X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=5413a30526531d4609f5a4996b4c201f6d355240;hb=961d720adf23c1206d8110f6b2d00f072872155a;hp=ba6d57fc69d36300c14cc0201c3af11a40259c57;hpb=301974b9fb0b89dbe5a931371084fc2936905f38;p=jalview.git
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ba6d57f..5413a30 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,37 +1,51 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
- *
- * 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 - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 org.exolab.castor.mapping.*;
-import org.exolab.castor.xml.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+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.gui.*;
-import jalview.ws.dbsources.Uniprot;
-import jalview.ws.ebi.EBIFetchClient;
+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 jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.lang.reflect.Array;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import uk.ac.ebi.picr.model.UPEntry;
/**
- * DOCUMENT ME!
+ * Implements a runnable for validating a sequence against external databases
+ * and then propagating references and features onto the sequence(s)
*
* @author $author$
* @version $Revision$
@@ -40,7 +54,7 @@ public class DBRefFetcher implements Runnable
{
SequenceI[] dataset;
- AlignFrame af;
+ IProgressIndicator af;
CutAndPasteTransfer output = new CutAndPasteTransfer();
@@ -48,47 +62,134 @@ 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;
- String[] dbSources;
+ DbSourceProxy[] dbSources;
SequenceFetcher sfetcher;
+ private SequenceI[] alseqs;
+
public DBRefFetcher()
{
}
/**
- * Creates a new SequenceFeatureFetcher object.
+ * 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.
+ *
+ * @param seqs
+ * 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
+ */
+ public DBRefFetcher(SequenceI[] seqs, AlignFrame af, DbSourceProxy[] 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
ds[i] = seqs[i];
}
this.dataset = ds;
- sfetcher = new SequenceFetcher();
- // select appropriate databases based on alignFrame context.
- if (af.getViewport().getAlignment().isNucleotide())
+ // TODO Jalview 2.5 lots of this code should be in the gui package!
+ sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+ if (sources == null)
{
- dbSources = DBRefSource.DNACODINGDBS;
+ // af.featureSettings_actionPerformed(null);
+ String[] defdb = null, otherdb = sfetcher
+ .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ List selsources = new ArrayList();
+ Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
+ .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+ .getSelectedSources();
+ Enumeration en = dasselsrc.elements();
+ while (en.hasMoreElements())
+ {
+ jalviewSourceI src = en.nextElement();
+ List sp=src.getSequenceSourceProxies();
+ selsources.addAll(sp);
+ if (sp.size()>1)
+ {
+ Cache.log.debug("Added many Db Sources for :"+src.getTitle());
+ }
+ }
+ // select appropriate databases based on alignFrame context.
+ if (af.getViewport().getAlignment().isNucleotide())
+ {
+ defdb = DBRefSource.DNACODINGDBS;
+ }
+ else
+ {
+ defdb = DBRefSource.PROTEINDBS;
+ }
+ List srces=new ArrayList();
+ for (String ddb:defdb) {
+ List srcesfordb=sfetcher.getSourceProxy(ddb);
+ if (srcesfordb!=null) {
+ srces.addAll(srcesfordb);
+ }
+ }
+
+ // append the selected sequence sources to the default dbs
+ srces.addAll(selsources);
+ dbSources = srces.toArray(new DbSourceProxy[0]);
}
else
{
- dbSources = DBRefSource.PROTEINDBS;
+ // we assume the caller knows what they're doing and ensured that all the
+ // db source names are valid
+ dbSources = sources;
+ }
+ }
+
+ /**
+ * retrieve all the das sequence sources and add them to the list of db
+ * sources to retrieve from
+ */
+ public void appendAllDasSources()
+ {
+ if (dbSources == null)
+ {
+ dbSources = new DbSourceProxy[0];
+ }
+ // append additional sources
+ DbSourceProxy[] otherdb=sfetcher
+ .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ if (otherdb != null && otherdb.length > 0)
+ {
+ DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length + otherdb.length];
+ System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
+ dbSources = newsrc;
}
}
@@ -96,7 +197,7 @@ public class DBRefFetcher implements Runnable
* 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)
{
@@ -123,9 +224,9 @@ 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)
{
@@ -165,9 +266,21 @@ 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++)
@@ -177,21 +290,9 @@ public class DBRefFetcher implements Runnable
while (sdataset.size() > 0 && db < dbSources.length)
{
int maxqlen = 1; // default number of queries made to at one time
- System.err.println("Verifying against " + dbSources[db]);
- jalview.ws.seqfetcher.DbSourceProxy dbsource = sfetcher
- .getSourceProxy(dbSources[db]);
- if (dbsource == null)
- {
- System.err.println("No proxy for " + dbSources[db]);
- db++;
- continue;
- }
- if (dbsource.getDbSourceProperties()
- .containsKey(DBRefSource.MULTIACC))
- {
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
- DBRefSource.MULTIACC)).intValue();
- }
+ System.err.println("Verifying against " + dbSources[db].getDbName());
+ boolean dn = false;
+
// iterate through db for each remaining un-verified sequence
SequenceI[] currSeqs = new SequenceI[sdataset.size()];
sdataset.copyInto(currSeqs);// seqs that are to be validated against
@@ -201,74 +302,133 @@ public class DBRefFetcher implements Runnable
int seqIndex = 0;
- while (queries.size() > 0 || seqIndex < currSeqs.length)
+ jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
{
- if (queries.size() > 0)
+ // for moment, we dumbly iterate over all retrieval sources for a particular database
+ // TODO: introduce multithread multisource queries and logic to remove a query from other sources if any source for a database returns a record
+ if (dbsource.getDbSourceProperties().containsKey(
+ DBRefSource.MULTIACC))
{
- // Still queries to make for current seqIndex
- StringBuffer queryString = new StringBuffer("");
- int nqSize = (maxqlen > queries.size()) ? queries.size()
- : maxqlen;
- for (int nq = 0, numq = 0; nq < nqSize; nq++)
- {
- String query = (String) queries.elementAt(nq);
- if (dbsource.isValidReference(query))
- {
- queryString.append((nq == 0) ? "" : dbsource
- .getAccessionSeparator());
- queryString.append(query);
- numq++;
- }
- }
- for (int nq = 0; nq < nqSize; nq++)
- {
- queries.removeElementAt(0);
- }
- // make the queries and process the response
- AlignmentI retrieved = null;
- try
- {
- retrieved = dbsource.getSequenceRecords(queryString.toString());
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- if (retrieved != null)
- {
- transferReferences(sdataset, dbSources[db], retrieved);
- }
+ maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
+ DBRefSource.MULTIACC)).intValue();
}
else
{
- // make some more strings for use as queries
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ maxqlen = 1;
+ }
+ while (queries.size() > 0 || seqIndex < currSeqs.length)
+ {
+ if (queries.size() > 0)
{
- SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
- // });
- // check for existing dbrefs to use
- if (uprefs != null)
+ // 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)
+ {
+ String query = (String) queries.elementAt(0);
+ if (dbsource.isValidReference(query))
+ {
+ queryString.append((numq == 0) ? "" : dbsource
+ .getAccessionSeparator());
+ queryString.append(query);
+ numq++;
+ }
+ // remove the extracted query string
+ queries.removeElementAt(0);
+ }
+ // make the queries and process the response
+ AlignmentI retrieved = null;
+ try
{
- for (int j = 0; j < uprefs.length; j++)
+ if (jalview.bin.Cache.log.isDebugEnabled())
{
- addSeqId(sequence, uprefs[j].getAccessionId());
- queries
- .addElement(uprefs[j].getAccessionId()
- .toUpperCase());
+ jalview.bin.Cache.log.debug("Querying "
+ + dbsource.getDbName() + " with : '"
+ + queryString.toString() + "'");
}
+ retrieved = dbsource.getSequenceRecords(queryString
+ .toString());
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } catch (OutOfMemoryError err)
+ {
+ new OOMWarning("retrieving database references ("
+ + queryString.toString() + ")", err);
}
- else
+ if (retrieved != null)
{
- // generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(sequence.getName(),
- "|");
- while (st.hasMoreTokens())
+ transferReferences(sdataset, dbsource.getDbSource(), retrieved);
+ }
+ }
+ else
+ {
+ // make some more strings for use as queries
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ {
+ SequenceI sequence = dataset[seqIndex];
+ DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
+ sequence.getDBRef(), new String[]
+ { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ // });
+ // check for existing dbrefs to use
+ 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());
+ }
+ }
+ else
{
- String token = st.nextToken();
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ // generate queries from sequence ID string
+ StringTokenizer st = new StringTokenizer(
+ sequence.getName(), "|");
+ while (st.hasMoreTokens())
+ {
+ String token = st.nextToken();
+ 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());
+ }
+ }
}
}
}
@@ -279,11 +439,10 @@ 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
@@ -306,13 +465,15 @@ 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);
@@ -326,9 +487,16 @@ 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();
@@ -346,14 +514,15 @@ public class DBRefFetcher implements Runnable
}
}
}
- if (sequenceMatches.size()==0)
+ if (sequenceMatches.size() == 0)
{
- // failed to match directly on accessionId==query so just compare all sequences to entry
+ // failed to match directly on accessionId==query so just compare all
+ // sequences to entry
Enumeration e = seqRefs.keys();
while (e.hasMoreElements())
{
Vector sqs = (Vector) seqRefs.get(e.nextElement());
- if (sqs!=null && sqs.size()>0)
+ if (sqs != null && sqs.size() > 0)
{
Enumeration sqe = sqs.elements();
while (sqe.hasMoreElements())
@@ -383,9 +552,12 @@ public class DBRefFetcher implements Runnable
for (int m = 0; m < sequenceMatches.size(); m++)
{
sequence = (SequenceI) sequenceMatches.elementAt(m);
- // only update start and end positions and shift features if there are no existing references
- // TODO: test for legacy where uniprot or EMBL refs exist but no mappings are made (but content matches retrieved set)
- boolean updateRefFrame = sequence.getDBRef()==null || sequence.getDBRef().length==0;
+ // only update start and end positions and shift features if there are
+ // no existing references
+ // TODO: test for legacy where uniprot or EMBL refs exist but no
+ // mappings are made (but content matches retrieved set)
+ boolean updateRefFrame = sequence.getDBRef() == null
+ || sequence.getDBRef().length == 0;
// verify sequence against the entry sequence
String nonGapped = AlignSeq.extractGaps("-. ",
@@ -401,27 +573,31 @@ 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");
+ + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
//
- // + " - ANY SEQUENCE FEATURES"
- // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
+ // + " - ANY SEQUENCE FEATURES"
+ // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
mp = new Mapping(null, new int[]
- { sequence.getStart()+absStart, sequence.getStart()+absStart+entrySeq.length()-1 }, new int[]
- { entry.getStart(),
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);
- updateRefFrame=false; // mapping is based on current start/end so don't modify start and end
+ { sequence.getStart() + absStart,
+ sequence.getStart() + absStart + entrySeq.length() - 1 },
+ new int[]
+ { entry.getStart(),
+ entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+ updateRefFrame = false; // mapping is based on current start/end so
+ // don't modify start and end
}
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
@@ -433,19 +609,24 @@ 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);
+ }
}
}
}
@@ -462,11 +643,74 @@ 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;
}
}