X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=c1fe276676973d08f180c17f30df232d0bb9c61d;hb=3bb3bf052916ca69a915a48324a122b0e3f20651;hp=1fd9f1c1078b210f835dab27133f9745e558d8c6;hpb=cb37b13542829ad0406c5f0ff8349334f83c31ae;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 1fd9f1c..c1fe276 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 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; @@ -74,6 +73,8 @@ public class DBRefFetcher implements Runnable SequenceFetcher sfetcher; + private SequenceI[] alseqs; + public DBRefFetcher() { } @@ -106,9 +107,11 @@ public class DBRefFetcher implements Runnable 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 @@ -123,8 +126,8 @@ public class DBRefFetcher implements Runnable 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(); + .getSelectedSources() : new jalview.gui.DasSourceBrowser() + .getSelectedSources(); Enumeration en = dasselsrc.elements(); while (en.hasMoreElements()) { @@ -190,9 +193,7 @@ public class DBRefFetcher implements Runnable { 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); + System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length); dbSources = newsrc; } } @@ -384,9 +385,7 @@ public class DBRefFetcher implements Runnable 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 @@ -404,8 +403,9 @@ public class DBRefFetcher implements Runnable try { presp = picrClient - .getUPIForAccession(token, null, picrClient - .getMappedDatabaseNames(), null, true); + .getUPIForAccession(token, null, + picrClient.getMappedDatabaseNames(), + null, true); } catch (Exception e) { System.err.println("Exception with Picr for '" + token @@ -444,11 +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 @@ -493,9 +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(); @@ -608,20 +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); + } } } } @@ -638,6 +648,29 @@ 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