X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=c1fe276676973d08f180c17f30df232d0bb9c61d;hb=e66322bfd895b80f19ae39ec0367a6c1cd4a93a3;hp=be0a8b0b67aead74f34ea35e26fa40c5e00d6f4d;hpb=1145380bdd6555637794c9db36624fa42a8818c8;p=jalview.git
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index be0a8b0..c1fe276 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,35 +1,45 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.ws;
-import java.io.*;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
+
+import java.lang.reflect.Array;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
import org.biojava.dasobert.dasregistry.DasSource;
-import org.exolab.castor.mapping.*;
-import org.exolab.castor.xml.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.datamodel.Mapping;
-import jalview.gui.*;
-import jalview.ws.dbsources.Uniprot;
-import jalview.ws.ebi.EBIFetchClient;
+
+import uk.ac.ebi.picr.model.UPEntry;
/**
* Implements a runnable for validating a sequence against external databases
@@ -50,6 +60,11 @@ public class DBRefFetcher implements Runnable
boolean running = false;
+ /**
+ * picr client instance
+ */
+ uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
+
// /This will be a collection of Vectors of sequenceI refs.
// The key will be the seq name or accession id of the seq
Hashtable seqRefs;
@@ -58,39 +73,45 @@ public class DBRefFetcher implements Runnable
SequenceFetcher sfetcher;
+ private SequenceI[] alseqs;
+
public DBRefFetcher()
{
}
/**
- * Creates a new SequenceFeatureFetcher object and fetches from the
- * currently selected set of databases.
+ * Creates a new SequenceFeatureFetcher object and fetches from the currently
+ * selected set of databases.
*
* @param seqs
- * fetch references for these sequences
+ * fetch references for these sequences
* @param af
- * the parent alignframe for progress bar monitoring.
+ * the parent alignframe for progress bar monitoring.
*/
public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
{
this(seqs, af, null);
}
+
/**
- * Creates a new SequenceFeatureFetcher object and fetches from the
- * currently selected set of databases.
+ * Creates a new SequenceFeatureFetcher object and fetches from the currently
+ * selected set of databases.
*
* @param seqs
- * fetch references for these sequences
+ * fetch references for these sequences
* @param af
- * the parent alignframe for progress bar monitoring.
- * @param sources array of database source strings to query references from
+ * the parent alignframe for progress bar monitoring.
+ * @param sources
+ * array of database source strings to query references from
*/
public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)
{
this.af = af;
+ alseqs = new SequenceI[seqs.length];
SequenceI[] ds = new SequenceI[seqs.length];
for (int i = 0; i < seqs.length; i++)
{
+ alseqs[i] = seqs[i];
if (seqs[i].getDatasetSequence() != null)
ds[i] = seqs[i].getDatasetSequence();
else
@@ -99,12 +120,14 @@ public class DBRefFetcher implements Runnable
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
- if (sources==null)
+ if (sources == null)
{
// af.featureSettings_actionPerformed(null);
- String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()
- : new jalview.gui.DasSourceBrowser().getSelectedSources();
+ String[] defdb = null, otherdb = sfetcher
+ .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings
+ .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+ .getSelectedSources();
Enumeration en = dasselsrc.elements();
while (en.hasMoreElements())
{
@@ -112,12 +135,14 @@ public class DBRefFetcher implements Runnable
selsources.addElement(src.getNickname());
}
int osel = 0;
- for (int o=0;otherdb!=null && o0)
+ String[] otherdb = sfetcher
+ .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+ if (otherdb != null && otherdb.length > 0)
{
- String[] newsrc = new String[dbSources.length+otherdb.length];
- System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);
- System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);
+ String[] newsrc = new String[dbSources.length + otherdb.length];
+ System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
dbSources = newsrc;
}
}
+
/**
* start the fetcher thread
*
* @param waitTillFinished
- * true to block until the fetcher has finished
+ * true to block until the fetcher has finished
*/
public void fetchDBRefs(boolean waitTillFinished)
{
@@ -195,9 +229,9 @@ public class DBRefFetcher implements Runnable
* could be either seq name or dbref id
*
* @param seq
- * SequenceI
+ * SequenceI
* @param key
- * String
+ * String
*/
void addSeqId(SequenceI seq, String key)
{
@@ -237,9 +271,21 @@ public class DBRefFetcher implements Runnable
{
throw new Error("Implementation error. Must initialise dbSources");
}
+ running = true;
long startTime = System.currentTimeMillis();
af.setProgressBar("Fetching db refs", startTime);
- running = true;
+ try
+ {
+ if (Cache.getDefault("DBREFFETCH_USEPICR", false))
+ {
+ picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+ .getAccessionMapperPort();
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't locate PICR service instance.\n");
+ e.printStackTrace();
+ }
int db = 0;
Vector sdataset = new Vector();
for (int s = 0; s < dataset.length; s++)
@@ -283,10 +329,10 @@ public class DBRefFetcher implements Runnable
{
// Still queries to make for current seqIndex
StringBuffer queryString = new StringBuffer("");
- int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()
- : maxqlen;
-
- while (queries.size()>0 && numq < nqSize)
+ int numq = 0, nqSize = (maxqlen > queries.size()) ? queries
+ .size() : maxqlen;
+
+ while (queries.size() > 0 && numq < nqSize)
{
String query = (String) queries.elementAt(0);
if (dbsource.isValidReference(query))
@@ -305,7 +351,9 @@ public class DBRefFetcher implements Runnable
{
if (jalview.bin.Cache.log.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");
+ jalview.bin.Cache.log.debug("Querying "
+ + dbsource.getDbName() + " with : '"
+ + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
} catch (Exception ex)
@@ -332,14 +380,12 @@ public class DBRefFetcher implements Runnable
{ dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
- if (uprefs != null && uprefs.length>0)
+ if (uprefs != null && uprefs.length > 0)
{
for (int j = 0; j < uprefs.length; j++)
{
addSeqId(sequence, uprefs[j].getAccessionId());
- queries
- .addElement(uprefs[j].getAccessionId()
- .toUpperCase());
+ queries.addElement(uprefs[j].getAccessionId().toUpperCase());
}
}
else
@@ -350,8 +396,44 @@ public class DBRefFetcher implements Runnable
while (st.hasMoreTokens())
{
String token = st.nextToken();
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ UPEntry[] presp = null;
+ if (picrClient != null)
+ {
+ // resolve the string against PICR to recover valid IDs
+ try
+ {
+ presp = picrClient
+ .getUPIForAccession(token, null,
+ picrClient.getMappedDatabaseNames(),
+ null, true);
+ } catch (Exception e)
+ {
+ System.err.println("Exception with Picr for '" + token
+ + "'\n");
+ e.printStackTrace();
+ }
+ }
+ if (presp != null && presp.length > 0)
+ {
+ for (int id = 0; id < presp.length; id++)
+ {
+ // construct sequences from response if sequences are
+ // present, and do a transferReferences
+ // otherwise transfer non sequence x-references directly.
+ }
+ System.out
+ .println("Validated ID against PICR... (for what its worth):"
+ + token);
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase());
+ }
+ else
+ {
+ // if ()
+ // System.out.println("Not querying source with token="+token+"\n");
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase());
+ }
}
}
}
@@ -362,11 +444,10 @@ public class DBRefFetcher implements Runnable
} // all databases have been queries.
if (sbuffer.length() > 0)
{
- output
- .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
- + "altered, most likely the start/end residue will have been updated.\n"
- + "Save your alignment to maintain the updated id.\n\n"
- + sbuffer.toString());
+ output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
+ + "altered, most likely the start/end residue will have been updated.\n"
+ + "Save your alignment to maintain the updated id.\n\n"
+ + sbuffer.toString());
Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
@@ -389,13 +470,15 @@ public class DBRefFetcher implements Runnable
AlignmentI retrievedAl) // File
// file)
{
-
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return;
}
- SequenceI[] retrieved = retrievedAl.getSequencesArray();
+ SequenceI[] retrieved = recoverDbSequences(retrievedAl
+ .getSequencesArray());
SequenceI sequence = null;
+ boolean transferred = false;
+ StringBuffer messages = new StringBuffer();
// Vector entries = new Uniprot().getUniprotEntries(file);
@@ -409,9 +492,16 @@ public class DBRefFetcher implements Runnable
// taking into account all accessionIds and names in the file
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
- .getDBRef(), new String[]
- { dbSource });
+ DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
+ entry.getDBRef(), new String[]
+ { dbSource });
+ if (entryRefs == null)
+ {
+ System.err
+ .println("Dud dbSource string ? no entryrefs selected for "
+ + dbSource + " on " + entry.getName());
+ continue;
+ }
for (int j = 0; j < entryRefs.length; j++)
{
String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();
@@ -488,11 +578,11 @@ public class DBRefFetcher implements Runnable
absStart = nonGapped.indexOf(entrySeq);
if (absStart == -1)
{ // verification failed.
- sbuffer.append(sequence.getName()
+ messages.append(sequence.getName()
+ " SEQUENCE NOT %100 MATCH \n");
continue;
}
-
+ transferred = true;
sbuffer.append(sequence.getName() + " HAS " + absStart
+ " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
//
@@ -512,6 +602,7 @@ public class DBRefFetcher implements Runnable
}
else
{
+ transferred = true;
// update start and end of local sequence to place it in entry's
// reference frame.
// apply identity map map from whole of local sequence to matching
@@ -523,20 +614,24 @@ public class DBRefFetcher implements Runnable
// absStart+sequence.getStart()+entrySeq.length()-1},
// new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
// relocate local features for updated start
- if (updateRefFrame && sequence.getSequenceFeatures() != null)
+ if (updateRefFrame)
{
- SequenceFeature[] sf = sequence.getSequenceFeatures();
- int start = sequence.getStart();
- int end = sequence.getEnd();
- int startShift = 1 - absStart - start; // how much the features are
- // to be shifted by
- for (int sfi = 0; sfi < sf.length; sfi++)
+ if (sequence.getSequenceFeatures() != null)
{
- if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
+ SequenceFeature[] sf = sequence.getSequenceFeatures();
+ int start = sequence.getStart();
+ int end = sequence.getEnd();
+ int startShift = 1 - absStart - start; // how much the features
+ // are
+ // to be shifted by
+ for (int sfi = 0; sfi < sf.length; sfi++)
{
- // shift feature along by absstart
- sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
- sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
+ if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
+ {
+ // shift feature along by absstart
+ sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
+ sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
+ }
}
}
}
@@ -553,11 +648,74 @@ public class DBRefFetcher implements Runnable
// finally, update local sequence reference frame if we're allowed
sequence.setStart(absStart);
sequence.setEnd(absEnd);
+ // search for alignment sequences to update coordinate frame for
+ for (int alsq = 0; alsq < alseqs.length; alsq++)
+ {
+ if (alseqs[alsq].getDatasetSequence() == sequence)
+ {
+ String ngAlsq = AlignSeq.extractGaps("-. ",
+ alseqs[alsq].getSequenceAsString()).toUpperCase();
+ int oldstrt = alseqs[alsq].getStart();
+ alseqs[alsq].setStart(sequence.getSequenceAsString()
+ .toUpperCase().indexOf(ngAlsq)
+ + sequence.getStart());
+ if (oldstrt != alseqs[alsq].getStart())
+ {
+ alseqs[alsq].setEnd(ngAlsq.length()
+ + alseqs[alsq].getStart() - 1);
+ }
+ }
+ }
+ // TODO: search for all other references to this dataset sequence, and
+ // update start/end
+ // TODO: update all AlCodonMappings which involve this alignment
+ // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas
+ // demo)
}
// and remove it from the rest
// TODO: decide if we should remove annotated sequence from set
sdataset.remove(sequence);
+ // TODO: should we make a note of sequences that have received new DB
+ // ids, so we can query all enabled DAS servers for them ?
}
}
+ if (!transferred)
+ {
+ // report the ID/sequence mismatches
+ sbuffer.append(messages);
+ }
+ }
+
+ /**
+ * loop thru and collect additional sequences in Map.
+ *
+ * @param sequencesArray
+ * @return
+ */
+ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
+ {
+ Vector nseq = new Vector();
+ for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
+ {
+ nseq.addElement(sequencesArray[i]);
+ DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+ jalview.datamodel.Mapping map = null;
+ for (int r = 0; (dbr != null) && r < dbr.length; r++)
+ {
+ if ((map = dbr[r].getMap()) != null)
+ {
+ if (map.getTo() != null && !nseq.contains(map.getTo()))
+ {
+ nseq.addElement(map.getTo());
+ }
+ }
+ }
+ }
+ if (nseq.size() > 0)
+ {
+ sequencesArray = new SequenceI[nseq.size()];
+ nseq.toArray(sequencesArray);
+ }
+ return sequencesArray;
}
}