X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=37108ca07c1d55047b9dcc057473ffb67d70e02a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d935db92629803b4e07ec5d860409f12f781d582;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index d935db9..37108ca 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
*
+ * Jalview 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 Jalview. If not, see .
*/
package jalview.ws.dbsources;
@@ -9,26 +23,35 @@ 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: later PFAM is a complex datasource - it could return a tree in addition
+ * to an alignment 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 Xfam implements
+ DbSourceProxy
{
public Pfam()
{
super();
-
+ // all extensions of this PFAM source base class are DOMAINDB sources
+ addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
+ addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
public String getAccessionSeparator()
@@ -37,7 +60,9 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
return null;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
public Regex getAccessionValidator()
@@ -46,67 +71,91 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
return null;
}
- /* (non-Javadoc)
- * @see jalview.ws.DbSourceProxy#getDbSource()
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
+ * 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; }
*/
- public String getDbSource()
- {
- return jalview.datamodel.DBRefSource.PFAM;
- }
- /* (non-Javadoc)
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+ * getDbSourceProperties() {
+ *
+ * return null; }
*/
- public Hashtable getDbSourceProperties()
- {
- // TODO Auto-generated method stub
- return null;
- }
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
- public String getDbVersion()
+ @Override
+public String getDbVersion()
{
// 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)
+
+ /**Returns base URL for selected Pfam alignment type
+ *
+ * @return PFAM URL stub for this DbSource
+ */
+ @Override
+protected abstract String getXFAMURL();
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
public AlignmentI getSequenceRecords(String queries) throws Exception
{
- // 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.
+ // 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