/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
import java.net.URL;\r
\r
import org.biojava.dasobert.das.FeatureThread;\r
-import org.biojava.dasobert.dasregistry.Das1Source;\r
import org.biojava.dasobert.eventmodel.FeatureEvent;\r
import org.biojava.dasobert.eventmodel.FeatureListener;\r
import org.biojava.dasobert.dasregistry.DasSource;\r
\r
\r
import jalview.bin.Cache;\r
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
\r
+import javax.swing.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class DasSequenceFeatureFetcher implements Runnable\r
{\r
- final AlignmentI dataset;\r
- final AlignmentPanel ap;\r
+ SequenceI [] sequences;\r
+ AlignFrame af;\r
StringBuffer sbuffer = new StringBuffer();\r
+ Vector selectedSources;\r
\r
+ long startTime;\r
+ int threadsRunning = 0;\r
+ boolean allBatchesComplete = false;\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, AlignmentPanel ap)\r
+ public DasSequenceFeatureFetcher(SequenceI [] sequences,\r
+ final AlignFrame af,\r
+ Vector selectedSources)\r
{\r
- this.dataset = align.getDataset();\r
- this.ap = ap;\r
+ this.selectedSources = selectedSources;\r
+ this.sequences = sequences;\r
+ this.af = af;\r
+\r
+ int uniprotCount = 0;\r
+ for (int i = 0; i < selectedSources.size(); i++)\r
+ {\r
+ DasSource source = (DasSource) selectedSources.elementAt(i);\r
+ DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
+ for (int c = 0; c < coords.length; c++)\r
+ {\r
+ if (coords[c].getName().indexOf("UniProt")>-1)\r
+ {\r
+ uniprotCount++;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ int refCount = 0;\r
+ for(int i=0; i<sequences.length; i++)\r
+ {\r
+ DBRefEntry [] dbref = sequences[i].getDBRef();\r
+ if(dbref!=null)\r
+ {\r
+ for(int j=0; j<dbref.length; j++)\r
+ {\r
+ if(dbref[j].getSource()\r
+ .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
+ {\r
+ refCount++;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
\r
+ if(refCount<sequences.length && uniprotCount>0)\r
+ {\r
+\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "Do you want Jalview to find\n"\r
+ +"Uniprot Accession ids for given sequence names?",\r
+ "Find Uniprot Accession Ids",\r
+ JOptionPane.YES_NO_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if(reply == JOptionPane.YES_OPTION)\r
+ {\r
+ Thread thread = new Thread(new FetchDBRefs());\r
+ thread.start();\r
+ }\r
+ else\r
+ startFetching();\r
+ }\r
+ else\r
+ startFetching();\r
+\r
+ /* System.out.println("User selection is " +\r
+ ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)\r
+ + " % Uniprot, and "+refCount+" / " +sequences.length+" have uniprot accession");\r
+*/\r
+ }\r
+\r
+ void startFetching()\r
+ {\r
Thread thread = new Thread(this);\r
thread.start();\r
}\r
+\r
+ class FetchDBRefs implements Runnable\r
+ {\r
+ public void run()\r
+ {\r
+ new DBRefFetcher(\r
+ af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
+ startFetching();\r
+ }\r
+ }\r
+\r
+\r
/**\r
* creates a jalview sequence feature from a das feature document\r
* @param dasfeature\r
// null\r
// );\r
\r
- // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
return f;\r
}\r
catch (Exception e) {\r
+ System.out.println("ERRR "+e);\r
e.printStackTrace();\r
+ System.out.println("############");\r
Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
return null;\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
+ String nickname)\r
+ {\r
//////////////\r
/// fetch DAS features\r
final Das1Source source = new Das1Source();\r
\r
Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
sourceUrl);\r
+\r
if (id != null && id.length() > 0)\r
{\r
+ setThreadsRunning(+1);\r
+\r
+ // int start=seq.getStart(), end = seq.getEnd();\r
+ /* if(af.getViewport().getSelectionGroup()!=null)\r
+ {\r
+ SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());\r
+ start = tmp.findPosition(\r
+ af.getViewport().getSelectionGroup().getStartRes()\r
+ );\r
+\r
+ end = tmp.findPosition(\r
+ af.getViewport().getSelectionGroup().getEndRes()\r
+ );\r
+ }*/\r
+\r
FeatureThread fetcher = new FeatureThread(id\r
- + ":" + seq.getStart() + "," +seq.getEnd()\r
- , source);\r
+ // + ":" + start + "," + end,\r
+ , source);\r
+\r
\r
fetcher.addFeatureListener(new FeatureListener()\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
\r
public void newFeatures(FeatureEvent e)\r
{\r
+ setThreadsRunning(-1);\r
Das1Source ds = e.getDasSource();\r
\r
Map[] features = e.getFeatures();\r
seq.addSequenceFeature(f);\r
}\r
}\r
- }\r
+ else\r
+ {\r
+ System.out.println("No features found for sequence " +seq.getName()\r
+ +" from: "+ e.getDasSource().getNickname());\r
+ }\r
\r
+ }\r
}\r
\r
);\r
\r
//NOTE alignPanel listener will be called after the previous\r
//anonymous listener!!!\r
- fetcher.addFeatureListener(ap);\r
+ fetcher.addFeatureListener(af);\r
\r
fetcher.start();\r
}\r
}\r
+\r
+ synchronized void setThreadsRunning(int i)\r
+ {\r
+ threadsRunning += i;\r
+ if(threadsRunning<1 && allBatchesComplete)\r
+ {\r
+ af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
+\r
+ if(af.featureSettings!=null)\r
+ af.featureSettings.setTableData();\r
+ }\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
+ startTime = System.currentTimeMillis();\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
- 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
- if(sources[i].getNickname().equals(token))\r
+ token = st.nextToken();\r
+ for (int i = 0; i < sources.length; i++)\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
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
try\r
{\r
+ //We must limit the feature fetching to 20 to prevent\r
+ //Servers being overloaded with too many requests\r
+ int batchCount = 0;\r
+ int batchMaxSize = 10;\r
int seqIndex = 0;\r
- Vector sequences = dataset.getSequences();\r
- while (seqIndex < sequences.size())\r
+ while (seqIndex < sequences.length)\r
{\r
- Sequence sequence = (Sequence) sequences.get(seqIndex);\r
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
+ batchCount ++;\r
+ if(batchCount>=batchMaxSize)\r
+ {\r
+ waitTillBatchComplete();\r
+ batchCount = 0;\r
+ }\r
+\r
+ DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
new String[] {\r
jalview.datamodel.DBRefSource.PDB,\r
jalview.datamodel.DBRefSource.UNIPROT});\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, k = uprefs.size(); j < k; j++)\r
+ for (int j = 0; j < uprefs.length; j++)\r
{\r
+\r
// Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
- org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
- for (int l=0; l<cs.length; l++) {\r
- if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
- uprefs.get(j)))\r
+ DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
+ for (int l=0; l<cs.length; l++)\r
+ {\r
+ if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r
{\r
Cache.log.debug("Launched fetcher for coordinate system " +\r
cs[l].getName());\r
- createFeatureFetcher(sequence,\r
+\r
+\r
+ createFeatureFetcher(sequences[seqIndex],\r
dasSource.getUrl(),\r
- ( (DBRefEntry) uprefs.get(j)).\r
- getAccessionId(),\r
+ uprefs[j].getAccessionId(),\r
dasSource.getNickname());\r
}\r
}\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
- 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
- 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
- createFeatureFetcher(sequence,\r
+ createFeatureFetcher(sequences[seqIndex],\r
dasSource.getUrl(),\r
id,\r
dasSource.getNickname());\r
{\r
ex.printStackTrace();\r
}\r
+ allBatchesComplete = true;\r
+ }\r
+\r
+ void waitTillBatchComplete()\r
+ {\r
+ while( threadsRunning > 0 )\r
+ {\r
+ try{\r
+ Thread.sleep(500);\r
+\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
}\r
\r
\r
{\r
DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
\r
- String registryURL = //jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- // "http://servlet.sanger.ac.uk/dasregistry/services/das_registry"\r
- "http://www.spice-3d.org/dasregistry/das1/sources";\r
- // );\r
+ String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
+ "http://das.sanger.ac.uk/registry/das1/sources/"\r
+ );\r
\r
try\r
{\r
git://source.jalview.org / jalview.git / blobdiff