X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=8bb1acde4ada8b20c8f5e4bac768d240482b781a;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=d363764857a9c85e105f3f6f2970993e13d4a921;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index d363764..8bb1acd 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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;
@@ -59,13 +62,17 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
colhash.put("YELLOW", new Color((float) 0.8, (float) 0.8, (float) 0.0));
}
- public ClustalxColourScheme(AnnotatedCollectionI alignment, Map hiddenReps)
+ public ClustalxColourScheme(AnnotatedCollectionI alignment,
+ Map hiddenReps)
{
- alignmentChanged(alignment,hiddenReps);
+ alignmentChanged(alignment, hiddenReps);
}
- public void alignmentChanged(AnnotatedCollectionI alignment, Map hiddenReps) {
- int maxWidth=alignment.getWidth();
- List seqs=alignment.getSequences(hiddenReps);
+
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps)
+ {
+ int maxWidth = alignment.getWidth();
+ List seqs = alignment.getSequences(hiddenReps);
cons2 = new int[maxWidth][24];
includeGaps = isIncludeGaps(); // does nothing - TODO replace with call to
// get the current setting of the
@@ -86,7 +93,7 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
int j = 0;
char[] seq;
- for (SequenceI sq: seqs)
+ for (SequenceI sq : seqs)
{
seq = sq.getSequence();
@@ -322,6 +329,14 @@ public class ClustalxColourScheme extends ResidueColourScheme // implements
{
this.includeGaps = includeGaps;
}
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ ClustalxColourScheme css= new ClustalxColourScheme(sg, hiddenRepSequences);
+ css.includeGaps = includeGaps;
+ return css;
+ }
}
class ConsensusColour