Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/schemes/CovariationColourScheme.java b/src/jalview/schemes/CovariationColourScheme.java
index dc7971b..4884283 100644 (file)
--- a/src/jalview/schemes/CovariationColourScheme.java
+++ b/src/jalview/schemes/CovariationColourScheme.java
@@ -65,9 +65,9 @@ public class CovariationColourScheme extends ResidueColourScheme
 
     for (int x = 0; x < this.annotation._rnasecstr.length; x++)
     {
-      // System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x] + " Begin" +
       // this.annotation._rnasecstr[x].getBegin());
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      // jalview.bin.Console.outPrintln(this.annotation._rnasecstr[x].getFeatureGroup());
       // pairs.put(this.annotation._rnasecstr[x].getBegin(),
       // this.annotation._rnasecstr[x].getEnd());
 
@@ -104,7 +104,7 @@ public class CovariationColourScheme extends ResidueColourScheme
   @Override
   public Color findColour(char c)
   {
-    // System.out.println("called"); log.debug
+    // jalview.bin.Console.outPrintln("called"); log.debug
     // Generate a random pastel color
 
     return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
@@ -124,16 +124,16 @@ public class CovariationColourScheme extends ResidueColourScheme
   {
     Color currentColour = Color.white;
     String currentHelix = null;
-    // System.out.println(c + " " + j);
+    // jalview.bin.Console.outPrintln(c + " " + j);
     currentHelix = positionsToHelix.get(j);
-    // System.out.println(positionsToHelix.get(j));
+    // jalview.bin.Console.outPrintln(positionsToHelix.get(j));
 
     if (currentHelix != null)
     {
       currentColour = helixcolorhash.get(currentHelix);
     }
 
-    // System.out.println(c + " " + j + " helix " + currentHelix + " " +
+    // jalview.bin.Console.outPrintln(c + " " + j + " helix " + currentHelix + " " +
     // currentColour);
     return currentColour;
   }