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Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application
[jalview.git]
/
src
/
jalview
/
gui
/
JalviewChimeraXBindingModel.java
diff --git
a/src/jalview/gui/JalviewChimeraXBindingModel.java
b/src/jalview/gui/JalviewChimeraXBindingModel.java
index
d7b5a94
..
cfd44c7
100644
(file)
--- a/
src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/
src/jalview/gui/JalviewChimeraXBindingModel.java
@@
-10,11
+10,13
@@
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.ChimeraXCommands;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.ext.rbvi.chimera.ChimeraXCommands;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
+import jalview.structure.AtomSpec;
import jalview.structure.StructureCommand;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
import jalview.structure.StructureCommand;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
+ public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
@@
-40,7
+42,7
@@
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
- executeCommand(new StructureCommand(command), false);
+ executeCommand(new StructureCommand(command), false);
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
@@
-65,7
+67,7
@@
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
@Override
public String getSessionFileExtension()
{
@Override
public String getSessionFileExtension()
{
- return ".cxs";
+ return CHIMERAX_SESSION_EXTENSION;
}
@Override
}
@Override
@@
-86,4
+88,15
@@
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
return String.valueOf(pdbfnum + 1);
}
return String.valueOf(pdbfnum + 1);
}
+ /**
+ * Returns a model of the structure positions described by the ChimeraX format atomspec
+ * @param atomSpec
+ * @return
+ */
+ @Override
+ protected AtomSpec parseAtomSpec(String atomSpec)
+ {
+ return AtomSpec.fromChimeraXAtomspec(atomSpec);
+ }
+
}
}