X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=9d092599860175227545083e840dbf595350b41a;hb=be1666f6c9be6b18051b233abdde85962ac0c89a;hp=d91d49fe0410f19ec7349259d745c6229e404936;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git
diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index d91d49f..9d09259 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,63 +1,106 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998 Michele Clamp
- *
- * 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jalview.schemes;
-
-
-import java.util.*;
-import java.awt.*;
-import jalview.gui.*;
-import jalview.datamodel.*;
-
-public class Blosum62ColourScheme extends ResidueColourScheme
-{
-
- // need to keep an eye on the changing visible consensus sequence
- AlignViewport av;
-
- public Blosum62ColourScheme(AlignViewport av)
- {
- super();
- this.av = av;
- }
-
- public Color findColour(SequenceI seq, String s, int j, Vector aa)
- {
- if (!s.equals("-") && !s.equals(".") && !s.equals(" "))
- {
- String max = av.getVisibleConsensus().charAt(j) + "";
-
- if (s.equals(max))
- return new Color(154, 154, 255);
- else if (ResidueProperties.getBLOSUM62(max, s) > 0)
- return new Color(204, 204, 255);
- else
- return Color.white;
-
- }
- else
- return Color.white;
-
- }
-
- public boolean canThreshold()
- {
- return false;
- }
-
-}
+/*
+ * 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.analysis.AAFrequency;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
+
+public class Blosum62ColourScheme extends ResidueColourScheme
+{
+ public Blosum62ColourScheme()
+ {
+ super();
+ }
+
+ @Override
+ public Color findColour(char res, int j, SequenceI seq)
+ {
+ if ('a' <= res && res <= 'z')
+ {
+ // TO UPPERCASE !!!
+ res -= ('a' - 'A');
+ }
+
+ if (consensus == null || j >= consensus.length || consensus[j] == null
+ || (threshold != 0 && !aboveThreshold(res, j)))
+ {
+ return Color.white;
+ }
+
+ Color currentColour;
+
+ if (!jalview.util.Comparison.isGap(res))
+ {
+ String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE);
+
+ if (max.indexOf(res) > -1)
+ {
+ // TODO use a constant here?
+ currentColour = new Color(154, 154, 255);
+ }
+ else
+ {
+ int c = 0;
+ int max_aa = 0;
+ int n = max.length();
+
+ do
+ {
+ c += ResidueProperties.getBLOSUM62(max.charAt(max_aa), res);
+ } while (++max_aa < n);
+
+ if (c > 0)
+ {
+ // TODO use a constant here?
+ currentColour = new Color(204, 204, 255);
+ }
+ else
+ {
+ currentColour = Color.white;
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+ }
+ else
+ {
+ return Color.white;
+ }
+
+ return currentColour;
+ }
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+ return newcs;
+ }
+}