.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm
- .findDistances(alf.getViewport().getAlignmentView(
- true));
+ MatrixI dm = fsm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm
- .findDistances(alf.getViewport().getAlignmentView(
- true));
+ MatrixI dm = fsm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm
- .findDistances(alf.getViewport().getAlignmentView(
- true));
+ MatrixI dm = fsm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
assertEquals(
dm.getValue(0, 2),
0d,
alf.selectAllSequenceMenuItem_actionPerformed(null);
MatrixI distances = fsm.findDistances(alf.getViewport()
- .getAlignmentView(true));
+ .getAlignmentView(true), SimilarityParams.Jalview);
assertEquals(distances.width(), 2);
assertEquals(distances.height(), 2);
assertEquals(distances.getValue(0, 0), 0d);