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JAL-2344 override to ignore (obsolete?) JalviewFileView
[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
746ae04
..
5b8a3ae
100644
(file)
--- a/
src/jalview/ws/dbsources/Pfam.java
+++ b/
src/jalview/ws/dbsources/Pfam.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
*
* This file is part of Jalview.
*
@@
-20,12
+20,14
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
-
-import com.stevesoft.pat.Regex;
-
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
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
/**
* TODO: later PFAM is a complex datasource - it could return a tree in addition
@@
-35,15
+37,12
@@
import jalview.ws.seqfetcher.DbSourceProxy;
* @author JimP
*
*/
* @author JimP
*
*/
-abstract public class Pfam extends Xfam implements DbSourceProxy
+abstract public class Pfam extends Xfam
{
public Pfam()
{
super();
{
public Pfam()
{
super();
- // all extensions of this PFAM source base class are DOMAINDB sources
- addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
- addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
}
/*
}
/*
@@
-51,6
+50,7
@@
abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
*/
+ @Override
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
public String getAccessionSeparator()
{
// TODO Auto-generated method stub
@@
-62,6
+62,7
@@
abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
public Regex getAccessionValidator()
{
// TODO Auto-generated method stub
@@
-112,22
+113,23
@@
abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
*/
*
* @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();
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(
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()));
// 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
{ // add the specific ref too
rcds.getSequenceAt(s).addDBRef(
new DBRefEntry(getDbSource(), getDbVersion(), queries
@@
-143,6
+145,7
@@
abstract public class Pfam extends Xfam implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
return accession.indexOf("PF") == 0;
public boolean isValidReference(String accession)
{
return accession.indexOf("PF") == 0;
@@
-152,9
+155,10
@@
abstract public class Pfam extends Xfam implements DbSourceProxy
* public String getDbName() { return "PFAM"; // getDbSource(); }
*/
* public String getDbName() { return "PFAM"; // getDbSource(); }
*/
+ @Override
public String getXfamSource()
{
public String getXfamSource()
{
- return jalview.datamodel.DBRefSource.PFAM;
+ return DBRefSource.PFAM;
}
}
}
}