X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=2075a0bd30502af112f62b66f1816007533925a3;hb=1facaef788a7570369f6f0e4fee6c8bce78335ea;hp=4077c51d885d29f3dc540b5be55caf81dbcb9739;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4077c51..2075a0b 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;
 
@@ -8,18 +23,28 @@ import java.util.Hashtable;
 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: 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)
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
@@ -40,22 +65,24 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
 
   /* (non-Javadoc)
    * @see jalview.ws.DbSourceProxy#getDbSource()
-   */
   public String getDbSource()
   {
-    // TODO Auto-generated method stub
+    ** 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;
   }
+   */
 
+  
   /* (non-Javadoc)
    * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
-   */
   public Hashtable getDbSourceProperties()
   {
-    // TODO Auto-generated method stub
+    
     return null;
   }
-
+ */
+  
   /* (non-Javadoc)
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
@@ -64,22 +91,33 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub
     return null;
   }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getRawRecords()
+  /**
+   * 
+   * @return PFAM URL stub for this DbSource
    */
-  public StringBuffer getRawRecords()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
+  protected abstract String getPFAMURL();
   /* (non-Javadoc)
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    throw new Exception("PFAM Retrieval not yet implemented - see jalview.gui.SequenceFetcher for current implementation");
+    // 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();
+    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(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)
@@ -87,22 +125,12 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
    */
   public boolean isValidReference(String accession)
   {
-    // TODO Auto-generated method stub
-    return false;
+    return accession.indexOf("PF")==0;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#queryInProgress()
-   */
-  public boolean queryInProgress()
-  {
-    // TODO Auto-generated method stub
-    return false;
-  }
 
-  public String getTestQuery()
+  /*public String getDbName()
   {
-    return "PF00535";
-  }
-
+    return "PFAM"; // getDbSource();
+  } */
 }