Merge branch 'develop' into releases/Release_2_11_2_Branch

diff --git a/help/markdown/releases/release-2_11_2_5.md b/help/markdown/releases/release-2_11_2_5.md
new file mode 100644 (file)
index 0000000..c9dc2b9
--- /dev/null
+++ b/help/markdown/releases/release-2_11_2_5.md
@@ -0,0 +1,12 @@
+---
+version: 2.11.2.5
+date: 2022-10-01
+channel: "release"
+---
+
+## New Features
+
+## Issues Resolved
+
+- <!-- JAL-3612 --> Overview doesn't colour nested features the same as in the alignment view 
+

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index a25114e..3843ddb 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -189,7 +189,7 @@ label.occupancy = Occupancy
 # delete Clustal - use FileFormat name instead
 label.clustal = Clustal
 # label.colourScheme_<schemeName> as in JalviewColourScheme, spaces removed
-label.colourScheme_clustal = Clustalx
+label.colourScheme_clustal = Clustal
 label.colourScheme_blosum62 = BLOSUM62 Score
 label.colourScheme_%identity = Percentage Identity
 label.colourScheme_zappo = Zappo
@@ -204,6 +204,10 @@ label.colourScheme_nucleotide = Nucleotide
 label.colourScheme_t-coffeescores = T-Coffee Scores
 label.colourScheme_rnahelices = By RNA Helices
 label.colourScheme_sequenceid = Sequence ID Colour
+label.colourScheme_gecos\:flower = gecos Flower
+label.colourScheme_gecos\:blossom = gecos Blossom
+label.colourScheme_gecos\:sunset = gecos Sunset
+label.colourScheme_gecos\:ocean = gecos Ocean
 label.blc = BLC
 label.fasta = Fasta
 label.msf = MSF

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 88fa161..d0bfd65 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -182,7 +182,7 @@ label.out_to_textbox = Generar cuadro de texto
 label.occupancy = Ocupación
 label.clustal = Clustal
 # label.colourScheme_<schemeName> as in JalviewColourScheme
-label.colourScheme_clustal = Clustalx
+label.colourScheme_clustal = Clustal
 label.colourScheme_blosum62 = Puntuación del BLOSUM62
 label.colourScheme_%identity = Porcentaje de identidad
 label.colourScheme_zappo = Zappo
@@ -197,6 +197,10 @@ label.colourScheme_nucleotide = Nucle
 label.colourScheme_t-coffeescores = Puntuación del T-Coffee
 label.colourScheme_rnahelices = Por hélices de RNA
 label.colourScheme_sequenceid = Color de ID de secuencia
+label.colourScheme_gecos\:flower = gecos Flower
+label.colourScheme_gecos\:blossom = gecos Blossom
+label.colourScheme_gecos\:sunset = gecos Sunset
+label.colourScheme_gecos\:ocean = gecos Ocean
 label.blc = BLC
 label.fasta = Fasta
 label.msf = MSF

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index ee12a5e..e66b7d5 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -537,10 +537,15 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
+      /*
+       * find features of this type, and the colour of the _last_ one
+       * (the one that would be drawn on top) that has a colour
+       */
       List<SequenceFeature> overlaps = seq.findFeatures(column, column,
               type);
-      for (SequenceFeature sequenceFeature : overlaps)
+      for (int i = overlaps.size() - 1 ; i >= 0 ; i--)
       {
+        SequenceFeature sequenceFeature = overlaps.get(i);
         if (!featureGroupNotShown(sequenceFeature))
         {
           Color col = getColour(sequenceFeature);

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 6b87dd4..637bbf4 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -26,6 +26,13 @@ import static org.testng.Assert.assertNotEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -37,13 +44,6 @@ import jalview.schemes.FeatureColour;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
-import java.awt.Color;
-import java.util.List;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
 /**
  * Unit tests for feature colour determination, including but not limited to
  * <ul>
@@ -162,6 +162,27 @@ public class FeatureColourFinderTest
     assertNull(c);
   }
 
+  /**
+   * Nested features coloured by label - expect the colour of the enclosed
+   * feature
+   */
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_nestedFeatures()
+  {
+    SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, 0f, null);
+    seq.addSequenceFeature(sf1);
+    SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20,
+            0f, null);
+    seq.addSequenceFeature(sf2);
+    FeatureColourI fc = new FeatureColour(Color.red);
+    fc.setColourByLabel(true);
+    fr.setColour("domain", fc);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+    Color c = finder.findFeatureColour(null, seq, 15);
+    assertEquals(c, fr.getColor(sf2, fc));
+  }
+
   @Test(groups = "Functional")
   public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
   {