Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index c61606e..70991c6 100644 (file)
--- 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;
@@ -69,8 +71,14 @@ public class AnnotationRenderer
 
   private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS();
 
-  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;
 
@@ -86,6 +94,8 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
+  private boolean av_ignoreBelowBackground;
+
   /**
    * attributes set from AwtRenderPanelI
    */
@@ -344,8 +354,12 @@ 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
@@ -361,17 +375,25 @@ 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
@@ -500,6 +522,28 @@ 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 if (row == consensusAnnot || row == structConsensusAnnot
+              || row == complementConsensusAnnot)
+      {
+        renderHistogram = av_renderHistogram;
+        renderProfile = av_renderProfile;
+        normaliseProfile = av_normaliseProfile;
+      }
 
       Annotation[] row_annotations = row.annotations;
       if (!row.visible)