--- /dev/null
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\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
+* 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 jalview.datamodel.*;\r
+\r
+import jalview.gui.*;\r
+\r
+import java.util.*;\r
+\r
+import java.net.URL;\r
+\r
+import org.biojava.dasobert.das.FeatureThread;\r
+import org.biojava.dasobert.eventmodel.FeatureEvent;\r
+import org.biojava.dasobert.eventmodel.FeatureListener;\r
+import org.biojava.dasobert.dasregistry.DasSource;\r
+\r
+import org.biojava.dasobert.das2.io.DasSourceReaderImpl;\r
+import org.biojava.dasobert.dasregistry.Das1Source;\r
+import org.biojava.dasobert.dasregistry.DasSource;\r
+import org.biojava.dasobert.das2.Das2Source;\r
+import org.biojava.dasobert.das2.DasSourceConverter;\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
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class DasSequenceFeatureFetcher implements Runnable\r
+{\r
+ SequenceI [] sequences;\r
+ AlignFrame af;\r
+ StringBuffer sbuffer = new StringBuffer();\r
+ Vector selectedSources;\r
+\r
+ long startTime;\r
+ int threadsRunning = 0;\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(SequenceI [] sequences,\r
+ final AlignFrame af,\r
+ Vector selectedSources)\r
+ {\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
+ * @return sequence feature object created using dasfeature information\r
+ */\r
+ SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
+ {\r
+ try {\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
+ desc+=(String) dasfeature.get("NOTE");\r
+\r
+\r
+ int start = 0, end = 0;\r
+ float score = 0f;\r
+\r
+ try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
+ catch( Exception ex){}\r
+ try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
+ catch (Exception ex){}\r
+ try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\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
+ // (String) dasfeature.get("ID"),\r
+ //// (String) dasfeature.get("METHOD"),\r
+ // (String) dasfeature.get("SCORE"),\r
+ // null\r
+ // );\r
+\r
+ return f;\r
+ }\r
+ catch (Exception e) {\r
+ e.printStackTrace();\r
+ Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
+ return null;\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
+ protected void createFeatureFetcher(final SequenceI seq,\r
+ final String sourceUrl,\r
+ String id,\r
+ String nickname)\r
+ {\r
+ //////////////\r
+ /// fetch DAS features\r
+ final Das1Source source = new Das1Source();\r
+ source.setUrl(sourceUrl);\r
+ source.setNickname(nickname);\r
+\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
+ // + ":" + 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
+\r
+ public void newFeatures(FeatureEvent e)\r
+ {\r
+ setThreadsRunning(-1);\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
+ 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(af);\r
+\r
+ fetcher.start();\r
+ }\r
+ }\r
+\r
+ synchronized void setThreadsRunning(int i)\r
+ {\r
+ threadsRunning += i;\r
+ if(threadsRunning<1)\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
+ if(selectedSources==null || selectedSources.size()==0)\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
+ {\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
+ try\r
+ {\r
+ int seqIndex = 0;\r
+ while (seqIndex < sequences.length)\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
+\r
+ for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
+ {\r
+ DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\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
+\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
+ 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
+\r
+\r
+ createFeatureFetcher(sequences[seqIndex],\r
+ dasSource.getUrl(),\r
+ uprefs[j].getAccessionId(),\r
+ dasSource.getNickname());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ String id = null;\r
+ // try and use the name as the sequence id\r
+ if (sequences[seqIndex].getName().indexOf("|") > -1)\r
+ {\r
+ id = sequences[seqIndex].getName().substring(\r
+ sequences[seqIndex].getName().lastIndexOf("|") + 1);\r
+ }\r
+ else\r
+ {\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(sequences[seqIndex],\r
+ dasSource.getUrl(),\r
+ id,\r
+ dasSource.getNickname());\r
+ }\r
+ }\r
+ }\r
+\r
+ seqIndex++;\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\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
+ "http://das.sanger.ac.uk/registry/das1/sources/"\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
+\r
git://source.jalview.org / jalview.git / blobdiff