X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=518c17924b7fea6fba291c2cefbc052e544c44c7;hb=19842e7d0674a3f4235e66605e4079b3dbd58bb8;hp=e30fb0c9c001b91695d9418b7f94b886632f4b21;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index e30fb0c..518c179 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -28,9 +28,12 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.ProfilesI;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.ResidueProperties;
+import jalview.schemes.ZappoColourScheme;
 import jalview.util.Platform;
 
 import java.awt.BasicStroke;
@@ -70,9 +73,11 @@ public class AnnotationRenderer
   boolean av_renderHistogram = true, av_renderProfile = true,
           av_normaliseProfile = false;
 
-  ColourSchemeI profcolour = null;
+  ResidueShaderI profcolour = null;
 
   private ColumnSelection columnSelection;
+  
+  private HiddenColumns hiddenColumns;
 
   private ProfilesI hconsensus;
 
@@ -305,22 +310,27 @@ public class AnnotationRenderer
   public void updateFromAlignViewport(AlignViewportI av)
   {
     charWidth = av.getCharWidth();
-    endRes = av.getEndRes();
+    endRes = av.getRanges().getEndRes();
     charHeight = av.getCharHeight();
     hasHiddenColumns = av.hasHiddenColumns();
     validCharWidth = av.isValidCharWidth();
     av_renderHistogram = av.isShowConsensusHistogram();
     av_renderProfile = av.isShowSequenceLogo();
     av_normaliseProfile = av.isNormaliseSequenceLogo();
-    profcolour = av.getGlobalColourScheme();
-    if (profcolour == null)
+    profcolour = av.getResidueShading();
+    if (profcolour == null || profcolour.getColourScheme() == null)
     {
-      // Set the default colour for sequence logo if the alignment has no
-      // colourscheme set
-      profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
-              : new jalview.schemes.ZappoColourScheme();
+      /*
+       * Use default colour for sequence logo if 
+       * the alignment has no colourscheme set
+       * (would like to use user preference but n/a for applet)
+       */
+      ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
+              : new ZappoColourScheme();
+      profcolour = new ResidueShader(col);
     }
     columnSelection = av.getColumnSelection();
+    hiddenColumns = av.getAlignment().getHiddenColumns();
     hconsensus = av.getSequenceConsensusHash();
     complementConsensus = av.getComplementConsensusHash();
     hStrucConsensus = av.getRnaStructureConsensusHash();
@@ -583,7 +593,7 @@ hconsensus.get(column),
         {
           if (hasHiddenColumns)
           {
-            column = columnSelection.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1225,7 +1235,7 @@ hconsensus.get(column),
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)
@@ -1304,7 +1314,7 @@ hconsensus.get(column),
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)
@@ -1423,11 +1433,12 @@ hconsensus.get(column),
             {
               final String codonTranslation = ResidueProperties
                       .codonTranslate(new String(dc));
-              colour = profcolour.findColour(codonTranslation.charAt(0));
+              colour = profcolour.findColour(codonTranslation.charAt(0),
+                      column, null);
             }
             else
             {
-              colour = profcolour.findColour(dc[0]);
+              colour = profcolour.findColour(dc[0], column, null);
             }
             g.setColor(colour == Color.white ? Color.lightGray : colour);