- Desktop d = Desktop.instance;
- assertNotNull(d);
-
- /*
- * alignment with reference to mappings
- */
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- mappings.add(acf1);
- mappings.add(acf2);
- af1.getViewport().getAlignment().setCodonFrames(mappings);
-
- /*
- * Add one and remove it.
- */
- ssm.registerMapping(acf1);
- ssm.deregisterMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- }
-
- /**
- * Test that a mapping is deregistered if no alignment holds a reference to it
- */
- @Test(groups ={ "Functional" })
- public void testDeregisterMapping_withNoReference()
- {
- Desktop d = Desktop.instance;
- assertNotNull(d);
-
- /*
- * alignment with reference to mappings
- */
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- mappings.add(acf2);
- af1.getViewport().getAlignment().setCodonFrames(mappings);
-
- /*
- * Add one and remove it.
- */
- ssm.registerMapping(acf1);
- assertEquals(1, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- ssm.deregisterMapping(acf1);
- assertEquals(0, ssm.seqmappings.size());
- }
-
- /**
- * Test that a mapping is not deregistered when a second view is closed but
- * the first still holds a reference to the mapping
- */
- @Test(groups ={ "Functional" })
- public void testDeregisterMapping_onCloseView()
- {
- /*
- * alignment with reference to mappings
- */
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- mappings.add(acf1);
- mappings.add(acf2);
- af1.getViewport().getAlignment().setCodonFrames(mappings);
- af1.newView_actionPerformed(null);
+ SequenceI seq = new Sequence(
+ "1GAQ|B",
+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
+ StructureSelectionManager sm = new StructureSelectionManager();
+ sm.setProcessSecondaryStructure(true);
+ sm.setAddTempFacAnnot(true);
+ StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
+ new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
+ assertTrue(pmap != null);
+
+ assertEquals(3, pmap.getSeqs().size());
+ assertEquals("1GAQ|A", pmap.getSeqs().get(0).getName());
+ assertEquals("1GAQ|B", pmap.getSeqs().get(1).getName());
+ assertEquals("1GAQ|C", pmap.getSeqs().get(2).getName());