X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=be4f49723b455cfa58fef0d918aae9ade6d4551e;hb=71a3cc0202bd8b731f01e5706372e9bae047d592;hp=1311405e8294cf3d2a6319a75aef1e459ebbdfdd;hpb=13f26fb9d1c8d6f27fcedbf5c760f8e3947fd145;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 1311405..be4f497 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,
@@ -1389,7 +1390,8 @@ public class AnnotationRenderer
           boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
           boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
           float ht = normaliseProfile ? y - _aa.graphHeight : y1;
-          final double normaliseFactor = normaliseProfile ? _aa.graphHeight : (y2 - y1);
+          final double normaliseFactor = normaliseProfile ? _aa.graphHeight
+                  : (y2 - y1);
 
           /**
            * Render a single base for a sequence profile, a base pair for
@@ -1440,7 +1442,7 @@ public class AnnotationRenderer
               s = new String(dc);
             }
             // next profl[] position is profile % for the character(s)
-            
+
             int percent = profl[c++];
             if (percent == 0)
             {
@@ -1473,9 +1475,9 @@ public class AnnotationRenderer
             // (int)(scl));
             // g.setColor(profcolour.findColour(dc[0]).darker());
 
-            double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);            
+            double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
             double sy = newHeight / asc;
-            double newAsc = asc * sy; 
+            double newAsc = asc * sy;
             double newDec = dec * sy;
             // it is not necessary to recalculate lm for the new font.
             // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
@@ -1501,15 +1503,21 @@ public class AnnotationRenderer
               ht2 += newHeight;
             }
             else
+            /**
+             * Java only
+             * 
+             * @j2sIgnore
+             */
             {
-              /*
-               * Java ('normal') method is to scale the font to fit
-               */
+              // Java ('normal') method is to scale the font to fit
+
               final int hght = (int) (ht + (newAsc - newDec));
               Font font = ofont
                       .deriveFont(AffineTransform.getScaleInstance(sx, sy));
               g.setFont(font);
               g.drawChars(dc, 0, dc.length, x * charWidth, hght);
+              g.setFont(ofont);
+
               ht += newHeight;
             }
           }
@@ -1523,7 +1531,7 @@ public class AnnotationRenderer
       Graphics2D g2 = (Graphics2D) g;
       g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
               BasicStroke.JOIN_ROUND, 3f, new float[]
-      { 5f, 3f }, 0f));
+              { 5f, 3f }, 0f));
 
       y2 = (int) (y
               - ((_aa.threshold.value - min) / range) * _aa.graphHeight);