/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.schemes;
-import jalview.analysis.AAFrequency;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import java.awt.Color;
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()
{
- this.pidColours = ResidueProperties.pidColours;
- this.thresholds = ResidueProperties.pidThresholds;
}
@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 (consensus == null || j >= consensus.length || consensus[j] == null)
+ if (consensusResidue == null || Comparison.isGap(c))
{
return Color.white;
}
- if ((threshold != 0) && !aboveThreshold(c, j))
- {
- return Color.white;
- }
-
- Color currentColour = Color.white;
-
- double sc = 0;
-
- if (consensus.length <= j)
- {
- return Color.white;
- }
+ Color colour = Color.white;
- if ((Integer
- .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
- && consensus[j].contains(String.valueOf(c)))
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
+ if (matchesConsensus)
{
- sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
-
- if (!jalview.util.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 colour;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.PID.toString();
+ }
- return currentColour;
+ /**
+ * 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;
}
}