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Align boxes
[jalview.git]
/
src
/
jalview
/
schemes
/
Consensus.java
diff --git
a/src/jalview/schemes/Consensus.java
b/src/jalview/schemes/Consensus.java
index
7b0dbbb
..
520196f
100755
(executable)
--- a/
src/jalview/schemes/Consensus.java
+++ b/
src/jalview/schemes/Consensus.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) 2006 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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@@
-13,60
+14,66
@@
*
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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
package jalview.schemes;
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\r
-import jalview.datamodel.*;
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-import java.util.*;
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////////////////////////////////////////////
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// This does nothing at all at the moment!!!!!!!!!!
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// AW 15th Dec 2004
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/////////////////////////////////////////
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////////////////////////////////////////////
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// This does nothing at all at the moment!!!!!!!!!!
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// AW 15th Dec 2004
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/////////////////////////////////////////
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-public class Consensus {
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-
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+public class Consensus
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+{
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int[] mask;
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double threshold;
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int[] mask;
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double threshold;
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+ String maskstr;
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\r
\r
- public Consensus(String m, double threshold)
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+ public Consensus(String mask, double threshold)
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{
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{
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- mask = setNums(m);
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+ // this.id = id;
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+ // this.mask = mask;
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+ this.maskstr = mask;
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+ setMask(mask);
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this.threshold = threshold;
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}
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this.threshold = threshold;
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}
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\r
+ public void setMask(String s)
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+ {
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+ this.mask = setNums(s);
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+
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+ // for (int i=0; i < mask.length; i++) {
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+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
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+ // }
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+ }
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\r
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- public boolean isConserved(int[][] cons2,int col, int res,int size)
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+ public boolean isConserved(int[][] cons2, int col, int size)
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{
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int tot = 0;
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{
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int tot = 0;
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-try{
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- for (int i=0; i < mask.length; i++)
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+ for (int i = 0; i < mask.length; i++)
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+ {
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tot += cons2[col][mask[i]];
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tot += cons2[col][mask[i]];
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-}catch(Exception ex)
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-{ return true; }
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+ }
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\r
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- if ((double)tot > threshold*size/100)
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+ if ( (double) tot > ( (threshold * size) / 100))
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+ {
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return true;
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return true;
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+ }
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return false;
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}
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\r
int[] setNums(String s)
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{
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return false;
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}
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int[] setNums(String s)
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{
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- int [] out = new int[s.length()];
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+ int[] out = new int[s.length()];
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int i = 0;
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int i = 0;
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+
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while (i < s.length())
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{
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while (i < s.length())
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{
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- out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
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+ out[i] = ResidueProperties.aaIndex[s.charAt(i)];
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i++;
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}
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i++;
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}
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+
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return out;
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}
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return out;
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}
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-
\r
-
\r
}
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}
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-
\r
-
\r
-
\r
-
\r