X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=95656796b40f8b432b5f0e8898dc7d4b6b318198;hb=98af16ccc5890b980f0c4f3acfb72d7128e3a6f0;hp=73d106a85fb60a9701d08bdc01ed3223fb05b24f;hpb=4ec235370b49c38ae7e7b3a46f92f926fc430bf1;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 73d106a..9565679 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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; @@ -31,6 +30,7 @@ import jalview.gui.CutAndPasteTransfer; import jalview.gui.Desktop; import jalview.gui.IProgressIndicator; import jalview.gui.OOMWarning; +import jalview.ws.dbsources.das.api.jalviewSourceI; import java.lang.reflect.Array; import java.util.Enumeration; @@ -38,8 +38,6 @@ import java.util.Hashtable; import java.util.StringTokenizer; import java.util.Vector; -import org.biojava.dasobert.dasregistry.DasSource; - import uk.ac.ebi.picr.model.UPEntry; /** @@ -125,15 +123,15 @@ public class DBRefFetcher implements Runnable { // af.featureSettings_actionPerformed(null); String[] defdb = null, otherdb = sfetcher - .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + .getDbInstances(jalview.ws.dbsources.das.datamodel.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()) { - DasSource src = (DasSource) en.nextElement(); - selsources.addElement(src.getNickname()); + jalviewSourceI src = (jalviewSourceI) en.nextElement(); + selsources.addElement(src.getTitle()); } int osel = 0; for (int o = 0; otherdb != null && o < otherdb.length; o++) @@ -189,14 +187,12 @@ public class DBRefFetcher implements Runnable } // append additional sources String[] otherdb = sfetcher - .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + .getDbInstances(jalview.ws.dbsources.das.datamodel.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); + System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length); dbSources = newsrc; } } @@ -388,9 +384,7 @@ 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 @@ -408,8 +402,9 @@ 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 @@ -448,11 +443,10 @@ 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 @@ -497,9 +491,16 @@ 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(); @@ -612,24 +613,26 @@ 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) { + if (updateRefFrame) + { if (sequence.getSequenceFeatures() != null) { - 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 (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); + } } } - } } } @@ -645,21 +648,28 @@ public class DBRefFetcher implements Runnable sequence.setStart(absStart); sequence.setEnd(absEnd); // search for alignment sequences to update coordinate frame for - for (int alsq = 0; alsq