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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
d62de27
..
9695891
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-27,6
+27,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
@@
-282,15
+283,14
@@
public class AppletFormatAdapter
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
boolean isParseWithJMOL = StructureImportSettings
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
boolean isParseWithJMOL = StructureImportSettings
- .getDefaultPDBFileParser()
- .equals(StructureImportSettings.StructureParser.JMOL_PARSER);
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
if (isParseWithJMOL)
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
+ alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
}
else
{
}
else
{
@@
-307,8
+307,7
@@
public class AppletFormatAdapter
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+ alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
@@
-442,8
+441,7
@@
public class AppletFormatAdapter
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
}
else
{
}
else
{
@@
-457,8
+455,7
@@
public class AppletFormatAdapter
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))
((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))