JAL-3438 spotless for 2.11.2.0

[jalview.git] / test / jalview / io / EmblFlatFileTest.java

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index ee853f3..e05b03b 100644 (file)
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -17,7 +17,7 @@ import java.util.Set;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence.DBModList;
@@ -31,7 +31,7 @@ public class EmblFlatFileTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
-    Cache.initLogger();
+    Console.initLogger();
   }
 
   /**
@@ -172,7 +172,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1579);
-          assertEquals(ranges.get(0)[1], 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 +184,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 2928);
-          assertEquals(ranges.get(0)[1], 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);
@@ -193,7 +193,7 @@ public class EmblFlatFileTest
         {
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 4054);
-          assertEquals(ranges.get(0)[1], 4848);
+          assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 264);
@@ -205,7 +205,7 @@ public class EmblFlatFileTest
           assertEquals(ranges.get(0)[0], 7022);
           assertEquals(ranges.get(0)[1], 7502);
           assertEquals(ranges.get(1)[0], 1);
-          assertEquals(ranges.get(1)[1], 437);
+          assertEquals(ranges.get(1)[1], 434); // excludes stop at 437
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 305);
@@ -215,7 +215,7 @@ public class EmblFlatFileTest
           // complement(488..1480)
           assertEquals((ranges = map.getFromRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1480);
-          assertEquals(ranges.get(0)[1], 488);
+          assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488
           assertEquals((ranges = map.getToRanges()).size(), 1);
           assertEquals(ranges.get(0)[0], 1);
           assertEquals(ranges.get(0)[1], 330);
@@ -231,6 +231,23 @@ public class EmblFlatFileTest
     assertEquals(uniprotCount, 8);
   }
 
+  /**
+   * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+   * one of them reverse strand
+   * 
+   * @throws MalformedURLException
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testParseToRNA() throws MalformedURLException, IOException
+  {
+    File dataFile = new File("test/jalview/io/J03321_rna.embl.txt");
+    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);
+  }
+
   @Test(groups = "Functional")
   public void testParse_codonStartNot1()
   {
@@ -271,7 +288,7 @@ 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");
@@ -285,7 +302,7 @@ 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");
@@ -313,21 +330,23 @@ public class EmblFlatFileTest
     // exact length match:
     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:
-    assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons));
+    int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
 
     // truncate last exon by 6bp
-    int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);
-    assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+    truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+    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("[11, 15, 21, 24]", Arrays.toString(truncated));
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 24]");
 
     // exact removal of exon case:
     exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
     truncated = EmblFlatFile.adjustForProteinLength(4, exons);
-    assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+    assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
 
     // what if exons are too short for protein?
     truncated = EmblFlatFile.adjustForProteinLength(7, exons);
@@ -338,8 +357,12 @@ 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");
   }
 }