X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignedCodonIteratorTest.java;h=af9bbb7087012947371bc0c6e28d25828f35999b;hb=a7169b1c72607f3c9357195b4999869650a2a891;hp=dd30b60b86ed046b0757f283a964fdd38f63537a;hpb=52288466dd1e71946a06fd1e6ea15fa8e652c693;p=jalview.git
diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java
index dd30b60..af9bbb7 100644
--- a/test/jalview/datamodel/AlignedCodonIteratorTest.java
+++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java
@@ -1,13 +1,35 @@
+/*
+ * 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.datamodel;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.Iterator;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
@@ -18,6 +40,14 @@ import org.testng.annotations.Test;
*/
public class AlignedCodonIteratorTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test normal case for iterating over aligned codons.
*/
@@ -28,9 +58,9 @@ public class AlignedCodonIteratorTest
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-R-");
to.createDatasetSequence();
- MapList map = new MapList(
- new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
- new int[] { 1, 3 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+ new int[]
+ { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator codons = m.getCodonIterator(from, '-');
@@ -56,9 +86,9 @@ public class AlignedCodonIteratorTest
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-TR-");
to.createDatasetSequence();
- MapList map = new MapList(
- new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[] { 1,
- 2, 4, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+ new int[]
+ { 1, 2, 4, 4 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator codons = m.getCodonIterator(from, '-');
@@ -85,7 +115,8 @@ public class AlignedCodonIteratorTest
SequenceI to = new Sequence("Seq1", "-PQ-R-");
to.createDatasetSequence();
MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
- new int[] { 1, 3 }, 3, 1);
+ new int[]
+ { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator codons = m.getCodonIterator(from, '-');
@@ -112,7 +143,8 @@ public class AlignedCodonIteratorTest
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "CHYQ");
to.createDatasetSequence();
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
+ 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator codons = m.getCodonIterator(from, '-');
@@ -130,4 +162,33 @@ public class AlignedCodonIteratorTest
assertEquals("Q", codon.product);
assertFalse(codons.hasNext());
}
+
+ /**
+ * Test for a case with sequence (and mappings) not starting at 1
+ */
+ @Test(groups = { "Functional" })
+ public void testNext_withOffset()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc", 7, 20);
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
+ to.createDatasetSequence();
+ MapList map = new MapList(
+ new int[]
+ { 7, 7, 9, 10, 12, 12, 14, 16, 18, 19 }, new int[] { 10, 12 },
+ 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ codon = codons.next();
+ assertEquals("[8, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ codon = codons.next();
+ assertEquals("[13, 15, 17]", codon.toString());
+ assertEquals("R", codon.product);
+ assertFalse(codons.hasNext());
+ }
}