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JAL-2520 improvement to download and update structure files loaded via URL to a local...
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
6ca1393
..
657d6b0
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
@@
-48,10
+47,9
@@
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');