X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=fa2900ddeda5743544d49e82185c9a2cf6a30d83;hb=6d03a7bc7ca503f0e845dcbc568e44a39c842612;hp=1cd3d3b5f55aa7b8af5111bc6cabf796a09a94ba;hpb=d9f0a24d9662a0b530fd79b51108dd074d03d6e0;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 1cd3d3b..fa2900d 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -80,9 +80,9 @@ public class AnnotationRenderer
 
   private ProfilesI hconsensus;
 
-  private Hashtable[] complementConsensus;
+  private Hashtable<String, Object>[] complementConsensus;
 
-  private Hashtable[] hStrucConsensus;
+  private Hashtable<String, Object>[] hStrucConsensus;
 
   private boolean av_ignoreGapsConsensus;
 
@@ -149,6 +149,7 @@ public class AnnotationRenderer
    */
   public void dispose()
   {
+    hiddenColumns = null;
     hconsensus = null;
     complementConsensus = null;
     hStrucConsensus = null;
@@ -446,7 +447,7 @@ public class AnnotationRenderer
     updateFromAwtRenderPanel(annotPanel, av);
     fm = g.getFontMetrics();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-    int temp = 0;
+    // int temp = 0;
     if (aa == null)
     {
       return false;
@@ -459,8 +460,8 @@ public class AnnotationRenderer
     boolean validRes = false;
     boolean validEnd = false;
     boolean labelAllCols = false;
-    boolean centreColLabels;
-    boolean centreColLabelsDef = av.isCentreColumnLabels();
+//    boolean centreColLabels;
+//    boolean centreColLabelsDef = av.isCentreColumnLabels();
     boolean scaleColLabel = false;
     final AlignmentAnnotation consensusAnnot = av
             .getAlignmentConsensusAnnotation();
@@ -506,7 +507,7 @@ public class AnnotationRenderer
       {
         continue;
       }
-      centreColLabels = row.centreColLabels || centreColLabelsDef;
+//      centreColLabels = row.centreColLabels || centreColLabelsDef;
       labelAllCols = row.showAllColLabels;
       scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
@@ -774,7 +775,7 @@ public class AnnotationRenderer
               if (x > -1)
               {
 
-                int nb_annot = x - temp;
+                // int nb_annot = x - temp;
                 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
                 // annot :"+nb_annot);
                 switch (lastSS)
@@ -783,7 +784,7 @@ public class AnnotationRenderer
                 case ')': // and opposite direction
                   drawStemAnnot(g, row_annotations, lastSSX, x, y,
                           iconOffset, startRes, column, validRes, validEnd);
-                  temp = x;
+                  // temp = x;
                   break;
 
                 case 'H':
@@ -866,13 +867,13 @@ public class AnnotationRenderer
                   drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
                           lastSSX, x, y, iconOffset, startRes, column,
                           validRes, validEnd);
-                  temp = x;
+                  // temp = x;
                   break;
                 default:
                   g.setColor(Color.gray);
                   g.fillRect(lastSSX, y + 6 + iconOffset,
                           (x * charWidth) - lastSSX, 2);
-                  temp = x;
+                  // temp = x;
                   break;
                 }
               }
@@ -1113,7 +1114,7 @@ public class AnnotationRenderer
 
   public static final Color STEM_COLOUR = Color.blue;
 
-  private Color sdNOTCANONICAL_COLOUR;
+  // private Color sdNOTCANONICAL_COLOUR;
 
   void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
           int y, int iconOffset, int startRes, int column, boolean validRes,
@@ -1505,7 +1506,7 @@ public class AnnotationRenderer
             /**
              * Java only
              * 
-             * @j2sNative
+             * @j2sIgnore
              */
             {
               // Java ('normal') method is to scale the font to fit