X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=2e0197c83b53d2e2dbaf216336744d5accfe8b2b;hb=7f8ddabd82dcf91860e0a8dc972cfd1ab6c59fc5;hp=d742eaa6ee8072a44b71e62788996ed9e644bd40;hpb=b60a5925d0ba5e99a9e4edf44a2ee6015775dd35;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index d742eaa..2e0197c 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; @@ -26,9 +28,9 @@ import jalview.datamodel.DBRefSource; 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; @@ -79,57 +81,55 @@ public class DBRefFetcher implements Runnable private SequenceI[] alseqs; /** - * when true - retrieved sequences will be trimmed to cover longest derived alignment sequence + * when true - retrieved sequences will be trimmed to cover longest derived + * alignment sequence */ - private boolean trimDsSeqs=true; + private boolean trimDsSeqs = true; public DBRefFetcher() { } /** - * 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. - */ - 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. + * 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); - // set default behaviour for transferring excess sequence data to the dataset + 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) { @@ -137,7 +137,7 @@ public class DBRefFetcher implements Runnable String[] defdb = null, otherdb = sfetcher .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class); List selsources = new ArrayList(); - Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings + Vector dasselsrc = (featureSettings != null) ? featureSettings .getSelectedSources() : new jalview.gui.DasSourceBrowser() .getSelectedSources(); Enumeration en = dasselsrc.elements(); @@ -155,7 +155,7 @@ public class DBRefFetcher implements Runnable } } // select appropriate databases based on alignFrame context. - if (af.getViewport().getAlignment().isNucleotide()) + if (isNucleotide) { defdb = DBRefSource.DNACODINGDBS; } @@ -275,15 +275,19 @@ 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)) @@ -379,7 +383,7 @@ public class DBRefFetcher implements Runnable if (retrieved != null) { transferReferences(sdataset, dbsource.getDbSource(), - retrieved,trimDsSeqs); + retrieved, trimDsSeqs); } } else @@ -389,8 +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.getDBRefs(), + new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT // }); // check for existing dbrefs to use if (uprefs != null && uprefs.length > 0) @@ -458,15 +462,20 @@ public class DBRefFetcher implements Runnable } // all databases have been queries. if (sbuffer.length() > 0) { - output.setText(MessageManager.getString("label.your_sequences_have_been_verified") + output.setText(MessageManager + .getString("label.your_sequences_have_been_verified") + sbuffer.toString()); - Desktop.addInternalFrame(output, MessageManager.getString("label.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(MessageManager.getString("label.dbref_search_completed"), startTime); + af.setProgressBar( + MessageManager.getString("label.dbref_search_completed"), + startTime); // promptBeforeBlast(); running = false; @@ -476,14 +485,15 @@ public class DBRefFetcher implements Runnable /** * Verify local sequences in seqRefs against the retrieved sequence database * records. - * @param trimDatasetSeqs + * + * @param trimDatasetSeqs * */ void transferReferences(Vector sdataset, String dbSource, AlignmentI retrievedAl, boolean trimDatasetSeqs) // File // file) { - System.out.println("trimming ? "+trimDatasetSeqs); + System.out.println("trimming ? " + trimDatasetSeqs); if (retrievedAl == null || retrievedAl.getHeight() == 0) { return; @@ -507,8 +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.getDBRefs(), new String[] { dbSource }); if (entryRefs == null) { System.err @@ -575,8 +584,8 @@ public class DBRefFetcher implements Runnable // 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 @@ -584,9 +593,9 @@ public class DBRefFetcher implements Runnable 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? @@ -606,12 +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 } @@ -634,7 +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 @@ -656,18 +663,22 @@ 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 - if (trimDatasetSeqs) { + if (trimDatasetSeqs) + { // just fix start/end sequence.setStart(absStart); sequence.setEnd(absEnd); - } else { - // insert full length sequence from record - sequence.setSequence(entry.getSequenceAsString()); } // search for alignment sequences to update coordinate frame for for (int alsq = 0; alsq < alseqs.length; alsq++) @@ -719,7 +730,7 @@ public class DBRefFetcher implements Runnable 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++) {