JAL-2446 merged to spike branch

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index e12b88a..518c179 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -22,15 +22,18 @@ package jalview.renderer;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.CodingUtils;
-import jalview.analysis.Profile;
 import jalview.analysis.Rna;
 import jalview.analysis.StructureFrequency;
 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;
@@ -70,11 +73,13 @@ 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 Profile[] hconsensus;
+  private ProfilesI hconsensus;
 
   private Hashtable[] complementConsensus;
 
@@ -152,9 +157,9 @@ 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;
@@ -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 alignnent 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();
@@ -352,7 +362,7 @@ 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
@@ -366,7 +376,8 @@ public class AnnotationRenderer
         }
         else
         {
-          return AAFrequency.extractProfile(hconsensus[column],
+          return AAFrequency.extractProfile(
+hconsensus.get(column),
                   av_ignoreGapsConsensus);
         }
       }
@@ -582,7 +593,7 @@ public class AnnotationRenderer
         {
           if (hasHiddenColumns)
           {
-            column = columnSelection.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1086,8 +1097,8 @@ 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);
@@ -1118,8 +1129,8 @@ 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);
@@ -1224,7 +1235,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)
@@ -1303,7 +1314,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)