test HMM annotaTION

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 640bf45..95bbf28 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.util.QuickSort;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -50,7 +48,6 @@ import java.awt.geom.AffineTransform;
 import java.awt.image.ImageObserver;
 import java.util.BitSet;
 import java.util.Hashtable;
-import java.util.List;
 
 public class AnnotationRenderer
 {
@@ -60,10 +57,6 @@ public class AnnotationRenderer
 
   private static final int CHAR_Z = 'Z'; // 90
 
-  private static final int AMINO = 0;
-
-  private static final int DNA = 1;
-
   /**
    * flag indicating if timing and redraw parameter info should be output
    */
@@ -344,94 +337,7 @@ public class AnnotationRenderer
     av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
   }
 
-  public int[] getHMMProfileFor(AlignmentAnnotation aa, int column,
-          boolean removeBelowBackground)
-  {
-
-    HiddenMarkovModel hmm;
-    hmm = aa.getHMM();
-    int size = 0;
-    int alphabet = 0;
-    String alph = hmm.getAlphabetType();
-    if (alph.equals("amino"))
-    {
-      size = 20;
-      alphabet = AMINO;
-    }
-    else if (alph.equals("DNA"))
-    {
-      size = 4;
-      alphabet = DNA;
-    }
-
-    char symbols[] = new char[size];
-    int values[] = new int[size];
 
-    List<Character> charList = hmm.getSymbols();
-
-    int i = 0;
-    for (char character : charList)
-    {
-      symbols[i] = character;
-      i++;
-    }
-
-    Integer totalCount = 0;
-    for (int j = 0; j < size; j++)
-    {
-      Double value;
-      char symbol = symbols[j];
-      value = hmm.getMatchEmissionProbability(column, symbol);
-      double freq;
-
-      if (alphabet == AMINO && removeBelowBackground)
-      {
-        freq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
-        if (value < freq)
-        {
-          value = 0d;
-        }
-      }
-      else if (alphabet == DNA && removeBelowBackground)
-      {
-        freq = ResidueProperties.nucleotideBackgroundFrequencies
-                .get(symbol);
-        if (value < freq)
-        {
-          value = 0d;
-        }
-      }
-      value = value * 10000;
-      values[j] = value.intValue();
-      totalCount += value.intValue();
-    }
-
-    QuickSort.sort(values, symbols);
-
-    int[] profile = new int[3 + size * 2];
-
-    profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
-    profile[1] = size;
-    profile[2] = totalCount;
-
-    if (totalCount != 0)
-    {
-      int arrayPos = 3;
-      for (int k = size - 1; k >= 0; k--)
-      {
-        Double percentage;
-        Integer value = values[k];
-        percentage = (value.doubleValue() / totalCount.doubleValue())
-                * 100d;
-        profile[arrayPos] = symbols[k];
-        profile[arrayPos + 1] = percentage.intValue();
-        arrayPos += 2;
-      }
-    }
-
-    return profile;
-
-  }
 
   /**
    * Returns profile data; the first element is the profile type, the second is
@@ -450,7 +356,8 @@ public class AnnotationRenderer
     //
     if (aa.label.startsWith("Information"))
     {
-      return getHMMProfileFor(aa, column, true);
+      return AAFrequency.getHMMProfileFor(aa, column,
+              true); // TODO detect setting
     }
     if (aa.autoCalculated
             && (aa.label.startsWith("Consensus") || aa.label