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JAL-4386 PCA/Tree Calculation for Secondary Structures: Changes related to dropdown...
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
cbc4dca
..
5bb0b09
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-243,13
+243,13
@@
public class Conservation
}
else
{
}
else
{
- System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+ jalview.bin.Console.outPrintln("SEQUENCE HAS BEEN DELETED!!!");
}
}
else
{
// JBPNote INFO level debug
}
}
else
{
// JBPNote INFO level debug
- System.err.println(
+ jalview.bin.Console.errPrintln(
"ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
}
}
"ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
}
}
@@
-711,7
+711,7
@@
public class Conservation
// tmp = ((max - tmp) * (size - cons2[j][23])) / size;
tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
// tmp = ((max - tmp) * (size - cons2[j][23])) / size;
tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
- // System.out.println(tmp+ " " + j);
+ // jalview.bin.Console.outPrintln(tmp+ " " + j);
quality.setElementAt(Double.valueOf(tmp), j);
if (tmp > newmax)
quality.setElementAt(Double.valueOf(tmp), j);
if (tmp > newmax)