X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblSource.java;h=44427a5bacc16b66014731033e706b3e7bdbd1c3;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=d4eb7c9007e8eb0416c61e4ed4a0d3e2bcbebd9a;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index d4eb7c9..44427a5 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,127 +1,124 @@
-/*
- * 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 java.io.File;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.StringTokenizer;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-/**
- * @author JimP
- * 
- */
-public class EmblSource extends EmblXmlSource implements DbSourceProxy
-{
-
-  public EmblSource()
-  {
-    addDbSourceProperty(DBRefSource.DNASEQDB);
-    addDbSourceProperty(DBRefSource.CODINGSEQDB);
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  public String getAccessionSeparator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  public Regex getAccessionValidator()
-  {
-    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbSource()
-   */
-  public String getDbSource()
-  {
-    return DBRefSource.EMBL;
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  public String getDbVersion()
-  {
-    // TODO Auto-generated method stub
-    return "0";
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
-  public AlignmentI getSequenceRecords(String queries) throws Exception
-  {
-    return getEmblSequenceRecords(DBRefSource.EMBL, queries);
-  }
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  public boolean isValidReference(String accession)
-  {
-    // most embl refs look like ..
-
-    return (accession == null || accession.length() < 2) ? false
-            : getAccessionValidator().search(accession);
-
-  }
-
-  /**
-   * return LHD_CHICK coding gene
-   */
-  public String getTestQuery()
-  {
-    return "X53828";
-  }
-
-  public String getDbName()
-  {
-    return "EMBL"; // getDbSource();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import com.stevesoft.pat.Regex;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * @author JimP
+ * 
+ */
+public class EmblSource extends EmblXmlSource implements DbSourceProxy
+{
+
+  public EmblSource()
+  {
+    addDbSourceProperty(DBRefSource.DNASEQDB);
+    addDbSourceProperty(DBRefSource.CODINGSEQDB);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+   */
+  public String getAccessionSeparator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+   */
+  public Regex getAccessionValidator()
+  {
+    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource()
+   */
+  public String getDbSource()
+  {
+    return DBRefSource.EMBL;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbVersion()
+   */
+  public String getDbVersion()
+  {
+    // TODO Auto-generated method stub
+    return "0";
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+   */
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return getEmblSequenceRecords(DBRefSource.EMBL, queries);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+   */
+  public boolean isValidReference(String accession)
+  {
+    // most embl refs look like ..
+
+    return (accession == null || accession.length() < 2) ? false
+            : getAccessionValidator().search(accession);
+
+  }
+
+  /**
+   * return LHD_CHICK coding gene
+   */
+  public String getTestQuery()
+  {
+    return "X53828";
+  }
+
+  public String getDbName()
+  {
+    return "EMBL"; // getDbSource();
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+}