JAL-3485 constants for CDNA_CONSENSUS, STRUCTURE_CONSENSUS added

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 683ca78..1e2cf76 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -35,6 +35,7 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.ZappoColourScheme;
 import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport.AutoAnnotation;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -162,7 +163,8 @@ public class AnnotationRenderer
           boolean validRes, boolean validEnd)
   {
     g.setColor(STEM_COLOUR);
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -228,7 +230,8 @@ public class AnnotationRenderer
     // System.out.println(nonCanColor);
 
     g.setColor(nonCanColor);
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -360,10 +363,13 @@ public class AnnotationRenderer
     // properties/rendering attributes as a global 'alignment group' which holds
     // all vis settings for the alignment as a whole rather than a subset
     //
-    if (aa.autoCalculated && (aa.label.startsWith("Consensus")
-            || aa.label.startsWith("cDNA Consensus")))
+    if (aa.autoCalculated
+            && (aa.label.startsWith(AutoAnnotation.CONSENSUS.label)
+                    || aa.label.startsWith(
+                            AutoAnnotation.CDNA_CONSENSUS.label)))
     {
-      boolean forComplement = aa.label.startsWith("cDNA Consensus");
+      boolean forComplement = aa.label
+              .startsWith(AutoAnnotation.CDNA_CONSENSUS.label);
       if (aa.groupRef != null && aa.groupRef.consensusData != null
               && aa.groupRef.isShowSequenceLogo())
       {
@@ -390,7 +396,8 @@ public class AnnotationRenderer
     }
     else
     {
-      if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+      if (aa.autoCalculated && aa.label
+              .startsWith(AutoAnnotation.STRUCTURE_CONSENSUS.label))
       {
         // TODO implement group structure consensus
         /*
@@ -600,7 +607,7 @@ public class AnnotationRenderer
         {
           if (hasHiddenColumns)
           {
-            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1148,7 +1155,7 @@ public class AnnotationRenderer
     g.setColor(HELIX_COLOUR);
 
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -1248,7 +1255,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)
@@ -1328,7 +1335,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)