/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
+ * This file is part of Jalview.\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
+ * Jalview 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 3 of the License, or (at your option) any later version.\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
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.ws;\r
\r
import jalview.gui.Desktop;\r
import jalview.gui.IProgressIndicator;\r
import jalview.gui.OOMWarning;\r
+import jalview.ws.dbsources.das.api.jalviewSourceI;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
import java.lang.reflect.Array;\r
+import java.util.ArrayList;\r
import java.util.Enumeration;\r
import java.util.Hashtable;\r
+import java.util.List;\r
import java.util.StringTokenizer;\r
import java.util.Vector;\r
\r
-import org.biojava.dasobert.dasregistry.DasSource;\r
-\r
import uk.ac.ebi.picr.model.UPEntry;\r
\r
/**\r
// The key will be the seq name or accession id of the seq\r
Hashtable seqRefs;\r
\r
- String[] dbSources;\r
+ DbSourceProxy[] dbSources;\r
\r
SequenceFetcher sfetcher;\r
\r
* @param sources\r
* array of database source strings to query references from\r
*/\r
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)\r
+ public DBRefFetcher(SequenceI[] seqs, AlignFrame af, DbSourceProxy[] sources)\r
{\r
this.af = af;\r
alseqs = new SequenceI[seqs.length];\r
{\r
// af.featureSettings_actionPerformed(null);\r
String[] defdb = null, otherdb = sfetcher\r
- .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
- .getSelectedSources()\r
- : new jalview.gui.DasSourceBrowser().getSelectedSources();\r
- Enumeration en = dasselsrc.elements();\r
+ .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
+ List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();\r
+ Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
+ .getSelectedSources() : new jalview.gui.DasSourceBrowser()\r
+ .getSelectedSources();\r
+ Enumeration<jalviewSourceI> en = dasselsrc.elements();\r
while (en.hasMoreElements())\r
{\r
- DasSource src = (DasSource) en.nextElement();\r
- selsources.addElement(src.getNickname());\r
- }\r
- int osel = 0;\r
- for (int o = 0; otherdb != null && o < otherdb.length; o++)\r
- {\r
- if (!selsources.contains(otherdb[o]))\r
+ jalviewSourceI src = en.nextElement();\r
+ List<DbSourceProxy> sp=src.getSequenceSourceProxies();\r
+ selsources.addAll(sp);\r
+ if (sp.size()>1)\r
{\r
- otherdb[o] = null;\r
- }\r
- else\r
- {\r
- osel++;\r
+ Cache.log.debug("Added many Db Sources for :"+src.getTitle());\r
}\r
}\r
// select appropriate databases based on alignFrame context.\r
{\r
defdb = DBRefSource.PROTEINDBS;\r
}\r
- // append the selected sequence sources to the default dbs\r
- dbSources = new String[defdb.length + osel];\r
- System.arraycopy(defdb, 0, dbSources, 0, defdb.length);\r
- for (int o = 0, op = defdb.length; otherdb != null\r
- && o < otherdb.length; o++)\r
- {\r
- if (otherdb[o] != null)\r
- {\r
- dbSources[op++] = otherdb[o];\r
+ List<DbSourceProxy> srces=new ArrayList<DbSourceProxy>();\r
+ for (String ddb:defdb) {\r
+ List<DbSourceProxy> srcesfordb=sfetcher.getSourceProxy(ddb);\r
+ if (srcesfordb!=null) {\r
+ srces.addAll(srcesfordb);\r
}\r
}\r
+ \r
+ // append the selected sequence sources to the default dbs\r
+ srces.addAll(selsources);\r
+ dbSources = srces.toArray(new DbSourceProxy[0]);\r
}\r
else\r
{\r
{\r
if (dbSources == null)\r
{\r
- dbSources = new String[]\r
- {};\r
+ dbSources = new DbSourceProxy[0];\r
}\r
// append additional sources\r
- String[] otherdb = sfetcher\r
- .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ DbSourceProxy[] otherdb=sfetcher\r
+ .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
if (otherdb != null && otherdb.length > 0)\r
{\r
- String[] newsrc = new String[dbSources.length + otherdb.length];\r
+ DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length + otherdb.length];\r
System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
- System\r
- .arraycopy(otherdb, 0, newsrc, dbSources.length,\r
- otherdb.length);\r
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);\r
dbSources = newsrc;\r
}\r
}\r
while (sdataset.size() > 0 && db < dbSources.length)\r
{\r
int maxqlen = 1; // default number of queries made to at one time\r
- System.err.println("Verifying against " + dbSources[db]);\r
- jalview.ws.seqfetcher.DbSourceProxy dbsource = sfetcher\r
- .getSourceProxy(dbSources[db]);\r
- if (dbsource == null)\r
- {\r
- System.err.println("No proxy for " + dbSources[db]);\r
- db++;\r
- continue;\r
- }\r
- if (dbsource.getDbSourceProperties()\r
- .containsKey(DBRefSource.MULTIACC))\r
- {\r
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(\r
- DBRefSource.MULTIACC)).intValue();\r
- }\r
- else\r
- {\r
- maxqlen = 1;\r
- }\r
+ System.err.println("Verifying against " + dbSources[db].getDbName());\r
+ boolean dn = false;\r
+\r
// iterate through db for each remaining un-verified sequence\r
SequenceI[] currSeqs = new SequenceI[sdataset.size()];\r
sdataset.copyInto(currSeqs);// seqs that are to be validated against\r
\r
int seqIndex = 0;\r
\r
- while (queries.size() > 0 || seqIndex < currSeqs.length)\r
+ jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];\r
{\r
- if (queries.size() > 0)\r
+ // for moment, we dumbly iterate over all retrieval sources for a particular database\r
+ // TODO: introduce multithread multisource queries and logic to remove a query from other sources if any source for a database returns a record\r
+ if (dbsource.getDbSourceProperties().containsKey(\r
+ DBRefSource.MULTIACC))\r
{\r
- // Still queries to make for current seqIndex\r
- StringBuffer queryString = new StringBuffer("");\r
- int numq = 0, nqSize = (maxqlen > queries.size()) ? queries\r
- .size() : maxqlen;\r
-\r
- while (queries.size() > 0 && numq < nqSize)\r
+ maxqlen = ((Integer) dbsource.getDbSourceProperties().get(\r
+ DBRefSource.MULTIACC)).intValue();\r
+ }\r
+ else\r
+ {\r
+ maxqlen = 1;\r
+ }\r
+ while (queries.size() > 0 || seqIndex < currSeqs.length)\r
+ {\r
+ if (queries.size() > 0)\r
{\r
- String query = (String) queries.elementAt(0);\r
- if (dbsource.isValidReference(query))\r
+ // Still queries to make for current seqIndex\r
+ StringBuffer queryString = new StringBuffer("");\r
+ int numq = 0, nqSize = (maxqlen > queries.size()) ? queries\r
+ .size() : maxqlen;\r
+\r
+ while (queries.size() > 0 && numq < nqSize)\r
{\r
- queryString.append((numq == 0) ? "" : dbsource\r
- .getAccessionSeparator());\r
- queryString.append(query);\r
- numq++;\r
+ String query = (String) queries.elementAt(0);\r
+ if (dbsource.isValidReference(query))\r
+ {\r
+ queryString.append((numq == 0) ? "" : dbsource\r
+ .getAccessionSeparator());\r
+ queryString.append(query);\r
+ numq++;\r
+ }\r
+ // remove the extracted query string\r
+ queries.removeElementAt(0);\r
}\r
- // remove the extracted query string\r
- queries.removeElementAt(0);\r
- }\r
- // make the queries and process the response\r
- AlignmentI retrieved = null;\r
- try\r
- {\r
- if (jalview.bin.Cache.log.isDebugEnabled())\r
+ // make the queries and process the response\r
+ AlignmentI retrieved = null;\r
+ try\r
{\r
- jalview.bin.Cache.log.debug("Querying "\r
- + dbsource.getDbName() + " with : '"\r
- + queryString.toString() + "'");\r
+ if (jalview.bin.Cache.log.isDebugEnabled())\r
+ {\r
+ jalview.bin.Cache.log.debug("Querying "\r
+ + dbsource.getDbName() + " with : '"\r
+ + queryString.toString() + "'");\r
+ }\r
+ retrieved = dbsource.getSequenceRecords(queryString\r
+ .toString());\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ } catch (OutOfMemoryError err)\r
+ {\r
+ new OOMWarning("retrieving database references ("\r
+ + queryString.toString() + ")", err);\r
+ }\r
+ if (retrieved != null)\r
+ {\r
+ transferReferences(sdataset, dbsource.getDbSource(), retrieved);\r
}\r
- retrieved = dbsource.getSequenceRecords(queryString.toString());\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- } catch (OutOfMemoryError err)\r
- {\r
- new OOMWarning("retrieving database references ("\r
- + queryString.toString() + ")", err);\r
- }\r
- if (retrieved != null)\r
- {\r
- transferReferences(sdataset, dbSources[db], retrieved);\r
}\r
- }\r
- else\r
- {\r
- // make some more strings for use as queries\r
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)\r
+ else\r
{\r
- SequenceI sequence = dataset[seqIndex];\r
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
- sequence.getDBRef(), new String[]\r
- { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
- // });\r
- // check for existing dbrefs to use\r
- if (uprefs != null && uprefs.length > 0)\r
+ // make some more strings for use as queries\r
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)\r
{\r
- for (int j = 0; j < uprefs.length; j++)\r
+ SequenceI sequence = dataset[seqIndex];\r
+ DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
+ sequence.getDBRef(), new String[]\r
+ { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT\r
+ // });\r
+ // check for existing dbrefs to use\r
+ if (uprefs != null && uprefs.length > 0)\r
{\r
- addSeqId(sequence, uprefs[j].getAccessionId());\r
- queries\r
- .addElement(uprefs[j].getAccessionId()\r
- .toUpperCase());\r
+ for (int j = 0; j < uprefs.length; j++)\r
+ {\r
+ addSeqId(sequence, uprefs[j].getAccessionId());\r
+ queries.addElement(uprefs[j].getAccessionId()\r
+ .toUpperCase());\r
+ }\r
}\r
- }\r
- else\r
- {\r
- // generate queries from sequence ID string\r
- StringTokenizer st = new StringTokenizer(sequence.getName(),\r
- "|");\r
- while (st.hasMoreTokens())\r
+ else\r
{\r
- String token = st.nextToken();\r
- UPEntry[] presp = null;\r
- if (picrClient != null)\r
+ // generate queries from sequence ID string\r
+ StringTokenizer st = new StringTokenizer(\r
+ sequence.getName(), "|");\r
+ while (st.hasMoreTokens())\r
{\r
- // resolve the string against PICR to recover valid IDs\r
- try\r
+ String token = st.nextToken();\r
+ UPEntry[] presp = null;\r
+ if (picrClient != null)\r
{\r
- presp = picrClient\r
- .getUPIForAccession(token, null, picrClient\r
- .getMappedDatabaseNames(), null, true);\r
- } catch (Exception e)\r
+ // resolve the string against PICR to recover valid IDs\r
+ try\r
+ {\r
+ presp = picrClient.getUPIForAccession(token, null,\r
+ picrClient.getMappedDatabaseNames(), null,\r
+ true);\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Exception with Picr for '"\r
+ + token + "'\n");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ if (presp != null && presp.length > 0)\r
{\r
- System.err.println("Exception with Picr for '" + token\r
- + "'\n");\r
- e.printStackTrace();\r
+ for (int id = 0; id < presp.length; id++)\r
+ {\r
+ // construct sequences from response if sequences are\r
+ // present, and do a transferReferences\r
+ // otherwise transfer non sequence x-references directly.\r
+ }\r
+ System.out\r
+ .println("Validated ID against PICR... (for what its worth):"\r
+ + token);\r
+ addSeqId(sequence, token);\r
+ queries.addElement(token.toUpperCase());\r
}\r
- }\r
- if (presp != null && presp.length > 0)\r
- {\r
- for (int id = 0; id < presp.length; id++)\r
+ else\r
{\r
- // construct sequences from response if sequences are\r
- // present, and do a transferReferences\r
- // otherwise transfer non sequence x-references directly.\r
+ // if ()\r
+ // System.out.println("Not querying source with token="+token+"\n");\r
+ addSeqId(sequence, token);\r
+ queries.addElement(token.toUpperCase());\r
}\r
- System.out\r
- .println("Validated ID against PICR... (for what its worth):"\r
- + token);\r
- addSeqId(sequence, token);\r
- queries.addElement(token.toUpperCase());\r
- }\r
- else\r
- {\r
- // if ()\r
- // System.out.println("Not querying source with token="+token+"\n");\r
- addSeqId(sequence, token);\r
- queries.addElement(token.toUpperCase());\r
}\r
}\r
}\r
} // all databases have been queries.\r
if (sbuffer.length() > 0)\r
{\r
- output\r
- .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
- + "altered, most likely the start/end residue will have been updated.\n"\r
- + "Save your alignment to maintain the updated id.\n\n"\r
- + sbuffer.toString());\r
+ output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
+ + "altered, most likely the start/end residue will have been updated.\n"\r
+ + "Save your alignment to maintain the updated id.\n\n"\r
+ + sbuffer.toString());\r
Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
// The above is the dataset, we must now find out the index\r
// of the viewed sequence\r
// taking into account all accessionIds and names in the file\r
Vector sequenceMatches = new Vector();\r
// look for corresponding accession ids\r
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry\r
- .getDBRef(), new String[]\r
- { dbSource });\r
+ DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(\r
+ entry.getDBRef(), new String[]\r
+ { dbSource });\r
+ if (entryRefs == null)\r
+ {\r
+ System.err\r
+ .println("Dud dbSource string ? no entryrefs selected for "\r
+ + dbSource + " on " + entry.getName());\r
+ continue;\r
+ }\r
for (int j = 0; j < entryRefs.length; j++)\r
{\r
String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();\r
// absStart+sequence.getStart()+entrySeq.length()-1},\r
// new int[] { entry.getStart(), entry.getEnd() }, 1, 1);\r
// relocate local features for updated start\r
- if (updateRefFrame) {\r
+ if (updateRefFrame)\r
+ {\r
if (sequence.getSequenceFeatures() != null)\r
{\r
- SequenceFeature[] sf = sequence.getSequenceFeatures();\r
- int start = sequence.getStart();\r
- int end = sequence.getEnd();\r
- int startShift = 1 - absStart - start; // how much the features are\r
- // to be shifted by\r
- for (int sfi = 0; sfi < sf.length; sfi++)\r
- {\r
- if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)\r
+ SequenceFeature[] sf = sequence.getSequenceFeatures();\r
+ int start = sequence.getStart();\r
+ int end = sequence.getEnd();\r
+ int startShift = 1 - absStart - start; // how much the features\r
+ // are\r
+ // to be shifted by\r
+ for (int sfi = 0; sfi < sf.length; sfi++)\r
{\r
- // shift feature along by absstart\r
- sf[sfi].setBegin(sf[sfi].getBegin() + startShift);\r
- sf[sfi].setEnd(sf[sfi].getEnd() + startShift);\r
+ if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)\r
+ {\r
+ // shift feature along by absstart\r
+ sf[sfi].setBegin(sf[sfi].getBegin() + startShift);\r
+ sf[sfi].setEnd(sf[sfi].getEnd() + startShift);\r
+ }\r
}\r
}\r
- }\r
}\r
}\r
\r
sequence.setStart(absStart);\r
sequence.setEnd(absEnd);\r
// search for alignment sequences to update coordinate frame for\r
- for (int alsq = 0; alsq<alseqs.length; alsq++)\r
+ for (int alsq = 0; alsq < alseqs.length; alsq++)\r
{\r
- if (alseqs[alsq].getDatasetSequence()==sequence)\r
+ if (alseqs[alsq].getDatasetSequence() == sequence)\r
{\r
String ngAlsq = AlignSeq.extractGaps("-. ",\r
alseqs[alsq].getSequenceAsString()).toUpperCase();\r
int oldstrt = alseqs[alsq].getStart();\r
- alseqs[alsq].setStart(sequence.getSequenceAsString().toUpperCase().indexOf(ngAlsq)+sequence.getStart());\r
- if (oldstrt != alseqs[alsq].getStart()) {\r
- alseqs[alsq].setEnd(ngAlsq.length()+alseqs[alsq].getStart()-1);\r
+ alseqs[alsq].setStart(sequence.getSequenceAsString()\r
+ .toUpperCase().indexOf(ngAlsq)\r
+ + sequence.getStart());\r
+ if (oldstrt != alseqs[alsq].getStart())\r
+ {\r
+ alseqs[alsq].setEnd(ngAlsq.length()\r
+ + alseqs[alsq].getStart() - 1);\r
}\r
}\r
}\r
- // TODO: search for all other references to this dataset sequence, and update start/end\r
- // TODO: update all AlCodonMappings which involve this alignment sequence (e.g. Q30167 cdna translation from exon2 product (vamsas demo)\r
+ // TODO: search for all other references to this dataset sequence, and\r
+ // update start/end\r
+ // TODO: update all AlCodonMappings which involve this alignment\r
+ // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas\r
+ // demo)\r
}\r
// and remove it from the rest\r
// TODO: decide if we should remove annotated sequence from set\r
git://source.jalview.org / jalview.git / blobdiff