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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
a6301fa
..
fc922b9
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-31,16
+31,15
@@
import java.util.Map;
public class PIDColourScheme extends ResidueColourScheme
{
public class PIDColourScheme extends ResidueColourScheme
{
- public Color[] pidColours;
+ private static final Color[] pidColours = { new Color(100, 100, 255),
+ new Color(153, 153, 255), new Color(204, 204, 255), };
- public float[] thresholds;
+ private static final float[] thresholds = { 80, 60, 40, };
SequenceGroup group;
public PIDColourScheme()
{
SequenceGroup group;
public PIDColourScheme()
{
- this.pidColours = ResidueProperties.pidColours;
- this.thresholds = ResidueProperties.pidThresholds;
}
@Override
}
@Override
@@
-48,16
+47,15
@@
public class PIDColourScheme extends ResidueColourScheme
String consensusResidue, float pid)
{
/*
String consensusResidue, float pid)
{
/*
- * make everything uppercase; note this does nothing (fast)
- * if consensusResidue is already uppercase
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
*/
*/
- consensusResidue = consensusResidue.toUpperCase();
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
- if (consensusResidue == null)
+ if (consensusResidue == null || Comparison.isGap(c))
{
return Color.white;
}
{
return Color.white;
}
@@
-67,19
+65,15
@@
public class PIDColourScheme extends ResidueColourScheme
/*
* test whether this is the consensus (or joint consensus) residue
*/
/*
* test whether this is the consensus (or joint consensus) residue
*/
- boolean matchesConsensus = consensusResidue.contains(
- String.valueOf(c));
+ boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
if (matchesConsensus)
{
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;
}
}
}
}
}
}