+++ /dev/null
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.net.*;\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-import org.biojava.dasobert.das.*;\r
-import org.biojava.dasobert.das2.*;\r
-import org.biojava.dasobert.das2.io.*;\r
-import org.biojava.dasobert.dasregistry.*;\r
-import org.biojava.dasobert.eventmodel.*;\r
-import jalview.bin.Cache;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class DasSequenceFeatureFetcher\r
-{\r
- SequenceI[] sequences;\r
- AlignFrame af;\r
- FeatureSettings fsettings;\r
- StringBuffer sbuffer = new StringBuffer();\r
- Vector selectedSources;\r
- boolean cancelled = false;\r
-\r
- long startTime;\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(SequenceI[] sequences,\r
- FeatureSettings fsettings,\r
- Vector selectedSources)\r
- {\r
- this.selectedSources = selectedSources;\r
- this.sequences = sequences;\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
- 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
- {\r
- startFetching();\r
- }\r
- }\r
- else\r
- {\r
- startFetching();\r
- }\r
-\r
- }\r
-\r
- class FetchDBRefs\r
- implements Runnable\r
- {\r
- public void run()\r
- {\r
- new DBRefFetcher(sequences, af).fetchDBRefs(true);\r
- startFetching();\r
- }\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
- 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
- cancelled = true;\r
- fsettings.noDasSourceActive();\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
- 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
- if (seq ==\r
- af.getViewport().getAlignment().getSequenceAt(index).getDatasetSequence())\r
- {\r
- af.alignPanel.paintAlignment(true);\r
- break;\r
- }\r
- }\r
- }\r
-\r
-\r
- void nextSequence(DasSource dasSource, SequenceI seq)\r
- {\r
- if (cancelled)\r
- return;\r
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),\r
- new String[]\r
- {\r
- // jalview.datamodel.DBRefSource.PDB,\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
-\r
- boolean dasCoordSysFound = false;\r
-\r
- if (uprefs != null)\r
- {\r
- // do any of these ids match the source's coordinate system ?\r
- for (int j = 0; !dasCoordSysFound && j < uprefs.length; j++)\r
- {\r
- DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
-\r
- for(int csIndex=0; csIndex<cs.length && !dasCoordSysFound; csIndex++)\r
- {\r
- if (cs.length > 0 && jalview.util.DBRefUtils\r
- .isDasCoordinateSystem(cs[csIndex].getName(), uprefs[j]))\r
- {\r
- Cache.log.debug("Launched fetcher for coordinate system " +\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
- System.out.println(seq.getName() + " " + (seq.getDatasetSequence() == null)\r
- + " " + dasSource.getUrl());\r
-\r
- dasCoordSysFound = true; // break's out of the loop\r
- createFeatureFetcher(seq,\r
- dasSource,\r
- uprefs[j]);\r
- }\r
- else\r
- System.out.println("IGNORE " + cs[csIndex].getName());\r
- }\r
- }\r
- }\r
-\r
- if(!dasCoordSysFound)\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
- 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
- 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[]=null;\r
- \r
- try {\r
- vf = dbref.getMap().locateFeature(f);\r
- }\r
- catch (Exception ex)\r
- {\r
- Cache.log.info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");\r
- Cache.log.info("Mapping feature from "+f.getBegin()+" to "+f.getEnd()+" in dbref "+dbref.getAccessionId()+" in "+dbref.getSource());\r
- Cache.log.info("using das Source "+ds.getUrl());\r
- Cache.log.info(ex);\r
- }\r
- \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
- fetcher.start();\r
- }\r
- protected void createFeatureFetcher(final SequenceI seq,\r
- final DasSource dasSource,\r
- String id)\r
- {\r
- //////////////\r
- /// fetch DAS features\r
- final Das1Source source = new Das1Source();\r
- source.setUrl(dasSource.getUrl());\r
- source.setNickname(dasSource.getNickname());\r
-\r
- Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
- dasSource.getUrl());\r
-\r
- if (id != null && id.length() > 0)\r
- {\r
- FeatureThread fetcher = new FeatureThread(id\r
- // + ":" + start + "," + end,\r
- , source);\r
-\r
- fetcher.addFeatureListener(new FeatureListener()\r
- {\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
-\r
- seq.addSequenceFeature(f);\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
- fetcher.start();\r
- }\r
- }\r
-\r
- /**\r
- * creates a jalview sequence feature from a das feature document\r
- * @param dasfeature\r
- * @return sequence feature object created using dasfeature information\r
- */\r
- SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
- {\r
- if (dasfeature==null)\r
- {\r
- return null;\r
- }\r
- try\r
- {\r
- /**\r
- * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
- * "METHOD") ||\r
- qName.equals("TYPE") ||\r
- qName.equals("START") ||\r
- qName.equals("END") ||\r
- qName.equals("NOTE") ||\r
- qName.equals("LINK") ||\r
- qName.equals("SCORE")\r
- */\r
- String desc = new String();\r
- if (dasfeature.containsKey("NOTE"))\r
- {\r
- desc += (String) dasfeature.get("NOTE");\r
- }\r
-\r
- int start = 0, end = 0;\r
- float score = 0f;\r
-\r
- try\r
- {\r
- start = Integer.parseInt(dasfeature.get("START").toString());\r
- }\r
- catch (Exception ex)\r
- {}\r
- try\r
- {\r
- end = Integer.parseInt(dasfeature.get("END").toString());\r
- }\r
- catch (Exception ex)\r
- {}\r
- try\r
- {\r
- score = Integer.parseInt(dasfeature.get("SCORE").toString());\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- SequenceFeature f = new SequenceFeature(\r
- (String) dasfeature.get("TYPE"),\r
- desc,\r
- start,\r
- end,\r
- score,\r
- nickname);\r
-\r
- if (dasfeature.containsKey("LINK"))\r
- {\r
- f.addLink(f.getType() + " " + f.begin + "_" + f.end\r
- + "|" + dasfeature.get("LINK"));\r
- }\r
-\r
- return f;\r
- }\r
- catch (Exception e)\r
- {\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
- }\r
-\r
- public static DasSource[] getDASSources()\r
- {\r
- DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
-\r
- String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- DasSourceBrowser.DEFAULT_REGISTRY\r
- );\r
-\r
- try\r
- {\r
- URL url = new URL(registryURL);\r
-\r
- DasSource[] sources = reader.readDasSource(url);\r
-\r
- List das1sources = new ArrayList();\r
- for (int i = 0; i < sources.length; i++)\r
- {\r
- DasSource ds = sources[i];\r
- if (ds instanceof Das2Source)\r
- {\r
- Das2Source d2s = (Das2Source) ds;\r
- if (d2s.hasDas1Capabilities())\r
- {\r
- Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
- das1sources.add(d1s);\r
- }\r
-\r
- }\r
- else if (ds instanceof Das1Source)\r
- {\r
- das1sources.add( (Das1Source) ds);\r
- }\r
- }\r
-\r
- return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- return null;\r
- }\r
- }\r
-\r
-}\r
-\r
git://source.jalview.org / jalview.git / blobdiff