X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=3e0004e0db6f888f4d50a1fabed513ffc473a31d;hb=7000ea3223f2f6a390f56341ba26850d2a137ae0;hp=d3788ea1ead1a96fa555c0956214a805c591f7ba;hpb=0d6e36143a2d7471edb7ef386d0b79095e0cd63e;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index d3788ea..3e0004e 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,48 +1,76 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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 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.
+ *
+ * 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
+ */
 package jalview.util;
 
 import java.util.*;
 
 import jalview.datamodel.*;
 
-
 public class DBRefUtils
 {
-    /**
-     * Utilities for handling DBRef objects and their collections.
-     */
-    /**
-     *
-     * @param dbrefs Vector of DBRef objects to search
-     * @param sources String[] array of source DBRef IDs to retrieve
-     * @return Vector
-     */
-    public static DBRefEntry [] selectRefs(DBRefEntry [] dbrefs, String[] sources) {
-      if (dbrefs==null)
-        return null;
-      if (sources==null)
-        return dbrefs;
-      Hashtable srcs = new Hashtable();
-      Vector res=new Vector();
+  /**
+   * Utilities for handling DBRef objects and their collections.
+   */
+  /**
+   *
+   * @param dbrefs Vector of DBRef objects to search
+   * @param sources String[] array of source DBRef IDs to retrieve
+   * @return Vector
+   */
+  public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs, String[] sources)
+  {
+    if (dbrefs == null)
+    {
+      return null;
+    }
+    if (sources == null)
+    {
+      return dbrefs;
+    }
+    Hashtable srcs = new Hashtable();
+    Vector res = new Vector();
 
-      for (int i=0; i<sources.length; i++)
-        srcs.put(new String(sources[i]), new Integer(i));
-      for (int i = 0, j = dbrefs.length; i < j; i++)
-        {
-          if (srcs.containsKey(dbrefs[i].getSource()))
-            res.add(dbrefs[i]);
-        }
+    for (int i = 0; i < sources.length; i++)
+    {
+      srcs.put(new String(sources[i]), new Integer(i));
+    }
+    for (int i = 0, j = dbrefs.length; i < j; i++)
+    {
+      if (srcs.containsKey(dbrefs[i].getSource()))
+      {
+        res.addElement(dbrefs[i]);
+      }
+    }
 
-      if (res.size()>0)
+    if (res.size() > 0)
+    {
+      DBRefEntry[] reply = new DBRefEntry[res.size()];
+      for (int i = 0; i < res.size(); i++)
       {
-        DBRefEntry [] reply = new DBRefEntry[res.size()];
-        for(int i=0; i<res.size(); i++)
-          reply[i] = (DBRefEntry)res.elementAt(i);
-        return reply;
+        reply[i] = (DBRefEntry) res.elementAt(i);
       }
-      res = null;
-      // there are probable  memory leaks in the hashtable!
-      return null;
+      return reply;
     }
+    res = null;
+    // there are probable  memory leaks in the hashtable!
+    return null;
+  }
 
   /**
    * isDasCoordinateSystem
@@ -55,18 +83,86 @@ public class DBRefUtils
   public static boolean isDasCoordinateSystem(String string,
                                               DBRefEntry dBRefEntry)
   {
-    if (DasCoordinateSystemsLookup==null)
+    if (DasCoordinateSystemsLookup == null)
     { // Initialise
       DasCoordinateSystemsLookup = new Hashtable();
       DasCoordinateSystemsLookup.put("pdbresnum",
                                      jalview.datamodel.DBRefSource.PDB);
       DasCoordinateSystemsLookup.put("uniprot",
                                      jalview.datamodel.DBRefSource.UNIPROT);
+      DasCoordinateSystemsLookup.put("EMBL",
+              jalview.datamodel.DBRefSource.EMBL);
+      //DasCoordinateSystemsLookup.put("EMBL",
+      //        jalview.datamodel.DBRefSource.EMBLCDS);
     }
 
-    String coordsys = (String) DasCoordinateSystemsLookup.get(string.toLowerCase());
-    if (coordsys!=null)
+    String coordsys = (String) DasCoordinateSystemsLookup.get(string.
+        toLowerCase());
+    if (coordsys != null)
+    {
       return coordsys.equals(dBRefEntry.getSource());
+    }
     return false;
   }
+  public static Hashtable CanonicalSourceNameLookup=null;
+  /**
+   * look up source in an internal list of database reference sources
+   * and return the canonical jalview name for the source, or the original
+   * string if it has no canonical form.
+   * @param source
+   * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or original source
+   */
+  public static String getCanonicalName(String source)
+  {
+    if (CanonicalSourceNameLookup==null) {
+      CanonicalSourceNameLookup = new Hashtable();
+      CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
+      CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
+      CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
+    }
+    String canonical = (String) CanonicalSourceNameLookup.get(source.
+        toLowerCase());
+    if (canonical==null)
+    {
+      return source;
+    }
+    return canonical;
+  }
+  /**
+   * find RefEntry corresponding to a particular pattern
+   * the equals method of each entry is used, from String attributes right down to Mapping attributes.
+   * @param ref Set of references to search
+   * @param entry pattern to collect - null any entry for wildcard match
+   * @return
+   */
+  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
+  {
+    if (ref==null || entry==null)
+      return null;
+    Vector rfs = new Vector();
+    for (int i=0; i<ref.length;i++)
+    {
+      if (entry.getSource()==null || ref[i].getSource().equals(entry.getSource()))
+      {
+        if (entry.getVersion()==null || ref[i].getVersion().equals(entry.getVersion()))
+        {
+          if (entry.getAccessionId()==null || ref[i].getAccessionId().equals(entry.getAccessionId()))
+          {
+            if (entry.getMap()==null || (ref[i].getMap()!=null && ref[i].getMap().equals(entry.getMap())))
+            {
+              rfs.addElement(ref[i]);
+            }
+          }
+        }
+      }
+    }
+    // TODO Auto-generated method stub
+    if (rfs.size()>0)
+    {
+      DBRefEntry[] rf = new DBRefEntry[rfs.size()];
+      rfs.copyInto(rf);
+      return rf;
+    }
+    return null;
+  }
 }