update spikes/mungo from JAL-3076 patch branch

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index b2e569e..adca17e 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -29,14 +29,12 @@ 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;
@@ -72,14 +70,8 @@ public class AnnotationRenderer
 
   private final boolean MAC = Platform.isAMac();
 
-  // 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;
+  boolean av_renderHistogram = true, av_renderProfile = true,
+          av_normaliseProfile = false;
 
   ResidueShaderI profcolour = null;
 
@@ -95,8 +87,6 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
-  private boolean av_ignoreBelowBackground;
-
   /**
    * attributes set from AwtRenderPanelI
    */
@@ -351,16 +341,12 @@ public class AnnotationRenderer
     }
     columnSelection = av.getColumnSelection();
     hiddenColumns = av.getAlignment().getHiddenColumns();
-    hconsensus = av.getConsensusProfiles();
+    hconsensus = av.getSequenceConsensusHash();
     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
@@ -376,25 +362,17 @@ 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 (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")))
+    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.getConsensusData() != null
+      if (aa.groupRef != null && aa.groupRef.consensusData != null
               && aa.groupRef.isShowSequenceLogo())
       {
         // TODO? group consensus for cDNA complement
         return AAFrequency.extractProfile(
-                aa.groupRef.getConsensusData().get(column),
-                aa.groupRef.isIgnoreGapsConsensus());
+                aa.groupRef.consensusData.get(column),
+                aa.groupRef.getIgnoreGapsConsensus());
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
@@ -527,21 +505,6 @@ 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;