diff --git a/CHANGELOG b/CHANGELOG
index dadb7279143d82cfb84765018ce6256269aeee10..a697bece18e21492292d8b148b9b47bcddc51c63 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -19,6 +19,7 @@ minerva (19.0.0~alpha.0) stable; urgency=medium
* Small improvement: layers called "text" are visible on the map (#2138)
* Small improvement: modification residues have text location (#2141)
* Small improvement: layers have z-index (#2215)
+ * Small improvement: NON_MATCHING_ALPHA attribute to overlay (#2263)
* Bug fix: text coordinates for multimer species are computed based on
multimer value when importing from CellDesigner (#2131)
* Bug fix: when removing project the layer texts/rectangles/ovals were not
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index cf641959f46da1474be42bb3c9da763077078201..d63ae8ef3ff2021a29f65e60737afd4d7c36a419 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -394,6 +394,11 @@ public class ComplexZipConverter {
colorSchemaType = DataOverlayType.GENERIC;
}
+ String nonMatchingAlpha = parameters.get(ZipEntryFileFactory.NON_MATCHING_ALPHA);
+ if (nonMatchingAlpha != null) {
+ layout.setNotMatchingAlpha(nonMatchingAlpha);
+ }
+
layout.setColorSchemaType(colorSchemaType);
layout.setInputData(fileEntry);
layout.setPublic(true);
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
index 8bc71e00b22f0b86c15142f679a7e9adea5d60ef..e1073b246fb7bf9426c09232553ca24453adf992 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
@@ -23,6 +23,8 @@ public class ZipEntryFileFactory {
* corresponding to the {@link LayoutZipEntryFile#type type}.
*/
public static final String LAYOUT_HEADER_PARAM_TYPE = "TYPE";
+
+ public static final String NON_MATCHING_ALPHA = "NON_MATCHING_ALPHA";
/**
* Name of the parameter in {@link LayoutZipEntryFile file describing layout}
* corresponding to the {@link LayoutZipEntryFile#genomeType genome type}.
diff --git a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlay.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlay.java
index d3847ea6ecf50ab2b267a96b575f83787bfc4a2a..a47fc95e5cda91dafad5f0b4065fb8349bbac74c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlay.java
+++ b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlay.java
@@ -28,6 +28,8 @@ import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.OneToOne;
import javax.persistence.Version;
+import javax.validation.constraints.Max;
+import javax.validation.constraints.Min;
import java.util.Collection;
import java.util.Comparator;
import java.util.HashSet;
@@ -73,6 +75,10 @@ public class DataOverlay implements MinervaEntity {
@JsonProperty("publicOverlay")
private boolean isPublic = false;
+ @Max(255)
+ @Min(0)
+ private Integer notMatchingAlpha;
+
/**
* Data overlay type. It can be null in such case it should be obtained from
* {@link #inputData}.
@@ -252,4 +258,16 @@ public class DataOverlay implements MinervaEntity {
public void setGroup(final DataOverlayGroup group) {
this.group = group;
}
+
+ public Integer getNotMatchingAlpha() {
+ return notMatchingAlpha;
+ }
+
+ public void setNotMatchingAlpha(final int notMatchingAlpha) {
+ this.notMatchingAlpha = notMatchingAlpha;
+ }
+
+ public void setNotMatchingAlpha(final String notMatchingAlpha) {
+ this.notMatchingAlpha = Integer.parseInt(notMatchingAlpha);
+ }
}
diff --git a/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250407__add_not_matching_alpha.sql b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250407__add_not_matching_alpha.sql
new file mode 100644
index 0000000000000000000000000000000000000000..455a10713843f6e6be5787f73eb87e47fc91c6f4
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/19.0.0~alpha.0/V19.0.0.20250407__add_not_matching_alpha.sql
@@ -0,0 +1,2 @@
+alter table public.data_overlay_table
+ add column not_matching_alpha integer;
diff --git a/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250407__add_not_matching_alpha.sql b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250407__add_not_matching_alpha.sql
new file mode 100644
index 0000000000000000000000000000000000000000..455a10713843f6e6be5787f73eb87e47fc91c6f4
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/19.0.0~alpha.0/V19.0.0.20250407__add_not_matching_alpha.sql
@@ -0,0 +1,2 @@
+alter table public.data_overlay_table
+ add column not_matching_alpha integer;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java b/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java
index 96fb86cac58facf86159d3fba4b0543477526728..bcbecca8fcfb386a5be64205eada01e771b123f7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/DataOverlayService.java
@@ -100,6 +100,11 @@ public class DataOverlayService implements IDataOverlayService {
overlay.setCreator(params.getUser());
overlay.addEntries(schemas);
+ String nonMatchingAlpha = parameters.get(ZipEntryFileFactory.NON_MATCHING_ALPHA);
+ if (nonMatchingAlpha != null) {
+ overlay.setNotMatchingAlpha(nonMatchingAlpha);
+ }
+
if (colorSchemaType == DataOverlayType.GENETIC_VARIANT) {
final String genomeVersion = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_GENOME_VERSION);
ReferenceGenomeType genomeType = ReferenceGenomeType.UCSC;
diff --git a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
index 6dd0ad29820357f0138b691d8e6f6e553abd8593..e6f02f2239e27e956164d1063da6dcd91f6a7c24 100644
--- a/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/OverlayControllerIntegrationTest.java
@@ -1365,6 +1365,10 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
fieldWithPath("order")
.description("sort order")
.type(JsonFieldType.NUMBER),
+ fieldWithPath("notMatchingAlpha")
+ .description("alpha to be used for all not matching bioEntities when highlighting this overlay")
+ .optional()
+ .type(JsonFieldType.NUMBER),
fieldWithPath("type")
.description("type; available options: " + new ProjectSnippets().getOptionsAsString(DataOverlayType.class))
.type(JsonFieldType.STRING),
@@ -1753,4 +1757,31 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
.andExpect(status().isForbidden());
}
+ @Test
+ public void testCreateOverlayWithNotMatchingAlpha() throws Exception {
+ final User admin = userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
+
+ final UploadedFileEntry file = createFile("#NON_MATCHING_ALPHA=243\nelement_identifier\tvalue\tcolor\n", admin);
+
+ final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ final String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+ new BasicNameValuePair("fileId", String.valueOf(file.getId())),
+ new BasicNameValuePair("name", "overlay name"),
+ new BasicNameValuePair("description", "overlay name"),
+ new BasicNameValuePair("filename", "overlay name"),
+ new BasicNameValuePair("type", "GENERIC"))));
+
+ final RequestBuilder request = post("/minerva/api/projects/{projectId}/overlays/", TEST_PROJECT)
+ .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+ .content(body)
+ .session(session);
+
+ mockMvc.perform(request)
+ .andExpect(status().is2xxSuccessful());
+
+ DataOverlay overlay = dataOverlayService.getDataOverlaysByProject(project).get(0);
+ assertEquals((Integer) 243, overlay.getNotMatchingAlpha());
+ }
+
}
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index b157a93fc5fc61d0a7185c38db8df4ddc85deb05..a0d15eec7cc54ae0aa11d5a3be2e4cca039b0564 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -487,6 +487,10 @@ public class NewApiDocs {
.description("group identifier")
.optional()
.type(JsonFieldType.NUMBER),
+ fieldWithPath(prefix + "notMatchingAlpha")
+ .description("alpha to be used for all not matching bioEntities when highlighting this overlay")
+ .optional()
+ .type(JsonFieldType.NUMBER),
fieldWithPath(prefix + "id")
.description("id")
.type(JsonFieldType.NUMBER),