X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;fp=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;h=fdb8b9a7c66b89eb4fb4d2a11f755f009e5a21db;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=f36e9357cda31610185e1d40c30ec20d760f77a3;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index f36e935..fdb8b9a 100644
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import static org.testng.Assert.assertEquals;
@@ -172,7 +192,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1579);
-          assertEquals(ranges.get(0)[1], 2931);  // excludes stop 2934 
+          assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 451);
@@ -184,7 +204,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 2928);
-          assertEquals(ranges.get(0)[1], 3989);  // excludes stop 3992
+          assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 354);
@@ -230,6 +250,7 @@ public class EmblFlatFileTest
     }
     assertEquals(uniprotCount, 8);
   }
+
   /**
    * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
    * one of them reverse strand
@@ -244,7 +265,7 @@ public class EmblFlatFileTest
     FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
     EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
     List<SequenceI> seqs = parser.getSeqs();
-    assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1);
+    assertTrue(seqs.get(0).getSequenceAsString().indexOf("u") > -1);
   }
 
   @Test(groups = "Functional")
@@ -287,7 +308,7 @@ public class EmblFlatFileTest
      * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
      */
     assertEquals(dbrefs.size(), 2);
-    
+
     // dbref to self
     DBRefEntry dbref = dbrefs.get(0);
     assertEquals(dbref.getSource(), "EMBLTEST");
@@ -301,7 +322,7 @@ public class EmblFlatFileTest
     assertEquals(map.getToHighest(), 40);
     assertEquals(map.getFromRatio(), 1);
     assertEquals(map.getToRatio(), 1);
-    
+
     // dbref to inferred EMBLCDSPROTEIN:
     dbref = dbrefs.get(1);
     assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
@@ -330,17 +351,17 @@ public class EmblFlatFileTest
     assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
 
     // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
-    // match if we assume exons include stop codon not in protein: 
+    // match if we assume exons include stop codon not in protein:
     int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
     assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
-    
+
     // truncate last exon by 6bp
     truncated = EmblFlatFile.adjustForProteinLength(4, exons);
-    assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 32]");
 
     // remove last exon and truncate preceding by 1bp (so 3bp in total)
     truncated = EmblFlatFile.adjustForProteinLength(3, exons);
-    assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 24]");
 
     // exact removal of exon case:
     exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
@@ -356,8 +377,12 @@ public class EmblFlatFileTest
   public void testRemoveQuotes()
   {
     assertNull(EmblFlatFile.removeQuotes(null));
-    assertEquals(EmblFlatFile.removeQuotes("No quotes here"), "No quotes here");
-    assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""), "Enclosing quotes");
-    assertEquals(EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""), "Escaped \"quotes\" example");
+    assertEquals(EmblFlatFile.removeQuotes("No quotes here"),
+            "No quotes here");
+    assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""),
+            "Enclosing quotes");
+    assertEquals(
+            EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""),
+            "Escaped \"quotes\" example");
   }
 }