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merge of SIFTs Branch
[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
4a50196
..
7f8c76c
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-97,7
+97,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
*/
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;
@@
-131,12
+131,12
@@
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;
@@
-188,18
+188,18
@@
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);
+ pdbAlignment.deleteSequence(pdbcs);
if (pdbcs.getAnnotation() != null)
{
for (AlignmentAnnotation aa : pdbcs.getAnnotation())
{
if (pdbcs.getAnnotation() != null)
{
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,
{
throw new Exception(MessageManager.formatMessage(
"exception.no_pdb_records_for_chain", new String[] { id,
@@
-211,7
+211,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
stopQuery();
throw (ex);
}
stopQuery();
throw (ex);
}
- return pdbfile;
+ return pdbAlignment;
}
/*
}
/*