/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
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.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.DbSourceProxy;
private SequenceI[] alseqs;
- public DBRefFetcher()
- {
- }
-
/**
- * 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.
+ * when true - retrieved sequences will be trimmed to cover longest derived
+ * alignment sequence
*/
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
+ private boolean trimDsSeqs = true;
+
+ public DBRefFetcher()
{
- this(seqs, af, null);
}
/**
- * Creates a new SequenceFeatureFetcher object and fetches from the currently
- * selected set of databases.
+ * Creates a new DBRefFetcher object and fetches from the currently selected
+ * set of databases, if this is null then it fetches based on feature settings
*
* @param seqs
- * fetch references for these sequences
- * @param af
- * the parent alignframe for progress bar monitoring.
+ * fetch references for these SequenceI array
+ * @param progressIndicatorFrame
+ * the frame for progress bar monitoring
* @param sources
- * array of database source strings to query references from
+ * array of DbSourceProxy to query references form
+ * @param featureSettings
+ * FeatureSettings to get alternative DbSourceProxy from
+ * @param isNucleotide
+ * indicates if the array of SequenceI are Nucleotides or not
*/
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af,
- DbSourceProxy[] sources)
+ public DBRefFetcher(SequenceI[] seqs,
+ IProgressIndicator progressIndicatorFrame,
+ DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide)
{
- this.af = af;
+ this.af = progressIndicatorFrame;
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;
// TODO Jalview 2.5 lots of this code should be in the gui package!
- sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+ sfetcher = jalview.gui.SequenceFetcher
+ .getSequenceFetcherSingleton(progressIndicatorFrame);
+ // set default behaviour for transferring excess sequence data to the
+ // dataset
+ trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
if (sources == null)
{
// af.featureSettings_actionPerformed(null);
String[] defdb = null, otherdb = sfetcher
.getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
+ Vector dasselsrc = (featureSettings != null) ? featureSettings
.getSelectedSources() : new jalview.gui.DasSourceBrowser()
.getSelectedSources();
Enumeration<jalviewSourceI> en = dasselsrc.elements();
}
}
// select appropriate databases based on alignFrame context.
- if (af.getViewport().getAlignment().isNucleotide())
+ if (isNucleotide)
{
defdb = DBRefSource.DNACODINGDBS;
}
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
if (dbSources == null)
{
- throw new Error("Implementation error. Must initialise dbSources");
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar("Fetching db refs", startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+ startTime);
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
if (retrieved != null)
{
transferReferences(sdataset, dbsource.getDbSource(),
- retrieved);
+ retrieved, trimDsSeqs);
}
}
else
{
SequenceI sequence = dataset[seqIndex];
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ sequence.getDBRefs(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
} // 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"
+ output.setText(MessageManager
+ .getString("label.your_sequences_have_been_verified")
+ sbuffer.toString());
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
+ Desktop.addInternalFrame(output,
+ MessageManager.getString("label.sequence_names_updated"),
+ 600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
}
- af.setProgressBar("DBRef search completed", startTime);
+ af.setProgressBar(
+ MessageManager.getString("label.dbref_search_completed"),
+ startTime);
// promptBeforeBlast();
running = false;
* Verify local sequences in seqRefs against the retrieved sequence database
* records.
*
+ * @param trimDatasetSeqs
+ *
*/
void transferReferences(Vector sdataset, String dbSource,
- AlignmentI retrievedAl) // File
+ AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
// file)
{
+ System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return;
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRef(), new String[]
- { dbSource });
+ entry.getDBRefs(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
// 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;
+ boolean updateRefFrame = sequence.getDBRefs() == null
+ || sequence.getDBRefs().length == 0;
+ // TODO:
// verify sequence against the entry sequence
String nonGapped = AlignSeq.extractGaps("-. ",
sequence.getSequenceAsString()).toUpperCase();
int absStart = entrySeq.indexOf(nonGapped);
- int mapStart = entry.getStart();
- jalview.datamodel.Mapping mp;
+ Mapping mp;
+ final int sequenceStart = sequence.getStart();
if (absStart == -1)
{
// Is local sequence contained in dataset sequence?
// 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);
+ mp = new Mapping(null, new int[] { sequenceStart + absStart,
+ sequenceStart + 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
}
if (sequence.getSequenceFeatures() != null)
{
SequenceFeature[] sf = sequence.getSequenceFeatures();
- int start = sequence.getStart();
+ int start = sequenceStart;
int end = sequence.getEnd();
int startShift = 1 - absStart - start; // how much the features
// are
+ " from " + dbSource + " sequence : " + entry.getName());
sequence.transferAnnotation(entry, mp);
// unknownSequences.remove(sequence);
- int absEnd = absStart + nonGapped.length();
- absStart += 1;
+ absStart += entry.getStart();
+ int absEnd = absStart + nonGapped.length() - 1;
+ if (!trimDatasetSeqs)
+ {
+ // insert full length sequence from record
+ sequence.setSequence(entry.getSequenceAsString());
+ sequence.setStart(entry.getStart());
+ }
if (updateRefFrame)
{
// finally, update local sequence reference frame if we're allowed
- sequence.setStart(absStart);
- sequence.setEnd(absEnd);
+ if (trimDatasetSeqs)
+ {
+ // just fix start/end
+ sequence.setStart(absStart);
+ sequence.setEnd(absEnd);
+ }
// search for alignment sequences to update coordinate frame for
for (int alsq = 0; alsq < alseqs.length; alsq++)
{
for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
{
nseq.addElement(sequencesArray[i]);
- DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+ DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
jalview.datamodel.Mapping map = null;
for (int r = 0; (dbr != null) && r < dbr.length; r++)
{
git://source.jalview.org / jalview.git / blobdiff