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refactor the command line executable launcher used in the test harness for running...
[jalview.git]
/
src
/
jalview
/
analysis
/
CrossRef.java
diff --git
a/src/jalview/analysis/CrossRef.java
b/src/jalview/analysis/CrossRef.java
index
1a56393
..
e6bae9b
100644
(file)
--- a/
src/jalview/analysis/CrossRef.java
+++ b/
src/jalview/analysis/CrossRef.java
@@
-619,28
+619,25
@@
public class CrossRef
* duplication (e.g. same variation from two
* transcripts)
*/
* duplication (e.g. same variation from two
* transcripts)
*/
- SequenceFeature[] sfs = ms.getSequenceFeatures();
- if (sfs != null)
+ List<SequenceFeature> sfs = ms.getFeatures()
+ .getAllFeatures();
+ for (SequenceFeature feat : sfs)
{
{
- for (SequenceFeature feat : sfs)
+ /*
+ * make a flyweight feature object which ignores Parent
+ * attribute in equality test; this avoids creating many
+ * otherwise duplicate exon features on genomic sequence
+ */
+ SequenceFeature newFeature = new SequenceFeature(feat)
{
{
- /*
- * make a flyweight feature object which ignores Parent
- * attribute in equality test; this avoids creating many
- * otherwise duplicate exon features on genomic sequence
- */
- SequenceFeature newFeature = new SequenceFeature(feat)
+ @Override
+ public boolean equals(Object o)
{
{
- @Override
- public boolean equals(Object o)
- {
- return super.equals(o, true);
- }
- };
- matched.addSequenceFeature(newFeature);
- }
+ return super.equals(o, true);
+ }
+ };
+ matched.addSequenceFeature(newFeature);
}
}
-
}
cf.addMap(retrievedSequence, map.getTo(), map.getMap());
} catch (Exception e)
}
cf.addMap(retrievedSequence, map.getTo(), map.getMap());
} catch (Exception e)
@@
-785,15
+782,15
@@
public class CrossRef
{
return false;
}
{
return false;
}
- char[] c1 = seq1.getSequence();
- char[] c2 = seq2.getSequence();
- if (c1.length != c2.length)
+
+ if (seq1.getLength() != seq2.getLength())
{
return false;
}
{
return false;
}
- for (int i = 0; i < c1.length; i++)
+ int length = seq1.getLength();
+ for (int i = 0; i < length; i++)
{
{
- int diff = c1[i] - c2[i];
+ int diff = seq1.getCharAt(i) - seq2.getCharAt(i);
/*
* same char or differ in case only ('a'-'A' == 32)
*/
/*
* same char or differ in case only ('a'-'A' == 32)
*/