X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=941bf1afa2330f293781c7df61cc1afe903ef3fc;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=b2443e8338cee2980efa996c5fee3db8706a705a;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index b2443e8..941bf1a 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,28 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+import com.stevesoft.pat.Regex;
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
@@ -32,15 +37,12 @@ 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);
}
/*
@@ -48,6 +50,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@ -59,6 +62,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
@@ -109,22 +113,22 @@ 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()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
+ AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+ + queries.trim().toUpperCase(), DataSourceType.URL,
+ FileFormat.Stockholm);
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
- rcds.getSequenceAt(s).addDBRef(
- new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
- // getDbSource(),
- getDbVersion(), queries.trim().toUpperCase()));
- if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
+ // getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
+ if (!getDbSource().equals(DBRefSource.PFAM))
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(
new DBRefEntry(getDbSource(), getDbVersion(), queries
@@ -140,6 +144,7 @@ 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;
@@ -149,9 +154,10 @@ 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;
}
}