X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=37108ca07c1d55047b9dcc057473ffb67d70e02a;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=4136e62834a95b9ec8159b4970df9675affde5b6;hpb=2de36153a84ca246643cd28b2ce05e9f4159dd89;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4136e62..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;
@@ -14,23 +28,30 @@ 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 could return a tree in addition to an alignment
- * TODO: create interface to pass alignment properties and tree back to sequence fetcher
+ * 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
- *
+ *
*/
-abstract 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
+ // 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()
@@ -39,7 +60,9 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
return null;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
public Regex getAccessionValidator()
@@ -48,74 +71,91 @@ abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
return null;
}
- /* (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;
- }
+ /*
+ * (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; }
*/
-
- /* (non-Javadoc)
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
- public Hashtable getDbSourceProperties()
- {
-
- return null;
- }
- */
-
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+ * getDbSourceProperties() {
+ *
+ * return null; }
+ */
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
- public String getDbVersion()
+ @Override
+public String getDbVersion()
{
// TODO Auto-generated method stub
return null;
}
- /**
+
+ /**Returns base URL for selected Pfam alignment type
*
* @return PFAM URL stub for this DbSource
*/
- protected abstract String getPFAMURL();
- /* (non-Javadoc)
+ @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();
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");
- for (int s=0,sNum=rcds.getHeight(); s