JAL-1065 JAL-1066 - use direct object reference rather then index into alignment

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 32ff59a..2bd3a9e 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -87,7 +87,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 4ebe3b7..19ca45d 100755 (executable)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -397,7 +397,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       try
       {
-        col = oldColourScheme.findColour(aa.charAt(0), -1, -1);
+        col = oldColourScheme.findColour(aa.charAt(0), -1, null);
       } catch (Exception ex)
       {
       }

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 15f1928..9c25e0d 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -115,7 +115,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq.getIndex());
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 8566e82..ca60354 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -386,7 +386,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         try
         {
-          col = oldColourScheme.findColour(aa.charAt(0), -1, -1);
+          col = oldColourScheme.findColour(aa.charAt(0), -1, null);
         } catch (Exception ex)
         {
         }

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 5d12cce..b0365ce 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -19,6 +19,7 @@ package jalview.schemes;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 
@@ -154,7 +155,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
    * @return DOCUMENT ME!
    */
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
 
@@ -204,7 +205,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
           if (colourScheme != null)
           {
-            currentColour = colourScheme.findColour(c, j, sequenceIndex);
+            currentColour = colourScheme.findColour(c, j, seq);
           }
           else if (range != 0)
           {

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index c511ded..27b8996 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -20,7 +20,7 @@ package jalview.schemes;
 import jalview.analysis.AAFrequency;
 
 import java.awt.Color;
-
+import jalview.datamodel.SequenceI;
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
   public Blosum62ColourScheme()
@@ -29,7 +29,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public Color findColour(char res, int j, int sequenceIndex)
+  public Color findColour(char res, int j, SequenceI seq)
   {
     if ('a' <= res && res <= 'z')
     {

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index ad6d37f..7258605 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -258,7 +258,7 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
   }
 
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index e8e5828..b197906 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -19,11 +19,12 @@ package jalview.schemes;
 
 import java.awt.Color;
 
+import jalview.datamodel.SequenceI;
 public interface ColourSchemeI
 {
   public Color findColour(char c);
 
-  public Color findColour(char c, int j, int sequenceIndex);
+  public Color findColour(char c, int j, SequenceI seq);
 
   public void setConsensus(java.util.Hashtable[] h);
 

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index df4d9a9..1de5764 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -17,6 +17,8 @@
  */
 package jalview.schemes;
 
+import jalview.datamodel.SequenceI;
+
 import java.awt.Color;
 
 /**
@@ -61,7 +63,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
    * @return DOCUMENT ME!
    */
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
     if ((threshold == 0) || aboveThreshold(c, j))

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index c4f7eb5..a64bf20 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -19,6 +19,7 @@ package jalview.schemes;
 
 import jalview.analysis.AAFrequency;
 import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 
@@ -38,7 +39,7 @@ public class PIDColourScheme extends ResidueColourScheme
 
   
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     if ('a' <= c && c <= 'z')
     {

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index cc7f0d8..5c0aa53 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -19,6 +19,7 @@ package jalview.schemes;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 import java.util.Hashtable;
@@ -83,7 +84,7 @@ public class ResidueColourScheme implements ColourSchemeI
   }
 
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
 

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 49aeeeb..7cd5cb6 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -17,6 +17,8 @@
  */
 package jalview.schemes;
 
+import jalview.datamodel.SequenceI;
+
 import java.awt.Color;
 
 /**
@@ -86,7 +88,7 @@ public class ScoreColourScheme extends ResidueColourScheme
    * @return DOCUMENT ME!
    */
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     if (threshold > 0)
     {

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 0c1e688..62dfec5 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -19,6 +19,7 @@ package jalview.schemes;
 
 import java.awt.Color;
 import java.util.StringTokenizer;
+import jalview.datamodel.SequenceI;
 
 public class UserColourScheme extends ResidueColourScheme
 {
@@ -201,7 +202,7 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public Color findColour(char c, int j, int sequenceIndex)
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];