updated jalview version of dasobert 1.53e client and added Das Sequence Source discov...

[jalview.git] / src / jalview / ws / dbsources / Pfam.java

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4d9c93d..db765eb 100644 (file)
--- 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;\r
 \r
 import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.io.FastaFile;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 /**\r
@@ -20,6 +22,12 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
 public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
 {\r
 \r
+  public Pfam()\r
+  {\r
+    super();\r
+    \r
+  }\r
+\r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
    */\r
@@ -43,8 +51,7 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
    */\r
   public String getDbSource()\r
   {\r
-    // TODO Auto-generated method stub\r
-    return null;\r
+    return jalview.datamodel.DBRefSource.PFAM;\r
   }\r
 \r
   /* (non-Javadoc)\r
@@ -64,22 +71,25 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub\r
     return null;\r
   }\r
-\r
-  /* (non-Javadoc)\r
-   * @see jalview.ws.DbSourceProxy#getRawRecords()\r
-   */\r
-  public StringBuffer getRawRecords()\r
-  {\r
-    // TODO Auto-generated method stub\r
-    return null;\r
-  }\r
-\r
+  public static String PFAMURL = "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=";\r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
    */\r
   public AlignmentI getSequenceRecords(String queries) throws Exception\r
   {\r
-    throw new Exception("PFAM Retrieval not yet implemented - see jalview.gui.SequenceFetcher for current implementation");\r
+    // 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. \r
+    startQuery();\r
+    results = new StringBuffer();\r
+    // split queries into many little ones.\r
+    results.append(new FastaFile(\r
+                PFAMURL+queries.trim().toUpperCase(), "URL").print());\r
+    stopQuery();\r
+    AlignmentI rcds = parseResult(results.toString());\r
+    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)\r
+    {\r
+      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), getDbVersion(), queries.trim().toUpperCase()));\r
+    }\r
+    return rcds;\r
   }\r
 \r
   /* (non-Javadoc)\r
@@ -87,17 +97,7 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
    */\r
   public boolean isValidReference(String accession)\r
   {\r
-    // TODO Auto-generated method stub\r
-    return false;\r
-  }\r
-\r
-  /* (non-Javadoc)\r
-   * @see jalview.ws.DbSourceProxy#queryInProgress()\r
-   */\r
-  public boolean queryInProgress()\r
-  {\r
-    // TODO Auto-generated method stub\r
-    return false;\r
+    return accession.indexOf("PF")==0;\r
   }\r
 \r
   public String getTestQuery()\r
@@ -105,4 +105,8 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return "PF00535";\r
   }\r
 \r
+  public String getDbName()\r
+  {\r
+    return "PFAM"; // getDbSource();\r
+  }\r
 }\r