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[jalview.git]
/
src
/
jalview
/
schemes
/
Blosum62ColourScheme.java
diff --git
a/src/jalview/schemes/Blosum62ColourScheme.java
b/src/jalview/schemes/Blosum62ColourScheme.java
index
6c83920
..
6e91e0b
100755
(executable)
--- a/
src/jalview/schemes/Blosum62ColourScheme.java
+++ b/
src/jalview/schemes/Blosum62ColourScheme.java
@@
-1,5
+1,6
@@
-/* Jalview - a java multiple alignment editor
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- * Copyright (C) 1998 Michele Clamp
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+/*
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+ * Jalview - A Sequence Alignment Editor and Viewer
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+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License
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@@
-13,67
+14,75
@@
*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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*/
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*/
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-
\r
package jalview.schemes;
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\r
\r
package jalview.schemes;
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\r
\r
-import java.util.*;
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import java.awt.*;
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import java.awt.*;
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-import jalview.gui.*;
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-import jalview.datamodel.*;
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\r
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-public class Blosum62ColourScheme extends ResidueColourScheme
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+public class Blosum62ColourScheme
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+ extends ResidueColourScheme
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{
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{
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-
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- // need to keep an eye on the changing visible consensus sequence
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- AlignViewport av;
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-
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- public Blosum62ColourScheme(AlignViewport av)
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+ public Blosum62ColourScheme()
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{
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super();
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{
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super();
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- this.av = av;
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}
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}
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\r
- public Color findColour(String s, int j, Vector aa)
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+ public Color findColour(String s, int j)
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{
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{
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- Hashtable hash;
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+ char res = s.charAt(0);
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+ if ('a' <= res && res <= 'z' )
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+ {
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+ // TO UPPERCASE !!!
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+ s = String.valueOf( res -= ('a' - 'A') );
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+ }
\r
\r
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- if (aa != null)
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- hash = (Hashtable)aa.elementAt(j);
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- else
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+
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+ if ( (threshold != 0) && !aboveThreshold(s, j))
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+ {
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return Color.white;
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return Color.white;
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+ }
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\r
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- if (!jalview.util.Comparison.isGap((s.charAt(0))))
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+ if (!jalview.util.Comparison.isGap( res ))
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{
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{
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- String max = (String)hash.get("maxResidue");
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+ String max = (String) consensus[j].get("maxResidue");
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\r
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- if (max.indexOf(s)>-1)
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- return new Color(154, 154, 255);
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- else {
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+ if (max.indexOf(s) > -1)
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+ {
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+ currentColour = new Color(154, 154, 255);
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+ }
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+ else
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+ {
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+ int c = 0;
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+ int max_aa = 0;
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+ int n = max.length();
\r
\r
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- int c = 0,
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- max_aa=0,
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- n=max.length();
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- do {
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- c+=ResidueProperties.getBLOSUM62(max.substring(max_aa, max_aa+1), s);
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- } while (++max_aa<n);
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+ do
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+ {
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+ c += ResidueProperties.getBLOSUM62(max.substring(max_aa,
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+ max_aa + 1), s);
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+ }
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+ while (++max_aa < n);
\r
\r
\r
- if (c>0)
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- return new Color(204, 204, 255);
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+ if (c > 0)
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+ {
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+ currentColour = new Color(204, 204, 255);
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+ }
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else
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else
\r
- return Color.white;
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+ {
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+ currentColour = Color.white;
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+ }
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}
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}
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+
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+ if(conservationColouring)
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+ applyConservation(j);
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}
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else
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}
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else
\r
- return Color.white;
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-
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- }
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+ {
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+ return Color.white;
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+ }
\r
\r
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- public boolean canThreshold()
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- {
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- return false;
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+ return currentColour;
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}
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}
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-
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}
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}
\r