JAL-2629 moved HMM storage location to placeholder sequence

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 3fdcb3b..78b3a88 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -28,8 +28,13 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
+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;
@@ -69,11 +74,13 @@ 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 Hashtable[] hconsensus;
+  private ProfilesI hconsensus;
 
   private Hashtable[] complementConsensus;
 
@@ -81,6 +88,8 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
+  private boolean av_ignoreBelowBackground;
+
   /**
    * attributes set from AwtRenderPanelI
    */
@@ -304,28 +313,36 @@ 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();
     av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+    av_ignoreBelowBackground = av.isIgnoreBelowBackground();
   }
 
+
+
   /**
    * Returns profile data; the first element is the profile type, the second is
    * the number of distinct values, the third the total count, and the remainder
@@ -341,6 +358,13 @@ public class AnnotationRenderer
     // properties/rendering attributes as a global 'alignment group' which holds
     // all vis settings for the alignment as a whole rather than a subset
     //
+    if (aa.label.startsWith("Information"))
+    {
+      HiddenMarkovModel hmm = aa.getHMM();
+      return AAFrequency.getHMMProfileFor(hmm, column,
+              av_ignoreBelowBackground); // TODO check if this follows standard
+                                         // pipeline
+    }
     if (aa.autoCalculated
             && (aa.label.startsWith("Consensus") || aa.label
                     .startsWith("cDNA Consensus")))
@@ -351,7 +375,7 @@ 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 +389,8 @@ public class AnnotationRenderer
         }
         else
         {
-          return AAFrequency.extractProfile(hconsensus[column],
+          return AAFrequency.extractProfile(
+hconsensus.get(column),
                   av_ignoreGapsConsensus);
         }
       }
@@ -581,7 +606,7 @@ public class AnnotationRenderer
         {
           if (hasHiddenColumns)
           {
-            column = columnSelection.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1223,7 +1248,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)
@@ -1302,7 +1327,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)