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[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
74381fd
..
deeb2e9
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-62,7
+62,7
@@
public class Conservation {
}
\r
} else {
\r
// JBPNote INFO level debug
\r
}
\r
} else {
\r
// JBPNote INFO level debug
\r
- System.out.println("calcSeqNum called with out of range sequence index for Alignment\n");
\r
+ System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
\r
}
\r
}
\r
Vector total = new Vector();
\r
}
\r
}
\r
Vector total = new Vector();
\r
@@
-351,7
+351,8
@@
public void findQuality(int start, int end) {
x[ii] += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;
\r
}
\r
} catch (Exception e) {
\r
x[ii] += (double)cons2[j][i2] * BLOSUM62[ii][i2]+4;
\r
}
\r
} catch (Exception e) {
\r
- System.out.println("Exception : " + e);
\r
+ System.err.println("Exception during quality calculation.");
\r
+ e.printStackTrace();
\r
}
\r
//System.out.println("X " + ii + " " + x[ii]);
\r
x[ii] /= (size);
\r
}
\r
//System.out.println("X " + ii + " " + x[ii]);
\r
x[ii] /= (size);
\r
@@
-373,6
+374,7
@@
public void findQuality(int start, int end) {
sr = (double)BLOSUM62[i][seqNum]+4;
\r
} catch (Exception e) {
\r
System.out.println("Exception in sr: " + e);
\r
sr = (double)BLOSUM62[i][seqNum]+4;
\r
} catch (Exception e) {
\r
System.out.println("Exception in sr: " + e);
\r
+ e.printStackTrace();
\r
}
\r
//Calculate X with another loop over residues
\r
\r
}
\r
//Calculate X with another loop over residues
\r
\r