X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=db765eb298332d064f57c585fddccca762ef405f;hb=54e003f9b2fff47dbfea6401c3944afdb7bd37b3;hp=4d9c93d6184928fb056033c2291277af376e89a9;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4d9c93d..db765eb 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -8,6 +8,8 @@ import java.util.Hashtable;
 import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.io.FastaFile;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 /**
@@ -20,6 +22,12 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
 public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
 {
 
+  public Pfam()
+  {
+    super();
+    
+  }
+
   /* (non-Javadoc)
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
@@ -43,8 +51,7 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
    */
   public String getDbSource()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return jalview.datamodel.DBRefSource.PFAM;
   }
 
   /* (non-Javadoc)
@@ -64,22 +71,25 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub
     return null;
   }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getRawRecords()
-   */
-  public StringBuffer getRawRecords()
-  {
-    // 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)
    * @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();
+    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++)
+    {
+      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), getDbVersion(), queries.trim().toUpperCase()));
+    }
+    return rcds;
   }
 
   /* (non-Javadoc)
@@ -87,17 +97,7 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
    */
   public boolean isValidReference(String accession)
   {
-    // TODO Auto-generated method stub
-    return false;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#queryInProgress()
-   */
-  public boolean queryInProgress()
-  {
-    // TODO Auto-generated method stub
-    return false;
+    return accession.indexOf("PF")==0;
   }
 
   public String getTestQuery()
@@ -105,4 +105,8 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return "PF00535";
   }
 
+  public String getDbName()
+  {
+    return "PFAM"; // getDbSource();
+  }
 }