/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+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;
}
- public Color findColour(char c, int j)
+ @Override
+ 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)
- {
- return Color.white;
- }
-
- if ((threshold != 0) && !aboveThreshold(c, j))
+ if (consensusResidue == null || Comparison.isGap(c))
{
return Color.white;
}
- Color currentColour = Color.white;
-
- double sc = 0;
+ Color colour = Color.white;
- if (consensus.length <= j)
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ boolean matchesConsensus = consensusResidue.contains(String.valueOf(c));
+ if (matchesConsensus)
{
- return Color.white;
- }
-
- if ((Integer
- .parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) != -1)
- && consensus[j].contains(String.valueOf(c)))
- {
- 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;
+ }
- return currentColour;
+ @Override
+ public String getSchemeName()
+ {
+ 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;
}
}