git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'Jalview-JS/develop' into merge_js_develop
[jalview.git]
/
src
/
jalview
/
analysis
/
CrossRef.java
diff --git
a/src/jalview/analysis/CrossRef.java
b/src/jalview/analysis/CrossRef.java
index
c54357e
..
1044802
100644
(file)
--- a/
src/jalview/analysis/CrossRef.java
+++ b/
src/jalview/analysis/CrossRef.java
@@
-20,6
+20,10
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
@@
-31,12
+35,7
@@
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
+import jalview.ws.SequenceFetcher;
/**
* Functions for cross-referencing sequence databases.
/**
* Functions for cross-referencing sequence databases.
@@
-402,7
+401,6
@@
public class CrossRef
private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
{
private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
{
- ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
SequenceI[] retrieved = null;
SequenceI dss = seq.getDatasetSequence() == null ? seq
: seq.getDatasetSequence();
SequenceI[] retrieved = null;
SequenceI dss = seq.getDatasetSequence() == null ? seq
: seq.getDatasetSequence();
@@
-418,7
+416,7
@@
public class CrossRef
}
try
{
}
try
{
- retrieved = sftch.getSequences(sourceRefs, !fromDna);
+ retrieved = SequenceFetcher.getInstance().getSequences(sourceRefs, !fromDna);
} catch (Exception e)
{
System.err.println(
} catch (Exception e)
{
System.err.println(