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JAL-2110 field 'cf' moved to stack
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 7 Jul 2016 15:51:21 +0000
(16:51 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 7 Jul 2016 15:51:21 +0000
(16:51 +0100)
src/jalview/analysis/CrossRef.java
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diff --git
a/src/jalview/analysis/CrossRef.java
b/src/jalview/analysis/CrossRef.java
index
df5ca10
..
288d60e
100644
(file)
--- a/
src/jalview/analysis/CrossRef.java
+++ b/
src/jalview/analysis/CrossRef.java
@@
-68,11
+68,6
@@
public class CrossRef
List<SequenceI> rseqs;
/**
List<SequenceI> rseqs;
/**
- * mappings constructed
- */
- AlignedCodonFrame cf;
-
- /**
* Constructor
*
* @param seqs
* Constructor
*
* @param seqs
@@
-213,7
+208,7
@@
public class CrossRef
{
rseqs = new ArrayList<SequenceI>();
{
rseqs = new ArrayList<SequenceI>();
- cf = new AlignedCodonFrame();
+ AlignedCodonFrame cf = new AlignedCodonFrame();
matcher = new SequenceIdMatcher(
dataset.getSequences());
matcher = new SequenceIdMatcher(
dataset.getSequences());
@@
-338,7
+333,7
@@
public class CrossRef
*/
if (!sourceRefs.isEmpty())
{
*/
if (!sourceRefs.isEmpty())
{
- retrieveCrossRef(sourceRefs, seq, xrfs, fromDna);
+ retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf);
}
}
}
}
@@
-355,7
+350,7
@@
public class CrossRef
}
private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
}
private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
- DBRefEntry[] xrfs, boolean fromDna)
+ DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf)
{
ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
SequenceI[] retrieved = null;
{
ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
SequenceI[] retrieved = null;