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ensure lastSeq is refreshed if new feature added
[jalview.git]
/
src
/
jalview
/
io
/
DasSequenceFeatureFetcher.java
diff --git
a/src/jalview/io/DasSequenceFeatureFetcher.java
b/src/jalview/io/DasSequenceFeatureFetcher.java
index
3186002
..
f6e6f9b
100755
(executable)
--- a/
src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/
src/jalview/io/DasSequenceFeatureFetcher.java
@@
-52,8
+52,10
@@
public class DasSequenceFeatureFetcher
{
\r
SequenceI[] sequences;
\r
AlignFrame af;
\r
{
\r
SequenceI[] sequences;
\r
AlignFrame af;
\r
+ FeatureSettings fsettings;
\r
StringBuffer sbuffer = new StringBuffer();
\r
Vector selectedSources;
\r
StringBuffer sbuffer = new StringBuffer();
\r
Vector selectedSources;
\r
+ boolean cancelled = false;
\r
\r
long startTime;
\r
\r
\r
long startTime;
\r
\r
@@
-65,12
+67,13
@@
public class DasSequenceFeatureFetcher
* @param ap DOCUMENT ME!
\r
*/
\r
public DasSequenceFeatureFetcher(SequenceI[] sequences,
\r
* @param ap DOCUMENT ME!
\r
*/
\r
public DasSequenceFeatureFetcher(SequenceI[] sequences,
\r
- final AlignFrame af,
\r
+ FeatureSettings fsettings,
\r
Vector selectedSources)
\r
{
\r
this.selectedSources = selectedSources;
\r
this.sequences = sequences;
\r
Vector selectedSources)
\r
{
\r
this.selectedSources = selectedSources;
\r
this.sequences = sequences;
\r
- this.af = af;
\r
+ this.af = fsettings.af;
\r
+ this.fsettings = fsettings;
\r
\r
int uniprotCount = 0;
\r
for (int i = 0; i < selectedSources.size(); i++)
\r
\r
int uniprotCount = 0;
\r
for (int i = 0; i < selectedSources.size(); i++)
\r
@@
-145,6
+148,7
@@
public class DasSequenceFeatureFetcher
*/
\r
void startFetching()
\r
{
\r
*/
\r
void startFetching()
\r
{
\r
+ cancelled = false;
\r
startTime = System.currentTimeMillis();
\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);
\r
\r
startTime = System.currentTimeMillis();
\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);
\r
\r
@@
-180,7
+184,9
@@
public class DasSequenceFeatureFetcher
\r
sourcesRemaining = selectedSources.size();
\r
//Now sending requests one at a time to each server
\r
\r
sourcesRemaining = selectedSources.size();
\r
//Now sending requests one at a time to each server
\r
- for (int sourceIndex = 0; sourceIndex < selectedSources.size();
\r
+ for (int sourceIndex = 0;
\r
+ sourceIndex < selectedSources.size()
\r
+ && !cancelled;
\r
sourceIndex++)
\r
{
\r
DasSource dasSource = (DasSource) selectedSources.elementAt(
\r
sourceIndex++)
\r
{
\r
DasSource dasSource = (DasSource) selectedSources.elementAt(
\r
@@
-190,12
+196,20
@@
public class DasSequenceFeatureFetcher
}
\r
}
\r
\r
}
\r
}
\r
\r
+ public void cancel()
\r
+ {
\r
+ af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
\r
+ cancelled = true;
\r
+ }
\r
+
\r
int sourcesRemaining=0;
\r
void responseComplete(DasSource dasSource, SequenceI seq)
\r
{
\r
if (seq != null)
\r
{
\r
int sourcesRemaining=0;
\r
void responseComplete(DasSource dasSource, SequenceI seq)
\r
{
\r
if (seq != null)
\r
{
\r
- for (int seqIndex = 0; seqIndex < sequences.length-1; seqIndex++)
\r
+ for (int seqIndex = 0;
\r
+ seqIndex < sequences.length-1
\r
+ && !cancelled; seqIndex++)
\r
{
\r
if (sequences[seqIndex] == seq)
\r
{
\r
{
\r
if (sequences[seqIndex] == seq)
\r
{
\r
@@
-213,6
+227,8
@@
public class DasSequenceFeatureFetcher
\r
if(af.featureSettings!=null)
\r
af.featureSettings.setTableData();
\r
\r
if(af.featureSettings!=null)
\r
af.featureSettings.setTableData();
\r
+
\r
+ fsettings.complete();
\r
}
\r
\r
}
\r
}
\r
\r
}
\r
@@
-443,7
+459,7
@@
public class DasSequenceFeatureFetcher
DasSourceReaderImpl reader = new DasSourceReaderImpl();
\r
\r
String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
\r
DasSourceReaderImpl reader = new DasSourceReaderImpl();
\r
\r
String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
\r
- "http://www.dasregistry.org/registry/das1/sources/"
\r
+ DasSourceBrowser.DEFAULT_REGISTRY
\r
);
\r
\r
try
\r
);
\r
\r
try
\r