X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=2abb60590aee7b8b5bc16468ad82af9c36fc86b1;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=814c5343d444572c0ab41e7251d394bad4aaac17;hpb=9f982f18f80a75d1be6f6c002c8ba81ff8a00a0a;p=jalview.git diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index 814c534..2abb605 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -1,28 +1,26 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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; import java.io.File; import java.io.FileReader; -import java.io.IOException; import java.util.Enumeration; -import java.util.Hashtable; import java.util.Vector; import org.exolab.castor.xml.Unmarshaller; @@ -38,9 +36,6 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.UniprotEntry; import jalview.datamodel.UniprotFile; -import jalview.io.FormatAdapter; -import jalview.io.IdentifyFile; -import jalview.ws.DBRefFetcher; import jalview.ws.ebi.EBIFetchClient; import jalview.ws.seqfetcher.DbSourceProxy; import jalview.ws.seqfetcher.DbSourceProxyImpl; @@ -76,7 +71,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy */ public Regex getAccessionValidator() { - return null; + return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)"); } /* @@ -101,22 +96,27 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy private EBIFetchClient ebi = null; + private static org.exolab.castor.mapping.Mapping map; + public Vector getUniprotEntries(File file) { UniprotFile uni = new UniprotFile(); try { - // 1. Load the mapping information from the file - org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping( - uni.getClass().getClassLoader()); - java.net.URL url = getClass().getResource("/uniprot_mapping.xml"); - map.loadMapping(url); + if (map == null) + { + // 1. Load the mapping information from the file + map = new org.exolab.castor.mapping.Mapping(uni.getClass() + .getClassLoader()); + java.net.URL url = getClass().getResource("/uniprot_mapping.xml"); + map.loadMapping(url); + } // 2. Unmarshal the data Unmarshaller unmar = new Unmarshaller(uni); unmar.setIgnoreExtraElements(true); unmar.setMapping(map); - if (file!=null) + if (file != null) { uni = (UniprotFile) unmar.unmarshal(new FileReader(file)); } @@ -138,7 +138,8 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy startQuery(); try { - queries = queries.toUpperCase().replaceAll("(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)",""); + queries = queries.toUpperCase().replaceAll( + "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", ""); Alignment al = null; ebi = new EBIFetchClient(); StringBuffer result = new StringBuffer(); @@ -208,10 +209,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy /** * add an ordered set of UniprotEntry objects to an ordered set of seuqences. * - * @param al - - * a sequence of n sequences + * @param al + * - a sequence of n sequences * @param entries - * a seuqence of n uniprot entries to be analysed. + * a seuqence of n uniprot entries to be analysed. */ public void addUniprotXrefs(Alignment al, Vector entries) { @@ -277,7 +278,9 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy */ public boolean isValidReference(String accession) { - return true; + // TODO: make the following a standard validator + return (accession == null || accession.length() < 2) ? false + : getAccessionValidator().search(accession); } /** @@ -292,4 +295,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy { return "Uniprot"; // getDbSource(); } + + @Override + public int getTier() + { + return 0; + } }