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 548291c..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;
 
@@ -80,12 +88,14 @@ public class AnnotationRenderer
 
   private ProfilesI hconsensus;
 
-  private Hashtable[] complementConsensus;
+  private Hashtable<String, Object>[] complementConsensus;
 
-  private Hashtable[] hStrucConsensus;
+  private Hashtable<String, Object>[] hStrucConsensus;
 
   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
@@ -446,7 +468,7 @@ public class AnnotationRenderer
     updateFromAwtRenderPanel(annotPanel, av);
     fm = g.getFontMetrics();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-    int temp = 0;
+    // int temp = 0;
     if (aa == null)
     {
       return false;
@@ -459,8 +481,8 @@ public class AnnotationRenderer
     boolean validRes = false;
     boolean validEnd = false;
     boolean labelAllCols = false;
-    boolean centreColLabels;
-    boolean centreColLabelsDef = av.isCentreColumnLabels();
+//    boolean centreColLabels;
+//    boolean centreColLabelsDef = av.isCentreColumnLabels();
     boolean scaleColLabel = false;
     final AlignmentAnnotation consensusAnnot = av
             .getAlignmentConsensusAnnotation();
@@ -500,13 +522,35 @@ 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)
       {
         continue;
       }
-      centreColLabels = row.centreColLabels || centreColLabelsDef;
+//      centreColLabels = row.centreColLabels || centreColLabelsDef;
       labelAllCols = row.showAllColLabels;
       scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
@@ -774,7 +818,7 @@ public class AnnotationRenderer
               if (x > -1)
               {
 
-                int nb_annot = x - temp;
+                // int nb_annot = x - temp;
                 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
                 // annot :"+nb_annot);
                 switch (lastSS)
@@ -783,7 +827,7 @@ public class AnnotationRenderer
                 case ')': // and opposite direction
                   drawStemAnnot(g, row_annotations, lastSSX, x, y,
                           iconOffset, startRes, column, validRes, validEnd);
-                  temp = x;
+                  // temp = x;
                   break;
 
                 case 'H':
@@ -866,13 +910,13 @@ public class AnnotationRenderer
                   drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
                           lastSSX, x, y, iconOffset, startRes, column,
                           validRes, validEnd);
-                  temp = x;
+                  // temp = x;
                   break;
                 default:
                   g.setColor(Color.gray);
                   g.fillRect(lastSSX, y + 6 + iconOffset,
                           (x * charWidth) - lastSSX, 2);
-                  temp = x;
+                  // temp = x;
                   break;
                 }
               }
@@ -1113,7 +1157,7 @@ public class AnnotationRenderer
 
   public static final Color STEM_COLOUR = Color.blue;
 
-  private Color sdNOTCANONICAL_COLOUR;
+  // private Color sdNOTCANONICAL_COLOUR;
 
   void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
           int y, int iconOffset, int startRes, int column, boolean validRes,