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JAL-3454 tidy comments
[jalview.git]
/
src
/
jalview
/
schemes
/
PIDColourScheme.java
diff --git
a/src/jalview/schemes/PIDColourScheme.java
b/src/jalview/schemes/PIDColourScheme.java
index
175e904
..
3a5c066
100755
(executable)
--- a/
src/jalview/schemes/PIDColourScheme.java
+++ b/
src/jalview/schemes/PIDColourScheme.java
@@
-20,7
+20,8
@@
*/
package jalview.schemes;
*/
package jalview.schemes;
-import jalview.datamodel.ProfileI;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
@@
-29,70
+30,54
@@
import java.awt.Color;
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
- public Color findColour(char c, int j, SequenceI seq)
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
{
{
+ /*
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
+ */
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
- if (consensus == null || consensus.get(j) == null)
- {
- return Color.white;
- }
-
- if ((threshold != 0) && !aboveThreshold(c, j))
+ if (consensusResidue == null || Comparison.isGap(c))
{
return Color.white;
}
{
return Color.white;
}
- Color currentColour = Color.white;
-
- double sc = 0;
-
+ Color colour = Color.white;
/*
* test whether this is the consensus (or joint consensus) residue
*/
/*
* test whether this is the consensus (or joint consensus) residue
*/
- ProfileI profile = consensus.get(j);
- boolean matchesConsensus = profile.getModalResidue().contains(
- String.valueOf(c));
+ boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
if (matchesConsensus)
{
if (matchesConsensus)
{
- sc = profile.getPercentageIdentity(ignoreGaps);
-
- 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 (sc > thresholds[i])
- {
- currentColour = pidColours[i];
- break;
- }
+ colour = pidColours[i];
+ break;
}
}
}
}
}
}
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return colour;
}
@Override
}
@Override
@@
-100,4
+85,21
@@
public class PIDColourScheme extends ResidueColourScheme
{
return JalviewColourScheme.PID.toString();
}
{
return JalviewColourScheme.PID.toString();
}
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new PIDColourScheme();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}
}