/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.datamodel.ProfileI;
+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
{
this.thresholds = ResidueProperties.pidThresholds;
}
- public Color findColour(char c, int j)
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
{
if ('a' <= c && c <= 'z')
{
c -= ('a' - 'A');
}
- if (consensus == null || j >= consensus.length || consensus[j] == null)
+ if (consensus == null || consensus.get(j) == null)
{
return Color.white;
}
double sc = 0;
- if (consensus.length <= j)
- {
- return 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
+ */
+ ProfileI profile = consensus.get(j);
+ boolean matchesConsensus = profile.getModalResidue().contains(
+ String.valueOf(c));
+ if (matchesConsensus)
{
- sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
+ sc = profile.getPercentageIdentity(ignoreGaps);
- if (!jalview.util.Comparison.isGap(c))
+ if (!Comparison.isGap(c))
{
for (int i = 0; i < thresholds.length; i++)
{
if (sc > thresholds[i])
{
currentColour = pidColours[i];
-
break;
}
}