JAL-2371 slight simplification of findColour overrides

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 49260a4..3c9f095 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
@@ -278,10 +279,8 @@ public class ClustalxColourScheme extends ResidueColourScheme
   @Override
   protected Color findColour(char c, int j, SequenceI seq)
   {
-    Color currentColour;
-
     // TODO why the test for includeGaps here?
-    if (cons2.length <= j
+    if (cons2.length <= j || Comparison.isGap(c)
     /*|| (includeGaps && threshold != 0 && !aboveThreshold(c, j))*/)
     {
       return Color.white;
@@ -289,11 +288,11 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     int i = ResidueProperties.aaIndex[c];
 
-    currentColour = Color.white;
+    Color colour = Color.white;
 
     if (i > 19)
     {
-      return currentColour;
+      return colour;
     }
 
     for (int k = 0; k < residueColour[i].cons.length; k++)
@@ -301,7 +300,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
       if (residueColour[i].cons[k].isConserved(cons2, j, size,
               includeGaps))
       {
-        currentColour = residueColour[i].c;
+        colour = residueColour[i].c;
       }
     }
 
@@ -312,11 +311,11 @@ public class ClustalxColourScheme extends ResidueColourScheme
        */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
-        currentColour = ClustalColour.PINK.colour;
+        colour = ClustalColour.PINK.colour;
       }
     }
 
-    return currentColour;
+    return colour;
   }
 
   /**

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index d1e18ef..abae733 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -24,7 +24,6 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
-import java.awt.Color;
 import java.util.Map;
 
 /**
@@ -43,20 +42,6 @@ public class NucleotideColourScheme extends ResidueColourScheme
     super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public Color findColour(char c)
-  {
-    return colors[ResidueProperties.nucleotideIndex[c]];
-  }
-
   @Override
   public boolean isNucleotideSpecific()
   {

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index a6301fa..6ca1393 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -57,7 +57,7 @@ public class PIDColourScheme extends ResidueColourScheme
       c -= ('a' - 'A');
     }
 
-    if (consensusResidue == null)
+    if (consensusResidue == null || Comparison.isGap(c))
     {
       return Color.white;
     }
@@ -71,15 +71,12 @@ public class PIDColourScheme extends ResidueColourScheme
             String.valueOf(c));
     if (matchesConsensus)
     {
-      if (!Comparison.isGap(c))
+      for (int i = 0; i < thresholds.length; i++)
       {
-        for (int i = 0; i < thresholds.length; i++)
+        if (pid > thresholds[i])
         {
-          if (pid > thresholds[i])
-          {
-            colour = pidColours[i];
-            break;
-          }
+          colour = pidColours[i];
+          break;
         }
       }
     }

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 47b80c2..1b36f30 100644 (file)
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -24,7 +24,6 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
-import java.awt.Color;
 import java.util.Map;
 
 /**
@@ -43,21 +42,6 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
             ResidueProperties.purinepyrimidine);
   }
 
-  /**
-   * Finds the corresponding color for the type of character inputed
-   * 
-   * @param c
-   *          Character in sequence
-   * 
-   * @return Color from purinepyrimidineIndex in
-   *         jalview.schemes.ResidueProperties
-   */
-  @Override
-  public Color findColour(char c)
-  {
-    return colors[ResidueProperties.purinepyrimidineIndex[c]];
-  }
-
   @Override
   public boolean isNucleotideSpecific()
   {

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index fc8b1b1..892c3e8 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
@@ -89,7 +90,16 @@ public abstract class ResidueColourScheme implements ColourSchemeI
   @Override
   public Color findColour(char c)
   {
-    return colors == null ? Color.white : colors[symbolIndex[c]];
+    Color colour = Color.white;
+
+    if (!Comparison.isGap(c) && colors != null && symbolIndex != null
+            && c < symbolIndex.length
+            && symbolIndex[c] < colors.length)
+    {
+      colour = colors[symbolIndex[c]];
+    }
+
+    return colour;
   }
 
   /**
@@ -104,18 +114,19 @@ public abstract class ResidueColourScheme implements ColourSchemeI
     return findColour(c, j, seq);
   }
 
+  /**
+   * Default implementation looks up the residue colour in a fixed scheme, or
+   * returns White if not found. Override this method for a colour scheme that
+   * depends on the column position or sequence.
+   * 
+   * @param c
+   * @param j
+   * @param seq
+   * @return
+   */
   protected Color findColour(char c, int j, SequenceI seq)
   {
-    Color colour = Color.white;
-
-    if (colors != null && symbolIndex != null && c < symbolIndex.length
-            && symbolIndex[c] < colors.length)
-    {
-      colour = colors[symbolIndex[c]];
-    }
-    // colour = adjustColour(c, j, colour);
-
-    return colour;
+    return findColour(c);
   }
 
   @Override

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 6850d79..aa20121 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -23,7 +23,6 @@ package jalview.schemes;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
-import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.Map;
@@ -88,27 +87,6 @@ public class ScoreColourScheme extends ResidueColourScheme
   /**
    * DOCUMENT ME!
    * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public Color findColour(char c, int j, SequenceI seq)
-  {
-    if (Comparison.isGap(c))
-    {
-      return Color.white;
-    }
-
-    return colors[ResidueProperties.aaIndex[c]];
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param c
    *          DOCUMENT ME!
    * 

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index d95652d..85bf54e 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -238,24 +238,6 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  @Override
-  public Color findColour(char c, int j, SequenceI seq)
-  {
-    Color colour;
-    int index = ResidueProperties.aaIndex[c];
-
-    if (lowerCaseColours != null && 'a' <= c && c <= 'z')
-    {
-      colour = lowerCaseColours[index];
-    }
-    else
-    {
-      colour = colors[index];
-    }
-
-    return colour;
-  }
-
   public void setLowerCaseColours(Color[] lcolours)
   {
     lowerCaseColours = lcolours;