From af57f0707e38303bc1bc98f4e99b21e712ae1a95 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Fri, 14 Mar 2025 10:14:06 +0100
Subject: [PATCH] fix tests after refactor
---
.../testFiles/artifitial_compartments.xml | 0
.../testFiles/coloring_model.xml | 0
.../testFiles/compartments.xml | 0
.../testFiles/complex_with_state.xml | 0
.../testFiles/custom_semantic_zooming.xml | 0
.../testFiles/cyclic_hierarchy_problem.xml | 0
.../testFiles/kinetics_with_compartment.xml | 0
.../testFiles/layer_text_with_notes.xml | 0
.../testFiles/nested_test.xml | 0
.../cutting_without_compartment.xml | 0
.../disconnected_child_in_complex.xml | 0
.../testFiles/problematic_description.xml | 0
.../testFiles/reactions_to_color.xml | 0
.../testFiles/spliting_test_Case.xml | 0
.../annotation/recon_annotation_example.xml | 228 +
.../annotation/sampleDescription.txt | 31 +
.../other_full/GSTP1 subnetwork_220214.xml | 12409 ----------------
.../compact_complex_view_problem.xml | 213 -
model-command/testFiles/sample.xml | 2420 ---
.../xmlNodeTestExamples/antisense_rna.xml | 15 +
.../xmlNodeTestExamples/block_diagrams.xml | 15 +
.../cd_antisense_rna_collection.xml | 4 +
.../cd_compartment_alias.xml | 8 +
.../cd_compartment_alias_collection.xml | 26 +
.../xmlNodeTestExamples/cd_complex_alias.xml | 21 +
.../cd_complex_alias_collection.xml | 65 +
.../cd_complex_alias_with_empty_state.xml | 21 +
.../cd_complex_alias_with_parent.xml | 21 +
.../cd_gene_collection.xml | 4 +
.../cd_included_species_collection.xml | 53 +
.../cd_protein_collection.xml | 6 +
.../xmlNodeTestExamples/cd_rna_collection.xml | 4 +
.../cd_sbml_collection.xml | 101 +
.../cd_species_alias_collection.xml | 78 +
.../xmlNodeTestExamples/compartment.xml | 16 +
.../testFiles/xmlNodeTestExamples/gene.xml | 12 +
.../testFiles/xmlNodeTestExamples/layer.xml | 34 +
.../xmlNodeTestExamples/layer_collection.xml | 36 +
.../xmlNodeTestExamples/layer_line.xml | 4 +
.../xmlNodeTestExamples/layer_oval.xml | 5 +
.../xmlNodeTestExamples/layer_square.xml | 5 +
.../xmlNodeTestExamples/layer_text.xml | 8 +
.../layer_text_with_z_index.xml | 9 +
.../xmlNodeTestExamples/nested_complex.xml | 490 +
.../testFiles/xmlNodeTestExamples/notes.xml | 10 +
.../testFiles/xmlNodeTestExamples/notes2.xml | 23 +
.../testFiles/xmlNodeTestExamples/notes3.xml | 11 +
.../testFiles/xmlNodeTestExamples/notes4.xml | 11 +
.../testFiles/xmlNodeTestExamples/notes5.xml | 43 +
.../notes_invalid_charge.xml | 11 +
.../testFiles/xmlNodeTestExamples/protein.xml | 16 +
.../reaction_dissociation_with_addition.xml | 102 +
.../reaction_heterodimer.xml | 54 +
.../reaction_heterodimer_with_additions.xml | 101 +
.../reaction_positive_influence.xml | 41 +
.../reaction_transcription.xml | 41 +
.../reaction_transcription_with_additions.xml | 80 +
.../reaction_transition.xml | 45 +
...reaction_transitionWithAdditionalNodes.xml | 86 +
.../reaction_transition_omitted.xml | 45 +
.../reaction_translation.xml | 77 +
.../reaction_transport.xml | 59 +
.../reaction_truncation.xml | 60 +
.../reaction_truncationWithModifier.xml | 187 +
.../reaction_unknown_transition.xml | 41 +
.../reaction_with_modifiers.xml | 91 +
.../reaction_with_operators.xml | 91 +
.../testFiles/xmlNodeTestExamples/rna.xml | 12 +
.../xmlNodeTestExamples/rna_with_region.xml | 5 +
.../sbml_antisense_rna.xml | 11 +
.../xmlNodeTestExamples/sbml_complex.xml | 11 +
.../xmlNodeTestExamples/sbml_degraded.xml | 11 +
.../xmlNodeTestExamples/sbml_drug.xml | 11 +
.../xmlNodeTestExamples/sbml_gene.xml | 73 +
.../xmlNodeTestExamples/sbml_ion.xml | 124 +
.../xmlNodeTestExamples/sbml_phenotype.xml | 15 +
.../xmlNodeTestExamples/sbml_protein.xml | 63 +
.../xmlNodeTestExamples/sbml_rna.xml | 78 +
.../sbml_simple_molecule.xml | 11 +
.../xmlNodeTestExamples/sbml_unknown.xml | 23 +
.../xmlNodeTestExamples/species_alias.xml | 19 +
.../species_alias_with_font.xml | 19 +
.../species_alias_with_state.xml | 19 +
.../species_alias_without_state.xml | 19 +
84 files changed, 3170 insertions(+), 15042 deletions(-)
rename {model-command => converter-CellDesigner}/testFiles/artifitial_compartments.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/coloring_model.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/compartments.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/complex_with_state.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/custom_semantic_zooming.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/cyclic_hierarchy_problem.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/kinetics_with_compartment.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/layer_text_with_notes.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/nested_test.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/problematic/cutting_without_compartment.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/problematic/disconnected_child_in_complex.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/problematic_description.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/reactions_to_color.xml (100%)
rename {model-command => converter-CellDesigner}/testFiles/spliting_test_Case.xml (100%)
create mode 100644 model-command/testFiles/annotation/recon_annotation_example.xml
create mode 100644 model-command/testFiles/annotation/sampleDescription.txt
delete mode 100644 model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml
delete mode 100644 model-command/testFiles/problematic/compact_complex_view_problem.xml
delete mode 100644 model-command/testFiles/sample.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/compartment.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/gene.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer_collection.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer_line.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer_oval.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer_square.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer_text.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/nested_complex.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/notes.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/notes2.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/notes3.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/notes4.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/notes5.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/protein.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/rna.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/species_alias.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml
create mode 100644 model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
diff --git a/model-command/testFiles/artifitial_compartments.xml b/converter-CellDesigner/testFiles/artifitial_compartments.xml
similarity index 100%
rename from model-command/testFiles/artifitial_compartments.xml
rename to converter-CellDesigner/testFiles/artifitial_compartments.xml
diff --git a/model-command/testFiles/coloring_model.xml b/converter-CellDesigner/testFiles/coloring_model.xml
similarity index 100%
rename from model-command/testFiles/coloring_model.xml
rename to converter-CellDesigner/testFiles/coloring_model.xml
diff --git a/model-command/testFiles/compartments.xml b/converter-CellDesigner/testFiles/compartments.xml
similarity index 100%
rename from model-command/testFiles/compartments.xml
rename to converter-CellDesigner/testFiles/compartments.xml
diff --git a/model-command/testFiles/complex_with_state.xml b/converter-CellDesigner/testFiles/complex_with_state.xml
similarity index 100%
rename from model-command/testFiles/complex_with_state.xml
rename to converter-CellDesigner/testFiles/complex_with_state.xml
diff --git a/model-command/testFiles/custom_semantic_zooming.xml b/converter-CellDesigner/testFiles/custom_semantic_zooming.xml
similarity index 100%
rename from model-command/testFiles/custom_semantic_zooming.xml
rename to converter-CellDesigner/testFiles/custom_semantic_zooming.xml
diff --git a/model-command/testFiles/cyclic_hierarchy_problem.xml b/converter-CellDesigner/testFiles/cyclic_hierarchy_problem.xml
similarity index 100%
rename from model-command/testFiles/cyclic_hierarchy_problem.xml
rename to converter-CellDesigner/testFiles/cyclic_hierarchy_problem.xml
diff --git a/model-command/testFiles/kinetics_with_compartment.xml b/converter-CellDesigner/testFiles/kinetics_with_compartment.xml
similarity index 100%
rename from model-command/testFiles/kinetics_with_compartment.xml
rename to converter-CellDesigner/testFiles/kinetics_with_compartment.xml
diff --git a/model-command/testFiles/layer_text_with_notes.xml b/converter-CellDesigner/testFiles/layer_text_with_notes.xml
similarity index 100%
rename from model-command/testFiles/layer_text_with_notes.xml
rename to converter-CellDesigner/testFiles/layer_text_with_notes.xml
diff --git a/model-command/testFiles/nested_test.xml b/converter-CellDesigner/testFiles/nested_test.xml
similarity index 100%
rename from model-command/testFiles/nested_test.xml
rename to converter-CellDesigner/testFiles/nested_test.xml
diff --git a/model-command/testFiles/problematic/cutting_without_compartment.xml b/converter-CellDesigner/testFiles/problematic/cutting_without_compartment.xml
similarity index 100%
rename from model-command/testFiles/problematic/cutting_without_compartment.xml
rename to converter-CellDesigner/testFiles/problematic/cutting_without_compartment.xml
diff --git a/model-command/testFiles/problematic/disconnected_child_in_complex.xml b/converter-CellDesigner/testFiles/problematic/disconnected_child_in_complex.xml
similarity index 100%
rename from model-command/testFiles/problematic/disconnected_child_in_complex.xml
rename to converter-CellDesigner/testFiles/problematic/disconnected_child_in_complex.xml
diff --git a/model-command/testFiles/problematic_description.xml b/converter-CellDesigner/testFiles/problematic_description.xml
similarity index 100%
rename from model-command/testFiles/problematic_description.xml
rename to converter-CellDesigner/testFiles/problematic_description.xml
diff --git a/model-command/testFiles/reactions_to_color.xml b/converter-CellDesigner/testFiles/reactions_to_color.xml
similarity index 100%
rename from model-command/testFiles/reactions_to_color.xml
rename to converter-CellDesigner/testFiles/reactions_to_color.xml
diff --git a/model-command/testFiles/spliting_test_Case.xml b/converter-CellDesigner/testFiles/spliting_test_Case.xml
similarity index 100%
rename from model-command/testFiles/spliting_test_Case.xml
rename to converter-CellDesigner/testFiles/spliting_test_Case.xml
diff --git a/model-command/testFiles/annotation/recon_annotation_example.xml b/model-command/testFiles/annotation/recon_annotation_example.xml
new file mode 100644
index 0000000000..78de9aec3c
--- /dev/null
+++ b/model-command/testFiles/annotation/recon_annotation_example.xml
@@ -0,0 +1,228 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="170.0" y="171.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="399.0" y="173.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>Symbol: S1_SYMB
+Abbreviation: ABREVIATION
+ChargedFormula: FORMULA
+Charge: 324
+Synonyms: syn44
+DESCRIPTION
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s1">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.compound:C05488"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28870"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hmdb:HMDB03141"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>s2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>Symbol: SAW
+Abbreviation: ABREVIATION2
+Formula: FORMULA2
+MechanicalConfidenceScore: 100
+LowerBound: 200.201
+UpperBound: 300.301
+Subsystem: SUBSYSTEM2
+GeneProteinReaction: (urn:miriam:ccds:CCDS8639.1) or (urn:miriam:ccds:CCDS26.1) or (urn:miriam:ccds:CCDS314.2) or (urn:miriam:ccds:CCDS314.1)
+Synonyms: SYN1
+DESCRIPTION2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re1">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:15035803"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:8920635"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:9653080"/>
+</rdf:Bag>
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+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/model-command/testFiles/annotation/sampleDescription.txt b/model-command/testFiles/annotation/sampleDescription.txt
new file mode 100644
index 0000000000..156cd8860b
--- /dev/null
+++ b/model-command/testFiles/annotation/sampleDescription.txt
@@ -0,0 +1,31 @@
+HGNC_ID: 1464
+Symbol: CAMK4
+Name: calcium/calmodulin-dependent protein kinase IV
+Description: RecName: Full=Calcium/calmodulin-dependent protein kinase type IV; Short=CaMK IV; EC=2.7.11.17; AltName: Full=CaM kinase-GR;
+Previous Symbols:
+Synonyms: CAMK, CAMKIV, CAMK-GR
+Chromosome: 5q21-q23
+UniProtKB_Acc: Q16566
+RefSeq_ID: NP_001735.1
+EntrezGene_ID: 814
+Ensembl_ID: ENSP00000282356, ENSG00000152495 , ENST00000282356
+UCSC_ID: uc003kpf.1
+Reactome_ID: REACT_16116
+Pubmed_ID: 2536634
+EMBL_ID: AAA18251.1, AAA35639.1, AAH16695.2, AAH25687.1, BAA06403.1, BC016695, BC025687, CH471086, D30742, EAW49033.1, EAW49034.1, L17000, L24959
+IPI_ID: IPI00430411
+UniGene_ID: Hs.591269
+PDB_ID: 2W4O
+DIP_ID: DIP-41997N
+MINT_ID:
+KEGG_ID: hsa:814
+GeneCards_ID: GC05P110587
+PharmGKB_ID: PA26050
+Pathway_Interaction_DB: hdac_classii_pathway, nfat_3pathway, pi3kplctrkpathway
+GO_Function: GO:0004683[calmodulin-dependent protein kinase activity][IEA:EC. ], GO:0005516[calmodulin binding][IEA:UniProtKB-KW. ], GO:0005524[ATP binding][IEA:UniProtKB-KW. ]
+GO_Process: GO:0006954[inflammatory response][IEA:UniProtKB-KW. ], GO:0007202[activation of phospholipase C activity][TAS:Reactome. ], GO:0007268[synaptic transmission][TAS:Reactome. ], GO:0007616[long-term memory][IGI:UniProtKB. ], GO:0033081[regulation of T cell differentiation in thymus][TAS:UniProtKB. ], GO:0043011[myeloid dendritic cell differentiation][IMP:UniProtKB. ], GO:0045670[regulation of osteoclast differentiation][TAS:UniProtKB. ], GO:0045893[positive regulation of transcription, DNA-dependent][IDA:UniProtKB. ], GO:0048011[nerve growth factor receptor signaling pathway][TAS:Reactome. ]
+GO_Component: GO:0005654[nucleoplasm][TAS:Reactome. ], GO:0005829[cytosol][TAS:Reactome. ]
+InterPro: IPR000719, IPR002290, IPR008271, IPR011009, IPR017441, IPR017442, Kinase-like_dom. , Protein_kinase_ATP_BS. , Prot_kinase_cat_dom. , Ser/Thr_kinase_AS. , Ser/Thr_kinase_dom. , Se/Thr_kinase-like_dom.
+Pfam: PF00069, Pkinase
+PANTHER:
+HOVERGEN: HBG108055
\ No newline at end of file
diff --git a/model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml b/model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml
deleted file mode 100644
index 90b3cdce6b..0000000000
--- a/model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml
+++ /dev/null
@@ -1,12409 +0,0 @@
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-<celldesigner:gene id="gn5" name="TXN" type="GENE"/>
-</celldesigner:listOfGenes>
-<celldesigner:listOfRNAs>
-<celldesigner:RNA id="rn1" name="GSS" type="RNA"/>
-<celldesigner:RNA id="rn2" name="SLC1A1" type="RNA"/>
-<celldesigner:RNA id="rn3" name="GGT1" type="RNA"/>
-<celldesigner:RNA id="rn4" name="GSTP1" type="RNA"/>
-<celldesigner:RNA id="rn5" name="TXN" type="RNA"/>
-</celldesigner:listOfRNAs>
-<celldesigner:listOfAntisenseRNAs/>
-<celldesigner:listOfLayers/>
-<celldesigner:listOfBlockDiagrams/>
-</celldesigner:extension>
-</annotation>
-<listOfUnitDefinitions>
-<unitDefinition metaid="substance" id="substance" name="substance">
-<listOfUnits>
-<unit metaid="CDMT00278" kind="mole"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="volume" id="volume" name="volume">
-<listOfUnits>
-<unit metaid="CDMT00279" kind="litre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="area" id="area" name="area">
-<listOfUnits>
-<unit metaid="CDMT00280" kind="metre" exponent="2"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="length" id="length" name="length">
-<listOfUnits>
-<unit metaid="CDMT00281" kind="metre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="time" id="time" name="time">
-<listOfUnits>
-<unit metaid="CDMT00282" kind="second"/>
-</listOfUnits>
-</unitDefinition>
-</listOfUnitDefinitions>
-<listOfCompartments>
-<compartment metaid="default" id="default" size="1" units="volume"/>
-<compartment metaid="c3" id="c3" name="Astrocyte" size="1" units="volume" outside="c5">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>Astrocyte</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment metaid="c6" id="c6" name="endothelial cell" size="1" units="volume" outside="c5">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>endothelial cell</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment metaid="c5" id="c5" name="blood vessel" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>blood vessel</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment metaid="c1" id="c1" name="Neuron" size="1" units="volume" outside="c5">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>Neuron</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment metaid="c7" id="c7" name="nucleus" size="1" units="volume" outside="c1">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>nucleus</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment metaid="c8" id="c8" name="Mitochondria" size="1" units="volume" outside="c1">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>Mitochondria</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-</listOfCompartments>
-<listOfSpecies>
-<species metaid="s2153" id="s2153" name="SLC7A11" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr867</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re3"/>
-<celldesigner:catalyzed reaction="re1"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2157" id="s2157" name="yGluCys" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>yGluCys</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2157">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17515"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2158" id="s2158" name="GCLM" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr868</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re82"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2159" id="s2159" name="GCLC" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr869</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re82"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2160" id="s2160" name="GSS" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr870</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re6"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2162" id="s2162" name="glutathione" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glutathione</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2162">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16856"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2163" id="s2163" name="glycine" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glycine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2163">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15428"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2164" id="s2164" name="glutathione" compartment="c5" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glutathione</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2164">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16856"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2165" id="s2165" name="ABCB1" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr872</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re7"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2166" id="s2166" name="GGT1" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr873</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re8"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2167" id="s2167" name="CysGly" compartment="c5" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>CysGly</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2167">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A4047"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2172" id="s2172" name="ANPEP" compartment="c1" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr875</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re9"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2173" id="s2173" name="cystine" compartment="c6" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>cystine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2173">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16283"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2174" id="s2174" name="cystine" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>cystine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2174">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16283"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2152" id="s2152" name="L-cysteine" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>L-cysteine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2152">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17561"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
-<species metaid="s2175" id="s2175" name="L-cysteine" compartment="c5" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>L-cysteine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17561"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr876</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
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-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>L-cysteine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17561"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
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-<annotation>
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-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glutathione</celldesigner:name>
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-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16856"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-</species>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr870</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
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-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr869</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re11"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
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diff --git a/model-command/testFiles/problematic/compact_complex_view_problem.xml b/model-command/testFiles/problematic/compact_complex_view_problem.xml
deleted file mode 100644
index d4dd9f7ba2..0000000000
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-</celldesigner:listOfComplexSpeciesAliases>
-<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa1" species="s2" complexSpeciesAlias="csa1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="308.0" y="139.0" w="103.0" h="56.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="brief"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10.0" y="7.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="103.0" height="56.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-</celldesigner:listOfSpeciesAliases>
-<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins>
-<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
-</celldesigner:listOfProteins>
-<celldesigner:listOfGenes/>
-<celldesigner:listOfRNAs/>
-<celldesigner:listOfAntisenseRNAs/>
-<celldesigner:listOfLayers/>
-<celldesigner:listOfBlockDiagrams/>
-</celldesigner:extension>
-</annotation>
-<listOfUnitDefinitions>
-<unitDefinition metaid="substance" id="substance" name="substance">
-<listOfUnits>
-<unit metaid="CDMT00001" kind="mole"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="volume" id="volume" name="volume">
-<listOfUnits>
-<unit metaid="CDMT00002" kind="litre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="area" id="area" name="area">
-<listOfUnits>
-<unit metaid="CDMT00003" kind="metre" exponent="2"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="length" id="length" name="length">
-<listOfUnits>
-<unit metaid="CDMT00004" kind="metre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="time" id="time" name="time">
-<listOfUnits>
-<unit metaid="CDMT00005" kind="second"/>
-</listOfUnits>
-</unitDefinition>
-</listOfUnitDefinitions>
-<listOfCompartments>
-<compartment metaid="default" id="default" size="1" units="volume"/>
-<compartment metaid="c3" id="c3" name="c3" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c3</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-</listOfCompartments>
-<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s5" id="s5" name="s5" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s5</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-</listOfSpecies>
-</model>
-</sbml>
diff --git a/model-command/testFiles/sample.xml b/model-command/testFiles/sample.xml
deleted file mode 100644
index 8a0755ad0a..0000000000
--- a/model-command/testFiles/sample.xml
+++ /dev/null
@@ -1,2420 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
-<model metaid="untitled" id="untitled">
-<annotation>
-<celldesigner:extension>
-<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
-<celldesigner:modelDisplay sizeX="1308" sizeY="600"/>
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s14" name="s14">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s12</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr5</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-</celldesigner:listOfIncludedSpecies>
-<celldesigner:listOfCompartmentAliases/>
-<celldesigner:listOfComplexSpeciesAliases>
-<celldesigner:complexSpeciesAlias id="csa1" species="s12">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="271.0" y="207.0" w="101.0" h="164.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="101.0" height="164.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-</celldesigner:listOfComplexSpeciesAliases>
-<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa1" species="s1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="12.0" y="6.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa2" species="s2">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="165.0" y="43.0" w="80.0" h="50.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="50.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffcc" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="289.0" y="39.0" w="80.0" h="40.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
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-<celldesigner:speciesAlias id="sa8" species="s8">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="358.5" y="125.5" w="25.0" h="25.0"/>
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-<celldesigner:speciesAlias id="sa9" species="s9">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="455.0" y="169.5" w="70.0" h="25.0"/>
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-<celldesigner:speciesAlias id="sa10" species="s10">
-<celldesigner:activity>inactive</celldesigner:activity>
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-<celldesigner:speciesAlias id="sa11" species="s11">
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-<body>ymbol: CNC
-Name: Carney complex, multiple neoplasia and lentiginosis
-Description: RecName: Full=Sodium/calcium exchanger 1; AltName: Full=Na(+)/Ca(2+)-exchange protein 1; Flags: Precursor;
-Previous Symbols:
-Synonyms: CNC, NCX1
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-fdghjkfdhgjkdfgjhdf
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-Symbol: CNC
-Name: Carney complex, multiple neoplasia and lentiginosis
-Description: RecName: Full=Sodium/calcium exchanger 1; AltName: Full=Na(+)/Ca(2+)-exchange protein 1; Flags: Precursor;
-Previous Symbols:
-Synonyms: CNC, NCX1
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-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00014" species="s12">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>csa1</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re8" id="re8" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s11" alias="sa11"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s6" alias="sa6"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00015" species="s11">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa11</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00016" species="s6">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa6</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re9" id="re9" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s12" alias="csa1"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s7" alias="sa7"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="2">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-<celldesigner:lineDirection index="1" value="unknown"/>
-<celldesigner:lineDirection index="2" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:editPoints>0.5575958068511513,0.2645369873821708 0.6392987775053893,-0.3332879174757498</celldesigner:editPoints>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00017" species="s12">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>csa1</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00018" species="s7">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa7</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re10" id="re10" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s6" alias="sa6"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s7" alias="sa7"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00019" species="s6">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa6</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00020" species="s7">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa7</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re11" id="re11" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s7" alias="sa7"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s3" alias="sa3"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00021" species="s7">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa7</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00022" species="s3">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re12" id="re12" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s7" alias="sa7"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00023" species="s7">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa7</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00024" species="s4">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re13" id="re13" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s2" alias="sa2"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s3" alias="sa3"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00025" species="s2">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa2</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00026" species="s3">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re14" id="re14" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00027" species="s3">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00028" species="s4">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re15" id="re15" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s4" alias="sa4"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s9" alias="sa9"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00029" species="s4">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00030" species="s9">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa9</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re16" id="re16" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s4" alias="sa4"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s8" alias="sa8"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00031" species="s4">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00032" species="s8">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa8</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re17" id="re17" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s8" alias="sa8"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s13" alias="sa12"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00033" species="s8">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa8</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00034" species="s13">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa12</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re18" id="re18" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
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-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s13" alias="sa12"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00035" species="s12">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>csa1</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00036" species="s13">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa12</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re19" id="re19" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s7" alias="sa7"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s8" alias="sa8"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00037" species="s7">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa7</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00038" species="s8">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa8</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re20" id="re20" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s9" alias="sa9"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s8" alias="sa8"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00039" species="s9">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa9</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00040" species="s8">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa8</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re21" id="re21" reversible="false">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>notes for reaction
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s15" alias="sa14"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s16" alias="sa15"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-<celldesigner:lineDirection index="1" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:editPoints>0.7118419617432699,-0.433495681498556</celldesigner:editPoints>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#re21">
-<bqmodel:is>
-<rdf:Bag>
-<rdf:li rdf:resource="urn:miriam:pubmed:123"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00041" species="s15">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa14</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00042" species="s16">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa15</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re22" id="re22" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s16" alias="sa15"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s15" alias="sa14"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00049" species="s16">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa15</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00050" species="s15">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa14</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re23" id="re23" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>DISSOCIATION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s12" alias="csa1"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s8" alias="sa8"/>
-<celldesigner:baseProduct species="s7" alias="sa7"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
-<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
-<celldesigner:lineDirection arm="0" index="2" value="unknown"/>
-<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
-<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
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-<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
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-<annotation>
-<celldesigner:extension>
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-</annotation>
-</speciesReference>
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-</annotation>
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-<speciesReference metaid="CDMT00064" species="s21">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa25</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re27" id="re27" reversible="false">
-<notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body>asd
-</body>
-</html>
-</notes>
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s23" alias="sa26">
-<celldesigner:linkAnchor position="E"/>
-</celldesigner:baseReactant>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s23" alias="sa27">
-<celldesigner:linkAnchor position="W"/>
-</celldesigner:baseProduct>
-</celldesigner:baseProducts>
-<celldesigner:listOfReactantLinks>
-<celldesigner:reactantLink reactant="s24" alias="sa28" targetLineIndex="-1,0">
-<celldesigner:linkAnchor position="S"/>
-<celldesigner:connectScheme connectPolicy="direct">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000" type="Curve"/>
-</celldesigner:reactantLink>
-</celldesigner:listOfReactantLinks>
-<celldesigner:listOfProductLinks>
-<celldesigner:productLink product="s25" alias="sa29" targetLineIndex="-1,1">
-<celldesigner:linkAnchor position="S"/>
-<celldesigner:connectScheme connectPolicy="direct">
-<celldesigner:listOfLineDirection>
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-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000" type="Curve"/>
-</celldesigner:productLink>
-</celldesigner:listOfProductLinks>
-<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-<celldesigner:lineDirection index="1" value="unknown"/>
-<celldesigner:lineDirection index="2" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:editPoints>-0.2598501687659524,-1.4924508108998107 0.1811739606709441,-1.5643296326517722</celldesigner:editPoints>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00065" species="s23">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa26</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-<speciesReference metaid="CDMT00066" species="s24">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa28</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00067" species="s23">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa27</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-<speciesReference metaid="CDMT00068" species="s25">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa29</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-<reaction metaid="re885" id="re28" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s4532" alias="sa35">
-<celldesigner:linkAnchor position="SSE"/>
-</celldesigner:baseReactant>
-</celldesigner:baseReactants>
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-</celldesigner:baseProduct>
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-<celldesigner:listOfLineDirection>
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-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
-</celldesigner:reactantLink>
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-<celldesigner:connectScheme connectPolicy="direct">
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-</celldesigner:listOfLineDirection>
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-<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
-</celldesigner:reactantLink>
-</celldesigner:listOfReactantLinks>
-<celldesigner:listOfProductLinks>
-<celldesigner:productLink product="s841" alias="sa31" targetLineIndex="-1,1">
-<celldesigner:connectScheme connectPolicy="direct">
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-</celldesigner:listOfLineDirection>
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-</celldesigner:productLink>
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-</celldesigner:modification>
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-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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-<celldesigner:extension>
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-<speciesReference metaid="CDMT00059" species="s4532">
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diff --git a/model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml b/model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml
new file mode 100644
index 0000000000..bba9ae5a93
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml
@@ -0,0 +1,15 @@
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
+</celldesigner:listOfRegions>
+</celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml b/model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml
new file mode 100644
index 0000000000..15d462cb5d
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml
@@ -0,0 +1,15 @@
+<celldesigner:listOfBlockDiagrams>
+<celldesigner:blockDiagram protein="pr1">
+<celldesigner:canvas height="312" width="476"/>
+<celldesigner:block height="90" nameOffsetX="-8.0" nameOffsetY="-8.0" width="140" x="100" y="50"/>
+<celldesigner:halo height="150" width="200" x="70" y="20"/>
+<celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:residueInBlockDiagram id="0" offsetX="-27.0" type="dontcare"/>
+</celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:listOfExternalNamesForResidue/>
+<celldesigner:listOfBindingSitesInBlockDiagram/>
+<celldesigner:listOfEffectSitesInBlockDiagram/>
+<celldesigner:listOfInternalOperatorsInBlockDiagram/>
+<celldesigner:listOfInternalLinksInBlockDiagram/>
+</celldesigner:blockDiagram>
+</celldesigner:listOfBlockDiagrams>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml
new file mode 100644
index 0000000000..36c6c6d596
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml
@@ -0,0 +1,4 @@
+<celldesigner:listOfAntisenseRNAs>
+<celldesigner:AntisenseRNA id="arn1" name="s6" type="ANTISENSE_RNA"/>
+<celldesigner:AntisenseRNA id="arn2" name="s8" type="ANTISENSE_RNA"/>
+</celldesigner:listOfAntisenseRNAs>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml
new file mode 100644
index 0000000000..f2f9049128
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml
@@ -0,0 +1,8 @@
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml
new file mode 100644
index 0000000000..a278e98f46
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml
@@ -0,0 +1,26 @@
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca2" compartment="c2">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="707.0" y="187.0" w="118.0" h="73.0"/>
+<celldesigner:namePoint x="758.5" y="223.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca3" compartment="c3">
+<celldesigner:class>OVAL</celldesigner:class>
+<celldesigner:bounds x="185.0" y="143.0" w="86.0" h="50.0"/>
+<celldesigner:namePoint x="220.5" y="156.11618483532334"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml
new file mode 100644
index 0000000000..95ff9bf415
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml
@@ -0,0 +1,21 @@
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml
new file mode 100644
index 0000000000..22c1ec5c43
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml
@@ -0,0 +1,65 @@
+<celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s2598">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="863.0" y="35.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa3" species="s2599" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="767.0" y="15.0" w="61.0" h="87.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="23.0" y="15.0"/>
+<celldesigner:boxSize width="61.0" height="87.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
new file mode 100644
index 0000000000..bf37613db8
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
@@ -0,0 +1,21 @@
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml
new file mode 100644
index 0000000000..032fdf22b5
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml
@@ -0,0 +1,21 @@
+<celldesigner:complexSpeciesAlias id="csa2" species="s2" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="183.0" y="156.0" w="78.0" h="101.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="11.0" y="9.0"/>
+<celldesigner:boxSize width="78.0" height="101.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml
new file mode 100644
index 0000000000..fc0f27d416
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml
@@ -0,0 +1,4 @@
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s3" type="GENE"/>
+<celldesigner:gene id="gn2" name="s4" type="GENE"/>
+</celldesigner:listOfGenes>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml
new file mode 100644
index 0000000000..9ac2917c63
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml
@@ -0,0 +1,53 @@
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml
new file mode 100644
index 0000000000..527d1e134c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml
@@ -0,0 +1,6 @@
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+<celldesigner:protein id="pr3" name="s11" type="GENERIC"/>
+<celldesigner:protein id="pr4" name="s12" type="GENERIC"/>
+</celldesigner:listOfProteins>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml
new file mode 100644
index 0000000000..fdee0dee3d
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml
@@ -0,0 +1,4 @@
+<celldesigner:listOfRNAs>
+<celldesigner:RNA id="rn1" name="s5" type="RNA"/>
+<celldesigner:RNA id="rn2" name="s7" type="RNA"/>
+</celldesigner:listOfRNAs>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml
new file mode 100644
index 0000000000..3d9b3b4af1
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml
@@ -0,0 +1,101 @@
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn2</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn1</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn2</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn2</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s9" id="s9" name="s9" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml
new file mode 100644
index 0000000000..8fe0e36940
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml
@@ -0,0 +1,78 @@
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa8" species="s2594">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="510.83547998986796" y="449.34999999999997" w="261.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.6161980749753" y="5346.0"/>
+<celldesigner:boxSize width="261.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa9" species="s2506">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="506.33547998986796" y="613.8499999999999" w="262.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.1161980749753" y="5539.5"/>
+<celldesigner:boxSize width="262.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa10" species="s2595">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="282.0" y="75.0" w="134.0" h="94.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="134.0" height="94.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa11" species="s2596">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="483.0" y="76.0" w="82.0" h="96.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
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new file mode 100644
index 0000000000..da23a06a1c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/compartment.xml
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new file mode 100644
index 0000000000..82e893f865
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new file mode 100644
index 0000000000..ac0718cca9
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+++ b/model-command/testFiles/xmlNodeTestExamples/layer.xml
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new file mode 100644
index 0000000000..818cce79cf
--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
index 0000000000..68185b6d00
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new file mode 100644
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+</celldesigner:speciesAlias>
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+<celldesigner:bounds x="204.0" y="94.0" w="80.0" h="40.0"/>
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+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="56.0" y="101.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
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+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="347.0" y="87.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
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+<celldesigner:briefView>
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+</celldesigner:speciesAlias>
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+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="350.0" y="139.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
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+<celldesigner:boxSize width="80.0" height="40.0"/>
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+</celldesigner:speciesAlias>
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+<celldesigner:bounds x="339.0" y="35.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
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+</celldesigner:usualView>
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+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s7" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s8" type="GENERIC"/>
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+<celldesigner:protein id="pr4" name="s11" type="TRUNCATED"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes>
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+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
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+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s6</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes.xml b/model-command/testFiles/xmlNodeTestExamples/notes.xml
new file mode 100644
index 0000000000..07e958faee
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes.xml
@@ -0,0 +1,10 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes2.xml b/model-command/testFiles/xmlNodeTestExamples/notes2.xml
new file mode 100644
index 0000000000..fe5db406a2
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes2.xml
@@ -0,0 +1,23 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: SNCA
+Previous Symbols: X1, X2, X3
+Synonyms: Y1, Y2, Y3
+Name: Synuclein alpha (or something)
+Abbreviation: SN
+Formula: form
+MechanicalConfidenceScore: 2
+LowerBound: 2
+UpperBound: 2
+Subsystem: 2
+GeneProteinReaction: 1
+ChargedFormula: 1
+Charge:15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes3.xml b/model-command/testFiles/xmlNodeTestExamples/notes3.xml
new file mode 100644
index 0000000000..68f0aadbf7
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes3.xml
@@ -0,0 +1,11 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes4.xml b/model-command/testFiles/xmlNodeTestExamples/notes4.xml
new file mode 100644
index 0000000000..444dade224
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes4.xml
@@ -0,0 +1,11 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes some notes Symbol: strange2
+some notes some notes Symbol: strange3
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes5.xml b/model-command/testFiles/xmlNodeTestExamples/notes5.xml
new file mode 100644
index 0000000000..b4d6531235
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes5.xml
@@ -0,0 +1,43 @@
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+<rdfa:Description rdf:about="#s6095">
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+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/></rdf:Bag>
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+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:PTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:ADH_Sf_Zn"/>
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+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml b/model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
new file mode 100644
index 0000000000..8e2a9d5f76
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
@@ -0,0 +1,11 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Charge:a15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/protein.xml b/model-command/testFiles/xmlNodeTestExamples/protein.xml
new file mode 100644
index 0000000000..835d0522dc
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/protein.xml
@@ -0,0 +1,16 @@
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
+</celldesigner:protein>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml
new file mode 100644
index 0000000000..15b2c0852a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml
@@ -0,0 +1,102 @@
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+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>DISSOCIATION</celldesigner:reactionType>
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+<celldesigner:linkAnchor position="NW"/>
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+<celldesigner:listOfReactantLinks>
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+<celldesigner:linkAnchor position="W"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
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+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
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+<celldesigner:linkAnchor position="WNW"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
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+</celldesigner:listOfLineDirection>
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+<celldesigner:line width="1.0" color="ff000000"/>
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+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00011" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00012" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml
new file mode 100644
index 0000000000..f759f74c79
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml
@@ -0,0 +1,54 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.3543143297380586,0.41502311248073964</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml
new file mode 100644
index 0000000000..83738af592
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml
@@ -0,0 +1,101 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s4" alias="sa4" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="SSE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="SSW"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="3" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="4" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="5" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="6" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="7" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="8" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="1" num1="2" num2="8" tShapeIndex="6">0.6898190045248871,0.41493212669683266 0.3690344574394102,0.4436355655530426 0.4067830423940162,-0.618154613466328 0.2057070196067705,0.27418031666165343 0.5573109932903977,0.24900556265208795 0.24307206195228326,0.011601570519530924 0.32722922889758355,-0.3519683205847308 0.23631167935790365,-0.6299101283205016 0.4451161869205815,-0.42463489483307004 2.1976031495216395,-0.051531612298451046 2.125528547270494,0.29079378866696914 0.34738186462324405,0.46335826795596924</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00009" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00010" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml
new file mode 100644
index 0000000000..6f969cbb9a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml
@@ -0,0 +1,41 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml
new file mode 100644
index 0000000000..ce5e630ed7
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml
@@ -0,0 +1,41 @@
+<reaction metaid="re4" id="re4" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSCRIPTION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s4" alias="sa4">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml
new file mode 100644
index 0000000000..5686ed8880
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml
@@ -0,0 +1,80 @@
+<reaction metaid="re4" id="re4" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSCRIPTION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s4" alias="sa4">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s6" alias="sa6" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="vertical"/>
+<celldesigner:lineDirection index="1" value="horizontal"/>
+<celldesigner:lineDirection index="2" value="vertical"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.3275574775411034,-0.25113523762663204 0.6977609748292235,0.23172381829317268</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00008" species="s6">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa6</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00009" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml
new file mode 100644
index 0000000000..0f8edfbdda
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml
@@ -0,0 +1,45 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="2">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+<celldesigner:lineDirection index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.24477145008979806,0.2737964196744106 0.3030703119434812,-0.2478987966128221 0.845451600125741,-0.29800234330419595</celldesigner:editPoints>
+<celldesigner:line width="2.0" color="ff120000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml
new file mode 100644
index 0000000000..2154bc1a73
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml
@@ -0,0 +1,86 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s4" alias="sa4" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.2694923595421561,0.03113391403065835</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="N"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.5963993894126993,-0.05429989069902841 0.5448875616378848,-1.603902125616216</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="2">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+<celldesigner:lineDirection index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.11233758456827642,0.12302432727767126 0.13628805800643468,-0.11389609817852006 0.7741123124570151,-0.15496432192880294</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00008" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00009" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml
new file mode 100644
index 0000000000..379f3cb933
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml
@@ -0,0 +1,45 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>KNOWN_TRANSITION_OMITTED</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+<celldesigner:lineDirection index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints omittedShapeIndex="1">0.1395721196429789,-0.2928391360632283 0.7711466302645423,0.20147252877787603 1.0166295304909794,0.12192232640388895</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml
new file mode 100644
index 0000000000..a39da86060
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml
@@ -0,0 +1,77 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSLATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s3" alias="sa3" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s6" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="N"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00004" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>csa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml
new file mode 100644
index 0000000000..99be4f1041
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml
@@ -0,0 +1,59 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>asd
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSPORT</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re885">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_631.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml
new file mode 100644
index 0000000000..393d0347e4
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml
@@ -0,0 +1,60 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRUNCATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="ESE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseProduct>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="1" num1="2" num2="3" tShapeIndex="0">0.584187648650865,0.5254654309849918 0.23345636699182837,-0.5527287107830219 0.4553770651333544,0.19492621754274708 1.948293047595317,1.096062795913281 2.214822748707086,-0.10695975741860275 0.932772869523844,-0.5673310998204193 0.3691743208436597,0.3600379064003501</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml
new file mode 100644
index 0000000000..dccad1d1d7
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml
@@ -0,0 +1,187 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRUNCATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="ESE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="S"/>
+</celldesigner:baseProduct>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="1" num1="0" num2="0" tShapeIndex="0">0.8318308545720352,-0.014828828365314406 2.21439801599832E-5,0.5674837795345327</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+<celldesigner:listOfModification>
+<celldesigner:modification type="CATALYSIS" modifiers="s4" aliases="sa4" targetLineIndex="0,5">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s4" alias="sa4">
+<celldesigner:linkAnchor position="SSE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="INHIBITION" modifiers="s10" aliases="sa10" targetLineIndex="0,3" editPoints="0.4895706964240256,0.34520664086062736 0.7400505289017092,-0.16597816296424608">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s10" alias="sa10">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="UNKNOWN_CATALYSIS" modifiers="s11" aliases="sa11" targetLineIndex="0,4">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s11" alias="sa11">
+<celldesigner:linkAnchor position="SSE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="UNKNOWN_INHIBITION" modifiers="s12" aliases="sa12" targetLineIndex="0,2">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s12" alias="sa12">
+<celldesigner:linkAnchor position="SSE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s13" aliases="sa13" targetLineIndex="0,6">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s13" alias="sa13">
+<celldesigner:linkAnchor position="NNW"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="MODULATION" modifiers="s14" aliases="sa14" targetLineIndex="0,7">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s14" alias="sa14">
+<celldesigner:linkAnchor position="NW"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="TRIGGER" modifiers="s15" aliases="sa15" targetLineIndex="0,3">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s15" alias="sa15">
+<celldesigner:linkAnchor position="NE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+</celldesigner:listOfModification>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference metaid="CDMT00009" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00014" species="s10">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa10</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00015" species="s11">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa11</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00016" species="s12">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa12</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00017" species="s13">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa13</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00018" species="s14">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa14</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00019" species="s15">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa15</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml
new file mode 100644
index 0000000000..546a2740e2
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml
@@ -0,0 +1,41 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>UNKNOWN_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="S"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml
new file mode 100644
index 0000000000..aa32d43ad2
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml
@@ -0,0 +1,91 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+<celldesigner:listOfModification>
+<celldesigner:modification type="BOOLEAN_LOGIC_GATE_AND" modifiers="s3,s4" aliases="sa3,sa4" modificationType="CATALYSIS" targetLineIndex="-1,2" editPoints="190.66666666666666,117.66666666666667">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="CATALYSIS" modifiers="s3" aliases="sa3" editPoints="0.3546405445791134,0.4532624937738668">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s3" alias="sa3">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="CATALYSIS" modifiers="s4" aliases="sa4" targetLineIndex="-1,0" editPoints="0.04371287754328368,-0.803475293820294">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s4" alias="sa4">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+</celldesigner:listOfModification>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00004" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml
new file mode 100644
index 0000000000..da5e508d96
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml
@@ -0,0 +1,91 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s3" alias="sa3" targetLineIndex="2,0">
+<celldesigner:linkAnchor position="INACTIVE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="2,1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="0" num1="0" num2="1" tShapeIndex="1">0.0339412438306228,-0.1656317895311532 0.7249666221628845,0.4813084112149532</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00004" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00005" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/rna.xml b/model-command/testFiles/xmlNodeTestExamples/rna.xml
new file mode 100644
index 0000000000..c6cf054847
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/rna.xml
@@ -0,0 +1,12 @@
+<celldesigner:RNA id="rn36" name="BCL6" type="RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+B-cell CLL/lymphoma 6
+</body>
+</html>
+</celldesigner:notes>
+</celldesigner:RNA>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml b/model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml
new file mode 100644
index 0000000000..52566ea024
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml
@@ -0,0 +1,5 @@
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
+</celldesigner:listOfRegions>
+</celldesigner:RNA>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml
new file mode 100644
index 0000000000..b3a9173dc8
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml
@@ -0,0 +1,11 @@
+<species metaid="s1" id="s2" name="s3" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml
new file mode 100644
index 0000000000..d51eb12845
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml
@@ -0,0 +1,11 @@
+<species metaid="s6549" id="s6549" name="LC3-II" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>LC3-II</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml
new file mode 100644
index 0000000000..0e8b347258
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml
@@ -0,0 +1,11 @@
+<species metaid="s1275" id="s1275" name="s1275" compartment="c20" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>DEGRADED</celldesigner:class>
+<celldesigner:name>s1275</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml
new file mode 100644
index 0000000000..ebb8c4a7a9
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml
@@ -0,0 +1,11 @@
+<species metaid="s6104" id="s6104" name="geldanamycin" compartment="c1" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>DRUG</celldesigner:class>
+<celldesigner:name>geldanamycin</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml
new file mode 100644
index 0000000000..3d176259f8
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml
@@ -0,0 +1,73 @@
+<species metaid="s5916" id="s5916" name="Ptgr1" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: PTGR1
+Name: prostaglandin reductase 1
+Description: RecName: Full=Prostaglandin reductase 1; Short=PRG-1; EC=1.3.1.-; AltName: Full=15-oxoprostaglandin 13-reductase; EC=1.3.1.48; AltName: Full=NADP-dependent leukotriene B4 12-hydroxydehydrogenase; EC=1.3.1.74;
+Previous Symbols: LTB4DH
+Synonyms: LTB4DH
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn95</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5916">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml
new file mode 100644
index 0000000000..5c2222a435
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml
@@ -0,0 +1,124 @@
+<species metaid="s6029" id="s6029" name="Pi" compartment="c1" initialConcentration="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Long Name: PiSynonym: Synonym not specifiedAccession: U02720
+Symbol: SERPINA1
+Name: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
+Description: RecName: Full=Alpha-1-antitrypsin; AltName: Full=Alpha-1 protease inhibitor; AltName: Full=Alpha-1-antiproteinase; AltName: Full=Serpin A1; Contains: RecName: Full=Short peptide from AAT; Short=SPAAT; Flags: Precursor;
+Previous Symbols: PI
+Synonyms: AAT, PI
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Pi</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6029">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121172.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AProt_inh_serpin"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA35509"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11461"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121174.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:8941"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002235.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121175.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121176.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121179.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121173.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121177.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_3705"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121178.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002236.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_000286.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml
new file mode 100644
index 0000000000..62bbee07b0
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml
@@ -0,0 +1,15 @@
+<species metaid="s5462" id="s5462" name="Neuronal damage and death" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>Neuronal damage and death</celldesigner:name>
+</celldesigner:speciesIdentity>
+<celldesigner:listOfCatalyzedReactions>
+<celldesigner:catalyzed reaction="re1435"/>
+<celldesigner:catalyzed reaction="re1434"/>
+</celldesigner:listOfCatalyzedReactions>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml
new file mode 100644
index 0000000000..0f8d55a9f6
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml
@@ -0,0 +1,63 @@
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>protein tyrosine phosphatase, receptor type, C
+also known as CED45
+Symbol: PTPRC
+Name: protein tyrosine phosphatase, receptor type, C
+Description: RecName: Full=Receptor-type tyrosine-protein phosphatase C; EC=3.1.3.48; AltName: Full=Leukocyte common antigen; Short=L-CA; AltName: Full=T200; AltName: CD_antigen=CD45; Flags: Precursor;
+Previous Symbols: CD45
+Synonyms: CD45
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:entrez.gene:5788"/></rdf:Bag>
+</bqbiol:is>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_002829.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_13296"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_563578.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA34011"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9666"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml
new file mode 100644
index 0000000000..a848f327dc
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml
@@ -0,0 +1,78 @@
+<species metaid="s5914" id="s5914" name="Fmo3" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: FMO3
+Name: flavin containing monooxygenase 3
+Description: RecName: Full=Dimethylaniline monooxygenase [N-oxide-forming] 3; EC=1.14.13.8; AltName: Full=Dimethylaniline oxidase 3; AltName: Full=FMO II; AltName: Full=FMO form 2; AltName: Full=Hepatic flavin-containing monooxygenase 3; Short=FMO 3;
+Previous Symbols:
+Synonyms:
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn101</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5914">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:8486388"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002294.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_5740"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA166"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_008825.4"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:3771"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:9417913"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml
new file mode 100644
index 0000000000..db9afbef08
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml
@@ -0,0 +1,11 @@
+<species metaid="s5463" id="s5463" name="Peroxides" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>Peroxides</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml
new file mode 100644
index 0000000000..e8891db4fb
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml
@@ -0,0 +1,23 @@
+<species metaid="s1356" id="s1356" name="unidentified caspase acting on Occludin" compartment="c1" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>UNKNOWN</celldesigner:class>
+<celldesigner:name>unidentified caspase acting on Occludin</celldesigner:name>
+</celldesigner:speciesIdentity>
+<celldesigner:listOfCatalyzedReactions>
+<celldesigner:catalyzed reaction="re514"/>
+</celldesigner:listOfCatalyzedReactions>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s1356">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_21584.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias.xml
new file mode 100644
index 0000000000..f3e98a7910
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
new file mode 100644
index 0000000000..893947c964
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa1" species="s78">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="78.0" y="207.0" w="307.0" h="110.0"/>
+<celldesigner:font size="30"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="307.0" height="110.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml
new file mode 100644
index 0000000000..86a9a41633
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa1" species="s78">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="69.0" y="75.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="open" prefix="free input" label="test" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
new file mode 100644
index 0000000000..267d16430a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
\ No newline at end of file
--
GitLab