X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcommands%2FEditCommandTest.java;fp=test%2Fjalview%2Fcommands%2FEditCommandTest.java;h=8e04cdd36293d9a44672fd694dc79937c9236cd0;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=91f844e2e755cc65c94e1c4520c1b1d8bacca584;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;p=jalview.git diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java index 91f844e..8e04cdd 100644 --- a/test/jalview/commands/EditCommandTest.java +++ b/test/jalview/commands/EditCommandTest.java @@ -313,8 +313,7 @@ public class EditCommandTest */ EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ", new SequenceI[] - { seq }, 2, - 4, al); + { seq }, 2, 4, al); assertEquals("ABxyZ-DEF", seq.getSequenceAsString()); assertEquals(1, seq.getStart()); assertEquals(8, seq.getEnd()); @@ -326,8 +325,9 @@ public class EditCommandTest /* * undo the edit */ - AlignmentI[] views = new AlignmentI[] - { new Alignment(new SequenceI[] { seq }) }; + AlignmentI[] views = new AlignmentI[] { + new Alignment(new SequenceI[] + { seq }) }; edit.undoCommand(views); assertEquals("ABC--DEF", seq.getSequenceAsString()); @@ -369,7 +369,8 @@ public class EditCommandTest // and ds is preserved assertTrue(dsseq == seqs[1].getDatasetSequence()); // and it is unchanged and UPPERCASE ! - assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString()); + assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), + dsseq.getSequenceAsString()); // and that alignment sequence start has been adjusted assertEquals(5, seqs[1].getStart()); assertEquals(11, seqs[1].getEnd()); @@ -396,7 +397,8 @@ public class EditCommandTest // and ds is preserved assertTrue(dsseq == seqs[1].getDatasetSequence()); // and it is unchanged AND UPPERCASE ! - assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString()); + assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), + dsseq.getSequenceAsString()); // and that alignment sequence start has been adjusted assertEquals(5, seqs[1].getStart()); assertEquals(11, seqs[1].getEnd()); @@ -414,17 +416,20 @@ public class EditCommandTest * 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); + 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); + 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); + new SequenceI[] + { edited }, 3, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); @@ -435,7 +440,8 @@ 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); + new SequenceI[] + { edited }, 5, 2, al); testee.addEdit(e); assertEquals(2, testee.getSize()); assertEquals(5, testee.getEdit(1).getPosition()); @@ -445,7 +451,8 @@ 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); + new SequenceI[] + { edited }, 6, 2, al); testee.addEdit(e); assertEquals(3, testee.getSize()); assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction()); @@ -465,21 +472,24 @@ public class EditCommandTest */ seqs[0].setSequence("a???bcdefghjk"); Edit e = new EditCommand().new Edit(Action.DELETE_GAP, - new SequenceI[] { seqs[0] }, 4, 1, al); + 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); + 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); + new SequenceI[] + { edited }, 2, 1, al); testee.addEdit(e); assertEquals(1, testee.getSize()); assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); @@ -490,7 +500,8 @@ 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); + new SequenceI[] + { edited }, 2, 1, al); testee.addEdit(e); assertEquals(2, testee.getSize()); assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); @@ -501,7 +512,8 @@ 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); + new SequenceI[] + { edited }, 1, 1, al); testee.addEdit(e); assertEquals(3, testee.getSize()); assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction()); @@ -519,12 +531,14 @@ public class EditCommandTest { seqs[0].setSequence("a???bcdefghjk"); Edit e = new EditCommand().new Edit(Action.DELETE_GAP, - new SequenceI[] { seqs[0] }, 4, 1, al); + new SequenceI[] + { seqs[0] }, 4, 1, al); testee.addEdit(e); seqs[1].setSequence("f??ghjklmnopq"); - Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] - { seqs[1] }, 3, 1, al); + Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, + new SequenceI[] + { seqs[1] }, 3, 1, al); testee.addEdit(e2); assertEquals(2, testee.getSize()); assertSame(e, testee.getEdit(0)); @@ -541,25 +555,27 @@ public class EditCommandTest /* * 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()); assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); assertEquals(1, testee.getEdit(0).getPosition()); assertEquals(2, testee.getEdit(0).getNumber()); - assertEquals(seqs[0].getDatasetSequence(), testee.getEdit(0) - .getSequences()[0].getDatasetSequence()); - assertEquals(seqs[1].getDatasetSequence(), testee.getEdit(0) - .getSequences()[1].getDatasetSequence()); + assertEquals(seqs[0].getDatasetSequence(), + testee.getEdit(0).getSequences()[0].getDatasetSequence()); + assertEquals(seqs[1].getDatasetSequence(), + testee.getEdit(0).getSequences()[1].getDatasetSequence()); } /** @@ -797,22 +813,22 @@ public class EditCommandTest * a cut of columns/residues 4-7 */ SequenceI seq0 = seqs[0]; // abcdefghjk/1-10 - seq0.addSequenceFeature(new SequenceFeature("before", "", 1, 3, 0f, - null)); - seq0.addSequenceFeature(new SequenceFeature("overlap left", "", 2, 6, - 0f, null)); - seq0.addSequenceFeature(new SequenceFeature("internal", "", 5, 6, 0f, - null)); - seq0.addSequenceFeature(new SequenceFeature("overlap right", "", 7, 8, - 0f, null)); - seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f, - null)); + seq0.addSequenceFeature( + new SequenceFeature("before", "", 1, 3, 0f, null)); + seq0.addSequenceFeature( + new SequenceFeature("overlap left", "", 2, 6, 0f, null)); + seq0.addSequenceFeature( + new SequenceFeature("internal", "", 5, 6, 0f, null)); + seq0.addSequenceFeature( + new SequenceFeature("overlap right", "", 7, 8, 0f, null)); + seq0.addSequenceFeature( + new SequenceFeature("after", "", 8, 10, 0f, null)); /* * add some contact features */ - SequenceFeature internalContact = new SequenceFeature("disulphide bond", "", 5, - 6, 0f, null); + SequenceFeature internalContact = new SequenceFeature("disulphide bond", + "", 5, 6, 0f, null); seq0.addSequenceFeature(internalContact); // should get deleted SequenceFeature overlapLeftContact = new SequenceFeature( "disulphide bond", "", 2, 6, 0f, null); @@ -820,8 +836,8 @@ public class EditCommandTest SequenceFeature overlapRightContact = new SequenceFeature( "disulphide bond", "", 5, 8, 0f, null); seq0.addSequenceFeature(overlapRightContact); // should get deleted - SequenceFeature spanningContact = new SequenceFeature( - "disulphide bond", "", 2, 9, 0f, null); + SequenceFeature spanningContact = new SequenceFeature("disulphide bond", + "", 2, 9, 0f, null); seq0.addSequenceFeature(spanningContact); // should get shortened 3' /* @@ -887,8 +903,8 @@ public class EditCommandTest for (int to = from; to <= end; to++) { String desc = String.format("%d-%d", from, to); - SequenceFeature sf = new SequenceFeature("test", desc, from, to, - 0f, null); + SequenceFeature sf = new SequenceFeature("test", desc, from, to, 0f, + null); sf.setValue("from", Integer.valueOf(from)); sf.setValue("to", Integer.valueOf(to)); seq0.addSequenceFeature(sf); @@ -910,8 +926,8 @@ public class EditCommandTest { for (int to = from; to < seq0.getLength(); to++) { - EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to - - from + 1), alignment); + 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(); @@ -1027,8 +1043,8 @@ public class EditCommandTest else { // failure in checkFeatureRelocation is more informative! - assertEquals(msg + "wrong number of features left", func(5) - - func(to - from + 1), sfs.size()); + assertEquals(msg + "wrong number of features left", + func(5) - func(to - from + 1), sfs.size()); } /* @@ -1055,9 +1071,8 @@ public class EditCommandTest { final int oldFrom = ((Integer) sf.getValue("from")).intValue(); final int oldTo = ((Integer) sf.getValue("to")).intValue(); - String msg = String.format( - "Undo cut of [%d-%d], feature at [%d-%d] ", from + 1, to + 1, - oldFrom, oldTo); + String msg = String.format("Undo cut of [%d-%d], feature at [%d-%d] ", + from + 1, to + 1, oldFrom, oldTo); assertEquals(msg + "start", oldFrom, sf.getBegin()); assertEquals(msg + "end", oldTo, sf.getEnd()); } @@ -1075,7 +1090,7 @@ public class EditCommandTest * @param seqStart */ private void verifyFeatureRelocation(SequenceFeature sf, int from, int to, - boolean newDataset, int seqStart) + boolean newDataset, int seqStart) { // TODO handle the gapped sequence case as well int cutSize = to - from + 1; @@ -1142,8 +1157,7 @@ public class EditCommandTest SequenceI seq0 = new Sequence("seq/8-11", "A-BCC"); seq0.createDatasetSequence(); assertEquals(8, seq0.getStart()); - seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f, - null)); + seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f, null)); SequenceI[] seqsArray = new SequenceI[] { seq0 }; AlignmentI alignment = new Alignment(seqsArray); @@ -1153,7 +1167,7 @@ public class EditCommandTest */ Edit ec = testee.new Edit(Action.CUT, seqsArray, 0, 3, alignment); EditCommand.cut(ec, new AlignmentI[] { alignment }); - + /* * feature on CC(10-11) should still be on CC(10-11) */