/**
* Test mapping a sequence group where sequences in and outside the group
* share a dataset sequence (e.g. alternative CDS for the same gene)
/**
* Test mapping a sequence group where sequences in and outside the group
* share a dataset sequence (e.g. alternative CDS for the same gene)
SequenceI pep1 = new Sequence("pep1", "KF");
SequenceI pep2 = new Sequence("pep2", "FG");
SequenceI pep3 = new Sequence("pep3", "GP");
SequenceI pep1 = new Sequence("pep1", "KF");
SequenceI pep2 = new Sequence("pep2", "FG");
SequenceI pep3 = new Sequence("pep3", "GP");
* Verify the mapped sequence group in dna is cds1 and cds3
*/
SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
* Verify the mapped sequence group in dna is cds1 and cds3
*/
SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg,
assertTrue(mappedGroup.getColourText());
assertSame(sg.getIdColour(), mappedGroup.getIdColour());
assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
assertTrue(mappedGroup.getColourText());
assertSame(sg.getIdColour(), mappedGroup.getIdColour());
assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
sg.addSequence(cds1, false);
sg.setStartRes(0);
sg.setEndRes(cdna.getWidth() - 1);
sg.addSequence(cds1, false);
sg.setStartRes(0);
sg.setEndRes(cdna.getWidth() - 1);
assertTrue(mappedGroup.getColourText());
assertSame(sg.getIdColour(), mappedGroup.getIdColour());
assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());
assertTrue(mappedGroup.getColourText());
assertSame(sg.getIdColour(), mappedGroup.getIdColour());
assertSame(sg.getOutlineColour(), mappedGroup.getOutlineColour());