X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcommands%2FEditCommandTest.java;h=348d87173cd9331e517e50375aa33ea6cbbf5f70;hb=8701f9ada6beaf1befdbd898f611228d255b9231;hp=3591648aa97753a1b94bbc8b6c7eacb6e4f4bc47;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git
diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 3591648..348d871 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -1,17 +1,46 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.JvOptionPane;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
import java.util.Map;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -23,6 +52,15 @@ import org.testng.annotations.Test;
*/
public class EditCommandTest
{
+ private static Comparator BY_DESCRIPTION = new Comparator()
+ {
+
+ @Override
+ public int compare(SequenceFeature o1, SequenceFeature o2)
+ {
+ return o1.getDescription().compareTo(o2.getDescription());
+ }
+ };
private EditCommand testee;
@@ -30,17 +68,33 @@ public class EditCommandTest
private Alignment al;
- @BeforeMethod
+ /*
+ * compute n(n+1)/2 e.g.
+ * func(5) = 5 + 4 + 3 + 2 + 1 = 15
+ */
+ private static int func(int i)
+ {
+ return i * (i + 1) / 2;
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
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);
@@ -50,7 +104,7 @@ 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 +121,7 @@ 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 +135,11 @@ 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 });
+ EditCommand.cut(ec, new AlignmentI[] { al });
assertEquals("abcdhjk", seqs[0].getSequenceAsString());
assertEquals("fghjnopq", seqs[1].getSequenceAsString());
assertEquals("qrstxyz", seqs[2].getSequenceAsString());
@@ -100,20 +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()
+ @Test(groups = { "Functional" }, enabled = false)
+ 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);
- testee.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());
@@ -123,15 +179,14 @@ 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 +196,13 @@ 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 +213,7 @@ 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 +232,7 @@ 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 +241,7 @@ 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 +249,7 @@ 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 +258,13 @@ 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());
@@ -223,41 +274,155 @@ 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);
+ seqs[1].createDatasetSequence();
+ 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());
+
}
/**
* 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 +432,8 @@ 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 +442,8 @@ 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 +455,29 @@ 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 +487,8 @@ 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 +498,8 @@ 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 +512,12 @@ 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 +533,21 @@ 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());
@@ -404,20 +569,19 @@ 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 };
- Edit e = command.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, sqs, 1, 2, '-');
command.addEdit(e);
- e = command.new Edit(Action.INSERT_GAP, seqs, 4, 1, '-');
+ e = command.new Edit(Action.INSERT_GAP, sqs, 4, 1, '-');
command.addEdit(e);
- e = command.new Edit(Action.INSERT_GAP, seqs, 0, 2, '-');
+ e = command.new Edit(Action.INSERT_GAP, sqs, 0, 2, '-');
command.addEdit(e);
Map unwound = command.priorState(false);
@@ -432,18 +596,17 @@ 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 };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-');
command.addEdit(e);
- e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-');
+ e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-');
command.addEdit(e);
Map unwound = command.priorState(false);
@@ -453,18 +616,17 @@ 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 };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 2, 2, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 2, 2, '-');
command.addEdit(e);
-
+
Map unwound = command.priorState(false);
assertEquals("AB--CDEF", unwound.get(ds).getSequenceAsString());
}
@@ -472,27 +634,52 @@ 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 };
- Edit e = command.new Edit(Action.INSERT_GAP, seqs, 2, 3, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-');
command.addEdit(e);
-
+
Map unwound = command.priorState(false);
- assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString());
+ SequenceI prior = unwound.get(ds);
+ assertEquals("ABCDEF", prior.getSequenceAsString());
+ assertEquals(1, prior.getStart());
+ assertEquals(6, prior.getEnd());
+ }
+
+ /**
+ * Test 'undoing' a single gap insertion edit command, on a sequence whose
+ * start residue is other than 1
+ */
+ @Test(groups = { "Functional" })
+ public void testPriorState_singleInsertWithOffset()
+ {
+ EditCommand command = new EditCommand();
+ SequenceI seq = new Sequence("", "AB---CDEF", 8, 13);
+ // SequenceI ds = new Sequence("", "ABCDEF", 8, 13);
+ // seq.setDatasetSequence(ds);
+ seq.createDatasetSequence();
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-');
+ command.addEdit(e);
+
+ Map unwound = command.priorState(false);
+ SequenceI prior = unwound.get(seq.getDatasetSequence());
+ assertEquals("ABCDEF", prior.getSequenceAsString());
+ assertEquals(8, prior.getStart());
+ assertEquals(13, prior.getEnd());
}
/**
* 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();
@@ -506,32 +693,28 @@ public class EditCommandTest
SequenceI seq = new Sequence("", "ABC-DEF");
SequenceI ds1 = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds1);
- SequenceI[] seqs = new SequenceI[]
- { seq };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 2, '-');
+ SequenceI[] sqs = new SequenceI[] { seq };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 2, '-');
command.addEdit(e);
seq = new Sequence("", "ABCDEF");
seq.setDatasetSequence(ds1);
- seqs = new SequenceI[]
- { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 3, 1, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 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 };
- e = command.new Edit(Action.DELETE_GAP, seqs, 2, 1, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-');
command.addEdit(e);
seq = new Sequence("", "FGHIJ");
seq.setDatasetSequence(ds2);
- seqs = new SequenceI[]
- { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-');
command.addEdit(e);
/*
@@ -540,9 +723,8 @@ public class EditCommandTest
seq = new Sequence("", "MNOPQ");
SequenceI ds3 = new Sequence("", "MNOPQ");
seq.setDatasetSequence(ds3);
- seqs = new SequenceI[]
- { seq };
- e = command.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
+ sqs = new SequenceI[] { seq };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-');
command.addEdit(e);
Map unwound = command.priorState(false);
@@ -556,7 +738,7 @@ 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();
@@ -576,9 +758,8 @@ 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 };
- Edit e = command.new Edit(Action.DELETE_GAP, seqs, 0, 1, '-');
+ SequenceI[] sqs = new SequenceI[] { seq1, seq2, seq3 };
+ Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 1, '-');
command.addEdit(e);
/*
@@ -590,9 +771,8 @@ public class EditCommandTest
seq2.setDatasetSequence(ds2);
seq3 = new Sequence("", "M-NOPQ");
seq3.setDatasetSequence(ds3);
- seqs = new SequenceI[]
- { seq1, seq2, seq3 };
- e = command.new Edit(Action.DELETE_GAP, seqs, 4, 2, '-');
+ sqs = new SequenceI[] { seq1, seq2, seq3 };
+ e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-');
command.addEdit(e);
Map unwound = command.priorState(false);
@@ -603,4 +783,384 @@ public class EditCommandTest
assertEquals(ds2, unwound.get(ds2).getDatasetSequence());
assertEquals(ds3, unwound.get(ds3).getDatasetSequence());
}
+
+ /**
+ * Test a cut action's relocation of sequence features
+ */
+ @Test(groups = { "Functional" })
+ public void testCut_withFeatures()
+ {
+ /*
+ * create sequence features before, after and overlapping
+ * 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));
+
+ /*
+ * add some contact features
+ */
+ 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);
+ seq0.addSequenceFeature(overlapLeftContact); // should get deleted
+ 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);
+ seq0.addSequenceFeature(spanningContact); // should get shortened 3'
+
+ /*
+ * cut columns 3-6 (base 0), residues d-g 4-7
+ */
+ Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); // cols 3-6 base 0
+ EditCommand.cut(ec, new AlignmentI[] { al });
+
+ List sfs = seq0.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(sfs, true);
+
+ assertEquals(5, sfs.size()); // features internal to cut were deleted
+ SequenceFeature sf = sfs.get(0);
+ assertEquals("before", sf.getType());
+ assertEquals(1, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ sf = sfs.get(1);
+ assertEquals("disulphide bond", sf.getType());
+ assertEquals(2, sf.getBegin());
+ assertEquals(5, sf.getEnd()); // truncated by cut
+ sf = sfs.get(2);
+ assertEquals("overlap left", sf.getType());
+ assertEquals(2, sf.getBegin());
+ assertEquals(3, sf.getEnd()); // truncated by cut
+ sf = sfs.get(3);
+ assertEquals("after", sf.getType());
+ assertEquals(4, sf.getBegin()); // shifted left by cut
+ assertEquals(6, sf.getEnd()); // shifted left by cut
+ sf = sfs.get(4);
+ assertEquals("overlap right", sf.getType());
+ assertEquals(4, sf.getBegin()); // shifted left by cut
+ assertEquals(4, sf.getEnd()); // truncated by cut
+ }
+
+ /**
+ * Test a cut action's relocation of sequence features, with full coverage of
+ * all possible feature and cut locations for a 5-position ungapped sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testCut_withFeatures_exhaustive()
+ {
+ /*
+ * create a sequence features on each subrange of 1-5
+ */
+ SequenceI seq0 = new Sequence("seq", "ABCDE");
+ int start = 8;
+ int end = 12;
+ seq0.setStart(start);
+ seq0.setEnd(end);
+ AlignmentI alignment = new Alignment(new SequenceI[] { seq0 });
+ alignment.setDataset(null);
+
+ /*
+ * create a new alignment with shared dataset sequence
+ */
+ AlignmentI copy = new Alignment(
+ new SequenceI[]
+ { alignment.getDataset().getSequenceAt(0).deriveSequence() });
+ SequenceI copySeq0 = copy.getSequenceAt(0);
+
+ for (int from = start; from <= end; from++)
+ {
+ 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);
+ sf.setValue("from", Integer.valueOf(from));
+ sf.setValue("to", Integer.valueOf(to));
+ seq0.addSequenceFeature(sf);
+ }
+ }
+ // sanity check
+ List sfs = seq0.getSequenceFeatures();
+ 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!
+ */
+ SequenceI[] sqs = new SequenceI[] { seq0 };
+
+ for (int from = 0; from < seq0.getLength(); from++)
+ {
+ for (int to = from; to < seq0.getLength(); to++)
+ {
+ 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);
+
+ /*
+ * verify copy alignment dataset sequence unaffected
+ */
+ assertEquals("Original dataset sequence was modified",
+ copySequenceFeatures,
+ copySeq0.getSequenceFeatures().toString());
+
+ /*
+ * verify any new dataset sequence was added to the
+ * alignment dataset
+ */
+ assertEquals("Wrong Dataset size after " + msg,
+ newDatasetSequence ? 2 : 1,
+ alignment.getDataset().getHeight());
+
+ /*
+ * undo and verify all restored
+ */
+ AlignmentI[] views = new AlignmentI[] { alignment };
+ ec.undoCommand(views);
+ sfs = seq0.getSequenceFeatures();
+ assertEquals("After undo of " + msg, func(5), sfs.size());
+ verifyUndo(from, to, sfs);
+
+ /*
+ * 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());
+ assertEquals("Wrong Dataset size after Undo of " + msg, 1,
+ alignment.getDataset().getHeight());
+
+ /*
+ * redo and verify
+ */
+ ec.doCommand(views);
+ verifyCut(seq0, from, to, msg, start);
+
+ /*
+ * 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());
+ assertEquals("Wrong Dataset size after Redo of " + msg,
+ newDatasetSequence ? 2 : 1,
+ alignment.getDataset().getHeight());
+
+ /*
+ * undo ready for next cut
+ */
+ ec.undoCommand(views);
+
+ /*
+ * 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());
+ assertEquals("Wrong Dataset size after final Undo of " + msg, 1,
+ alignment.getDataset().getHeight());
+ }
+ }
+ }
+
+ /**
+ * Verify by inspection that the sequence features left on the sequence after
+ * a cut match the expected results. The trick to this is that we can parse
+ * each feature's original start-end positions from its description.
+ *
+ * @param seq0
+ * @param from
+ * @param to
+ * @param msg
+ * @param seqStart
+ */
+ protected void verifyCut(SequenceI seq0, int from, int to,
+ final String msg, int seqStart)
+ {
+ List sfs;
+ sfs = seq0.getSequenceFeatures();
+
+ Collections.sort(sfs, BY_DESCRIPTION);
+
+ /*
+ * confirm the number of features has reduced by the
+ * number of features within the cut region i.e. by
+ * func(length of cut); exception is a cut at start or end of sequence,
+ * which retains the original coordinates, dataset sequence
+ * and all its features
+ */
+ boolean datasetRetained = from == 0 || to == 4;
+ if (datasetRetained)
+ {
+ // dataset and all features retained
+ assertEquals(msg, func(5), sfs.size());
+ }
+ else if (to - from == 4)
+ {
+ // all columns were cut
+ assertTrue(sfs.isEmpty());
+ }
+ else
+ {
+ // failure in checkFeatureRelocation is more informative!
+ assertEquals(msg + "wrong number of features left", func(5)
+ - func(to - from + 1), sfs.size());
+ }
+
+ /*
+ * inspect individual features
+ */
+ for (SequenceFeature sf : sfs)
+ {
+ verifyFeatureRelocation(sf, from + 1, to + 1, !datasetRetained,
+ seqStart);
+ }
+ }
+
+ /**
+ * Check that after Undo, every feature has start/end that match its original
+ * "start" and "end" properties
+ *
+ * @param from
+ * @param to
+ * @param sfs
+ */
+ protected void verifyUndo(int from, int to, List sfs)
+ {
+ for (SequenceFeature sf : sfs)
+ {
+ 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);
+ assertEquals(msg + "start", oldFrom, sf.getBegin());
+ assertEquals(msg + "end", oldTo, sf.getEnd());
+ }
+ }
+
+ /**
+ * Helper method to check a feature has been correctly relocated after a cut
+ *
+ * @param sf
+ * @param from
+ * start of cut (first residue cut 1..)
+ * @param to
+ * end of cut (last residue cut 1..)
+ * @param newDataset
+ * @param seqStart
+ */
+ private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,
+ boolean newDataset, int seqStart)
+ {
+ // TODO handle the gapped sequence case as well
+ int cutSize = to - from + 1;
+ final int oldFrom = ((Integer) sf.getValue("from")).intValue();
+ final int oldTo = ((Integer) sf.getValue("to")).intValue();
+ final int oldFromPosition = oldFrom - seqStart + 1; // 1..
+ final int oldToPosition = oldTo - seqStart + 1; // 1..
+
+ String msg = String.format(
+ "Feature %s relocated to %d-%d after cut of %d-%d",
+ sf.getDescription(), sf.getBegin(), sf.getEnd(), from, to);
+ if (!newDataset)
+ {
+ // dataset retained with all features unchanged
+ assertEquals("0: " + msg, oldFrom, sf.getBegin());
+ assertEquals("0: " + msg, oldTo, sf.getEnd());
+ }
+ else if (oldToPosition < from)
+ {
+ // before cut region so unchanged
+ assertEquals("1: " + msg, oldFrom, sf.getBegin());
+ assertEquals("2: " + msg, oldTo, sf.getEnd());
+ }
+ else if (oldFromPosition > to)
+ {
+ // follows cut region - shift by size of cut
+ assertEquals("3: " + msg, newDataset ? oldFrom - cutSize : oldFrom,
+ sf.getBegin());
+ assertEquals("4: " + msg, newDataset ? oldTo - cutSize : oldTo,
+ sf.getEnd());
+ }
+ else if (oldFromPosition < from && oldToPosition > to)
+ {
+ // feature encloses cut region - shrink it right
+ assertEquals("5: " + msg, oldFrom, sf.getBegin());
+ assertEquals("6: " + msg, oldTo - cutSize, sf.getEnd());
+ }
+ else if (oldFromPosition < from)
+ {
+ // feature overlaps left side of cut region - truncated right
+ assertEquals("7: " + msg, from - 1 + seqStart - 1, sf.getEnd());
+ }
+ else if (oldToPosition > to)
+ {
+ // feature overlaps right side of cut region - truncated left
+ assertEquals("8: " + msg, newDataset ? from + seqStart - 1 : to + 1,
+ sf.getBegin());
+ assertEquals("9: " + msg, newDataset ? from + oldTo - to - 1 : oldTo,
+ sf.getEnd());
+ }
+ else
+ {
+ // feature internal to cut - should have been deleted!
+ Assert.fail(msg + " - should have been deleted");
+ }
+ }
+
+ /**
+ * Test a cut action's relocation of sequence features
+ */
+ @Test(groups = { "Functional" })
+ public void testCut_withFeatures5prime()
+ {
+ SequenceI seq0 = new Sequence("seq/8-11", "A-BCC");
+ seq0.createDatasetSequence();
+ assertEquals(8, seq0.getStart());
+ seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f,
+ null));
+ SequenceI[] seqsArray = new SequenceI[] { seq0 };
+ AlignmentI alignment = new Alignment(seqsArray);
+
+ /*
+ * cut columns of A-B; same dataset sequence is retained, aligned sequence
+ * start becomes 10
+ */
+ 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)
+ */
+ assertSame(seq0, alignment.getSequenceAt(0));
+ assertEquals(10, seq0.getStart());
+ List sfs = seq0.getSequenceFeatures();
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(0);
+ assertEquals(10, sf.getBegin());
+ assertEquals(11, sf.getEnd());
+ }
}