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JAL-2344 corrected conversion of Type enum to FileFormat
[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
a50ed14
..
68dda88
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-29,6
+29,9
@@
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
@@
-47,9
+50,10
@@
import com.stevesoft.pat.Regex;
public class Pdb extends EbiFileRetrievedProxy
{
private static final String SEPARATOR = "|";
public class Pdb extends EbiFileRetrievedProxy
{
private static final String SEPARATOR = "|";
+
private static final String COLON = ":";
private static final String COLON = ":";
- private static final int PDB_ID_LENGTH = 4;
+ private static final int PDB_ID_LENGTH = 4;
public Pdb()
{
public Pdb()
{
@@
-137,12
+141,11
@@
public class Pdb extends EbiFileRetrievedProxy
stopQuery();
return null;
}
stopQuery();
return null;
}
- String ext = StructureImportSettings.getDefaultStructureFileFormat()
- .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
+ Type pdbFileFormat = StructureImportSettings
+ .getDefaultStructureFileFormat();
+ String ext = "." + pdbFileFormat.getExtension();
EBIFetchClient ebi = new EBIFetchClient();
EBIFetchClient ebi = new EBIFetchClient();
- file = ebi.fetchDataAsFile("pdb:" + id,
- StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
- ext)
+ file = ebi.fetchDataAsFile("pdb:" + id, pdbFileFormat.getFormat(), ext)
.getAbsolutePath();
stopQuery();
if (file == null)
.getAbsolutePath();
stopQuery();
if (file == null)
@@
-151,10
+154,12
@@
public class Pdb extends EbiFileRetrievedProxy
}
try
{
}
try
{
-
+ // todo get rid of Type and use FileFormatI instead?
+ // todo get rid of "ext" and just use "tmp"?
+ FileFormatI fileFormat = pdbFileFormat == Type.PDB ? FileFormat.PDB
+ : FileFormat.MMCif;
pdbAlignment = new FormatAdapter().readFile(file,
pdbAlignment = new FormatAdapter().readFile(file,
- jalview.io.AppletFormatAdapter.FILE,
- StructureImportSettings.getDefaultStructureFileFormat());
+ DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
@@
-177,8
+182,8
@@
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 + 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
/*
@@
-269,7
+274,6
@@
public class Pdb extends EbiFileRetrievedProxy
return 0;
}
return 0;
}
-
/**
* Returns a descriptor for suitable feature display settings with
* <ul>
/**
* Returns a descriptor for suitable feature display settings with
* <ul>