X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=7e069e3d7b4feeef15d19c691b7059f258729537;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=6a31956eadb3f54e7ff72aa4ac8c48ef3e42b3c2;hpb=2ca2207a05be706b6b068839e9f752d8c0744315;p=jalview.git
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 6a31956..7e069e3 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,894 +1,931 @@
-/*
- * 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 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.
- *
- * 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;
-
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.FeatureSettings;
-import jalview.util.UrlLink;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-
-import org.biodas.jdas.client.FeaturesClient;
-import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
-import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
-import org.biodas.jdas.client.threads.FeaturesClientMultipleSources;
-import org.biodas.jdas.schema.features.ERRORSEGMENT;
-import org.biodas.jdas.schema.features.FEATURE;
-import org.biodas.jdas.schema.features.LINK;
-import org.biodas.jdas.schema.features.SEGMENT;
-import org.biodas.jdas.schema.features.TYPE;
-import org.biodas.jdas.schema.features.UNKNOWNFEATURE;
-import org.biodas.jdas.schema.features.UNKNOWNSEGMENT;
-import org.biodas.jdas.schema.sources.COORDINATES;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class DasSequenceFeatureFetcher
-{
- SequenceI[] sequences;
-
- AlignFrame af;
-
- FeatureSettings fsettings;
-
- StringBuffer sbuffer = new StringBuffer();
-
- List selectedSources;
-
- boolean cancelled = false;
-
- private void debug(String mesg)
- {
- debug(mesg, null);
- }
-
- private void debug(String mesg, Exception e)
- {
- if (Cache.log != null)
- {
- Cache.log.debug(mesg, e);
- }
- else
- {
- System.err.println(mesg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
- long startTime;
-
- private DasSourceRegistryI sourceRegistry;
- private boolean useJDASMultiThread=true;
- /**
- * Creates a new SequenceFeatureFetcher object. Uses default
- *
- * @param align
- * DOCUMENT ME!
- * @param ap
- * DOCUMENT ME!
- */
- public DasSequenceFeatureFetcher(SequenceI[] sequences,
- FeatureSettings fsettings, Vector selectedSources)
- {
- this(sequences, fsettings, selectedSources, true, true, true);
- }
-
- public DasSequenceFeatureFetcher(SequenceI[] oursequences,
- FeatureSettings fsettings, List selectedSources2,
- boolean checkDbrefs, boolean promptFetchDbrefs)
- {
- this(oursequences,fsettings,selectedSources2,checkDbrefs,promptFetchDbrefs,true);
- }
- public DasSequenceFeatureFetcher(SequenceI[] oursequences,
- FeatureSettings fsettings, List selectedSources2,
- boolean checkDbrefs, boolean promptFetchDbrefs, boolean useJDasMultiThread)
- {
- this.useJDASMultiThread=useJDasMultiThread;
- this.selectedSources = new ArrayList();
- // filter both sequences and sources to eliminate duplicates
- for (jalviewSourceI src : selectedSources2)
- {
- if (!selectedSources.contains(src))
- {
- selectedSources.add(src);
- }
- ;
- }
- Vector sqs = new Vector();
- for (int i = 0; i < oursequences.length; i++)
- {
- if (!sqs.contains(oursequences[i]))
- {
- sqs.addElement(oursequences[i]);
- }
- }
- sequences = new SequenceI[sqs.size()];
- for (int i = 0; i < sequences.length; i++)
- {
- sequences[i] = (SequenceI) sqs.elementAt(i);
- }
- if (fsettings != null)
- {
- this.fsettings = fsettings;
- this.af = fsettings.af;
- af.setShowSeqFeatures(true);
- }
- int uniprotCount = 0;
- for (jalviewSourceI source : selectedSources)
- {
- for (COORDINATES coords : source.getVersion().getCOORDINATES())
- {
- // TODO: match UniProt coord system canonically (?) - does
- // UniProt==uniprot==UNIPROT ?
- if (coords.getAuthority().toLowerCase().equals("uniprot"))
- {
- uniprotCount++;
- break;
- }
- }
- }
-
- int refCount = 0;
- for (int i = 0; i < sequences.length; i++)
- {
- DBRefEntry[] dbref = sequences[i].getDBRef();
- if (dbref != null)
- {
- for (int j = 0; j < dbref.length; j++)
- {
- if (dbref[j].getSource().equals(
- jalview.datamodel.DBRefSource.UNIPROT))
- {
- refCount++;
- break;
- }
- }
- }
- }
-
- if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
- {
-
- int reply = JOptionPane.YES_OPTION;
- if (promptFetchDbrefs)
- {
- reply = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- "Do you want Jalview to find\n"
- + "Uniprot Accession ids for given sequence names?",
- "Find Uniprot Accession Ids",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
- }
-
- if (reply == JOptionPane.YES_OPTION)
- {
- Thread thread = new Thread(new FetchDBRefs());
- thread.start();
- }
- else
- {
- _startFetching();
- }
- }
- else
- {
- _startFetching();
- }
-
- }
- private void _startFetching()
- {
- running=true;
- new Thread(new FetchSeqFeatures()).start();
- }
- class FetchSeqFeatures implements Runnable
- {
- public void run()
- {
- startFetching();
- setGuiFetchComplete();
- }
- }
- class FetchDBRefs implements Runnable
- {
- public void run()
- {
- running=true;
- new DBRefFetcher(sequences, af).fetchDBRefs(true);
- startFetching();
- setGuiFetchComplete();
- }
- }
-
- /**
- * Spawns Fetcher threads to add features to sequences in the dataset
- */
- void startFetching()
- {
- running=true;
- cancelled = false;
- startTime = System.currentTimeMillis();
- if (af != null)
- {
- af.setProgressBar("Fetching DAS Sequence Features", startTime);
- }
- if (sourceRegistry == null)
- {
- sourceRegistry = Cache.getDasSourceRegistry();
- }
- if (selectedSources == null || selectedSources.size() == 0)
- {
- try
- {
- jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
- new jalviewSourceI[0]);
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
- "uniprot");
- StringTokenizer st = new StringTokenizer(active, "\t");
- selectedSources = new Vector();
- String token;
- while (st.hasMoreTokens())
- {
- token = st.nextToken();
- for (int i = 0; i < sources.length; i++)
- {
- if (sources[i].getTitle().equals(token))
- {
- selectedSources.add(sources[i]);
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- debug("Exception whilst setting default feature sources from registry and local preferences.",
- ex);
- }
- }
-
- if (selectedSources == null || selectedSources.size() == 0)
- {
- System.out.println("No DAS Sources active");
- cancelled = true;
- setGuiNoDassourceActive();
- return;
- }
-
- sourcesRemaining = selectedSources.size();
- FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();
- fc.setConnProps(sourceRegistry.getSessionHandler());
- // Now sending requests one at a time to each server
- ArrayList srcobj = new ArrayList();
- ArrayList src = new ArrayList();
- List> ids = new ArrayList>();
- List> idobj = new ArrayList>();
- List