X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FAlignedCodonIteratorTest.java;h=60042c48f6bfa3dee62725a09f0cd6531a1f8e01;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d9c7e120018b48e00546529ab83961d720763fbc;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git
diff --git a/test/jalview/datamodel/AlignedCodonIteratorTest.java b/test/jalview/datamodel/AlignedCodonIteratorTest.java
index d9c7e12..60042c4 100644
--- a/test/jalview/datamodel/AlignedCodonIteratorTest.java
+++ b/test/jalview/datamodel/AlignedCodonIteratorTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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;
@@ -21,16 +41,16 @@ public class AlignedCodonIteratorTest
/**
* Test normal case for iterating over aligned codons.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testNext()
{
SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
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, '-');
@@ -49,16 +69,16 @@ public class AlignedCodonIteratorTest
/**
* Test weird case where the mapping skips over a peptide.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testNext_unmappedPeptide()
{
SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc");
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, '-');
@@ -73,20 +93,19 @@ public class AlignedCodonIteratorTest
assertEquals("R", codon.product);
assertFalse(codons.hasNext());
}
-
+
/**
* Test for exception thrown for an incomplete codon.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testNext_incompleteCodon()
{
SequenceI from = new Sequence("Seq1", "-CgC-C-cCgTt");
from.createDatasetSequence();
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);
+ MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
+ new int[] { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator codons = m.getCodonIterator(from, '-');
@@ -106,18 +125,16 @@ public class AlignedCodonIteratorTest
/**
* Test normal case for iterating over aligned codons.
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testAnother()
{
SequenceI from = new Sequence("Seq1", "TGCCATTACCAG-");
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, '-');
AlignedCodon codon = codons.next();
assertEquals("[0, 1, 2]", codon.toString());