@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
- "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
+ Jalview.main(
+ new String[]
+ { "-noquestionnaire", "-nonews", "-props",
+ "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
ViewerType.CHIMERA.name());
Cache.setProperty("SHOW_ANNOTATIONS", "false");
assertEquals(pdbIds.size(), 1);
PDBEntry pdbEntry = pdbIds.get(0);
assertEquals(pdbEntry.getId(), "1GAQ");
- StructureViewer structureViewer = new StructureViewer(af.getViewport()
- .getStructureSelectionManager());
+ StructureViewer structureViewer = new StructureViewer(
+ af.getViewport().getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
- new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
.getBinding();
} catch (InterruptedException e)
{
}
- } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
+ } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
assertTrue(chimeraViewer.hasViewerActionsMenu());
// now add another sequence and bind to view
- //
+ //
AlignmentI al = af.getViewport().getAlignment();
PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
- sq = new Sequence("1GAQ", al.getSequenceAt(0).getSequence(25, 95).toString());
+ sq = new Sequence("1GAQ",
+ al.getSequenceAt(0).getSequence(25, 95).toString());
al.addSequence(sq);
- structureViewer.viewStructures(new PDBEntry[] { xpdb }, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ structureViewer.viewStructures(new PDBEntry[] { xpdb },
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
/*
* Wait for viewer load thread to complete
*/
- do
+ do
{
- try {
+ try
+ {
Thread.sleep(1500);
- } catch (InterruptedException q) {};
+ } catch (InterruptedException q)
+ {
+ }
+ ;
} while (!binding.isLoadingFinished());
-
+
// still just one PDB structure shown
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
// and the viewer action menu should still be visible
/*
* use local test PDB and SIFTS files
*/
- String pdbFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+ String pdbFilePath = new File("test/jalview/ext/rbvi/chimera/4zho.pdb")
+ .getPath();
PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
String siftsFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
- .getPath();
+ "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
SiftsClient.setMockSiftsFile(new File(siftsFilePath));
- StructureViewer structureViewer = new StructureViewer(af.getViewport()
- .getStructureSelectionManager());
+ StructureViewer structureViewer = new StructureViewer(
+ af.getViewport().getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
- new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
.getBinding();
sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
"Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
// on a sequence region that is partially mapped to structure:
- sq.addSequenceFeature(new SequenceFeature("helix", null, 50, 60,
- Float.NaN, null));
+ sq.addSequenceFeature(
+ new SequenceFeature("helix", null, 50, 60, Float.NaN, null));
// and again:
- sq.addSequenceFeature(new SequenceFeature("chain", null, 50, 70,
- Float.NaN, null));
+ sq.addSequenceFeature(
+ new SequenceFeature("chain", null, 50, 70, Float.NaN, null));
// add numeric valued features - score is set as attribute value
sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
62, -2.1f, null));
new StructureCommand("list resi att jv_metal_ion_binding_site"),
true);
assertEquals(reply.size(), 4);
- assertTrue(reply
- .contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
- assertTrue(reply
- .contains("residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
- assertTrue(reply
- .contains("residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
- assertTrue(reply
- .contains("residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+ assertTrue(reply.contains(
+ "residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+ assertTrue(reply.contains(
+ "residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+ assertTrue(reply.contains(
+ "residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+ assertTrue(reply.contains(
+ "residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
/*
* check attributes with score values
SequenceI fer2Arath = af.getViewport().getAlignment()
.findName("FER2_ARATH");
assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
-
+
/*
* need a Uniprot dbref for SIFTS mapping to work!!
*/
fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
-
+
/*
* use local test PDB and SIFTS files
*/
- String pdbFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+ String pdbFilePath = new File("test/jalview/ext/rbvi/chimera/4zho.pdb")
+ .getPath();
PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
String siftsFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
- .getPath();
+ "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
SiftsClient.setMockSiftsFile(new File(siftsFilePath));
-
- StructureViewer structureViewer = new StructureViewer(af.getViewport()
- .getStructureSelectionManager());
+
+ StructureViewer structureViewer = new StructureViewer(
+ af.getViewport().getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
- new SequenceI[] { fer2Arath }, af.getCurrentView()
- .getAlignPanel());
-
+ new SequenceI[]
+ { fer2Arath }, af.getCurrentView().getAlignPanel());
+
JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
.getBinding();
do
{
}
} while (!binding.isFinishedInit());
-
+
assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
-
+
assertEquals(binding.getPdbCount(), 1);
-
+
/*
* 'perform' menu action to copy Chimera attributes
* to features in Jalview
*/
// TODO rename and pull up method to binding interface
// once functionality is added for Jmol as well
- binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
- .getAlignPanel());
+ binding.copyStructureAttributesToFeatures("isHelix",
+ af.getViewport().getAlignPanel());
/*
* verify 22 residues have isHelix feature
/*
* fetch a numeric valued attribute
*/
- binding.copyStructureAttributesToFeatures("phi", af.getViewport()
- .getAlignPanel());
+ binding.copyStructureAttributesToFeatures("phi",
+ af.getViewport().getAlignPanel());
fr.setVisible("phi");
List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54,
"phi");
git://source.jalview.org / jalview.git / blobdiff