X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FUniprot.java;h=167758f8815a60e57614971edbbd5964135fdc55;hb=e9aa1cee679000405c5549829ee08e1c08b2ffd5;hp=f29a555c4c74c9c3f81f01a2a63b9cd55a5fedcf;hpb=25ae256a88bf092f45a78b649a48f41e6fd5d70b;p=jalview.git diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java index f29a555..167758f 100644 --- a/src/jalview/ws/dbsources/Uniprot.java +++ b/src/jalview/ws/dbsources/Uniprot.java @@ -1,5 +1,19 @@ -/** +/* + * 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.dbsources; @@ -36,11 +50,12 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl; */ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy { - public Uniprot() { + public Uniprot() + { super(); addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB); addDbSourceProperty(DBRefSource.PROTSEQDB); -// addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50)); + // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50)); } /* @@ -60,7 +75,7 @@ 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]+)"); } /* @@ -91,7 +106,8 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy try { // 1. Load the mapping information from the file - org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader()); + 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); @@ -99,10 +115,11 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy Unmarshaller unmar = new Unmarshaller(uni); unmar.setIgnoreExtraElements(true); unmar.setMapping(map); - - uni = (UniprotFile) unmar.unmarshal(new FileReader(file)); - } - catch (Exception e) + if (file != null) + { + uni = (UniprotFile) unmar.unmarshal(new FileReader(file)); + } + } catch (Exception e) { System.out.println("Error getUniprotEntries() " + e); } @@ -120,11 +137,15 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy startQuery(); try { - Alignment al=null; + queries = queries.toUpperCase().replaceAll( + "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", ""); + Alignment al = null; ebi = new EBIFetchClient(); - StringBuffer result=new StringBuffer(); + StringBuffer result = new StringBuffer(); // uniprotxml parameter required since december 2007 - File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null); + // uniprotkb dbname changed introduced december 2008 + File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml", + null); Vector entries = getUniprotEntries(file); if (entries != null) @@ -149,12 +170,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy name.append(en2.nextElement()); } - if (entry.getProtein()!=null && entry.getProtein().getName()!=null) + if (entry.getProtein() != null + && entry.getProtein().getName() != null) { - for (int nm=0,nmSize=entry.getProtein().getName().size(); nm