X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=3a7173261417c3d355b1d9d9b306b950c09812ed;hb=ca0a70b02a67f842a195319414d241ffa336656b;hp=0f2101e06a089a7fe5d8a1ab3788ba00746b17aa;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 0f2101e..3a71732 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,54 +1,121 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
-*/
-
-package jalview.schemes;
-
-import java.awt.*;
-
-public class NucleotideColourScheme extends ResidueColourScheme
-{
- public NucleotideColourScheme() {
- super(ResidueProperties.nucleotide,0);
- }
-
-
- public Color findColour(String n)
- {
- // System.out.println("called"); log.debug
- return colors[((Integer)(ResidueProperties.nucleotideHash.get(n))).intValue()];
- }
-
-
- public Color findColour(String n, int j) {
-
- if (threshold == 0 || aboveThreshold( n, j))
- try
- {
- return colors[ ( (Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
- }
- catch (Exception ex)
- {
- return Color.white;
- }
- else
- return Color.white;
-
- }
-
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new NucleotideColourScheme object.
+ */
+ public NucleotideColourScheme()
+ {
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
+ 0);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c)
+ {
+ // System.out.println("called"); log.debug
+ return colors[ResidueProperties.nucleotideIndex[c]];
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ 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;
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Nucleotide.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
+ {
+ return new NucleotideColourScheme();
+ }
+}