X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=4f081ee3bb1a76a0ad4fb8d5f5b6e908720330a7;hb=27c7530b396a5dd1addc4ab346ef2823d34fb335;hp=3f0ec1188724a6cecc835d0756f6b5f8fc1cbff2;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 3f0ec11..4f081ee 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,29 +1,31 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.dbsources;
-
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.datamodel.DBRefSource;
+import jalview.io.FormatAdapter;
+
+import com.stevesoft.pat.Regex;
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
@@ -33,15 +35,12 @@ import jalview.ws.seqfetcher.DbSourceProxy;
* @author JimP
*
*/
-abstract public class Pfam extends Xfam implements DbSourceProxy
+abstract public class Pfam extends Xfam
{
public Pfam()
{
super();
- // all extensions of this PFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
}
/*
@@ -49,6 +48,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@ -60,6 +60,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
@@ -110,22 +111,23 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
+ @Override
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.
startQuery();
- AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
+ AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+ queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
"STH");
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
+new DBRefEntry(DBRefSource.PFAM,
// getDbSource(),
getDbVersion(), queries.trim().toUpperCase()));
- if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
+ if (!getDbSource().equals(DBRefSource.PFAM))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(
new DBRefEntry(getDbSource(), getDbVersion(), queries
@@ -141,6 +143,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
return accession.indexOf("PF") == 0;
@@ -150,9 +153,10 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
* public String getDbName() { return "PFAM"; // getDbSource(); }
*/
+ @Override
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.PFAM;
+ return DBRefSource.PFAM;
}
}