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no need to send pid, seqnum
[jalview.git]
/
src
/
jalview
/
schemes
/
Consensus.java
diff --git
a/src/jalview/schemes/Consensus.java
b/src/jalview/schemes/Consensus.java
index
7b0dbbb
..
17cb789
100755
(executable)
--- a/
src/jalview/schemes/Consensus.java
+++ b/
src/jalview/schemes/Consensus.java
@@
-18,8
+18,6
@@
\r
package jalview.schemes;
\r
\r
\r
package jalview.schemes;
\r
\r
-import jalview.datamodel.*;
\r
-import java.util.*;
\r
////////////////////////////////////////////
\r
// This does nothing at all at the moment!!!!!!!!!!
\r
// AW 15th Dec 2004
\r
////////////////////////////////////////////
\r
// This does nothing at all at the moment!!!!!!!!!!
\r
// AW 15th Dec 2004
\r
@@
-28,25
+26,29
@@
public class Consensus {
\r
int[] mask;
\r
double threshold;
\r
\r
int[] mask;
\r
double threshold;
\r
+ String maskstr;
\r
\r
\r
- public Consensus(String m, double threshold)
\r
- {
\r
- mask = setNums(m);
\r
+ public Consensus(String mask, double threshold) {
\r
+ // this.id = id;
\r
+ // this.mask = mask;
\r
+ this.maskstr = mask;
\r
+ setMask(mask);
\r
this.threshold = threshold;
\r
}
\r
\r
this.threshold = threshold;
\r
}
\r
\r
+ public void setMask(String s) {
\r
+ this.mask = setNums(s);
\r
+ // for (int i=0; i < mask.length; i++) {
\r
+ // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
\r
+ // }
\r
+ }
\r
\r
\r
- public boolean isConserved(int[][] cons2,int col, int res,int size)
\r
- {
\r
+ public boolean isConserved(int[][] cons2,int col ,int size) {
\r
int tot = 0;
\r
int tot = 0;
\r
-
\r
-try{
\r
- for (int i=0; i < mask.length; i++)
\r
+ for (int i = 0; i < mask.length; i++)
\r
tot += cons2[col][mask[i]];
\r
tot += cons2[col][mask[i]];
\r
-}catch(Exception ex)
\r
-{ return true; }
\r
\r
\r
- if ((double)tot > threshold*size/100)
\r
+ if ( (double) tot > threshold * size / 100)
\r
return true;
\r
\r
return false;
\r
return true;
\r
\r
return false;
\r
@@
-60,7
+62,9
@@
try{
{
\r
out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
\r
i++;
\r
{
\r
out[i] = ( (Integer) ResidueProperties.aaHash.get(s.substring(i, i + 1))).intValue();
\r
i++;
\r
+
\r
}
\r
}
\r
+
\r
return out;
\r
}
\r
\r
return out;
\r
}
\r
\r