X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=abae7337da966fc1711bebe73d42f5c3e024b5c4;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=7906ed11cd60ccdd5fc5c6f5c513a67e304af066;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 7906ed1..abae733 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,24 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
/**
* DOCUMENT ME!
@@ -33,56 +39,29 @@ public class NucleotideColourScheme extends ResidueColourScheme
*/
public NucleotideColourScheme()
{
- super(ResidueProperties.nucleotide, 0);
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(char c)
+ @Override
+ public boolean isNucleotideSpecific()
{
- // System.out.println("called"); log.debug
- return colors[ResidueProperties.nucleotideIndex[c]];
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Nucleotide.toString();
}
/**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
*/
- public Color findColour(char c, int j)
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
{
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ return new NucleotideColourScheme();
}
}