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Selected DAS sources may differ from default
author
amwaterhouse
<Andrew Waterhouse>
Thu, 13 Jul 2006 17:00:47 +0000
(17:00 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 13 Jul 2006 17:00:47 +0000
(17:00 +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
7dbb183
..
dc51617
100755
(executable)
--- a/
src/jalview/io/DasSequenceFeatureFetcher.java
+++ b/
src/jalview/io/DasSequenceFeatureFetcher.java
@@
-53,18
+53,24
@@
public class DasSequenceFeatureFetcher implements Runnable
final AlignmentI dataset;
\r
final AlignFrame af;
\r
StringBuffer sbuffer = new StringBuffer();
\r
final AlignmentI dataset;
\r
final AlignFrame af;
\r
StringBuffer sbuffer = new StringBuffer();
\r
+ Vector selectedSources;
\r
\r
\r
+ long startTime;
\r
+ int threadsRunning = 0;
\r
\r
\r
/**
\r
* Creates a new SequenceFeatureFetcher object.
\r
\r
\r
/**
\r
* Creates a new SequenceFeatureFetcher object.
\r
+ * Uses default
\r
*
\r
* @param align DOCUMENT ME!
\r
* @param ap DOCUMENT ME!
\r
*/
\r
public DasSequenceFeatureFetcher(AlignmentI align,
\r
*
\r
* @param align DOCUMENT ME!
\r
* @param ap DOCUMENT ME!
\r
*/
\r
public DasSequenceFeatureFetcher(AlignmentI align,
\r
- AlignFrame af)
\r
+ AlignFrame af,
\r
+ Vector selectedSources)
\r
{
\r
{
\r
+ this.selectedSources = selectedSources;
\r
this.dataset = align.getDataset();
\r
this.af = af;
\r
\r
this.dataset = align.getDataset();
\r
this.af = af;
\r
\r
@@
-154,6
+160,8
@@
public class DasSequenceFeatureFetcher implements Runnable
sourceUrl);
\r
if (id != null && id.length() > 0)
\r
{
\r
sourceUrl);
\r
if (id != null && id.length() > 0)
\r
{
\r
+ setThreadsRunning(+1);
\r
+
\r
FeatureThread fetcher = new FeatureThread(id
\r
+ ":" + seq.getStart() + "," +seq.getEnd()
\r
, source);
\r
FeatureThread fetcher = new FeatureThread(id
\r
+ ":" + seq.getStart() + "," +seq.getEnd()
\r
, source);
\r
@@
-162,6
+170,7
@@
public class DasSequenceFeatureFetcher implements Runnable
{
\r
public void comeBackLater(FeatureEvent e)
\r
{
\r
{
\r
public void comeBackLater(FeatureEvent e)
\r
{
\r
+ setThreadsRunning(-1);
\r
Cache.log.debug("das source " + e.getDasSource().getNickname() +
\r
" asked us to come back in " + e.getComeBackLater() +
\r
" secs.");
\r
Cache.log.debug("das source " + e.getDasSource().getNickname() +
\r
" asked us to come back in " + e.getComeBackLater() +
\r
" secs.");
\r
@@
-169,6
+178,7
@@
public class DasSequenceFeatureFetcher implements Runnable
\r
public void newFeatures(FeatureEvent e)
\r
{
\r
\r
public void newFeatures(FeatureEvent e)
\r
{
\r
+ setThreadsRunning(-1);
\r
Das1Source ds = e.getDasSource();
\r
\r
Map[] features = e.getFeatures();
\r
Das1Source ds = e.getDasSource();
\r
\r
Map[] features = e.getFeatures();
\r
@@
-204,34
+214,44
@@
public class DasSequenceFeatureFetcher implements Runnable
fetcher.start();
\r
}
\r
}
\r
fetcher.start();
\r
}
\r
}
\r
+
\r
+ synchronized void setThreadsRunning(int i)
\r
+ {
\r
+ threadsRunning += i;
\r
+ if(threadsRunning<1)
\r
+ af.setProgressBar("DAS Feature Fetching Complete", startTime);
\r
+ }
\r
+
\r
/**
\r
* Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
\r
*/
\r
public void run()
\r
{
\r
/**
\r
* Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset
\r
*/
\r
public void run()
\r
{
\r
- long startTime = System.currentTimeMillis();
\r
+ startTime = System.currentTimeMillis();
\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);
\r
\r
DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
\r
\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);
\r
\r
DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();
\r
\r
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
\r
- StringTokenizer st = new StringTokenizer(active, "\t");
\r
- Vector selectedSources = new Vector();
\r
- String token;
\r
- while (st.hasMoreTokens())
\r
+ if(selectedSources==null || selectedSources.size()==0)
\r
{
\r
{
\r
- token = st.nextToken();
\r
- for(int i=0; i<sources.length; i++)
\r
+ String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
\r
+ StringTokenizer st = new StringTokenizer(active, "\t");
\r
+ Vector selectedSources = new Vector();
\r
+ String token;
\r
+ while (st.hasMoreTokens())
\r
{
\r
{
\r
- if(sources[i].getNickname().equals(token))
\r
+ token = st.nextToken();
\r
+ for (int i = 0; i < sources.length; i++)
\r
{
\r
{
\r
- selectedSources.addElement(sources[i]);
\r
- break;
\r
+ if (sources[i].getNickname().equals(token))
\r
+ {
\r
+ selectedSources.addElement(sources[i]);
\r
+ break;
\r
+ }
\r
}
\r
}
\r
}
\r
\r
}
\r
}
\r
}
\r
\r
-
\r
if(selectedSources == null || selectedSources.size()==0)
\r
{
\r
System.out.println("No DAS Sources active");
\r
if(selectedSources == null || selectedSources.size()==0)
\r
{
\r
System.out.println("No DAS Sources active");
\r
@@
-312,8
+332,6
@@
public class DasSequenceFeatureFetcher implements Runnable
{
\r
ex.printStackTrace();
\r
}
\r
{
\r
ex.printStackTrace();
\r
}
\r
-
\r
- af.setProgressBar("DAS Feature Fetching Complete", startTime);
\r
}
\r
\r
\r
}
\r
\r
\r