From 94c90874868e68016e7521e4f28738b3f5436dde Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 10 Jun 2019 11:18:36 +0100 Subject: [PATCH 1/1] JAL-3296 ensure sequence cursor reset when sequence start changes --- src/jalview/datamodel/Sequence.java | 1 + test/jalview/datamodel/SequenceTest.java | 119 ++++++++++++++++++------------ 2 files changed, 72 insertions(+), 48 deletions(-) diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 6f5c18a..566898e 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -496,6 +496,7 @@ public class Sequence extends ASequence implements SequenceI public void setStart(int start) { this.start = start; + sequenceChanged(); } /** diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java index c344645..4ac8c5b 100644 --- a/test/jalview/datamodel/SequenceTest.java +++ b/test/jalview/datamodel/SequenceTest.java @@ -358,7 +358,7 @@ public class SequenceTest SequenceI sq = new Sequence("test/8-13", "ABCDEF"); assertEquals(8, sq.findPosition(0)); // Sequence should now hold a cursor at [8, 0] - assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0", + assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1", PA.getValue(sq, "cursor").toString()); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); int token = (int) PA.getValue(sq, "changeCount"); @@ -374,24 +374,24 @@ public class SequenceTest cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(++token, (int) PA.getValue(sq, "changeCount")); assertEquals(new SequenceCursor(sq, 13, 6, token), cursor); - assertEquals("test:Pos13:Col6:startCol1:endCol6:tok1", + assertEquals("test:Pos13:Col6:startCol1:endCol6:tok2", PA.getValue(sq, "cursor").toString()); // assertEquals(-1, seq.findPosition(6)); // fails sq = new Sequence("test/8-11", "AB-C-D--"); - token = (int) PA.getValue(sq, "changeCount"); // 0 + token = (int) PA.getValue(sq, "changeCount"); // 1 for setStart assertEquals(8, sq.findPosition(0)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 8, 1, token), cursor); - assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0", + assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(9, sq.findPosition(1)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor); - assertEquals("test:Pos9:Col2:startCol1:endCol0:tok1", + assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -400,14 +400,14 @@ public class SequenceTest assertEquals(10, sq.findPosition(2)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor); - assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2", + assertEquals("test:Pos9:Col2:startCol1:endCol0:tok3", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(10, sq.findPosition(3)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor); - assertEquals("test:Pos10:Col4:startCol1:endCol0:tok3", + assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -416,7 +416,7 @@ public class SequenceTest assertEquals(11, sq.findPosition(4)); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor); - assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4", + assertEquals("test:Pos10:Col4:startCol1:endCol0:tok5", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -424,7 +424,7 @@ public class SequenceTest cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor); // lastCol has been found and saved in the cursor - assertEquals("test:Pos11:Col6:startCol1:endCol6:tok5", + assertEquals("test:Pos11:Col6:startCol1:endCol6:tok6", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); @@ -440,6 +440,7 @@ public class SequenceTest sq = new Sequence("test/8-13", "--AB-C-DEF--"); assertEquals(8, sq.findPosition(0)); assertNull(PA.getValue(sq, "cursor")); + assertEquals(1, PA.getValue(sq, "changeCount")); sq.sequenceChanged(); assertEquals(8, sq.findPosition(1)); @@ -447,41 +448,41 @@ public class SequenceTest sq.sequenceChanged(); assertEquals(8, sq.findPosition(2)); - assertEquals("test:Pos8:Col3:startCol3:endCol0:tok2", + assertEquals("test:Pos8:Col3:startCol3:endCol0:tok3", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(9, sq.findPosition(3)); - assertEquals("test:Pos9:Col4:startCol3:endCol0:tok3", + assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[4] is a gap, returns next residue pos (C10) // cursor is set to last residue found [B] assertEquals(10, sq.findPosition(4)); - assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4", + assertEquals("test:Pos9:Col4:startCol3:endCol0:tok5", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(10, sq.findPosition(5)); - assertEquals("test:Pos10:Col6:startCol3:endCol0:tok5", + assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); // column[6] is a gap, returns next residue pos (D11) // cursor is set to last residue found [C] assertEquals(11, sq.findPosition(6)); - assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6", + assertEquals("test:Pos10:Col6:startCol3:endCol0:tok7", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(11, sq.findPosition(7)); - assertEquals("test:Pos11:Col8:startCol3:endCol0:tok7", + assertEquals("test:Pos11:Col8:startCol3:endCol0:tok8", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(12, sq.findPosition(8)); - assertEquals("test:Pos12:Col9:startCol3:endCol0:tok8", + assertEquals("test:Pos12:Col9:startCol3:endCol0:tok9", PA.getValue(sq, "cursor").toString()); /* @@ -489,12 +490,12 @@ public class SequenceTest */ sq.sequenceChanged(); assertEquals(13, sq.findPosition(9)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok9", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(14, sq.findPosition(10)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11", PA.getValue(sq, "cursor").toString()); /* @@ -503,12 +504,12 @@ public class SequenceTest */ sq.sequenceChanged(); assertEquals(14, sq.findPosition(11)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(14, sq.findPosition(99)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok13", PA.getValue(sq, "cursor").toString()); /* @@ -516,19 +517,19 @@ public class SequenceTest */ sq = new Sequence("test/8-13", "--AB-C-DEF"); assertEquals(13, sq.findPosition(9)); - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1", PA.getValue(sq, "cursor").toString()); sq.sequenceChanged(); assertEquals(12, sq.findPosition(8)); // E12 // sequenceChanged() invalidates cursor.lastResidueColumn cursor = (SequenceCursor) PA.getValue(sq, "cursor"); - assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1", + assertEquals("test:Pos12:Col9:startCol3:endCol0:tok2", cursor.toString()); // findPosition with cursor accepts base 1 column values assertEquals(13, ((Sequence) sq).findPosition(10, cursor)); assertEquals(13, sq.findPosition(9)); // F13 // lastResidueColumn has now been found and saved in cursor - assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1", + assertEquals("test:Pos13:Col10:startCol3:endCol10:tok2", PA.getValue(sq, "cursor").toString()); } @@ -1501,21 +1502,23 @@ public class SequenceTest public void testFindIndex_withCursor() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); + final int tok = (int) PA.getValue(sq, "changeCount"); + assertEquals(1, tok); // find F given A, check cursor is now at the found position - assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0))); + assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, tok))); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(13, cursor.residuePosition); assertEquals(10, cursor.columnPosition); // find A given F - assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0))); + assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, tok))); cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(8, cursor.residuePosition); assertEquals(2, cursor.columnPosition); // find C given C (no cursor update is done for this case) - assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0))); + assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, tok))); SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor"); assertSame(cursor2, cursor); @@ -1563,41 +1566,48 @@ public class SequenceTest public void testFindPosition_withCursor() { Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--"); + final int tok = (int) PA.getValue(sq, "changeCount"); + assertEquals(1, tok); // find F pos given A - lastCol gets set in cursor - assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0))); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals(13, + sq.findPosition(10, new SequenceCursor(sq, 8, 2, tok))); + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); // find A pos given F - first residue column is saved in cursor - assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0))); - assertEquals("test:Pos8:Col2:startCol2:endCol10:tok0", + assertEquals(8, + sq.findPosition(2, new SequenceCursor(sq, 13, 10, tok))); + assertEquals("test:Pos8:Col2:startCol2:endCol10:tok1", PA.getValue(sq, "cursor").toString()); // find C pos given C (neither startCol nor endCol is set) - assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0))); - assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0", + assertEquals(10, + sq.findPosition(6, new SequenceCursor(sq, 10, 6, tok))); + assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1", PA.getValue(sq, "cursor").toString()); // now the grey area - what residue position for a gapped column? JAL-2562 // find 'residue' for column 3 given cursor for D (so working left) // returns B9; cursor is updated to [B 5] - assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0))); - assertEquals("test:Pos9:Col5:startCol0:endCol0:tok0", + assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, tok))); + assertEquals("test:Pos9:Col5:startCol0:endCol0:tok1", PA.getValue(sq, "cursor").toString()); // find 'residue' for column 8 given cursor for D (so working right) // returns E12; cursor is updated to [D 7] - assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0))); - assertEquals("test:Pos11:Col7:startCol0:endCol0:tok0", + assertEquals(12, + sq.findPosition(8, new SequenceCursor(sq, 11, 7, tok))); + assertEquals("test:Pos11:Col7:startCol0:endCol0:tok1", PA.getValue(sq, "cursor").toString()); // find 'residue' for column 12 given cursor for B // returns 1 more than last residue position; cursor is updated to [F 10] // lastCol position is saved in cursor - assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0))); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals(14, + sq.findPosition(12, new SequenceCursor(sq, 9, 5, tok))); + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); /* @@ -1605,8 +1615,9 @@ public class SequenceTest * returns 1 more than the last residue position * cursor is set to last real residue position [F 10] */ - assertEquals(14, sq.findPosition(99, new SequenceCursor(sq, 8, 2, 0))); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals(14, + sq.findPosition(99, new SequenceCursor(sq, 8, 2, tok))); + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); /* @@ -1614,14 +1625,14 @@ public class SequenceTest */ sq = new Sequence("test/8-13", "-A--BCD-EF"); // first find C from A - assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, 0))); + assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, tok))); SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor"); - assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0", + assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1", cursor.toString()); // now 'find' 99 from C // cursor is set to [F 10] and saved lastCol assertEquals(14, sq.findPosition(99, cursor)); - assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0", + assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1", PA.getValue(sq, "cursor").toString()); } @@ -1728,6 +1739,17 @@ public class SequenceTest // cursor should now be at [F 10] cursor = (SequenceCursor) PA.getValue(sq, "cursor"); assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor); + + /* + * changing sequence start should invalidate cursor + */ + sq = new Sequence("test/8-13", "-A--BCD-EF--"); + assertEquals(8, sq.getStart()); + assertEquals(9, sq.findPosition(4)); // B(9) + sq.setStart(7); + assertEquals(8, sq.findPosition(4)); // is now B(8) + sq.setStart(10); + assertEquals(11, sq.findPosition(4)); // is now B(11) } @Test(groups = { "Functional" }) @@ -1752,23 +1774,24 @@ public class SequenceTest { String seqstring = "-A--BCD-EF--"; SequenceI sq = new Sequence("test/8-13", seqstring); - assertEquals(0, PA.getValue(sq, "changeCount")); + // changeCount is incremented for setStart + assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(0, sq.replace('A', 'A')); // same char assertEquals(seqstring, sq.getSequenceAsString()); - assertEquals(0, PA.getValue(sq, "changeCount")); + assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(0, sq.replace('X', 'Y')); // not there assertEquals(seqstring, sq.getSequenceAsString()); - assertEquals(0, PA.getValue(sq, "changeCount")); + assertEquals(1, PA.getValue(sq, "changeCount")); assertEquals(1, sq.replace('A', 'K')); assertEquals("-K--BCD-EF--", sq.getSequenceAsString()); - assertEquals(1, PA.getValue(sq, "changeCount")); + assertEquals(2, PA.getValue(sq, "changeCount")); assertEquals(6, sq.replace('-', '.')); assertEquals(".K..BCD.EF..", sq.getSequenceAsString()); - assertEquals(2, PA.getValue(sq, "changeCount")); + assertEquals(3, PA.getValue(sq, "changeCount")); } @Test(groups = { "Functional" }) -- 1.7.10.2