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JAL-4059 New namespaced query string parameters.
[jalview.git]
/
src
/
jalview
/
schemes
/
Consensus.java
diff --git
a/src/jalview/schemes/Consensus.java
b/src/jalview/schemes/Consensus.java
index
cccc995
..
fe71d31
100755
(executable)
--- a/
src/jalview/schemes/Consensus.java
+++ b/
src/jalview/schemes/Consensus.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-46,15
+46,17
@@
public class Consensus
this.mask = setNums(s);
// for (int i=0; i < mask.length; i++) {
this.mask = setNums(s);
// for (int i=0; i < mask.length; i++) {
- // System.out.println(mask[i] + " " + ResidueProperties.aa[mask[i]]);
+ // jalview.bin.Console.outPrintln(mask[i] + " " + ResidueProperties.aa[mask[i]]);
// }
}
/**
* @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
*/
// }
}
/**
* @deprecated Use {@link #isConserved(int[][],int,int,boolean)} instead
*/
+ @Deprecated
public boolean isConserved(int[][] cons2, int col, int size)
{
public boolean isConserved(int[][] cons2, int col, int size)
{
+ jalview.bin.Console.outPrintln("DEPRECATED!!!!");
return isConserved(cons2, col, size, true);
}
return isConserved(cons2, col, size, true);
}
@@
-71,9
+73,9
@@
public class Consensus
tot += cons2[col][mask[i]];
}
tot += cons2[col][mask[i]];
}
- if ((double) tot > ((threshold * size) / 100))
+ if (tot > ((threshold * size) / 100))
{
{
- // System.out.println("True conserved "+tot+" from "+threshold+" out of
+ // jalview.bin.Console.outPrintln("True conserved "+tot+" from "+threshold+" out of
// "+size+" : "+maskstr);
return true;
}
// "+size+" : "+maskstr);
return true;
}