X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPdb.java;h=f222aaabcb338c076e1b1cae3daf814540e82344;hb=5f090b7d1cb8836903474f8f4d5e475be142d30c;hp=631a79f3854d393ed11d5006269ac1d6abc5f462;hpb=e1d776602ceedd69cae590bcf85836d7b32c5993;p=jalview.git
diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 631a79f..f222aaa 100644
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,28 +1,34 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.SequenceI;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import MCview.PDBChain;
@@ -32,6 +38,7 @@ 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;
@@ -133,6 +140,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
jalview.io.AppletFormatAdapter.FILE, "PDB");
if (pdbfile != null)
{
+ List toremove = new ArrayList();
for (SequenceI pdbcs : pdbfile.getSequences())
{
String chid = null;
@@ -177,17 +185,30 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
}
else
{
- // remove this sequence from the alignment - since it's not from the
- // right chain
- pdbfile.deleteSequence(pdbcs);
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
+ {
+ pdbfile.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation()!=null)
+ {
+ for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+ {
+ pdbfile.deleteAnnotation(aa);
+ }
}
}
}
+
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
{
stopQuery();