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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[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
982c399
..
d502f74
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-36,6
+36,7
@@
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.ebi.EBIFetchClient;
import java.io.File;
import jalview.ws.ebi.EBIFetchClient;
import java.io.File;
@@
-56,6
+57,8
@@
public class Pdb extends EbiFileRetrievedProxy
private static final int PDB_ID_LENGTH = 4;
private static final int PDB_ID_LENGTH = 4;
+ private static Regex ACCESSION_REGEX;
+
public Pdb()
{
super();
public Pdb()
{
super();
@@
-80,7
+83,12
@@
public class Pdb extends EbiFileRetrievedProxy
@Override
public Regex getAccessionValidator()
{
@Override
public Regex getAccessionValidator()
{
- return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform
+ .newRegex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
+ }
+ return ACCESSION_REGEX;
}
/*
}
/*
@@
-165,7
+173,7
@@
public class Pdb extends EbiFileRetrievedProxy
// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(file,
+ pdbAlignment = new FormatAdapter().readFile(tmpFile,
DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
@@
-182,15
+190,14
@@
public class Pdb extends EbiFileRetrievedProxy
}
}
}
}
- if (chain == null
- || (chid != null && (chid.equals(chain)
- || chid.trim().equals(chain.trim()) || (chain
- .trim().length() == 0 && chid.equals("_")))))
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
{
// 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 + SEPARATOR
- + id + SEPARATOR + 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
/*
@@
-236,8
+243,8
@@
public class Pdb extends EbiFileRetrievedProxy
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
throw new Exception(MessageManager.formatMessage(
- "exception.no_pdb_records_for_chain", new String[] { id,
- ((chain == null) ? "' '" : chain) }));
+ "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