JAL-2189 format tests

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 2f5d0c5..602ce9f 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -153,7 +153,8 @@ public class FeaturesFileTest
     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
             .getFeatureColours();
     // GFF2 uses space as name/value separator in column 9
-    String gffData = "METAL\tcc9900\n" + "GFF\n"
+    String gffData = "METAL\tcc9900\n"
+            + "GFF\n"
             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
@@ -304,7 +305,7 @@ public class FeaturesFileTest
   {
     assertEquals("no sequences extracted from GFF3 file", 2,
             dataset.getHeight());
-  
+
     SequenceI seq1 = dataset.findName("seq1");
     SequenceI seq2 = dataset.findName("seq2");
     assertNotNull(seq1);
@@ -335,7 +336,7 @@ public class FeaturesFileTest
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null
                     && dataset.getCodonFrame(seq1).size() > 0);
-  
+
   }
 
   @Test(groups = { "Functional" })
@@ -352,9 +353,8 @@ public class FeaturesFileTest
   public void simpleGff3FileClass() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
-            FormatAdapter.FILE);
-  
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
     boolean parseResult = ffile.parse(dataset, null, false, false);
     assertTrue("return result should be true", parseResult);
     checkDatasetfromSimpleGff3(dataset);
@@ -375,9 +375,8 @@ public class FeaturesFileTest
   public void simpleGff3RelaxedIdMatching() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
-            FormatAdapter.FILE);
-  
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
     boolean parseResult = ffile.parse(dataset, null, false, true);
     assertTrue("return result (relaxedID matching) should be true",
             parseResult);
@@ -408,8 +407,7 @@ public class FeaturesFileTest
      * first with no features displayed
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
-    Map<String, FeatureColourI> visible = fr
-            .getDisplayedFeatureCols();
+    Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
     String exported = featuresFile.printJalviewFormat(
             al.getSequencesArray(), visible);
     String expected = "No Features Visible";