- /**\r
- * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
- */\r
- void startFetching()\r
- {\r
- startTime = System.currentTimeMillis();\r
- af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
-\r
- DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
-\r
- if (selectedSources == null || selectedSources.size() == 0)\r
- {\r
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
- "uniprot");\r
- StringTokenizer st = new StringTokenizer(active, "\t");\r
- Vector selectedSources = new Vector();\r
- String token;\r
- while (st.hasMoreTokens())\r
- {\r
- token = st.nextToken();\r
- for (int i = 0; i < sources.length; i++)\r
- {\r
- if (sources[i].getNickname().equals(token))\r
- {\r
- selectedSources.addElement(sources[i]);\r
- break;\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (selectedSources == null || selectedSources.size() == 0)\r
- {\r
- System.out.println("No DAS Sources active");\r
- af.setProgressBar("No DAS Sources Active", startTime);\r
- return;\r
- }\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
- sourceIndex++)\r
- {\r
- DasSource dasSource = (DasSource) selectedSources.elementAt(\r
- sourceIndex);\r
-\r
- nextSequence(dasSource, sequences[0]);\r
- }\r
- }\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
- {\r
- if (sequences[seqIndex] == seq)\r
- {\r
- nextSequence(dasSource, sequences[++seqIndex]);\r
- return;\r
- }\r
- }\r
- }\r
-\r
- sourcesRemaining --;\r
-\r
- if(sourcesRemaining==0)\r
- {\r
- af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
-\r
- if(af.featureSettings!=null)\r
- af.featureSettings.setTableData();\r
- }\r
-\r
- }\r
-\r
- void featuresAdded(SequenceI seq)\r
- {\r
- af.getFeatureRenderer().featuresAdded();\r
-\r
- int start = af.getViewport().getStartSeq();\r
- int end = af.getViewport().getEndSeq();\r
- int index;\r
- for(index=start; index<end; index++)\r
- if(seq == af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())\r
- {\r
- af.alignPanel.repaint();\r
- break;\r
- }\r
- }\r
+ if (selectedSources == null || selectedSources.size() == 0)\r
+ {\r
+ String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
+ "uniprot");\r
+ StringTokenizer st = new StringTokenizer(active, "\t");\r
+ Vector selectedSources = new Vector();\r
+ String token;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ token = st.nextToken();\r
+ for (int i = 0; i < sources.length; i++)\r
+ {\r
+ if (sources[i].getNickname().equals(token))\r
+ {\r
+ selectedSources.addElement(sources[i]);\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ if (selectedSources == null || selectedSources.size() == 0)\r
+ {\r
+ System.out.println("No DAS Sources active");\r
+ af.setProgressBar("No DAS Sources Active", startTime);\r
+ return;\r
+ }\r
+\r
+ sourcesRemaining = selectedSources.size();\r
+ //Now sending requests one at a time to each server\r
+ for (int sourceIndex = 0;\r
+ sourceIndex < selectedSources.size()\r
+ && !cancelled;\r
+ sourceIndex++)\r
+ {\r
+ DasSource dasSource = (DasSource) selectedSources.elementAt(\r
+ sourceIndex);\r
+\r
+ nextSequence(dasSource, sequences[0]);\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
+ for (int seqIndex = 0;\r
+ seqIndex < sequences.length - 1\r
+ && !cancelled; seqIndex++)\r
+ {\r
+ if (sequences[seqIndex] == seq)\r
+ {\r
+ nextSequence(dasSource, sequences[++seqIndex]);\r
+ return;\r
+ }\r
+ }\r
+ }\r