/**
* Test inserting gap characters
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAppendEdit_insertGap()
{
// set a non-standard gap character to prove it is actually used
* Test deleting characters from sequences. Note the deleteGap() action does
* not check that only gap characters are being removed.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAppendEdit_deleteGap()
{
testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true);
* Test a cut action. The command should store the cut characters to support
* undo.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testCut()
{
Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al);
/**
* Test a Paste action, where this adds sequences to an alignment.
*/
- @Test(enabled = false)
+ @Test(groups =
+ { "Functional" }, enabled = false)
// TODO fix so it works
public void testPaste_addToAlignment()
{
/**
* Test insertGap followed by undo command
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testUndo_insertGap()
{
// Edit ec = testee.new Edit(Action.INSERT_GAP, seqs, 4, 3, '?');
/**
* Test deleteGap followed by undo command
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testUndo_deleteGap()
{
testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true);
/**
* Test several commands followed by an undo command
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testUndo_multipleCommands()
{
// delete positions 3/4/5 (counting from 1)
* Unit test for JAL-1594 bug: click and drag sequence right to insert gaps -
* undo did not remove them all.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testUndo_multipleInsertGaps()
{
testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true);
/**
* Test cut followed by undo command
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testUndo_cut()
{
testee.appendEdit(Action.CUT, seqs, 4, 3, al, true);
/**
* Test the replace command (used to manually edit a sequence)
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testReplace()
{
// seem to need a dataset sequence on the edited sequence here
* Test that the addEdit command correctly merges insert gap commands when
* possible.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAddEdit_multipleInsertGap()
{
/*
* Test that the addEdit command correctly merges delete gap commands when
* possible.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAddEdit_multipleDeleteGap()
{
/*
* case when they appear contiguous but are acting on different sequences.
* They should not be merged.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAddEdit_removeAllGaps()
{
seqs[0].setSequence("a???bcdefghjk");
* Test that the addEdit command correctly merges insert gap commands acting
* on a multi-sequence selection.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAddEdit_groupInsertGaps()
{
/*
* <li>last: --A--B-CDEF</li>
* </ul>
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testPriorState_multipleInserts()
{
EditCommand command = new EditCommand();
* <li>End: ABC</li>
* </ul>
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testPriorState_removeAllGaps()
{
EditCommand command = new EditCommand();
/**
* Test for 'undoing' a single delete edit.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testPriorState_singleDelete()
{
EditCommand command = new EditCommand();
/**
* Test 'undoing' a single gap insertion edit command.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testPriorState_singleInsert()
{
EditCommand command = new EditCommand();
* Test that mimics 'remove all gaps' action. This generates delete gap edits
* for contiguous gaps in each sequence separately.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testPriorState_removeGapsMultipleSeqs()
{
EditCommand command = new EditCommand();
* series Delete Gap edits that each act on all sequences that share a gapped
* column region.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testPriorState_removeGappedCols()
{
EditCommand command = new EditCommand();