JAL-98 ProfilesI container for profiles for columns

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index e58ba02..a0e530c 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -28,6 +28,7 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ProfilesI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Platform;
@@ -73,7 +74,7 @@ public class AnnotationRenderer
 
   private ColumnSelection columnSelection;
 
-  private Hashtable[] hconsensus;
+  private ProfilesI hconsensus;
 
   private Hashtable[] complementConsensus;
 
@@ -151,9 +152,9 @@ public class AnnotationRenderer
     annotationPanel = null;
   }
 
-  void drawStemAnnot(Graphics g, Annotation[] row_annotations,
-          int lastSSX, int x, int y, int iconOffset, int startRes,
-          int column, boolean validRes, boolean validEnd)
+  void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
+          int x, int y, int iconOffset, int startRes, int column,
+          boolean validRes, boolean validEnd)
   {
     g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth) + startRes;
@@ -351,7 +352,7 @@ public class AnnotationRenderer
       {
         // TODO? group consensus for cDNA complement
         return AAFrequency.extractProfile(
-                aa.groupRef.consensusData[column],
+                aa.groupRef.consensusData.get(column),
                 aa.groupRef.getIgnoreGapsConsensus());
       }
       // TODO extend annotation row to enable dynamic and static profile data to
@@ -365,7 +366,8 @@ public class AnnotationRenderer
         }
         else
         {
-          return AAFrequency.extractProfile(hconsensus[column],
+          return AAFrequency.extractProfile(
+hconsensus.get(column),
                   av_ignoreGapsConsensus);
         }
       }
@@ -1085,8 +1087,8 @@ public class AnnotationRenderer
 
   private Color sdNOTCANONICAL_COLOUR;
 
-  void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
-          int x, int y, int iconOffset, int startRes, int column,
+  void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
+          int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
     g.setColor(GLYPHLINE_COLOR);
@@ -1117,8 +1119,8 @@ public class AnnotationRenderer
 
   }
 
-  void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
-          int x, int y, int iconOffset, int startRes, int column,
+  void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
+          int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
     g.setColor(HELIX_COLOUR);