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JAL-1683 replace year/version strings with tokens in source
[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
b252900
..
76e8351
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 2.8.2)
- * 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.
*
@@
-21,6
+21,7
@@
package jalview.ws.dbsources;
import jalview.datamodel.Alignment;
package jalview.ws.dbsources;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
@@
-37,6
+38,7
@@
import com.stevesoft.pat.Regex;
import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
import jalview.datamodel.AlignmentI;
import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxy;
@@
-138,7
+140,7
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
jalview.io.AppletFormatAdapter.FILE, "PDB");
if (pdbfile != null)
{
jalview.io.AppletFormatAdapter.FILE, "PDB");
if (pdbfile != null)
{
- List<SequenceI> toremove=new ArrayList<SequenceI>();
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
for (SequenceI pdbcs : pdbfile.getSequences())
{
String chid = null;
for (SequenceI pdbcs : pdbfile.getSequences())
{
String chid = null;
@@
-183,21
+185,28
@@
public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
}
else
{
}
else
{
- // mark this sequence to be removed from the alignment
+ // mark this sequence to be removed from the alignment
// - since it's not from the right chain
toremove.add(pdbcs);
}
}
// - since it's not from the right chain
toremove.add(pdbcs);
}
}
- // now remove marked sequences
- for (SequenceI pdbcs:toremove) {
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
+ {
pdbfile.deleteSequence(pdbcs);
pdbfile.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation()!=null)
+ {
+ for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+ {
+ pdbfile.deleteAnnotation(aa);
+ }
+ }
}
}
}
}
-
+
if (pdbfile == null || pdbfile.getHeight() < 1)
{
if (pdbfile == null || pdbfile.getHeight() < 1)
{
- throw new Exception("No PDB Records for " + id + " chain "
- + ((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