X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=91ffbca2d29c4f85539be361f010a656a81673a6;hb=7d4f1d8e997964bef5c351d04fbdafe4401cf5d7;hp=d935db92629803b4e07ec5d860409f12f781d582;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d935db9..91ffbca 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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.ws.dbsources;
 
@@ -9,26 +24,34 @@ import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.FastaFile;
+import jalview.io.StockholmFile;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
+
 /**
- * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.
- * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment
- * TODO: HP: Incorporate jalview.gui.SequenceFetcher retrieval code here.
+ * TODO: later PFAM is a complex datasource - it could return a tree in addition
+ * to an alignment TODO: create interface to pass alignment properties and tree
+ * back to sequence fetcher
+ * 
  * @author JimP
- *
+ * 
  */
-public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
+abstract public class Pfam extends DbSourceProxyImpl implements
+        DbSourceProxy
 {
 
   public Pfam()
   {
     super();
-    
+    // all extensions of this PFAM source base class are DOMAINDB sources
+    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -37,7 +60,9 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
@@ -46,24 +71,28 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSource()
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
+   *      this doesn't work - DbSource is key for the hash of DbSourceProxy
+   *      instances - 1:many mapping for DbSource to proxy will be lost. *
+   *      suggest : PFAM is an 'alignment' source - means proxy is higher level
+   *      than a sequence source. return jalview.datamodel.DBRefSource.PFAM; }
    */
-  public String getDbSource()
-  {
-    return jalview.datamodel.DBRefSource.PFAM;
-  }
 
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+   *      getDbSourceProperties() {
+   * 
+   * return null; }
    */
-  public Hashtable getDbSourceProperties()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
@@ -71,42 +100,55 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub
     return null;
   }
-  public static String PFAMURL = "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=";
-  /* (non-Javadoc)
+
+  /**
+   * 
+   * @return PFAM URL stub for this DbSource
+   */
+  protected abstract String getPFAMURL();
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    // TODO: this is not a perfect implementation. We need to be able to add individual references to each sequence in each family alignment that's retrieved. 
+    // TODO: this is not a perfect implementation. We need to be able to add
+    // individual references to each sequence in each family alignment that's
+    // retrieved.
     startQuery();
-    results = new StringBuffer();
-    // split queries into many little ones.
-    results.append(new FastaFile(
-                PFAMURL+queries.trim().toUpperCase(), "URL").print());
-    stopQuery();
-    AlignmentI rcds = parseResult(results.toString());
-    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()
+            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
+            "STH");
+    for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
-      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), getDbVersion(), queries.trim().toUpperCase()));
+      rcds.getSequenceAt(s).addDBRef(
+              new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
+              // getDbSource(),
+                      getDbVersion(), queries.trim().toUpperCase()));
+      if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
+      { // add the specific ref too
+        rcds.getSequenceAt(s).addDBRef(
+                new DBRefEntry(getDbSource(), getDbVersion(), queries
+                        .trim().toUpperCase()));
+      }
     }
+    stopQuery();
     return rcds;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
   {
-    return accession.indexOf("PF")==0;
+    return accession.indexOf("PF") == 0;
   }
 
-  public String getTestQuery()
-  {
-    return "PF00535";
-  }
-
-  public String getDbName()
-  {
-    return getDbSource();
-  }
+  /*
+   * public String getDbName() { return "PFAM"; // getDbSource(); }
+   */
 }