'Add Rfam database sequence retrieval' merged; JAL-580

[jalview.git] / src / jalview / ws / dbsources / RfamSeed.java

diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
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+++ b/src/jalview/ws/dbsources/RfamSeed.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws.dbsources;
+
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * Flyweight class specifying retrieval of Seed family alignments from RFAM
+ * 
+ * @author Lauren Michelle Lui
+ * 
+ */
+public class RfamSeed extends Rfam implements DbSourceProxy
+{
+  public RfamSeed()
+  {
+    super();
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.dbsources.Rfam#getRFAMURL()
+   */
+  protected String getXFAMURL()
+  {
+    return "http://rfam.sanger.ac.uk/family/alignment/download/format?alnType=seed&nseLabels=0&format=stockholm&acc=";
+    // Janelia Farms url
+    // "http://rfam.janelia.org/cgi-bin/getalignment?type=seed&fmt=stockholm&acc=";
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.seqfetcher.DbSourceProxy#getDbName()
+   */
+  public String getDbName()
+  {
+    return "RFAM (Seed)";
+  }
+
+  public String getDbSource()
+  {
+    return getDbName(); // so we have unique DbSource string.
+  }
+
+  public String getTestQuery()
+  {
+    return "RF00014";
+  } // http://rfam.janelia.org/cgi-bin/getdesc?acc=RF00014
+
+  public String getDbVersion()
+  {
+    return null;
+  }
+
+}