JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / test / jalview / datamodel / AlignmentTest.java

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 2eaae94..f5f271d 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -79,7 +99,7 @@ public class AlignmentTest
    * Read in Stockholm format test data including secondary structure
    * annotations.
    */
- @BeforeMethod(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws IOException
   {
     al = loadAlignment(TEST_DATA, "STH");
@@ -94,7 +114,7 @@ public class AlignmentTest
   /**
    * Test method that returns annotations that match on calcId.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testFindAnnotation_byCalcId()
   {
     Iterable<AlignmentAnnotation> anns = al
@@ -106,7 +126,7 @@ public class AlignmentTest
     assertFalse(iter.hasNext());
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeleteAllAnnotations_includingAutocalculated()
   {
     AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
@@ -120,7 +140,7 @@ public class AlignmentTest
     assertEquals("Not all deleted", 0, al.getAlignmentAnnotation().length);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testDeleteAllAnnotations_excludingAutocalculated()
   {
     AlignmentAnnotation aa = new AlignmentAnnotation("Consensus",
@@ -144,7 +164,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAlignAs_dnaAsDna() throws IOException
   {
     // aligned cDNA:
@@ -157,9 +177,7 @@ public class AlignmentTest
      * of what would normally be protein here.
      */
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList ml = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 12 }, 1, 1);
+    MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 12 }, 1, 1);
     acf.addMap(al2.getSequenceAt(0), al1.getSequenceAt(0), ml);
     acf.addMap(al2.getSequenceAt(1), al1.getSequenceAt(1), ml);
     al1.addCodonFrame(acf);
@@ -176,16 +194,14 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAlignAs_proteinAsCdna() throws IOException
   {
     // see also AlignmentUtilsTests
     AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
     AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList ml = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 4 }, 3, 1);
+    MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
     acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
     acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
     al2.addCodonFrame(acf);
@@ -200,7 +216,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAlignAs_cdnaAsProtein() throws IOException
   {
     /*
@@ -209,9 +225,7 @@ public class AlignmentTest
     AlignmentI al1 = loadAlignment(CDNA_SEQS_1, "FASTA");
     AlignmentI al2 = loadAlignment(AA_SEQS_1, "FASTA");
     AlignedCodonFrame acf = new AlignedCodonFrame();
-    MapList ml = new MapList(new int[]
-    { 1, 12 }, new int[]
-    { 1, 4 }, 3, 1);
+    MapList ml = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
     acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
     acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
     al2.addCodonFrame(acf);
@@ -232,7 +246,7 @@ public class AlignmentTest
    * 
    * @throws IOException
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testAlignAs_dnaAsProtein_withIntrons() throws IOException
   {
     /*
@@ -247,13 +261,11 @@ public class AlignmentTest
     AlignedCodonFrame acf = new AlignedCodonFrame();
     // Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
     // Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
-    MapList ml1 = new MapList(new int[]
-    { 1, 2, 5, 8, 10, 12 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList ml1 = new MapList(new int[] { 1, 2, 5, 8, 10, 12 }, new int[] {
+        1, 3 }, 3, 1);
     acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
-    MapList ml2 = new MapList(new int[]
-    { 2, 4, 7, 12 }, new int[]
-    { 1, 3 }, 3, 1);
+    MapList ml2 = new MapList(new int[] { 2, 4, 7, 12 },
+            new int[] { 1, 3 }, 3, 1);
     acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
     al2.addCodonFrame(acf);