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Just fetch features for selected seqs
author
amwaterhouse
<Andrew Waterhouse>
Fri, 14 Jul 2006 08:58:11 +0000
(08:58 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 14 Jul 2006 08:58:11 +0000
(08:58 +0000)
src/jalview/io/DasSequenceFeatureFetcher.java
patch
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diff --git
a/src/jalview/io/DasSequenceFeatureFetcher.java
b/src/jalview/io/DasSequenceFeatureFetcher.java
index
dc51617
..
1295520
100755
(executable)
--- a/
src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/
src/jalview/io/DasSequenceFeatureFetcher.java
@@
-50,8
+50,8
@@
import jalview.bin.Cache;
*/
\r
public class DasSequenceFeatureFetcher implements Runnable
\r
{
\r
*/
\r
public class DasSequenceFeatureFetcher implements Runnable
\r
{
\r
- final AlignmentI dataset;
\r
- final AlignFrame af;
\r
+ SequenceI [] sequences;
\r
+ AlignFrame af;
\r
StringBuffer sbuffer = new StringBuffer();
\r
Vector selectedSources;
\r
\r
StringBuffer sbuffer = new StringBuffer();
\r
Vector selectedSources;
\r
\r
@@
-66,12
+66,12
@@
public class DasSequenceFeatureFetcher implements Runnable
* @param align DOCUMENT ME!
\r
* @param ap DOCUMENT ME!
\r
*/
\r
* @param align DOCUMENT ME!
\r
* @param ap DOCUMENT ME!
\r
*/
\r
- public DasSequenceFeatureFetcher(AlignmentI align,
\r
+ public DasSequenceFeatureFetcher(SequenceI [] sequences,
\r
AlignFrame af,
\r
Vector selectedSources)
\r
{
\r
this.selectedSources = selectedSources;
\r
AlignFrame af,
\r
Vector selectedSources)
\r
{
\r
this.selectedSources = selectedSources;
\r
- this.dataset = align.getDataset();
\r
+ this.sequences = sequences;
\r
this.af = af;
\r
\r
Thread thread = new Thread(this);
\r
this.af = af;
\r
\r
Thread thread = new Thread(this);
\r
@@
-145,7
+145,7
@@
public class DasSequenceFeatureFetcher implements Runnable
* @param SourceUrl
\r
* @param id
\r
*/
\r
* @param SourceUrl
\r
* @param id
\r
*/
\r
- protected void createFeatureFetcher(final Sequence seq,
\r
+ protected void createFeatureFetcher(final SequenceI seq,
\r
final String sourceUrl,
\r
String id,
\r
String nickname) {
\r
final String sourceUrl,
\r
String id,
\r
String nickname) {
\r
@@
-262,11
+262,9
@@
public class DasSequenceFeatureFetcher implements Runnable
try
\r
{
\r
int seqIndex = 0;
\r
try
\r
{
\r
int seqIndex = 0;
\r
- Vector sequences = dataset.getSequences();
\r
- while (seqIndex < sequences.size())
\r
+ while (seqIndex < sequences.length)
\r
{
\r
{
\r
- Sequence sequence = (Sequence) sequences.get(seqIndex);
\r
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),
\r
+ Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),
\r
new String[] {
\r
jalview.datamodel.DBRefSource.PDB,
\r
jalview.datamodel.DBRefSource.UNIPROT});
\r
new String[] {
\r
jalview.datamodel.DBRefSource.PDB,
\r
jalview.datamodel.DBRefSource.UNIPROT});
\r
@@
-292,7
+290,7
@@
public class DasSequenceFeatureFetcher implements Runnable
cs[l].getName());
\r
\r
\r
cs[l].getName());
\r
\r
\r
- createFeatureFetcher(sequence,
\r
+ createFeatureFetcher(sequences[seqIndex],
\r
dasSource.getUrl(),
\r
( (DBRefEntry) uprefs.get(j)).
\r
getAccessionId(),
\r
dasSource.getUrl(),
\r
( (DBRefEntry) uprefs.get(j)).
\r
getAccessionId(),
\r
@@
-305,19
+303,19
@@
public class DasSequenceFeatureFetcher implements Runnable
{
\r
String id = null;
\r
// try and use the name as the sequence id
\r
{
\r
String id = null;
\r
// try and use the name as the sequence id
\r
- if (sequence.getName().indexOf("|") > -1)
\r
+ if (sequences[seqIndex].getName().indexOf("|") > -1)
\r
{
\r
{
\r
- id = sequence.getName().substring(
\r
- sequence.getName().lastIndexOf("|") + 1);
\r
+ id = sequences[seqIndex].getName().substring(
\r
+ sequences[seqIndex].getName().lastIndexOf("|") + 1);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- id = sequence.getName();
\r
+ id = sequences[seqIndex].getName();
\r
}
\r
if (id != null)
\r
{
\r
// Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
\r
}
\r
if (id != null)
\r
{
\r
// Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references
\r
- createFeatureFetcher(sequence,
\r
+ createFeatureFetcher(sequences[seqIndex],
\r
dasSource.getUrl(),
\r
id,
\r
dasSource.getNickname());
\r
dasSource.getUrl(),
\r
id,
\r
dasSource.getNickname());
\r