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Merge branch 'JAL-1956_featureStyles' into features/JAL-653_JAL-1766_htslib_refseqsupport
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Pdb.java
diff --git
a/src/jalview/ws/dbsources/Pdb.java
b/src/jalview/ws/dbsources/Pdb.java
index
8503167
..
3fd7541
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
*
@@
-20,38
+20,31
@@
*/
package jalview.ws.dbsources;
*/
package jalview.ws.dbsources;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
-import MCview.PDBChain;
-import MCview.PDBfile;
-
import com.stevesoft.pat.Regex;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.AlignmentI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
/**
* @author JimP
*
*/
/**
* @author JimP
*
*/
-public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
+public class Pdb extends EbiFileRetrievedProxy
{
public Pdb()
{
super();
{
public Pdb()
{
super();
- addDbSourceProperty(DBRefSource.PROTSEQDB);
}
/*
}
/*
@@
-59,6
+52,7
@@
public class Pdb extends EbiFileRetrievedProxy 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
@@
-70,6
+64,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
*
* @see jalview.ws.DbSourceProxy#getAccessionValidator()
*/
+ @Override
public Regex getAccessionValidator()
{
return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
public Regex getAccessionValidator()
{
return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
@@
-80,6
+75,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
*
* @see jalview.ws.DbSourceProxy#getDbSource()
*/
+ @Override
public String getDbSource()
{
return DBRefSource.PDB;
public String getDbSource()
{
return DBRefSource.PDB;
@@
-90,6
+86,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
*
* @see jalview.ws.DbSourceProxy#getDbVersion()
*/
+ @Override
public String getDbVersion()
{
return "0";
public String getDbVersion()
{
return "0";
@@
-100,9
+97,10
@@
public class Pdb extends EbiFileRetrievedProxy 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
{
public AlignmentI getSequenceRecords(String queries) throws Exception
{
- AlignmentI pdbfile = null;
+ AlignmentI pdbAlignment = null;
Vector result = new Vector();
String chain = null;
String id = null;
Vector result = new Vector();
String chain = null;
String id = null;
@@
-136,20
+134,20
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
try
{
try
{
- pdbfile = new FormatAdapter().readFile(file,
+ pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE, "PDB");
jalview.io.AppletFormatAdapter.FILE, "PDB");
- if (pdbfile != null)
+ if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
- for (SequenceI pdbcs : pdbfile.getSequences())
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
{
String chid = null;
// Mapping map=null;
{
String chid = null;
// Mapping map=null;
- for (PDBEntry pid : (Vector<PDBEntry>) pdbcs.getPDBId())
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
{
if (pid.getFile() == file)
{
{
if (pid.getFile() == file)
{
- chid = (String) pid.getProperty().get("CHAIN");
+ chid = pid.getChainCode();
}
;
}
;
@@
-193,20
+191,22
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
// now remove marked sequences
for (SequenceI pdbcs : toremove)
{
// now remove marked sequences
for (SequenceI pdbcs : toremove)
{
- pdbfile.deleteSequence(pdbcs);
- if (pdbcs.getAnnotation()!=null)
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
{
{
- for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
{
{
- pdbfile.deleteAnnotation(aa);
+ pdbAlignment.deleteAnnotation(aa);
}
}
}
}
}
}
}
}
- if (pdbfile == null || pdbfile.getHeight() < 1)
+ if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
{
- throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
+ throw new Exception(MessageManager.formatMessage(
+ "exception.no_pdb_records_for_chain", new String[] { id,
+ ((chain == null) ? "' '" : chain) }));
}
} catch (Exception ex) // Problem parsing PDB file
}
} catch (Exception ex) // Problem parsing PDB file
@@
-214,7
+214,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
stopQuery();
throw (ex);
}
stopQuery();
throw (ex);
}
- return pdbfile;
+ return pdbAlignment;
}
/*
}
/*
@@
-222,6
+222,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
*
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
*/
+ @Override
public boolean isValidReference(String accession)
{
Regex r = getAccessionValidator();
public boolean isValidReference(String accession)
{
Regex r = getAccessionValidator();
@@
-231,11
+232,13
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
/**
* obtain human glyoxalase chain A sequence
*/
/**
* obtain human glyoxalase chain A sequence
*/
+ @Override
public String getTestQuery()
{
return "1QIPA";
}
public String getTestQuery()
{
return "1QIPA";
}
+ @Override
public String getDbName()
{
return "PDB"; // getDbSource();
public String getDbName()
{
return "PDB"; // getDbSource();