else\r
{\r
startFetching();\r
- }\r
+ }\r
}\r
else\r
{\r
startFetching();\r
}\r
\r
- }\r
+ }\r
\r
class FetchDBRefs\r
implements Runnable\r
}\r
}\r
\r
- /**\r
- * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
- */\r
- void startFetching()\r
- {\r
- cancelled = false;\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
+ * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
+ */\r
+ void startFetching()\r
+ {\r
+ cancelled = false;\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;\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
+\r
+ sourcesRemaining --;\r
+\r
+ if(sourcesRemaining==0)\r
+ {\r
+ af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
+\r
+ if(af.featureSettings!=null)\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
+ af.featureSettings.setTableData();\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
+ fsettings.complete();\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
+ }\r
\r
- sourcesRemaining--;\r
+ void featuresAdded(SequenceI seq)\r
+ {\r
+ af.getFeatureRenderer().featuresAdded();\r
\r
- if (sourcesRemaining == 0)\r
- {\r
- af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
-\r
- if (af.featureSettings != null)\r
- {\r
- af.featureSettings.setTableData();\r
- }\r
-\r
- fsettings.complete();\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
- {\r
+ int start = af.getViewport().getStartSeq();\r
+ int end = af.getViewport().getEndSeq();\r
+ int index;\r
+ for(index=start; index<end; index++)\r
+ {\r
if (seq ==\r
af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())\r
{\r
af.alignPanel.paintAlignment(true);\r
- break;\r
- }\r
- }\r
+ break;\r
+ }\r
+ }\r
}\r
\r
+\r
void nextSequence(DasSource dasSource, SequenceI seq)\r
{\r
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),\r
- new String[]\r
- {\r
+ DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),\r
+ new String[]\r
+ {\r
// jalview.datamodel.DBRefSource.PDB,\r
- jalview.datamodel.DBRefSource.UNIPROT\r
- });\r
-\r
- if (uprefs != null)\r
- {\r
- // we know the id for this entry, so don't note its ID in the unknownSequences list\r
- // for (int j = 0; j < uprefs.length; j++)\r
- {\r
- // Will have to pass any mapping information to the fetcher\r
- //- the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
- DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
- if (cs.length > 0)\r
+ jalview.datamodel.DBRefSource.UNIPROT,\r
+ // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord sys sources\r
+ });\r
+// TODO: minimal list of DAS queries to make by querying with untyped ID if distinct from any typed IDs\r
+ if (uprefs != null)\r
{\r
- // for (int l = 0; l < cs.length; l++)\r
+ // do any of these ids match the source's coordinate system ?\r
+ for (int j = 0; j < uprefs.length; j++)\r
{\r
- //\r
- if (jalview.util.DBRefUtils\r
- .isDasCoordinateSystem(cs[0].getName(), uprefs[0]))\r
+ DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
+ \r
+ if(cs.length>0 && jalview.util.DBRefUtils\r
+ .isDasCoordinateSystem(cs[0].getName(), uprefs[j]))\r
{\r
Cache.log.debug("Launched fetcher for coordinate system " +\r
- cs[0].getName());\r
-\r
+ cs[0].getName());\r
+ // Will have to pass any mapping information to the fetcher\r
+ //- the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
+ \r
createFeatureFetcher(seq,\r
- dasSource,\r
- uprefs[0].getAccessionId());\r
+ dasSource,\r
+ uprefs[j]);\r
+ break; // only do this for one reference - assume same source will send same features for all IDs\r
}\r
}\r
}\r
- }\r
- }\r
- else\r
+ else\r
+ {\r
+ String id = null;\r
+ // try and use the name as the sequence id\r
+ if (seq.getName().indexOf("|") > -1)\r
+ {\r
+ id = seq.getName().substring(\r
+ seq.getName().lastIndexOf("|") + 1);\r
+ }\r
+ else\r
+ {\r
+ id = seq.getName();\r
+ }\r
+ if (id != null)\r
+ {\r
+ // Should try to call a general feature fetcher that\r
+ // queries many sources with name to discover applicable ID references\r
+ createFeatureFetcher(seq,\r
+ dasSource,\r
+ id);\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+\r
+/**\r
+ * fetch and add das features to a sequence using the given source URL and compatible DbRef id.\r
+ * new features are mapped using the DbRef mapping to the local coordinate system.\r
+ * @param seq\r
+ * @param SourceUrl\r
+ * @param dbref\r
+ */ \r
+ protected void createFeatureFetcher(final SequenceI seq, final DasSource dasSource,\r
+ final DBRefEntry dbref) {\r
+ \r
+ //////////////\r
+ /// fetch DAS features\r
+ final Das1Source source = new Das1Source();\r
+ source.setUrl(dasSource.getUrl());\r
+ source.setNickname(dasSource.getNickname());\r
+ if (dbref==null || dbref.getAccessionId()==null || dbref.getAccessionId().length()<1) \r
{\r
- String id = null;\r
- // try and use the name as the sequence id\r
- if (seq.getName().indexOf("|") > -1)\r
- {\r
- id = seq.getName().substring(\r
- seq.getName().lastIndexOf("|") + 1);\r
- }\r
- else\r
- {\r
- id = seq.getName();\r
- }\r
- if (id != null)\r
+ return;\r
+ }\r
+ Cache.log.debug("new Das Feature Fetcher for " + dbref.getSource()+":"+dbref.getAccessionId() + " querying " +\r
+ dasSource.getUrl());\r
+ FeatureThread fetcher = new FeatureThread(dbref.getAccessionId()\r
+ // + ":" + start + "," + end,\r
+ , source);\r
+\r
+ fetcher.addFeatureListener(new FeatureListener()\r
{\r
- // Should try to call a general feature fetcher that\r
- // queries many sources with name to discover applicable ID references\r
- createFeatureFetcher(seq,\r
- dasSource,\r
- id);\r
+ public void comeBackLater(FeatureEvent e)\r
+ {\r
+ responseComplete(dasSource, seq);\r
+ Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
+ " asked us to come back in " + e.getComeBackLater() +\r
+ " secs.");\r
+ }\r
+\r
+ public void newFeatures(FeatureEvent e)\r
+ {\r
+\r
+ Das1Source ds = e.getDasSource();\r
+\r
+ Map[] features = e.getFeatures();\r
+ // add features to sequence\r
+ Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
+ features.length + " features");\r
+\r
+ if (features.length > 0)\r
+ {\r
+ for (int i = 0; i < features.length; i++)\r
+ {\r
+ SequenceFeature f = newSequenceFeature(features[i],\r
+ source.getNickname());\r
+ if (dbref.getMap()!=null && f.getBegin()>0 && f.getEnd()>0) {\r
+ Cache.log.debug("mapping from "+f.getBegin()+" - "+f.getEnd());\r
+ SequenceFeature vf[] = dbref.getMap().locateFeature(f);\r
+ if (vf!=null) {\r
+ for (int v=0;v<vf.length;v++) \r
+ {\r
+ Cache.log.debug("mapping to "+v+": "+vf[v].getBegin()+" - "+vf[v].getEnd());\r
+ seq.addSequenceFeature(vf[v]);\r
+ }\r
+ }\r
+ } else {\r
+ seq.addSequenceFeature(f);\r
+ }\r
+ }\r
+\r
+ featuresAdded(seq);\r
+ }\r
+ else\r
+ {\r
+ // System.out.println("No features found for " + seq.getName()\r
+ // + " from: " + e.getDasSource().getNickname());\r
+ }\r
+ responseComplete(dasSource, seq);\r
+\r
+ }\r
}\r
- }\r
\r
- }\r
+ );\r
\r
- /**\r
- * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
- * @param seq\r
- * @param SourceUrl\r
- * @param id\r
- */\r
+ fetcher.start();\r
+ }\r
protected void createFeatureFetcher(final SequenceI seq,\r
final DasSource dasSource,\r
String id)\r
}\r
else\r
{\r
- // System.out.println("No features found for " + seq.getName()\r
- // + " from: " + e.getDasSource().getNickname());\r
+ // System.out.println("No features found for " + seq.getName()\r
+ // + " from: " + e.getDasSource().getNickname());\r
}\r
responseComplete(dasSource, seq);\r
\r
}\r
\r
}\r
+\r
git://source.jalview.org / jalview.git / commitdiff