X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcommands%2FEditCommandTest.java;h=7ce01380191aa54b2ea2919e574c1bc66f6aac69;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3591648aa97753a1b94bbc8b6c7eacb6e4f4bc47;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 3591648..7ce0138 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.commands; import static org.testng.AssertJUnit.assertEquals; @@ -30,7 +50,7 @@ public class EditCommandTest private Alignment al; - @BeforeMethod + @BeforeMethod(alwaysRun = true) public void setUp() { testee = new EditCommand(); @@ -50,7 +70,7 @@ public class EditCommandTest /** * Test inserting gap characters */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testAppendEdit_insertGap() { // set a non-standard gap character to prove it is actually used @@ -67,7 +87,7 @@ public class EditCommandTest * Test deleting characters from sequences. Note the deleteGap() action does * not check that only gap characters are being removed. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testAppendEdit_deleteGap() { testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); @@ -81,12 +101,11 @@ public class EditCommandTest * Test a cut action. The command should store the cut characters to support * undo. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testCut() { Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al); - testee.cut(ec, new AlignmentI[] - { al }); + testee.cut(ec, new AlignmentI[] { al }); assertEquals("abcdhjk", seqs[0].getSequenceAsString()); assertEquals("fghjnopq", seqs[1].getSequenceAsString()); assertEquals("qrstxyz", seqs[2].getSequenceAsString()); @@ -102,8 +121,7 @@ public class EditCommandTest /** * Test a Paste action, where this adds sequences to an alignment. */ - @Test(groups = - { "Functional" }, enabled = false) + @Test(groups = { "Functional" }, enabled = false) // TODO fix so it works public void testPaste_addToAlignment() { @@ -112,8 +130,7 @@ public class EditCommandTest newSeqs[1] = new Sequence("newseq1", "JWMPDH"); Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al); - testee.paste(ec, new AlignmentI[] - { al }); + testee.paste(ec, new AlignmentI[] { al }); assertEquals(6, al.getSequences().size()); assertEquals("1234567890", seqs[3].getSequenceAsString()); assertEquals("ACEFKL", seqs[4].getSequenceAsString()); @@ -123,15 +140,14 @@ public class EditCommandTest /** * Test insertGap followed by undo command */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testUndo_insertGap() { // Edit ec = testee.new Edit(Action.INSERT_GAP, seqs, 4, 3, '?'); testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true); // check something changed assertEquals("abcd???efghjk", seqs[0].getSequenceAsString()); - testee.undoCommand(new AlignmentI[] - { al }); + testee.undoCommand(new AlignmentI[] { al }); assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); @@ -141,14 +157,13 @@ public class EditCommandTest /** * Test deleteGap followed by undo command */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testUndo_deleteGap() { testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); // check something changed assertEquals("abcdhjk", seqs[0].getSequenceAsString()); - testee.undoCommand(new AlignmentI[] - { al }); + testee.undoCommand(new AlignmentI[] { al }); // deleteGap doesn't 'remember' deleted characters, only gaps get put back assertEquals("abcd???hjk", seqs[0].getSequenceAsString()); assertEquals("fghj???nopq", seqs[1].getSequenceAsString()); @@ -159,7 +174,7 @@ public class EditCommandTest /** * Test several commands followed by an undo command */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testUndo_multipleCommands() { // delete positions 3/4/5 (counting from 1) @@ -178,8 +193,7 @@ public class EditCommandTest assertEquals("12?890", seqs[3].getSequenceAsString()); // undo edit commands - testee.undoCommand(new AlignmentI[] - { al }); + testee.undoCommand(new AlignmentI[] { al }); assertEquals("ab?????hjk", seqs[0].getSequenceAsString()); assertEquals("12?????890", seqs[3].getSequenceAsString()); } @@ -188,7 +202,7 @@ public class EditCommandTest * Unit test for JAL-1594 bug: click and drag sequence right to insert gaps - * undo did not remove them all. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testUndo_multipleInsertGaps() { testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true); @@ -196,8 +210,7 @@ public class EditCommandTest testee.appendEdit(Action.INSERT_GAP, seqs, 6, 1, al, true); // undo edit commands - testee.undoCommand(new AlignmentI[] - { al }); + testee.undoCommand(new AlignmentI[] { al }); assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); assertEquals("1234567890", seqs[3].getSequenceAsString()); @@ -206,14 +219,13 @@ public class EditCommandTest /** * Test cut followed by undo command */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testUndo_cut() { testee.appendEdit(Action.CUT, seqs, 4, 3, al, true); // check something changed assertEquals("abcdhjk", seqs[0].getSequenceAsString()); - testee.undoCommand(new AlignmentI[] - { al }); + testee.undoCommand(new AlignmentI[] { al }); assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); @@ -223,13 +235,13 @@ public class EditCommandTest /** * Test the replace command (used to manually edit a sequence) */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testReplace() { // seem to need a dataset sequence on the edited sequence here seqs[1].setDatasetSequence(seqs[1]); - new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] - { seqs[1] }, 4, 8, al); + new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] }, + 4, 8, al); assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); assertEquals("1234567890", seqs[3].getSequenceAsString()); @@ -240,24 +252,24 @@ public class EditCommandTest * Test that the addEdit command correctly merges insert gap commands when * possible. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testAddEdit_multipleInsertGap() { /* * 3 insert gap in a row (aka mouse drag right): */ - Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { seqs[0] }, 1, 1, al); + Edit e = new EditCommand().new Edit(Action.INSERT_GAP, + new SequenceI[] { seqs[0] }, 1, 1, al); testee.addEdit(e); SequenceI edited = new Sequence("seq0", "a?bcdefghjk"); edited.setDatasetSequence(seqs[0].getDatasetSequence()); - e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { edited }, 2, 1, al); + e = new EditCommand().new Edit(Action.INSERT_GAP, + new SequenceI[] { edited }, 2, 1, al); testee.addEdit(e); edited = new Sequence("seq0", "a??bcdefghjk"); edited.setDatasetSequence(seqs[0].getDatasetSequence()); - e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { edited }, 3, 1, al); + e = new EditCommand().new Edit(Action.INSERT_GAP, + new SequenceI[] { edited }, 3, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); @@ -267,8 +279,8 @@ public class EditCommandTest /* * Add a non-contiguous edit - should not be merged. */ - e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { edited }, 5, 2, al); + e = new EditCommand().new Edit(Action.INSERT_GAP, + new SequenceI[] { edited }, 5, 2, al); testee.addEdit(e); assertEquals(2, testee.getSize()); assertEquals(5, testee.getEdit(1).getPosition()); @@ -277,8 +289,8 @@ public class EditCommandTest /* * Add a Delete after the Insert - should not be merged. */ - e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { edited }, 6, 2, al); + e = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] { edited }, 6, 2, al); testee.addEdit(e); assertEquals(3, testee.getSize()); assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction()); @@ -290,29 +302,29 @@ public class EditCommandTest * Test that the addEdit command correctly merges delete gap commands when * possible. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testAddEdit_multipleDeleteGap() { /* * 3 delete gap in a row (aka mouse drag left): */ seqs[0].setSequence("a???bcdefghjk"); - Edit e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { seqs[0] }, 4, 1, al); + Edit e = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] { seqs[0] }, 4, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); SequenceI edited = new Sequence("seq0", "a??bcdefghjk"); edited.setDatasetSequence(seqs[0].getDatasetSequence()); - e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { edited }, 3, 1, al); + e = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] { edited }, 3, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); edited = new Sequence("seq0", "a?bcdefghjk"); edited.setDatasetSequence(seqs[0].getDatasetSequence()); - e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { edited }, 2, 1, al); + e = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] { edited }, 2, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); @@ -322,8 +334,8 @@ public class EditCommandTest /* * Add a non-contiguous edit - should not be merged. */ - e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { edited }, 2, 1, al); + e = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] { edited }, 2, 1, al); testee.addEdit(e); assertEquals(2, testee.getSize()); assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); @@ -333,8 +345,8 @@ public class EditCommandTest /* * Add an Insert after the Delete - should not be merged. */ - e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { edited }, 1, 1, al); + e = new EditCommand().new Edit(Action.INSERT_GAP, + new SequenceI[] { edited }, 1, 1, al); testee.addEdit(e); assertEquals(3, testee.getSize()); assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction()); @@ -347,12 +359,12 @@ public class EditCommandTest * case when they appear contiguous but are acting on different sequences. * They should not be merged. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testAddEdit_removeAllGaps() { seqs[0].setSequence("a???bcdefghjk"); - Edit e = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { seqs[0] }, 4, 1, al); + Edit e = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] { seqs[0] }, 4, 1, al); testee.addEdit(e); seqs[1].setSequence("f??ghjklmnopq"); @@ -368,21 +380,21 @@ public class EditCommandTest * Test that the addEdit command correctly merges insert gap commands acting * on a multi-sequence selection. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testAddEdit_groupInsertGaps() { /* * 2 insert gap in a row (aka mouse drag right), on two sequences: */ - Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { seqs[0], seqs[1] }, 1, 1, al); + Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] { + seqs[0], seqs[1] }, 1, 1, al); testee.addEdit(e); SequenceI seq1edited = new Sequence("seq0", "a?bcdefghjk"); seq1edited.setDatasetSequence(seqs[0].getDatasetSequence()); SequenceI seq2edited = new Sequence("seq1", "f?ghjklmnopq"); seq2edited.setDatasetSequence(seqs[1].getDatasetSequence()); - e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] - { seq1edited, seq2edited }, 2, 1, al); + e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] { + seq1edited, seq2edited }, 2, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); @@ -404,15 +416,14 @@ public class EditCommandTest *
  • last: --A--B-CDEF
    • * */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testPriorState_multipleInserts() { EditCommand command = new EditCommand(); SequenceI seq = new Sequence("", "--A--B-CDEF"); SequenceI ds = new Sequence("", "ABCDEF"); seq.setDatasetSequence(ds); - SequenceI[] seqs = new SequenceI[] - { seq }; + SequenceI[] seqs = new SequenceI[] { seq }; Edit e = command.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-'); command.addEdit(e); e = command.new Edit(Action.INSERT_GAP, seqs, 4, 1, '-'); @@ -432,15 +443,14 @@ public class EditCommandTest *
  • End: ABC
    • * */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testPriorState_removeAllGaps() { EditCommand command = new EditCommand(); SequenceI seq = new Sequence("", "ABC"); SequenceI ds = new Sequence("", "ABC"); seq.setDatasetSequence(ds); - SequenceI[] seqs = new SequenceI[] - { seq }; + SequenceI[] seqs = new SequenceI[] { seq }; Edit e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'); command.addEdit(e); e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-'); @@ -453,18 +463,17 @@ public class EditCommandTest /** * Test for 'undoing' a single delete edit. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testPriorState_singleDelete() { EditCommand command = new EditCommand(); SequenceI seq = new Sequence("", "ABCDEF"); SequenceI ds = new Sequence("", "ABCDEF"); seq.setDatasetSequence(ds); - SequenceI[] seqs = new SequenceI[] - { seq }; + SequenceI[] seqs = new SequenceI[] { seq }; Edit e = command.new Edit(Action.DELETE_GAP, seqs, 2, 2, '-'); command.addEdit(e); - + Map unwound = command.priorState(false); assertEquals("AB--CDEF", unwound.get(ds).getSequenceAsString()); } @@ -472,18 +481,17 @@ public class EditCommandTest /** * Test 'undoing' a single gap insertion edit command. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testPriorState_singleInsert() { EditCommand command = new EditCommand(); SequenceI seq = new Sequence("", "AB---CDEF"); SequenceI ds = new Sequence("", "ABCDEF"); seq.setDatasetSequence(ds); - SequenceI[] seqs = new SequenceI[] - { seq }; + SequenceI[] seqs = new SequenceI[] { seq }; Edit e = command.new Edit(Action.INSERT_GAP, seqs, 2, 3, '-'); command.addEdit(e); - + Map unwound = command.priorState(false); assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString()); } @@ -492,7 +500,7 @@ public class EditCommandTest * Test that mimics 'remove all gaps' action. This generates delete gap edits * for contiguous gaps in each sequence separately. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testPriorState_removeGapsMultipleSeqs() { EditCommand command = new EditCommand(); @@ -506,31 +514,27 @@ public class EditCommandTest SequenceI seq = new Sequence("", "ABC-DEF"); SequenceI ds1 = new Sequence("", "ABCDEF"); seq.setDatasetSequence(ds1); - SequenceI[] seqs = new SequenceI[] - { seq }; + SequenceI[] seqs = new SequenceI[] { seq }; Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 2, '-'); command.addEdit(e); seq = new Sequence("", "ABCDEF"); seq.setDatasetSequence(ds1); - seqs = new SequenceI[] - { seq }; + seqs = new SequenceI[] { seq }; e = command.new Edit(Action.DELETE_GAP, seqs, 3, 1, '-'); command.addEdit(e); - + /* * Two edits for the second sequence */ seq = new Sequence("", "FGHI--J"); SequenceI ds2 = new Sequence("", "FGHIJ"); seq.setDatasetSequence(ds2); - seqs = new SequenceI[] - { seq }; + seqs = new SequenceI[] { seq }; e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-'); command.addEdit(e); seq = new Sequence("", "FGHIJ"); seq.setDatasetSequence(ds2); - seqs = new SequenceI[] - { seq }; + seqs = new SequenceI[] { seq }; e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-'); command.addEdit(e); @@ -540,8 +544,7 @@ public class EditCommandTest seq = new Sequence("", "MNOPQ"); SequenceI ds3 = new Sequence("", "MNOPQ"); seq.setDatasetSequence(ds3); - seqs = new SequenceI[] - { seq }; + seqs = new SequenceI[] { seq }; e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'); command.addEdit(e); @@ -556,7 +559,7 @@ public class EditCommandTest * series Delete Gap edits that each act on all sequences that share a gapped * column region. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testPriorState_removeGappedCols() { EditCommand command = new EditCommand(); @@ -576,8 +579,7 @@ public class EditCommandTest SequenceI seq3 = new Sequence("", "M-NO--PQ"); SequenceI ds3 = new Sequence("", "MNOPQ"); seq3.setDatasetSequence(ds3); - SequenceI[] seqs = new SequenceI[] - { seq1, seq2, seq3 }; + SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 }; Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 1, '-'); command.addEdit(e); @@ -590,8 +592,7 @@ public class EditCommandTest seq2.setDatasetSequence(ds2); seq3 = new Sequence("", "M-NOPQ"); seq3.setDatasetSequence(ds3); - seqs = new SequenceI[] - { seq1, seq2, seq3 }; + seqs = new SequenceI[] { seq1, seq2, seq3 }; e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-'); command.addEdit(e);