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JAL-3375 format validate VCF Integer and Float fields
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
6ca1393
..
3a5c066
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-20,27
+20,25
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.awt.Color;
-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
+46,9
@@
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');
@@
-67,8
+64,7
@@
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)
{
for (int i = 0; i < thresholds.length; i++)
if (matchesConsensus)
{
for (int i = 0; i < thresholds.length; i++)
@@
-95,8
+91,8
@@
public class PIDColourScheme extends ResidueColourScheme
* be coloured
*/
@Override
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
- Map<SequenceI, SequenceCollectionI> hrs)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
{
return new PIDColourScheme();
}
{
return new PIDColourScheme();
}