X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=3ba0e3454db16f5357a25e3498ba20e5c236fb3d;hb=32522ec3c4179494249e085506977f21f83e9b2e;hp=9f8fb82bde033a6fa1b46bb906fef830489b91e7;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 9f8fb82..3ba0e34 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * 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. * @@ -28,9 +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; @@ -55,9 +55,16 @@ import uk.ac.ebi.picr.model.UPEntry; */ public class DBRefFetcher implements Runnable { + public interface FetchFinishedListenerI + { + void finished(); + } + + private List listeners; + SequenceI[] dataset; - IProgressIndicator af; + IProgressIndicator progressWindow; CutAndPasteTransfer output = new CutAndPasteTransfer(); @@ -86,52 +93,45 @@ public class DBRefFetcher implements Runnable */ 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; + listeners = new ArrayList(); + this.progressWindow = 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); @@ -141,7 +141,7 @@ 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(); @@ -159,7 +159,7 @@ public class DBRefFetcher implements Runnable } } // select appropriate databases based on alignFrame context. - if (af.getViewport().getAlignment().isNucleotide()) + if (isNucleotide) { defdb = DBRefSource.DNACODINGDBS; } @@ -190,6 +190,26 @@ public class DBRefFetcher implements Runnable } /** + * Constructor with only sequences provided + * + * @param sequences + */ + public DBRefFetcher(SequenceI[] sequences) + { + this(sequences, null, null, null, false); + } + + /** + * Add a listener to be notified when sequence fetching is complete + * + * @param l + */ + public void addListener(FetchFinishedListenerI l) + { + listeners.add(l); + } + + /** * retrieve all the das sequence sources and add them to the list of db * sources to retrieve from */ @@ -279,15 +299,23 @@ public class DBRefFetcher implements Runnable /** * DOCUMENT ME! */ + @Override public void run() { if (dbSources == null) { - throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources")); + throw new Error( + MessageManager + .getString("error.implementation_error_must_init_dbsources")); } running = true; long startTime = System.currentTimeMillis(); - af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime); + if (progressWindow != null) + { + progressWindow.setProgressBar( + MessageManager.getString("status.fetching_db_refs"), + startTime); + } try { if (Cache.getDefault("DBREFFETCH_USEPICR", false)) @@ -328,16 +356,8 @@ 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) @@ -393,8 +413,8 @@ 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) @@ -472,14 +492,18 @@ public class DBRefFetcher implements Runnable // of the viewed sequence } + if (progressWindow != null) + { + progressWindow.setProgressBar( + MessageManager.getString("label.dbref_search_completed"), + startTime); + } - af.setProgressBar( - MessageManager.getString("label.dbref_search_completed"), - startTime); - // promptBeforeBlast(); - + for (FetchFinishedListenerI listener : listeners) + { + listener.finished(); + } running = false; - } /** @@ -517,8 +541,7 @@ 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 @@ -585,8 +608,8 @@ 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 @@ -594,9 +617,9 @@ 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? @@ -616,12 +639,10 @@ 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 } @@ -644,7 +665,7 @@ 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 @@ -666,8 +687,8 @@ 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 @@ -733,7 +754,7 @@ 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++) {