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JAL-2168 document '-nonews' parameter
[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
b2063c1
..
61c5c04
100644
(file)
--- a/
src/jalview/ws/dbsources/Pdb.java
+++ b/
src/jalview/ws/dbsources/Pdb.java
@@
-1,3
+1,4
@@
+
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
@@
-26,9
+27,11
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
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.StructureImportSettings;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
import jalview.util.MessageManager;
import jalview.ws.ebi.EBIFetchClient;
@@
-53,8
+56,6
@@
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)
*
@@
-132,11
+133,12
@@
public class Pdb extends EbiFileRetrievedProxy
stopQuery();
return null;
}
stopQuery();
return null;
}
- String ext = getCurrentDefaultFormat().equalsIgnoreCase("mmcif") ? ".cif"
- : ".xml";
+ String ext = StructureImportSettings.getDefaultStructureFileFormat()
+ .equalsIgnoreCase(Type.MMCIF.toString()) ? ".cif" : ".xml";
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
EBIFetchClient ebi = new EBIFetchClient();
file = ebi.fetchDataAsFile("pdb:" + id,
- getCurrentDefaultFormat().toLowerCase(), "raw", ext)
+ StructureImportSettings.getDefaultStructureFileFormat().toLowerCase(),
+ ext)
.getAbsolutePath();
stopQuery();
if (file == null)
.getAbsolutePath();
stopQuery();
if (file == null)
@@
-148,7
+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());
+ StructureImportSettings.getDefaultStructureFileFormat());
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
@@
-243,12
+245,12
@@
public class Pdb extends EbiFileRetrievedProxy
}
/**
}
/**
- * obtain human glyoxalase chain A sequence
+ * human glyoxalase
*/
@Override
public String getTestQuery()
{
*/
@Override
public String getTestQuery()
{
- return "1QIPA";
+ return "1QIP";
}
@Override
}
@Override
@@
-263,15
+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