sensibly sized example for PFAM source

[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 d935db9..2075a0b 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,5 +1,20 @@
-/**\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
  * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  */\r
 package jalview.ws.dbsources;\r
 \r
@@ -9,23 +24,25 @@ import com.stevesoft.pat.Regex;
 \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
-    \r
+    // all extensions of this PFAM source base class are DOMAINDB sources \r
+    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
   }\r
 \r
   /* (non-Javadoc)\r
@@ -48,21 +65,24 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
 \r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getDbSource()\r
-   */\r
   public String getDbSource()\r
   {\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
@@ -71,7 +91,11 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     // TODO Auto-generated method stub\r
     return null;\r
   }\r
-  public static String PFAMURL = "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=";\r
+  /**\r
+   * \r
+   * @return PFAM URL stub for this DbSource\r
+   */\r
+  protected abstract String getPFAMURL();\r
   /* (non-Javadoc)\r
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
    */\r
@@ -79,16 +103,20 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
   {\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
+    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(getDbSource(), getDbVersion(), queries.trim().toUpperCase()));\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
@@ -100,13 +128,9 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
     return accession.indexOf("PF")==0;\r
   }\r
 \r
-  public String getTestQuery()\r
-  {\r
-    return "PF00535";\r
-  }\r
 \r
-  public String getDbName()\r
+  /*public String getDbName()\r
   {\r
-    return getDbSource();\r
-  }\r
+    return "PFAM"; // getDbSource();\r
+  } */\r
 }\r