JAL-1066 - T-Coffee color scheme + signature change on findColour method

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index e265598..5d12cce 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -17,9 +17,10 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
 
-import jalview.datamodel.*;
+import java.awt.Color;
 
 public class AnnotationColourGradient extends ResidueColourScheme
 {
@@ -152,7 +153,8 @@ public class AnnotationColourGradient extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     Color currentColour = Color.white;
 
@@ -202,7 +204,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
           if (colourScheme != null)
           {
-            currentColour = colourScheme.findColour(c, j);
+            currentColour = colourScheme.findColour(c, j, sequenceIndex);
           }
           else if (range != 0)
           {

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 3236b55..c511ded 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -17,9 +17,9 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.analysis.AAFrequency;
 
-import jalview.analysis.*;
+import java.awt.Color;
 
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
@@ -28,7 +28,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
     super();
   }
 
-  public Color findColour(char res, int j)
+  @Override
+  public Color findColour(char res, int j, int sequenceIndex)
   {
     if ('a' <= res && res <= 'z')
     {

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 309bdc2..ad6d37f 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -17,11 +17,11 @@
  */
 package jalview.schemes;
 
-import java.util.*;
+import jalview.datamodel.SequenceI;
 
-import java.awt.*;
-
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class ClustalxColourScheme extends ResidueColourScheme // implements
 // IParameterizable
@@ -251,12 +251,14 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
     ResidueColour[19] = colours[0]; // V
   }
 
+  @Override
   public Color findColour(char c)
   {
     return Color.pink;
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     Color currentColour;
 

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index fdda463..e8e5828 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -17,13 +17,13 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 public interface ColourSchemeI
 {
   public Color findColour(char c);
 
-  public Color findColour(char c, int j);
+  public Color findColour(char c, int j, int sequenceIndex);
 
   public void setConsensus(java.util.Hashtable[] h);
 

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 0f758e0..3738f61 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -17,7 +17,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
@@ -81,6 +81,9 @@ public class ColourSchemeProperty
   public static final int PURINEPYRIMIDINE = 13;
 
   public static final int COVARIATION = 14;
+  
+  public static final int TCOFFEE = 15;
+  
 
   /**
    * index of first colourscheme (includes 'None')
@@ -145,6 +148,11 @@ public class ColourSchemeProperty
     {
       ret = NUCLEOTIDE;
     }
+    else if (name.equalsIgnoreCase("T-Coffee scores"))
+    {
+      ret = TCOFFEE;
+    }
+
     else if (name.equalsIgnoreCase("User Defined"))
     {
       ret = USER_DEFINED;

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 249d87d..df4d9a9 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -17,7 +17,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
@@ -43,6 +43,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color findColour(char c)
   {
     // System.out.println("called"); log.debug
@@ -59,7 +60,8 @@ public class NucleotideColourScheme extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     Color currentColour;
     if ((threshold == 0) || aboveThreshold(c, j))

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 23a2ee2..c4f7eb5 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -17,10 +17,10 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.SequenceGroup;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import java.awt.Color;
 
 public class PIDColourScheme extends ResidueColourScheme
 {
@@ -36,7 +36,9 @@ public class PIDColourScheme extends ResidueColourScheme
     this.thresholds = ResidueProperties.pidThresholds;
   }
 
-  public Color findColour(char c, int j)
+  
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     if ('a' <= c && c <= 'z')
     {

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 5402d75..cc7f0d8 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -17,11 +17,11 @@
  */
 package jalview.schemes;
 
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
 
-import java.awt.*;
-
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Hashtable;
 
 /**
  * DOCUMENT ME!
@@ -82,7 +82,8 @@ public class ResidueColourScheme implements ColourSchemeI
             : colors[ResidueProperties.aaIndex[c]];
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     Color currentColour;
 

diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java
index 37dd9e5..49aeeeb 100755 (executable)
--- a/src/jalview/schemes/ScoreColourScheme.java
+++ b/src/jalview/schemes/ScoreColourScheme.java
@@ -17,7 +17,7 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
@@ -85,7 +85,8 @@ public class ScoreColourScheme extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     if (threshold > 0)
     {

diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
new file mode 100644 (file)
index 0000000..740c15e
--- /dev/null
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -0,0 +1,66 @@
+package jalview.schemes;
+
+import jalview.io.TCoffeeScoreFile;
+
+import java.awt.Color;
+
+/**
+ * Defines the color score for T-Coffee MSA 
+ * <p>
+ * See http://tcoffee.org
+ * 
+ * 
+ * @author Paolo Di Tommaso
+ *
+ */
+public class TCoffeeColourScheme extends ResidueColourScheme {
+
+       static final Color[] colors = {
+               new Color( 102, 102, 255 ),     // #6666FF
+               new Color( 0, 255, 0),          // #00FF00
+               new Color( 102, 255, 0),        // #66FF00
+               new Color( 204, 255, 0),        // #CCFF00
+               new Color( 255, 255, 0),        // #FFFF00
+               new Color( 255, 204, 0),        // #FFCC00
+               new Color( 255, 153, 0),        // #FF9900
+               new Color( 255, 102, 0),        // #FF6600
+               new Color( 255, 51, 0),         // #FF3300
+               new Color( 255, 34, 0)          // #FF2000
+       };
+
+
+       byte[][] scoreMatrix = null;
+
+       /**
+        * Initialize the color sheme based on the content of the T-Coffee score file 
+        * 
+        * @param scoreFile
+        */
+       public TCoffeeColourScheme(TCoffeeScoreFile scoreFile) {
+
+               scoreMatrix = scoreFile != null ? scoreFile.getScoresArray() : null;
+
+       }
+
+       @Override
+       public Color findColour(char c, int j, int sequenceIndex) {
+
+               if( scoreMatrix == null ) {
+                       return Color.white;
+               }
+               
+               if( sequenceIndex<0  || sequenceIndex >= scoreMatrix.length ) {
+                       System.out.printf("Sequence index out of range for the T-Coffee color scheme. Index:  %s\n", sequenceIndex);
+                       return Color.white;
+               }
+
+               byte[] seqScores = scoreMatrix[sequenceIndex]; 
+               if( j < 0 || j>= seqScores.length ) {
+                       System.out.printf("Residue index out of range for the T-Coffee color scheme. Sequence %s - residue: %s\n", sequenceIndex, j);
+                       return Color.white;
+               }
+               
+               byte val = seqScores[j];
+               return val >= 0 && val < colors.length ? colors[val] : Color.white;
+       }
+}

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index b6602ea..0c1e688 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -17,9 +17,8 @@
  */
 package jalview.schemes;
 
-import java.util.*;
-
-import java.awt.*;
+import java.awt.Color;
+import java.util.StringTokenizer;
 
 public class UserColourScheme extends ResidueColourScheme
 {
@@ -201,7 +200,8 @@ public class UserColourScheme extends ResidueColourScheme
 
   }
 
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, int sequenceIndex)
   {
     Color currentColour;
     int index = ResidueProperties.aaIndex[c];