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JAL-2213 code warnings addressed (typed collections, string / magic
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 29 Sep 2016 12:20:30 +0000
(13:20 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 29 Sep 2016 12:20:30 +0000
(13:20 +0100)
number constants)
src/jalview/ws/dbsources/Pdb.java
patch
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diff --git
a/src/jalview/ws/dbsources/Pdb.java
b/src/jalview/ws/dbsources/Pdb.java
index
04c23a2
..
a50ed14
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-37,7
+37,6
@@
import jalview.ws.ebi.EBIFetchClient;
import java.util.ArrayList;
import java.util.List;
import java.util.ArrayList;
import java.util.List;
-import java.util.Vector;
import com.stevesoft.pat.Regex;
import com.stevesoft.pat.Regex;
@@
-47,15
+46,16
@@
import com.stevesoft.pat.Regex;
*/
public class Pdb extends EbiFileRetrievedProxy
{
*/
public class Pdb extends EbiFileRetrievedProxy
{
+ private static final String SEPARATOR = "|";
+ private static final String COLON = ":";
+ private static final int PDB_ID_LENGTH = 4;
+
+
public Pdb()
{
super();
}
public Pdb()
{
super();
}
- public static final String FEATURE_INSERTION = "INSERTION";
-
- public static final String FEATURE_RES_NUM = "RESNUM";
-
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
@@
-64,7
+64,6
@@
public class Pdb extends EbiFileRetrievedProxy
@Override
public String getAccessionSeparator()
{
@Override
public String getAccessionSeparator()
{
- // TODO Auto-generated method stub
return null;
}
return null;
}
@@
-110,23
+109,28
@@
public class Pdb extends EbiFileRetrievedProxy
public AlignmentI getSequenceRecords(String queries) throws Exception
{
AlignmentI pdbAlignment = null;
public AlignmentI getSequenceRecords(String queries) throws Exception
{
AlignmentI pdbAlignment = null;
- Vector result = new Vector();
String chain = null;
String id = null;
String chain = null;
String id = null;
- if (queries.indexOf(":") > -1)
+ if (queries.indexOf(COLON) > -1)
{
{
- chain = queries.substring(queries.indexOf(":") + 1);
- id = queries.substring(0, queries.indexOf(":"));
+ chain = queries.substring(queries.indexOf(COLON) + 1);
+ id = queries.substring(0, queries.indexOf(COLON));
}
else
{
id = queries;
}
}
else
{
id = queries;
}
- if (queries.length() > 4 && chain == null)
+
+ /*
+ * extract chain code if it is appended to the id and we
+ * don't already have one
+ */
+ if (queries.length() > PDB_ID_LENGTH && chain == null)
{
{
- chain = queries.substring(4, 5);
- id = queries.substring(0, 4);
+ chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
+ id = queries.substring(0, PDB_ID_LENGTH);
}
}
+
if (!isValidReference(id))
{
System.err.println("Ignoring invalid pdb query: '" + id + "'");
if (!isValidReference(id))
{
System.err.println("Ignoring invalid pdb query: '" + id + "'");
@@
-165,8
+169,6
@@
public class Pdb extends EbiFileRetrievedProxy
chid = pid.getChainCode();
}
chid = pid.getChainCode();
}
- ;
-
}
if (chain == null
|| (chid != null && (chid.equals(chain)
}
if (chain == null
|| (chid != null && (chid.equals(chain)
@@
-175,8
+177,8
@@
public class Pdb extends EbiFileRetrievedProxy
{
// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
// TODO: suggest simplify naming to 1qip|A as default name defined
{
// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
// TODO: suggest simplify naming to 1qip|A as default name defined
- pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
- + "|" + pdbcs.getName());
+ pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
+ + SEPARATOR + pdbcs.getName());
// Might need to add more metadata to the PDBEntry object
// like below
/*
// Might need to add more metadata to the PDBEntry object
// like below
/*