X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=9d91e310b88d4bd9f8041ea4eb329cc1ee70cbb7;hb=ac599db2d506591153433ffbf1e6ea2ef4be4943;hp=12b4158dba2969975cc3a98a031c493d53fca778;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 12b4158..9d91e31 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,19 +1,21 @@
/*
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws;
@@ -31,6 +33,7 @@ import jalview.gui.CutAndPasteTransfer;
import jalview.gui.Desktop;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.jalviewSourceI;
import jalview.ws.seqfetcher.DbSourceProxy;
@@ -77,6 +80,12 @@ public class DBRefFetcher implements Runnable
private SequenceI[] alseqs;
+ /**
+ * when true - retrieved sequences will be trimmed to cover longest derived
+ * alignment sequence
+ */
+ private boolean trimDsSeqs = true;
+
public DBRefFetcher()
{
}
@@ -116,13 +125,20 @@ public class DBRefFetcher implements Runnable
{
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);
+ // 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);
@@ -267,15 +283,19 @@ public class DBRefFetcher implements Runnable
/**
* 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))
@@ -316,16 +336,8 @@ public class DBRefFetcher implements Runnable
// 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))
- {
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
- DBRefSource.MULTIACC)).intValue();
- }
- else
- {
- maxqlen = 1;
- }
+ maxqlen = dbsource.getMaximumQueryCount();
+
while (queries.size() > 0 || seqIndex < currSeqs.length)
{
if (queries.size() > 0)
@@ -371,7 +383,7 @@ public class DBRefFetcher implements Runnable
if (retrieved != null)
{
transferReferences(sdataset, dbsource.getDbSource(),
- retrieved);
+ retrieved, trimDsSeqs);
}
}
else
@@ -381,8 +393,8 @@ public class DBRefFetcher implements Runnable
{
SequenceI sequence = dataset[seqIndex];
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ sequence.getDBRef(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
@@ -450,17 +462,20 @@ 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"
+ 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;
@@ -471,11 +486,14 @@ public class DBRefFetcher implements Runnable
* 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;
@@ -499,8 +517,7 @@ public class DBRefFetcher implements Runnable
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRef(), new String[]
- { dbSource });
+ entry.getDBRef(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
@@ -569,15 +586,16 @@ public class DBRefFetcher implements Runnable
// mappings are made (but content matches retrieved set)
boolean updateRefFrame = sequence.getDBRef() == null
|| sequence.getDBRef().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?
@@ -597,12 +615,10 @@ public class DBRefFetcher implements Runnable
// 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
}
@@ -625,7 +641,7 @@ public class DBRefFetcher implements Runnable
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
@@ -647,13 +663,23 @@ public class DBRefFetcher implements Runnable
+ " 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++)
{