X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=40fb513b158e3a5a2ec77730f56463bef87f48f4;hb=6398c0217546a4d6943f63f670c2684c7c7274be;hp=8a80d41f149c11d1f17cd782c887f3b8354adbcb;hpb=14b1b2a878190d5fffda298c4b9a901c72c74ad3;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 8a80d41..40fb513 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -29,12 +29,14 @@ 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 jalview.workers.InformationThread;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -70,8 +72,14 @@ public class AnnotationRenderer
 
   private final boolean MAC = Platform.isAMac();
 
-  boolean av_renderHistogram = true, av_renderProfile = true,
-          av_normaliseProfile = false;
+  // todo remove these flags, read from group/viewport where needed
+  boolean av_renderHistogram = true;
+
+  boolean av_renderProfile = true;
+
+  boolean av_normaliseProfile = false;
+
+  boolean av_infoHeight = false;
 
   ResidueShaderI profcolour = null;
 
@@ -87,6 +95,8 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
+  private boolean av_ignoreBelowBackground;
+
   /**
    * attributes set from AwtRenderPanelI
    */
@@ -163,7 +173,7 @@ public class AnnotationRenderer
   {
     g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -230,7 +240,7 @@ public class AnnotationRenderer
 
     g.setColor(nonCanColor);
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -345,8 +355,12 @@ public class AnnotationRenderer
     complementConsensus = av.getComplementConsensusHash();
     hStrucConsensus = av.getRnaStructureConsensusHash();
     av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+    av_ignoreBelowBackground = av.isIgnoreBelowBackground();
+    av_infoHeight = av.isInfoLetterHeight();
   }
 
+
+
   /**
    * 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
@@ -362,17 +376,25 @@ 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.autoCalculated && (aa.label.startsWith("Consensus")
-            || aa.label.startsWith("cDNA Consensus")))
+    if (InformationThread.HMM_CALC_ID.equals(aa.getCalcId()))
+    {
+      HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
+      return AAFrequency.extractHMMProfile(hmm, column,
+              av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
+                                         // pipeline
+    }
+    if (aa.autoCalculated
+            && (aa.label.startsWith("Consensus") || aa.label
+                    .startsWith("cDNA Consensus")))
     {
       boolean forComplement = aa.label.startsWith("cDNA Consensus");
-      if (aa.groupRef != null && aa.groupRef.consensusData != null
+      if (aa.groupRef != null && aa.groupRef.getConsensusData() != null
               && aa.groupRef.isShowSequenceLogo())
       {
         // TODO? group consensus for cDNA complement
         return AAFrequency.extractProfile(
-                aa.groupRef.consensusData.get(column),
-                aa.groupRef.getIgnoreGapsConsensus());
+                aa.groupRef.getConsensusData().get(column),
+						aa.groupRef.getIgnoreGapsConsensus());
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
@@ -505,6 +527,21 @@ public class AnnotationRenderer
           renderProfile = av_renderProfile;
           normaliseProfile = av_normaliseProfile;
         }
+        else if (InformationThread.HMM_CALC_ID.equals(row.getCalcId()))
+        {
+          if (row.groupRef != null)
+          {
+            renderHistogram = row.groupRef.isShowInformationHistogram();
+            renderProfile = row.groupRef.isShowHMMSequenceLogo();
+            normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo();
+          }
+          else
+          {
+            renderHistogram = av.isShowInformationHistogram();
+            renderProfile = av.isShowHMMSequenceLogo();
+            normaliseProfile = av.isNormaliseHMMSequenceLogo();
+          }
+        }
         else
         {
           renderHistogram = true;
@@ -602,7 +639,7 @@ public class AnnotationRenderer
         {
           if (hasHiddenColumns)
           {
-            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1150,7 +1187,7 @@ public class AnnotationRenderer
     g.setColor(HELIX_COLOUR);
 
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -1250,7 +1287,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)
@@ -1330,7 +1367,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)