JAL-98 use Profile to store consensus, ResidueCount for fast compact

[jalview.git] / src / jalview / schemes / ResidueColourScheme.java

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index bca98cf..e6b28db 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -20,15 +20,14 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
+import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
-import java.util.Hashtable;
 import java.util.Map;
 
 /**
@@ -48,10 +47,10 @@ public class ResidueColourScheme implements ColourSchemeI
   int threshold = 0;
 
   /* Set when threshold colouring to either pid_gaps or pid_nogaps */
-  protected String ignoreGaps = AAFrequency.PID_GAPS;
+  protected boolean ignoreGaps = false;
 
   /** Consenus as a hashtable array */
-  Hashtable[] consensus;
+  Profile[] consensus;
 
   /** Conservation string as a char array */
   char[] conservation;
@@ -100,6 +99,7 @@ public class ResidueColourScheme implements ColourSchemeI
   /**
    * Find a colour without an index in a sequence
    */
+  @Override
   public Color findColour(char c)
   {
     return colors == null ? Color.white : colors[symbolIndex[c]];
@@ -133,6 +133,7 @@ public class ResidueColourScheme implements ColourSchemeI
    * 
    * @return Returns the percentage threshold
    */
+  @Override
   public int getThreshold()
   {
     return threshold;
@@ -144,17 +145,11 @@ public class ResidueColourScheme implements ColourSchemeI
    * @param ct
    *          DOCUMENT ME!
    */
+  @Override
   public void setThreshold(int ct, boolean ignoreGaps)
   {
     threshold = ct;
-    if (ignoreGaps)
-    {
-      this.ignoreGaps = AAFrequency.PID_NOGAPS;
-    }
-    else
-    {
-      this.ignoreGaps = AAFrequency.PID_GAPS;
-    }
+    this.ignoreGaps = ignoreGaps;
   }
 
   /**
@@ -181,10 +176,9 @@ public class ResidueColourScheme implements ColourSchemeI
       return false;
     }
 
-    if ((((Integer) consensus[j].get(AAFrequency.MAXCOUNT)).intValue() != -1)
-            && consensus[j].contains(String.valueOf(c)))
+    if (consensus[j].getMaxCount() > 0) // != -1))
     {
-      if (((Float) consensus[j].get(ignoreGaps)).floatValue() >= threshold)
+      if (consensus[j].getPercentageIdentity(ignoreGaps) >= threshold)
       {
         return true;
       }
@@ -193,6 +187,7 @@ public class ResidueColourScheme implements ColourSchemeI
     return false;
   }
 
+  @Override
   public boolean conservationApplied()
   {
     return conservationColouring;
@@ -204,11 +199,13 @@ public class ResidueColourScheme implements ColourSchemeI
     conservationColouring = conservationApplied;
   }
 
+  @Override
   public void setConservationInc(int i)
   {
     inc = i;
   }
 
+  @Override
   public int getConservationInc()
   {
     return inc;
@@ -220,7 +217,8 @@ public class ResidueColourScheme implements ColourSchemeI
    * @param consensus
    *          DOCUMENT ME!
    */
-  public void setConsensus(Hashtable[] consensus)
+  @Override
+  public void setConsensus(Profile[] consensus)
   {
     if (consensus == null)
     {
@@ -230,6 +228,7 @@ public class ResidueColourScheme implements ColourSchemeI
     this.consensus = consensus;
   }
 
+  @Override
   public void setConservation(Conservation cons)
   {
     if (cons == null)