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Merge branch 'develop' into features/JAL-4219_extended_fasta_rna_ss
[jalview.git]
/
src
/
jalview
/
schemes
/
CovariationColourScheme.java
diff --git
a/src/jalview/schemes/CovariationColourScheme.java
b/src/jalview/schemes/CovariationColourScheme.java
index
dc7971b
..
c91380e
100644
(file)
--- a/
src/jalview/schemes/CovariationColourScheme.java
+++ b/
src/jalview/schemes/CovariationColourScheme.java
@@
-65,9
+65,10
@@
public class CovariationColourScheme extends ResidueColourScheme
for (int x = 0; x < this.annotation._rnasecstr.length; x++)
{
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());
// 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());
// pairs.put(this.annotation._rnasecstr[x].getBegin(),
// this.annotation._rnasecstr[x].getEnd());
@@
-104,7
+105,7
@@
public class CovariationColourScheme extends ResidueColourScheme
@Override
public Color findColour(char c)
{
@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);
// Generate a random pastel color
return ResidueProperties.purinepyrimidine[ResidueProperties.purinepyrimidineIndex[c]];// jalview.util.ColorUtils.generateRandomColor(Color.white);
@@
-124,16
+125,17
@@
public class CovariationColourScheme extends ResidueColourScheme
{
Color currentColour = Color.white;
String currentHelix = null;
{
Color currentColour = Color.white;
String currentHelix = null;
- // System.out.println(c + " " + j);
+ // jalview.bin.Console.outPrintln(c + " " + j);
currentHelix = positionsToHelix.get(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);
}
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;
}
// currentColour);
return currentColour;
}