X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcommands%2FEditCommandTest.java;h=9afae3741cd8f067b7427b2afd17340bbe0339fb;hb=2438d989181ffbe05c7a8096c328b76bff4bb080;hp=984cda44e87047e57a3d4778cf066dd9bd4cb6e1;hpb=52288466dd1e71946a06fd1e6ea15fa8e652c693;p=jalview.git
diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 984cda4..9afae37 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * 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;
@@ -85,7 +105,7 @@ public class EditCommandTest
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());
@@ -110,7 +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 });
+ EditCommand.paste(ec, new AlignmentI[] { al });
assertEquals(6, al.getSequences().size());
assertEquals("1234567890", seqs[3].getSequenceAsString());
assertEquals("ACEFKL", seqs[4].getSequenceAsString());
@@ -403,12 +423,12 @@ public class EditCommandTest
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);
@@ -430,10 +450,10 @@ public class EditCommandTest
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);
@@ -450,8 +470,8 @@ public class EditCommandTest
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);
@@ -468,12 +488,38 @@ public class EditCommandTest
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());
}
/**
@@ -494,13 +540,13 @@ 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);
/*
@@ -509,13 +555,13 @@ public class EditCommandTest
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);
/*
@@ -524,8 +570,8 @@ 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);
@@ -559,8 +605,8 @@ 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);
/*
@@ -572,8 +618,8 @@ 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);