public void setUp()
{
StructureImportSettings.setShowSeqFeatures(true);
- ssm = new StructureSelectionManager();
+ StructureSelectionManager.release(null);
+ ssm = StructureSelectionManager.getStructureSelectionManager(null);
}
@Test(groups = { "Functional" })
acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
- List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set1 = new ArrayList<>();
set1.add(acf1);
set1.add(acf2);
- List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> set2 = new ArrayList<>();
set2.add(acf2);
set2.add(acf3);
SequenceI seq = new Sequence(
"1GAQ|B",
"ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
- StructureSelectionManager sm = new StructureSelectionManager();
+ StructureSelectionManager sm = StructureSelectionManager
+ .getStructureSelectionManager(null);
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
{
// for some reason 'BeforeMethod' (which should be inherited from
// Jalview2XmlBase isn't always called)...
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.getInstance().closeAll_actionPerformed(null);
try {
Thread.sleep(200);
- } catch (Exception foo) {};
+ } catch (Exception foo) {}
SequenceI seq = new Sequence("4IM2|A",
"LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
- StructureSelectionManager sm = new StructureSelectionManager();
+ StructureSelectionManager sm = StructureSelectionManager
+ .getStructureSelectionManager(null);
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
DataSourceType.PASTE);
Desktop.addInternalFrame(alf, "Foo", 800, 600);
- ;
+
AlignmentI al = alf.getViewport().getAlignment();
SequenceI seq = al.getSequenceAt(0);
assertEquals(470, seq.getStart());
PDBID);
AlignmentAnnotation subseq_tf=null;
- assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0);
+ assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
{
Assert.assertNull(subseq,
"Expected no annotation transferred at position " + p);
}
- ;
if (orig != null)
{
Assert.assertNotNull(subseq,
"Expected annotation transfer at position " + p);
assertEquals(orig.value, subseq.value);
}
- ;
}
}
} catch (InterruptedException q)
{
}
- ;
Assert.assertTrue(schoose.selectStructure(pDBID),
"Couldn't select structure via structure chooser: " + pDBID);
schoose.showStructures(true);