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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
util
/
DBRefUtils.java
diff --git
a/src/jalview/util/DBRefUtils.java
b/src/jalview/util/DBRefUtils.java
index
9765a1a
..
32589f7
100755
(executable)
--- a/
src/jalview/util/DBRefUtils.java
+++ b/
src/jalview/util/DBRefUtils.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,6
+20,11
@@
*/
package jalview.util;
*/
package jalview.util;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
@@
-28,11
+33,6
@@
import java.util.Map;
import com.stevesoft.pat.Regex;
import com.stevesoft.pat.Regex;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-
public class DBRefUtils
{
private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
public class DBRefUtils
{
private static Map<String, String> canonicalSourceNameLookup = new HashMap<String, String>();
@@
-118,8
+118,7
@@
public class DBRefUtils
{
return false;
}
{
return false;
}
- String coordsys = dasCoordinateSystemsLookup.get(string
- .toLowerCase());
+ String coordsys = dasCoordinateSystemsLookup.get(string.toLowerCase());
return coordsys == null ? false : coordsys.equals(dBRefEntry
.getSource());
}
return coordsys == null ? false : coordsys.equals(dBRefEntry
.getSource());
}
@@
-139,8
+138,7
@@
public class DBRefUtils
{
return null;
}
{
return null;
}
- String canonical = canonicalSourceNameLookup.get(source
- .toLowerCase());
+ String canonical = canonicalSourceNameLookup.get(source.toLowerCase());
return canonical == null ? source : canonical;
}
return canonical == null ? source : canonical;
}
@@
-436,7
+434,7
@@
public class DBRefUtils
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
{
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
- if (chaincode==null)
+ if (chaincode == null)
{
chaincode = " ";
}
{
chaincode = " ";
}
@@
-450,11
+448,15
@@
public class DBRefUtils
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setType(PDBEntry.Type.PDB);
pdbr.setProperty(new Hashtable());
pdbr.setProperty(new Hashtable());
- pdbr.getProperty().put("CHAIN", chaincode);
+ pdbr.setChainCode(chaincode);
+ // pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
seq.addPDBId(pdbr);
- } else {
- System.err.println("Malformed PDB DR line:"+acn);
+ }
+ else
+ {
+ System.err.println("Malformed PDB DR line:" + acn);
}
}
else
}
}
else