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JAL-1919 updated PDBSequenceFetcherTest and JMol parser config settings to enable...
[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
b0b5e92
..
d3a6238
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-30,6
+30,7
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
import jalview.datamodel.SequenceI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureViewSettings;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
@@
-54,8
+55,6
@@
public class Pdb extends EbiFileRetrievedProxy
public static final String FEATURE_RES_NUM = "RESNUM";
public static final String FEATURE_RES_NUM = "RESNUM";
- private static String currentDefaultFormat = DBRefSource.PDB;
-
/*
* (non-Javadoc)
*
/*
* (non-Javadoc)
*
@@
-133,11
+132,13
@@
public class Pdb extends EbiFileRetrievedProxy
stopQuery();
return null;
}
stopQuery();
return null;
}
- String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
+ String ext = StructureViewSettings.getCurrentDefaultFormat()
+ .equalsIgnoreCase("mmcif") ? ".cif"
: ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
: ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
- getCurrentDefaultFormat().toLowerCase(), ext)
+ StructureViewSettings.getCurrentDefaultFormat().toLowerCase(),
+ ext)
.getAbsolutePath();
stopQuery();
if (file == null)
.getAbsolutePath();
stopQuery();
if (file == null)
@@
-149,7
+150,7
@@
public class Pdb extends EbiFileRetrievedProxy
pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE,
pdbAlignment = new FormatAdapter().readFile(file,
jalview.io.AppletFormatAdapter.FILE,
- getCurrentDefaultFormat());
+ StructureViewSettings.getCurrentDefaultFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
@@
-264,15
+265,6
@@
public class Pdb extends EbiFileRetrievedProxy
return 0;
}
return 0;
}
- public static String getCurrentDefaultFormat()
- {
- return currentDefaultFormat;
- }
-
- public static void setCurrentDefaultFormat(String currentDefaultFomart)
- {
- Pdb.currentDefaultFormat = currentDefaultFomart;
- }
/**
* Returns a descriptor for suitable feature display settings with
/**
* Returns a descriptor for suitable feature display settings with