pdb xrefs added as dbrefs and as PDB file links

[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..4136e62 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -8,18 +8,28 @@ import java.util.Hashtable;
 import com.stevesoft.pat.Regex;\r
 \r
 import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FastaFile;\r
+import jalview.io.StockholmFile;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 /**\r
- * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.\r
  * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment\r
- * TODO: HP: Incorporate jalview.gui.SequenceFetcher retrieval code here.\r
+ * TODO: create interface to pass alignment properties and tree back to sequence fetcher\r
  * @author JimP\r
  *\r
  */\r
-public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
+abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
 {\r
 \r
+  public Pfam()\r
+  {\r
+    super();\r
+    // all extensions of this PFAM source base class are DOMAINDB sources \r
+    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
+  }\r
+\r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
    */\r
@@ -40,22 +50,24 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
 \r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getDbSource()\r
-   */\r
   public String getDbSource()\r
   {\r
-    // TODO Auto-generated method stub\r
-    return null;\r
+    ** this doesn't work - DbSource is key for the hash of DbSourceProxy instances - 1:many mapping for DbSource to proxy will be lost.\r
+    ** suggest : PFAM is an 'alignment' source - means proxy is higher level than a sequence source.\r
+    return jalview.datamodel.DBRefSource.PFAM;\r
   }\r
+   */\r
 \r
+  \r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getDbSourceProperties()\r
-   */\r
   public Hashtable getDbSourceProperties()\r
   {\r
-    // TODO Auto-generated method stub\r
+    \r
     return null;\r
   }\r
-\r
+ */\r
+  \r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getDbVersion()\r
    */\r
@@ -64,22 +76,33 @@ 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
+   * \r
+   * @return PFAM URL stub for this DbSource\r
    */\r
-  public StringBuffer getRawRecords()\r
-  {\r
-    // TODO Auto-generated method stub\r
-    return null;\r
-  }\r
-\r
+  protected abstract String getPFAMURL();\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
+    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");\r
+    for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)\r
+    {\r
+      rcds.getSequenceAt(s).addDBRef(new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,\r
+              // getDbSource(), \r
+              getDbVersion(), queries.trim().toUpperCase()));\r
+      if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))\r
+      {         // add the specific ref too\r
+        rcds.getSequenceAt(s).addDBRef(\r
+                new DBRefEntry( getDbSource(), \r
+                        getDbVersion(), queries.trim().toUpperCase()));\r
+      }\r
+    }\r
+    stopQuery();\r
+    return rcds;\r
   }\r
 \r
   /* (non-Javadoc)\r
@@ -87,22 +110,12 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
    */\r
   public boolean isValidReference(String accession)\r
   {\r
-    // TODO Auto-generated method stub\r
-    return false;\r
+    return accession.indexOf("PF")==0;\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
-  }\r
 \r
-  public String getTestQuery()\r
+  /*public String getDbName()\r
   {\r
-    return "PF00535";\r
-  }\r
-\r
+    return "PFAM"; // getDbSource();\r
+  } */\r
 }\r