From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 8 Jul 2024 11:02:00 +0000 (+0100)
Subject: JAL-4392 check if we are rendering a ss-consensus logo *just once* per row
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fspike%2FJAL-4386_develop_trial_merge;p=jalview.git

JAL-4392 check if we are rendering a ss-consensus logo *just once* per row
---

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 3235624..1ab9e48 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1508,6 +1508,14 @@ public class AnnotationRenderer
 
     int column;
     int aaMax = aa_annotations.length - 1;
+
+    /**
+     * TODO Should really set this using a constant local to AlignmentAnnotation
+     * in the same way as the cDNA and rna structure profiles are typed
+     */
+    boolean _aa_is_dssp3 = _aa.autoCalculated && _aa.label
+            .startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL);
+
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -1563,6 +1571,7 @@ public class AnnotationRenderer
         // just try to draw the logo if profl is not null
         if (profl != null && profl[2] != 0)
         {
+          // TODO do we ever have different profiles for different columns ?  Move up to where we set _aa_is_dssp3
           boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
           boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
           float ht = normaliseProfile ? y - _aa.graphHeight : y1;
@@ -1639,15 +1648,13 @@ public class AnnotationRenderer
                       .codonTranslate(s);
               colour = profcolour.findColour(codonTranslation.charAt(0),
                       column, null);
-            }
-            if(_aa.label.startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL)) {
+            } else if(_aa_is_dssp3) {
+              // TODO - would be nice to get rid of the special 'findSSColour' here ? 
               colour = profcolour.findSSColour(dc[0], column);
             }
             else
             {
-              
               colour = profcolour.findColour(dc[0], column, null);
-
             }
             g.setColor(colour == Color.white ? Color.lightGray : colour);