X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FRfamFull.java;h=e6fc8ffcacc875b2015cd1321f3130e8ac974bf4;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=f8b1952d4b14431be3722e8c7ef71ca7f604fd47;hpb=8daeb715c3e8ec8486f26708361698095084232f;p=jalview.git diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java index f8b1952..e6fc8ff 100644 --- a/src/jalview/ws/dbsources/RfamFull.java +++ b/src/jalview/ws/dbsources/RfamFull.java @@ -1,32 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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; -import jalview.ws.seqfetcher.DbSourceProxy; - /** * Flyweight class specifying retrieval of Full family alignments from RFAM * * @author Lauren Michelle Lui * */ -public class RfamFull extends Rfam implements DbSourceProxy +public class RfamFull extends Rfam { public RfamFull() { @@ -38,9 +38,11 @@ public class RfamFull extends Rfam implements DbSourceProxy * * @see jalview.ws.dbsources.Rfam#getXFAMURL() */ + @Override protected String getXFAMURL() { - return "http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc="; + return "http://rfam.xfam.org/family/alignment/download/format?alnType=full&nseLabels=0&format=stockholm&acc="; + } /* @@ -48,16 +50,19 @@ public class RfamFull extends Rfam implements DbSourceProxy * * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName() */ + @Override public String getDbName() { return "RFAM (Full)"; } + @Override public String getDbSource() { return getDbName(); // so we have unique DbSource string. } + @Override public String getTestQuery() { // Can be retrieved from http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014 @@ -66,9 +71,15 @@ public class RfamFull extends Rfam implements DbSourceProxy return "RF00014"; } + @Override public String getDbVersion() { return null; } + @Override + public int getTier() + { + return 0; + } }