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JAL-98 JAL-1854 encapsulate 'magic number' threshold 3 in Conservation
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
34fdabe
..
61a30f8
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-1637,9
+1637,8
@@
public class AnnotationFile
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group", 3,
- sg.getSequences(null), sg.getStartRes(),
- sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold