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JAL-2349 rename ContactMatrixTest to SeqDistanceContactMatrix
[jalview.git]
/
src
/
jalview
/
io
/
AnnotationFile.java
diff --git
a/src/jalview/io/AnnotationFile.java
b/src/jalview/io/AnnotationFile.java
index
6e121b3
..
82e71b5
100755
(executable)
--- a/
src/jalview/io/AnnotationFile.java
+++ b/
src/jalview/io/AnnotationFile.java
@@
-32,7
+32,6
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import java.io.BufferedReader;
import jalview.schemes.UserColourScheme;
import java.io.BufferedReader;
@@
-1638,8
+1637,7
@@
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",
- ResidueProperties.propHash, 3, sg.getSequences(null),
+ Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();