From: Renia Correya <rcorreya001@dundee.ac.uk>
Date: Thu, 4 Jul 2024 09:30:25 +0000 (+0100)
Subject: JAL-4392 Updated the colouring of consensus logo
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a8367f07f487bcf754bd249b5f90889f7f630aa4;p=jalview.git

JAL-4392 Updated the colouring of consensus logo
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0284498..99d3d6e 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2914,7 +2914,7 @@ public class AlignmentUtils
       return Color.red;
     }
 
-    return Color.gray;
+    return Color.white;
   }
 
   public static char findSSAnnotationForGivenSeqposition(AlignmentAnnotation aa,
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index f46019e..3235624 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1641,7 +1641,7 @@ public class AnnotationRenderer
                       column, null);
             }
             if(_aa.label.startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL)) {
-              colour = AlignmentUtils.getSecondaryStructureAnnotationColour(dc[0]);              
+              colour = profcolour.findSSColour(dc[0], column);
             }
             else
             {
diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index 00c228f..0b191ec 100644
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -20,6 +20,7 @@
  */
 package jalview.renderer;
 
+import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -304,24 +305,15 @@ public class ResidueShader implements ResidueShaderI
   }
   
   @Override
-  public Color findSSColour(char symbol, int position, SequenceI seq, String source)
+  public Color findSSColour(char symbol, int position)
   {
     if (colourScheme == null)
     {
       return Color.white; // Colour is 'None'
     }
 
-    /*
-     * get 'base' colour
-     */
-    ProfileI profile = ssConsensusProfileMap.get(source) == null ? null : ssConsensusProfileMap.get(source).get(position);
-    String modalSS = profile == null ? null
-            : profile.getModalSS();
-    float pid = profile == null ? 0f
-            : profile.getSSPercentageIdentity(ignoreGaps);
-    Color colour = colourScheme.findColour(symbol, position, seq,
-            modalSS, pid);
-
+    Color colour = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol);
+        
     /*
      * apply PID threshold and consensus fading if in force
      */
diff --git a/src/jalview/renderer/ResidueShaderI.java b/src/jalview/renderer/ResidueShaderI.java
index 38a466b..c35f208 100644
--- a/src/jalview/renderer/ResidueShaderI.java
+++ b/src/jalview/renderer/ResidueShaderI.java
@@ -84,8 +84,7 @@ public interface ResidueShaderI
 
   public abstract void setColourScheme(ColourSchemeI cs);
 
-  Color findSSColour(char symbol, int position, SequenceI seq,
-          String source);
+  Color findSSColour(char symbol, int position);
 
   int getConsensusSecondaryStructureThreshold();