/*\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, 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.analysis.AlignSeq;\r
+import jalview.bin.Cache;\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.DBRefEntry;\r
import jalview.datamodel.DBRefSource;\r
import jalview.gui.IProgressIndicator;\r
import jalview.gui.OOMWarning;\r
\r
+import java.lang.reflect.Array;\r
import java.util.Enumeration;\r
import java.util.Hashtable;\r
import java.util.StringTokenizer;\r
StringBuffer sbuffer = new StringBuffer();\r
\r
boolean running = false;\r
+\r
/**\r
* picr client instance\r
*/\r
\r
SequenceFetcher sfetcher;\r
\r
+ private SequenceI[] alseqs;\r
+\r
public DBRefFetcher()\r
{\r
}\r
\r
/**\r
- * Creates a new SequenceFeatureFetcher object and fetches from the\r
- * currently selected set of databases.\r
+ * Creates a new SequenceFeatureFetcher object and fetches from the currently\r
+ * selected set of databases.\r
* \r
* @param seqs\r
- * fetch references for these sequences\r
+ * fetch references for these sequences\r
* @param af\r
- * the parent alignframe for progress bar monitoring.\r
+ * the parent alignframe for progress bar monitoring.\r
*/\r
public DBRefFetcher(SequenceI[] seqs, AlignFrame af)\r
{\r
this(seqs, af, null);\r
}\r
+\r
/**\r
- * Creates a new SequenceFeatureFetcher object and fetches from the\r
- * currently selected set of databases.\r
+ * Creates a new SequenceFeatureFetcher object and fetches from the currently\r
+ * selected set of databases.\r
* \r
* @param seqs\r
- * fetch references for these sequences\r
+ * fetch references for these sequences\r
* @param af\r
- * the parent alignframe for progress bar monitoring.\r
- * @param sources array of database source strings to query references from\r
+ * the parent alignframe for progress bar monitoring.\r
+ * @param sources\r
+ * array of database source strings to query references from\r
*/\r
public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)\r
{\r
this.af = af;\r
+ alseqs = new SequenceI[seqs.length];\r
SequenceI[] ds = new SequenceI[seqs.length];\r
for (int i = 0; i < seqs.length; i++)\r
{\r
+ alseqs[i] = seqs[i];\r
if (seqs[i].getDatasetSequence() != null)\r
ds[i] = seqs[i].getDatasetSequence();\r
else\r
this.dataset = ds;\r
// TODO Jalview 2.5 lots of this code should be in the gui package!\r
sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);\r
- if (sources==null)\r
+ if (sources == null)\r
{\r
// af.featureSettings_actionPerformed(null);\r
- String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()\r
- : new jalview.gui.DasSourceBrowser().getSelectedSources();\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() : new jalview.gui.DasSourceBrowser()\r
+ .getSelectedSources();\r
Enumeration en = dasselsrc.elements();\r
while (en.hasMoreElements())\r
{\r
selsources.addElement(src.getNickname());\r
}\r
int osel = 0;\r
- for (int o=0;otherdb!=null && o<otherdb.length;o++)\r
+ for (int o = 0; otherdb != null && o < otherdb.length; o++)\r
{\r
if (!selsources.contains(otherdb[o]))\r
{\r
otherdb[o] = null;\r
- } else {\r
+ }\r
+ else\r
+ {\r
osel++;\r
}\r
}\r
{\r
defdb = DBRefSource.PROTEINDBS;\r
}\r
- // append the selected sequence sources to the default dbs \r
- dbSources = new String[defdb.length+osel];\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 && o<otherdb.length; o++)\r
+ for (int o = 0, op = defdb.length; otherdb != null\r
+ && o < otherdb.length; o++)\r
{\r
- if (otherdb[o]!=null)\r
+ if (otherdb[o] != null)\r
{\r
dbSources[op++] = otherdb[o];\r
}\r
}\r
- } else {\r
- // we assume the caller knows what they're doing and ensured that all the db source names are valid\r
+ }\r
+ else\r
+ {\r
+ // we assume the caller knows what they're doing and ensured that all the\r
+ // db source names are valid\r
dbSources = sources;\r
}\r
}\r
+\r
/**\r
- * retrieve all the das sequence sources and add them to the list of db sources to retrieve from \r
+ * retrieve all the das sequence sources and add them to the list of db\r
+ * sources to retrieve from\r
*/\r
public void appendAllDasSources()\r
{\r
if (dbSources == null)\r
{\r
- dbSources = new String[] {};\r
+ dbSources = new String[]\r
+ {};\r
}\r
// append additional sources\r
- String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- if (otherdb!=null && otherdb.length>0)\r
+ String[] otherdb = sfetcher\r
+ .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
+ if (otherdb != null && otherdb.length > 0)\r
{\r
- String[] newsrc = new String[dbSources.length+otherdb.length];\r
- System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);\r
- System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);\r
+ String[] newsrc = new String[dbSources.length + otherdb.length];\r
+ System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);\r
dbSources = newsrc;\r
}\r
}\r
+\r
/**\r
* start the fetcher thread\r
* \r
* @param waitTillFinished\r
- * true to block until the fetcher has finished\r
+ * true to block until the fetcher has finished\r
*/\r
public void fetchDBRefs(boolean waitTillFinished)\r
{\r
* could be either seq name or dbref id\r
* \r
* @param seq\r
- * SequenceI\r
+ * SequenceI\r
* @param key\r
- * String\r
+ * String\r
*/\r
void addSeqId(SequenceI seq, String key)\r
{\r
running = true;\r
long startTime = System.currentTimeMillis();\r
af.setProgressBar("Fetching db refs", startTime);\r
- try {\r
- picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); \r
+ try\r
+ {\r
+ if (Cache.getDefault("DBREFFETCH_USEPICR", false))\r
+ {\r
+ picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()\r
+ .getAccessionMapperPort();\r
+ }\r
} catch (Exception e)\r
{\r
System.err.println("Couldn't locate PICR service instance.\n");\r
{\r
// Still queries to make for current seqIndex\r
StringBuffer queryString = new StringBuffer("");\r
- int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()\r
- : maxqlen;\r
- \r
- while (queries.size()>0 && numq < nqSize)\r
+ int numq = 0, nqSize = (maxqlen > queries.size()) ? queries\r
+ .size() : maxqlen;\r
+\r
+ while (queries.size() > 0 && numq < nqSize)\r
{\r
String query = (String) queries.elementAt(0);\r
if (dbsource.isValidReference(query))\r
{\r
if (jalview.bin.Cache.log.isDebugEnabled())\r
{\r
- jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");\r
+ jalview.bin.Cache.log.debug("Querying "\r
+ + dbsource.getDbName() + " with : '"\r
+ + queryString.toString() + "'");\r
}\r
retrieved = dbsource.getSequenceRecords(queryString.toString());\r
} catch (Exception ex)\r
{ dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
// });\r
// check for existing dbrefs to use\r
- if (uprefs != null && uprefs.length>0)\r
+ if (uprefs != null && uprefs.length > 0)\r
{\r
for (int j = 0; j < uprefs.length; j++)\r
{\r
addSeqId(sequence, uprefs[j].getAccessionId());\r
- queries\r
- .addElement(uprefs[j].getAccessionId()\r
- .toUpperCase());\r
+ queries.addElement(uprefs[j].getAccessionId().toUpperCase());\r
}\r
}\r
else\r
{\r
String token = st.nextToken();\r
UPEntry[] presp = null;\r
- try {\r
- presp=picrClient.getUPIForAccession(token, null, picrClient.getMappedDatabaseNames(), null, true);\r
- } catch (Exception e) {\r
- System.err.println("Exception with Picr for '"+token+"'\n");\r
- e.printStackTrace();\r
+ if (picrClient != null)\r
+ {\r
+ // resolve the string against PICR to recover valid IDs\r
+ try\r
+ {\r
+ presp = picrClient\r
+ .getUPIForAccession(token, null,\r
+ picrClient.getMappedDatabaseNames(),\r
+ null, true);\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Exception with Picr for '" + token\r
+ + "'\n");\r
+ e.printStackTrace();\r
+ }\r
}\r
- if (presp!=null && presp.length>0)\r
+ if (presp != null && presp.length > 0)\r
{\r
- for (int id=0;id<presp.length; id++)\r
+ for (int id = 0; id < presp.length; id++)\r
{\r
- // construct sequences from response if sequences are present, and do a transferReferences\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
+ 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
- } else {\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
AlignmentI retrievedAl) // File\r
// file)\r
{\r
-\r
if (retrievedAl == null || retrievedAl.getHeight() == 0)\r
{\r
return;\r
}\r
- SequenceI[] retrieved = retrievedAl.getSequencesArray();\r
+ SequenceI[] retrieved = recoverDbSequences(retrievedAl\r
+ .getSequencesArray());\r
SequenceI sequence = null;\r
+ boolean transferred = false;\r
+ StringBuffer messages = new StringBuffer();\r
\r
// Vector entries = new Uniprot().getUniprotEntries(file);\r
\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 = nonGapped.indexOf(entrySeq);\r
if (absStart == -1)\r
{ // verification failed.\r
- sbuffer.append(sequence.getName()\r
+ messages.append(sequence.getName()\r
+ " SEQUENCE NOT %100 MATCH \n");\r
continue;\r
}\r
-\r
+ transferred = true;\r
sbuffer.append(sequence.getName() + " HAS " + absStart\r
+ " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");\r
//\r
}\r
else\r
{\r
+ transferred = true;\r
// update start and end of local sequence to place it in entry's\r
// reference frame.\r
// apply identity map map from whole of local sequence to matching\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 && sequence.getSequenceFeatures() != null)\r
+ if (updateRefFrame)\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
+ if (sequence.getSequenceFeatures() != null)\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
// finally, update local sequence reference frame if we're allowed\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
+ {\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()\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\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
sdataset.remove(sequence);\r
- // TODO: should we make a note of sequences that have received new DB ids, so we can query all enabled DAS servers for them ?\r
+ // TODO: should we make a note of sequences that have received new DB\r
+ // ids, so we can query all enabled DAS servers for them ?\r
}\r
}\r
+ if (!transferred)\r
+ {\r
+ // report the ID/sequence mismatches\r
+ sbuffer.append(messages);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * loop thru and collect additional sequences in Map.\r
+ * \r
+ * @param sequencesArray\r
+ * @return\r
+ */\r
+ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)\r
+ {\r
+ Vector nseq = new Vector();\r
+ for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)\r
+ {\r
+ nseq.addElement(sequencesArray[i]);\r
+ DBRefEntry dbr[] = sequencesArray[i].getDBRef();\r
+ jalview.datamodel.Mapping map = null;\r
+ for (int r = 0; (dbr != null) && r < dbr.length; r++)\r
+ {\r
+ if ((map = dbr[r].getMap()) != null)\r
+ {\r
+ if (map.getTo() != null && !nseq.contains(map.getTo()))\r
+ {\r
+ nseq.addElement(map.getTo());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (nseq.size() > 0)\r
+ {\r
+ sequencesArray = new SequenceI[nseq.size()];\r
+ nseq.toArray(sequencesArray);\r
+ }\r
+ return sequencesArray;\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff