X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=67b44d73b220edbda12416ae7900cc676c6f0303;hb=57b4d7111e3f745aa6f1ec40f518fe1a6073e8e3;hp=b1c987ecd8400a39093002c31c0cfc846a76fa88;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index b1c987e..67b44d7 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -20,7 +20,22 @@ */ package jalview.ws; +import java.util.Locale; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; +import java.util.regex.Matcher; +import java.util.regex.Pattern; + import jalview.analysis.AlignSeq; +import jalview.api.FeatureSettingsModelI; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; @@ -35,15 +50,6 @@ import jalview.gui.OOMWarning; import jalview.util.DBRefUtils; import jalview.util.MessageManager; import jalview.ws.seqfetcher.DbSourceProxy; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.StringTokenizer; -import java.util.Vector; - import uk.ac.ebi.picr.model.UPEntry; import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator; @@ -71,8 +77,6 @@ public class DBRefFetcher implements Runnable CutAndPasteTransfer output = new CutAndPasteTransfer(); - boolean running = false; - /** * picr client instance */ @@ -222,24 +226,13 @@ public class DBRefFetcher implements Runnable */ public void fetchDBRefs(boolean waitTillFinished) { - // TODO can we not simply write - // if (waitTillFinished) { run(); } else { new Thread(this).start(); } - - Thread thread = new Thread(this); - thread.start(); - running = true; - if (waitTillFinished) { - while (running) - { - try - { - Thread.sleep(500); - } catch (Exception ex) - { - } - } + run(); + } + else + { + new Thread(this).start(); } } @@ -254,7 +247,7 @@ public class DBRefFetcher implements Runnable */ void addSeqId(SequenceI seq, String key) { - key = key.toUpperCase(); + key = key.toUpperCase(Locale.ROOT); Vector seqs; if (seqRefs.containsKey(key)) @@ -292,7 +285,6 @@ public class DBRefFetcher implements Runnable throw new Error(MessageManager .getString("error.implementation_error_must_init_dbsources")); } - running = true; long startTime = System.currentTimeMillis(); if (progressWindow != null) { @@ -317,6 +309,9 @@ public class DBRefFetcher implements Runnable Arrays.asList(dataset)); List warningMessages = new ArrayList<>(); + // clear any old feature display settings recorded from past sessions + featureDisplaySettings = null; + int db = 0; while (sdataset.size() > 0 && db < dbSources.length) { @@ -383,7 +378,7 @@ public class DBRefFetcher implements Runnable } if (retrieved != null) { - transferReferences(sdataset, dbsource.getDbSource(), retrieved, + transferReferences(sdataset, dbsource, retrieved, trimDsSeqs, warningMessages); } } @@ -406,17 +401,19 @@ public class DBRefFetcher implements Runnable DBRefEntry upref = uprefs.get(j); addSeqId(sequence, upref.getAccessionId()); queries.addElement( - upref.getAccessionId().toUpperCase()); + upref.getAccessionId().toUpperCase(Locale.ROOT)); } } else { + Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+"); // generate queries from sequence ID string - StringTokenizer st = new StringTokenizer(sequence.getName(), - "|"); - while (st.hasMoreTokens()) + Matcher tokens = possibleIds.matcher(sequence.getName()); + int p=0; + while (tokens.find(p)) { - String token = st.nextToken(); + String token = tokens.group(); + p = tokens.end(); UPEntry[] presp = null; if (picrClient != null) { @@ -445,7 +442,7 @@ public class DBRefFetcher implements Runnable "Validated ID against PICR... (for what its worth):" + token); addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + queries.addElement(token.toUpperCase(Locale.ROOT)); } else { @@ -453,7 +450,7 @@ public class DBRefFetcher implements Runnable // System.out.println("Not querying source with // token="+token+"\n"); addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + queries.addElement(token.toUpperCase(Locale.ROOT)); } } } @@ -492,7 +489,6 @@ public class DBRefFetcher implements Runnable { listener.finished(); } - running = false; } /** @@ -512,7 +508,8 @@ public class DBRefFetcher implements Runnable * @param warningMessages * a list of messages to add to */ - boolean transferReferences(Vector sdataset, String dbSource, + boolean transferReferences(Vector sdataset, + DbSourceProxy dbSourceProxy, AlignmentI retrievedAl, boolean trimDatasetSeqs, List warningMessages) { @@ -522,6 +519,7 @@ public class DBRefFetcher implements Runnable return false; } + String dbSource = dbSourceProxy.getDbName(); boolean modified = false; SequenceI[] retrieved = recoverDbSequences( retrievedAl.getSequencesArray()); @@ -548,7 +546,7 @@ public class DBRefFetcher implements Runnable DBRefEntry ref = entryRefs.get(j); String accessionId = ref.getAccessionId(); // match up on accessionId - if (seqRefs.containsKey(accessionId.toUpperCase())) + if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT))) { Vector seqs = seqRefs.get(accessionId); for (int jj = 0; jj < seqs.size(); jj++) @@ -593,10 +591,14 @@ public class DBRefFetcher implements Runnable * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) { * sequenceMatches.addElement(sequence); } } } } */ + if (sequenceMatches.size() > 0) + { + addFeatureSettings(dbSourceProxy); + } // sequenceMatches now contains the set of all sequences associated with // the returned db record final String retrievedSeqString = retrievedSeq.getSequenceAsString(); - String entrySeq = retrievedSeqString.toUpperCase(); + String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT); for (int m = 0; m < sequenceMatches.size(); m++) { sequence = sequenceMatches.elementAt(m); @@ -615,7 +617,7 @@ public class DBRefFetcher implements Runnable boolean remoteEnclosesLocal = false; String nonGapped = AlignSeq .extractGaps("-. ", sequence.getSequenceAsString()) - .toUpperCase(); + .toUpperCase(Locale.ROOT); int absStart = entrySeq.indexOf(nonGapped); if (absStart == -1) { @@ -735,10 +737,10 @@ public class DBRefFetcher implements Runnable String ngAlsq = AlignSeq .extractGaps("-. ", alseqs[alsq].getSequenceAsString()) - .toUpperCase(); + .toUpperCase(Locale.ROOT); int oldstrt = alseqs[alsq].getStart(); alseqs[alsq].setStart(sequence.getSequenceAsString() - .toUpperCase().indexOf(ngAlsq) + sequence.getStart()); + .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart()); if (oldstrt != alseqs[alsq].getStart()) { alseqs[alsq].setEnd( @@ -761,6 +763,33 @@ public class DBRefFetcher implements Runnable return modified; } + Map featureDisplaySettings = null; + + private void addFeatureSettings(DbSourceProxy dbSourceProxy) + { + FeatureSettingsModelI fsettings = dbSourceProxy + .getFeatureColourScheme(); + if (fsettings != null) + { + if (featureDisplaySettings == null) + { + featureDisplaySettings = new HashMap<>(); + } + featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings); + } + } + + /** + * + * @return any feature settings associated with sources that have provided sequences + */ + public ListgetFeatureSettingsModels() + { + return featureDisplaySettings == null + ? Arrays.asList(new FeatureSettingsModelI[0]) + : Arrays.asList(featureDisplaySettings.values() + .toArray(new FeatureSettingsModelI[1])); + } /** * Adds the message to the list unless it already contains it *