X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=84f6d4da05261611adecb02f8da8dda0787adbcf;hb=1c52130ad032d77caac874c3a8be23a399a3ec93;hp=c677fdcc573806234bf729b599c074f2ae436343;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java index c677fdc..84f6d4d 100644 --- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java +++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java @@ -1,23 +1,36 @@ /* - * 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.dbsources.das.datamodel; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; +import jalview.ws.dbsources.das.api.jalviewSourceI; +import jalview.ws.seqfetcher.DbSourceProxy; +import jalview.ws.seqfetcher.DbSourceProxyImpl; + import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; @@ -37,15 +50,6 @@ import org.biodas.jdas.schema.sources.VERSION; import com.stevesoft.pat.Regex; -import jalview.ws.dbsources.das.api.jalviewSourceI; -import jalview.ws.seqfetcher.*; -import jalview.bin.Cache; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceI; - /** * an instance of this class is created for each unique DAS Sequence source (ie * one capable of handling the 'sequence' for a particular MapMaster) @@ -53,8 +57,8 @@ import jalview.datamodel.SequenceI; * @author JimP * */ -public class DasSequenceSource extends DbSourceProxyImpl implements - DbSourceProxy +public class DasSequenceSource extends DbSourceProxyImpl + implements DbSourceProxy { private jalviewSourceI jsrc; @@ -71,9 +75,10 @@ public class DasSequenceSource extends DbSourceProxyImpl implements protected MultipleConnectionPropertyProviderI connprops = null; /** - * DAS sources are tier 1 - if we have a direct DB connection then we should prefer it + * DAS sources are tier 1 - if we have a direct DB connection then we should + * prefer it */ - private int tier=1; + private int tier = 1; /** * create a new DbSource proxy for a DAS 1 source @@ -97,10 +102,12 @@ public class DasSequenceSource extends DbSourceProxyImpl implements if (!(jsrc = new JalviewSource(source, connprops, false)) .isSequenceSource()) { - throw new Exception("Source " + source.getTitle() - + " does not support the sequence command."); + throw new Exception(MessageManager.formatMessage( + "exception.das_source_doesnt_support_sequence_command", + new String[] + { source.getTitle() })); } - this.tier = 1+((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1); + this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1); this.source = source; this.dbname = dbname; this.dbrefname = dbrefname.toUpperCase(); @@ -141,7 +148,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements public AlignmentI getSequenceRecords(String queries) throws Exception { StringTokenizer st = new StringTokenizer(queries, "\t"); - List toks = new ArrayList(), src = new ArrayList(), acIds = new ArrayList(); + List toks = new ArrayList(), + src = new ArrayList(), acIds = new ArrayList(); while (st.hasMoreTokens()) { String t; @@ -162,24 +170,21 @@ public class DasSequenceSource extends DbSourceProxyImpl implements // slow, fetch one at a time. for (String sr : src) { - System.err - .println("Retrieving IDs individually from das source: " - + sr); + System.err.println( + "Retrieving IDs individually from das source: " + sr); org.biodas.jdas.client.SequenceClient sq = new SequenceClient( connprops.getConnectionPropertyProviderFor(sr)); for (String q : toks) { - List qset = Arrays.asList(new String[] - { q }); + List qset = Arrays.asList(new String[] { q }); try { DasSequenceAdapter s = sq.fetchData(sr, qset); Map, DasSequenceAdapter> dss = resultset.get(sr); if (dss == null) { - resultset - .put(sr, - dss = new HashMap, DasSequenceAdapter>()); + resultset.put(sr, + dss = new HashMap, DasSequenceAdapter>()); } dss.put(qset, s); } catch (Exception x) @@ -187,7 +192,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements Map, Exception> ers = errors.get(sr); if (ers == null) { - errors.put(sr, ers = new HashMap, Exception>()); + errors.put(sr, + ers = new HashMap, Exception>()); } ers.put(qset, x); } @@ -241,8 +247,8 @@ public class DasSequenceSource extends DbSourceProxyImpl implements if (acIds.indexOf(lbl) == -1) { - System.err - .println("Warning - received sequence event for strange accession code (" + System.err.println( + "Warning - received sequence event for strange accession code (" + lbl + ")"); } else @@ -251,11 +257,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements { if (e.getContent().length() == 0) { - System.err - .println("Empty sequence returned for accession code (" - + lbl - + ") from " - + resset.getKey() + System.err.println( + "Empty sequence returned for accession code (" + + lbl + ") from " + resset.getKey() + " (source is " + getDbName()); continue; } @@ -263,11 +267,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements seqs = new java.util.Vector(); // JDAS returns a sequence complete with any newlines and spaces // in the XML - Sequence sq = new Sequence(lbl, e.getContent().replaceAll( - "\\s+", "")); + Sequence sq = new Sequence(lbl, + e.getContent().replaceAll("\\s+", "")); sq.setStart(e.getStart().intValue()); - sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion() - + ":" + e.getVersion(), lbl)); + sq.addDBRef(new DBRefEntry(getDbSource(), + getDbVersion() + ":" + e.getVersion(), lbl)); seqs.addElement(sq); } } @@ -303,9 +307,9 @@ public class DasSequenceSource extends DbSourceProxyImpl implements } catch (Exception x) { - Cache.log - .error("Couldn't retrieve features for sequence from its source.", - x); + Cache.log.error( + "Couldn't retrieve features for sequence from its source.", + x); } }