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Use Selection group to define sequence range to fetch features
author
amwaterhouse
<Andrew Waterhouse>
Wed, 19 Jul 2006 10:39:38 +0000
(10:39 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 19 Jul 2006 10:39:38 +0000
(10:39 +0000)
src/jalview/io/DasSequenceFeatureFetcher.java
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diff --git
a/src/jalview/io/DasSequenceFeatureFetcher.java
b/src/jalview/io/DasSequenceFeatureFetcher.java
index
70af276
..
20ae27c
100755
(executable)
--- a/
src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/
src/jalview/io/DasSequenceFeatureFetcher.java
@@
-94,13
+94,14
@@
public class DasSequenceFeatureFetcher implements Runnable
int refCount = 0;
\r
for(int i=0; i<sequences.length; i++)
\r
{
\r
int refCount = 0;
\r
for(int i=0; i<sequences.length; i++)
\r
{
\r
- if(sequences[i].getDBRef()!=null)
\r
+ Vector dbref = sequences[i].getDBRef();
\r
+ if(dbref!=null)
\r
{
\r
{
\r
- for(int j=0; j<sequences[i].getDBRef().size(); j++)
\r
+ for(int j=0; j<dbref.size(); j++)
\r
{
\r
{
\r
- System.out.println(sequences[i].getDBRef().elementAt(j)
\r
+ System.out.println(dbref.elementAt(j)
\r
+" "+jalview.datamodel.DBRefSource.UNIPROT);
\r
+" "+jalview.datamodel.DBRefSource.UNIPROT);
\r
- if(sequences[i].getDBRef().elementAt(j)
\r
+ if(dbref.elementAt(j)
\r
.equals(jalview.datamodel.DBRefSource.UNIPROT))
\r
{
\r
System.out.println("got a match");
\r
.equals(jalview.datamodel.DBRefSource.UNIPROT))
\r
{
\r
System.out.println("got a match");
\r
@@
-210,7
+211,8
@@
public class DasSequenceFeatureFetcher implements Runnable
protected void createFeatureFetcher(final SequenceI seq,
\r
final String sourceUrl,
\r
String id,
\r
protected void createFeatureFetcher(final SequenceI seq,
\r
final String sourceUrl,
\r
String id,
\r
- String nickname) {
\r
+ String nickname)
\r
+ {
\r
//////////////
\r
/// fetch DAS features
\r
final Das1Source source = new Das1Source();
\r
//////////////
\r
/// fetch DAS features
\r
final Das1Source source = new Das1Source();
\r
@@
-220,13
+222,27
@@
public class DasSequenceFeatureFetcher implements Runnable
\r
Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
\r
sourceUrl);
\r
\r
Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +
\r
sourceUrl);
\r
+
\r
if (id != null && id.length() > 0)
\r
{
\r
setThreadsRunning(+1);
\r
\r
if (id != null && id.length() > 0)
\r
{
\r
setThreadsRunning(+1);
\r
\r
+ int start=seq.getStart(), end = seq.getEnd();
\r
+
\r
+ if(af.getViewport().getSelectionGroup()!=null)
\r
+ {
\r
+ SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());
\r
+ start = tmp.findPosition(
\r
+ af.getViewport().getSelectionGroup().getStartRes()
\r
+ );
\r
+
\r
+ end = tmp.findPosition(
\r
+ af.getViewport().getSelectionGroup().getEndRes()
\r
+ );
\r
+ }
\r
+
\r
FeatureThread fetcher = new FeatureThread(id
\r
FeatureThread fetcher = new FeatureThread(id
\r
- + ":" + seq.getStart() + "," +seq.getEnd()
\r
- , source);
\r
+ + ":" + start + "," + end, source);
\r
\r
fetcher.addFeatureListener(new FeatureListener()
\r
{
\r
\r
fetcher.addFeatureListener(new FeatureListener()
\r
{
\r