X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=c59d5791418ab7e387681235aa18598e7426df46;hb=bdbd32582db88724697211a25b08f9cb8958bcb1;hp=23a2ee286f5906cdf05cdd64dc633a8837c7fdb8;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 23a2ee2..c59d579 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,26 +1,31 @@
/*
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+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
{
@@ -36,7 +41,8 @@ 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')
{
@@ -68,7 +74,7 @@ public class PIDColourScheme extends ResidueColourScheme
{
sc = ((Float) consensus[j].get(ignoreGaps)).floatValue();
- if (!jalview.util.Comparison.isGap(c))
+ if (!Comparison.isGap(c))
{
for (int i = 0; i < thresholds.length; i++)
{