X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcommands%2FEditCommandTest.java;h=348d87173cd9331e517e50375aa33ea6cbbf5f70;hb=e88567692c9f1f3adfb9764a802474e83ff4c69f;hp=63ceebe2ac53c68e11e5cb246a79ced4dca47857;hpb=d04ceb9a223fe6eeb504d23f7bc85c519d75a255;p=jalview.git diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 63ceebe..348d871 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -90,11 +90,11 @@ public class EditCommandTest testee = new EditCommand(); seqs = new SequenceI[4]; seqs[0] = new Sequence("seq0", "abcdefghjk"); - seqs[0].setDatasetSequence(new Sequence("seq0ds", "abcdefghjk")); + seqs[0].setDatasetSequence(new Sequence("seq0ds", "ABCDEFGHJK")); seqs[1] = new Sequence("seq1", "fghjklmnopq"); - seqs[1].setDatasetSequence(new Sequence("seq1ds", "fghjklmnopq")); + seqs[1].setDatasetSequence(new Sequence("seq1ds", "FGHJKLMNOPQ")); seqs[2] = new Sequence("seq2", "qrstuvwxyz"); - seqs[2].setDatasetSequence(new Sequence("seq2ds", "qrstuvwxyz")); + seqs[2].setDatasetSequence(new Sequence("seq2ds", "QRSTUVWXYZ")); seqs[3] = new Sequence("seq3", "1234567890"); seqs[3].setDatasetSequence(new Sequence("seq3ds", "1234567890")); al = new Alignment(seqs); @@ -153,18 +153,23 @@ public class EditCommandTest } /** - * Test a Paste action, where this adds sequences to an alignment. + * Test a Paste action, followed by Undo and Redo */ @Test(groups = { "Functional" }, enabled = false) - // TODO fix so it works - public void testPaste_addToAlignment() + public void testPaste_undo_redo() { + // TODO code this test properly, bearing in mind that: + // Paste action requires something on the clipboard (Cut/Copy) + // - EditCommand.paste doesn't add sequences to the alignment + // ... that is done in AlignFrame.paste() + // ... unless as a Redo + // ... + SequenceI[] newSeqs = new SequenceI[2]; newSeqs[0] = new Sequence("newseq0", "ACEFKL"); newSeqs[1] = new Sequence("newseq1", "JWMPDH"); - Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al); - EditCommand.paste(ec, new AlignmentI[] { al }); + new EditCommand("Paste", Action.PASTE, newSeqs, 0, al.getWidth(), al); assertEquals(6, al.getSequences().size()); assertEquals("1234567890", seqs[3].getSequenceAsString()); assertEquals("ACEFKL", seqs[4].getSequenceAsString()); @@ -274,12 +279,126 @@ public class EditCommandTest { // seem to need a dataset sequence on the edited sequence here seqs[1].createDatasetSequence(); - new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] }, + assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); + // NB command.number holds end position for a Replace command + new EditCommand("", Action.REPLACE, "Z-xY", new SequenceI[] { seqs[1] }, 4, 8, al); assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); + assertEquals("fghjZ-xYopq", seqs[1].getSequenceAsString()); + // Dataset Sequence should always be uppercase + assertEquals("fghjZxYopq".toUpperCase(), + seqs[1].getDatasetSequence().getSequenceAsString()); assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); assertEquals("1234567890", seqs[3].getSequenceAsString()); - seqs[1] = new Sequence("seq1", "fghjZXYnopq"); + } + + /** + * Test the replace command (used to manually edit a sequence) + */ + @Test(groups = { "Functional" }) + public void testReplace_withGaps() + { + SequenceI seq = new Sequence("seq", "ABC--DEF"); + seq.createDatasetSequence(); + assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString()); + assertEquals(1, seq.getStart()); + assertEquals(6, seq.getEnd()); + + /* + * replace C- with XYZ + * NB arg4 = start column of selection for edit (base 0) + * arg5 = column after end of selection for edit + */ + EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ", + new SequenceI[] + { seq }, 2, + 4, al); + assertEquals("ABxyZ-DEF", seq.getSequenceAsString()); + assertEquals(1, seq.getStart()); + assertEquals(8, seq.getEnd()); + // Dataset sequence always uppercase + assertEquals("ABxyZDEF".toUpperCase(), + seq.getDatasetSequence().getSequenceAsString()); + assertEquals(8, seq.getDatasetSequence().getEnd()); + + /* + * undo the edit + */ + AlignmentI[] views = new AlignmentI[] + { new Alignment(new SequenceI[] { seq }) }; + edit.undoCommand(views); + + assertEquals("ABC--DEF", seq.getSequenceAsString()); + assertEquals("ABCDEF", seq.getDatasetSequence().getSequenceAsString()); + assertEquals(1, seq.getStart()); + assertEquals(6, seq.getEnd()); + assertEquals(6, seq.getDatasetSequence().getEnd()); + + /* + * redo the edit + */ + edit.doCommand(views); + + assertEquals("ABxyZ-DEF", seq.getSequenceAsString()); + assertEquals(1, seq.getStart()); + assertEquals(8, seq.getEnd()); + // dataset sequence should be Uppercase + assertEquals("ABxyZDEF".toUpperCase(), + seq.getDatasetSequence().getSequenceAsString()); + assertEquals(8, seq.getDatasetSequence().getEnd()); + + } + + /** + * Test replace command when it doesn't cause a sequence edit (see comment in + */ + @Test(groups = { "Functional" }) + public void testReplaceFirstResiduesWithGaps() + { + // test replace when gaps are inserted at start. Start/end should change + // w.r.t. original edited sequence. + SequenceI dsseq = seqs[1].getDatasetSequence(); + EditCommand edit = new EditCommand("", Action.REPLACE, "----", + new SequenceI[] + { seqs[1] }, 0, 4, al); + + // trimmed start + assertEquals("----klmnopq", seqs[1].getSequenceAsString()); + // and ds is preserved + assertTrue(dsseq == seqs[1].getDatasetSequence()); + // and it is unchanged and UPPERCASE ! + assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString()); + // and that alignment sequence start has been adjusted + assertEquals(5, seqs[1].getStart()); + assertEquals(11, seqs[1].getEnd()); + + AlignmentI[] views = new AlignmentI[] { new Alignment(seqs) }; + // and undo + edit.undoCommand(views); + + // dataset sequence unchanged + assertTrue(dsseq == seqs[1].getDatasetSequence()); + // restore sequence + assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); + // and start/end numbering also restored + assertEquals(1, seqs[1].getStart()); + assertEquals(11, seqs[1].getEnd()); + + // now redo + edit.undoCommand(views); + + // and repeat asserts for the original edit + + // trimmed start + assertEquals("----klmnopq", seqs[1].getSequenceAsString()); + // and ds is preserved + assertTrue(dsseq == seqs[1].getDatasetSequence()); + // and it is unchanged AND UPPERCASE ! + assertEquals("fghjklmnopq".toUpperCase(), dsseq.getSequenceAsString()); + // and that alignment sequence start has been adjusted + assertEquals(5, seqs[1].getStart()); + assertEquals(11, seqs[1].getEnd()); + } /** @@ -752,6 +871,7 @@ public class EditCommandTest seq0.setEnd(end); AlignmentI alignment = new Alignment(new SequenceI[] { seq0 }); alignment.setDataset(null); + /* * create a new alignment with shared dataset sequence */ @@ -777,6 +897,7 @@ public class EditCommandTest assertEquals(func(5), sfs.size()); assertEquals(sfs, copySeq0.getSequenceFeatures()); String copySequenceFeatures = copySeq0.getSequenceFeatures().toString(); + /* * now perform all possible cuts of subranges of columns 1-5 * and validate the resulting remaining sequence features! @@ -790,6 +911,8 @@ public class EditCommandTest EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to - from + 1), alignment); final String msg = String.format("Cut %d-%d ", from + 1, to + 1); + boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0 + .getDatasetSequence(); verifyCut(seq0, from, to, msg, start); @@ -799,10 +922,13 @@ public class EditCommandTest assertEquals("Original dataset sequence was modified", copySequenceFeatures, copySeq0.getSequenceFeatures().toString()); + /* - * verify a new dataset sequence has appeared + * verify any new dataset sequence was added to the + * alignment dataset */ - assertEquals("Wrong Dataset size after cut", 2, + assertEquals("Wrong Dataset size after " + msg, + newDatasetSequence ? 2 : 1, alignment.getDataset().getHeight()); /* @@ -816,15 +942,12 @@ public class EditCommandTest /* * verify copy alignment dataset sequence still unaffected + * and alignment dataset has shrunk (if it was added to) */ assertEquals("Original dataset sequence was modified", copySequenceFeatures, copySeq0.getSequenceFeatures().toString()); - - /* - * verify dataset sequence has shrunk - */ - assertEquals("Wrong Dataset size after cut", 1, + assertEquals("Wrong Dataset size after Undo of " + msg, 1, alignment.getDataset().getHeight()); /* @@ -835,15 +958,13 @@ public class EditCommandTest /* * verify copy alignment dataset sequence unaffected + * and any new dataset sequence readded to alignment dataset */ assertEquals("Original dataset sequence was modified", copySequenceFeatures, copySeq0.getSequenceFeatures().toString()); - - /* - * verify a new dataset sequence has appeared again - */ - assertEquals("Wrong Dataset size after cut", 2, + assertEquals("Wrong Dataset size after Redo of " + msg, + newDatasetSequence ? 2 : 1, alignment.getDataset().getHeight()); /* @@ -853,16 +974,13 @@ public class EditCommandTest /* * final verify that copy alignment dataset sequence is still unaffected + * and that alignment dataset has shrunk */ assertEquals("Original dataset sequence was modified", copySequenceFeatures, copySeq0.getSequenceFeatures().toString()); - /* - * and that dataset sequence has shrunk - */ - assertEquals("Wrong Dataset size after cut", 1, + assertEquals("Wrong Dataset size after final Undo of " + msg, 1, alignment.getDataset().getHeight()); - } } }