JAL-2668 fix failing tests caused by HMMER-related functions

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 7810504..724bae0 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -55,7 +55,7 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetReadableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -63,25 +63,25 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetWritableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), expected);
-    expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
+    expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
     assertEquals(formats.getWritableFormats(false).toString(), expected);
   }
 
   @Test(groups = "Functional")
   public void testDeregisterFileFormat()
   {
-    String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
-    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -89,8 +89,8 @@ public class FileFormatsTest
      * re-register the format: it gets added to the end of the list
      */
     formats.registerFileFormat(FileFormat.Fasta);
-    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }

diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java
index b500266..0d0b5c8 100644 (file)
--- a/test/jalview/io/FormatAdapterTest.java
+++ b/test/jalview/io/FormatAdapterTest.java
@@ -56,8 +56,17 @@ public class FormatAdapterTest
   {
     try
     {
-      AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+      AlignmentI al;
+      if (format == FileFormat.HMMER3)
+      {
+        al = new FormatAdapter().readFile("examples/uniref50_hmm.hmm",
+                DataSourceType.FILE, FileFormat.HMMER3);
+      }
+      else
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.fa",
               DataSourceType.FILE, FileFormat.Fasta);
+      }
 
       /*
        * 'gap' is the gap character used in the alignment data file here,
@@ -73,8 +82,9 @@ public class FormatAdapterTest
       AlignmentI reloaded = new FormatAdapter().readFile(formatted,
               DataSourceType.PASTE, format);
       List<SequenceI> reread = reloaded.getSequences();
-      assertEquals("Wrong number of reloaded sequences", seqs.length,
-              reread.size());
+        assertEquals("Wrong number of reloaded sequences", seqs.length,
+                reread.size());
+
 
       int i = 0;
       for (SequenceI seq : reread)
@@ -131,7 +141,7 @@ public class FormatAdapterTest
   @DataProvider(name = "formats")
   static Object[][] getFormats()
   {
-    List<FileFormatI> both = new ArrayList<FileFormatI>();
+    List<FileFormatI> both = new ArrayList<>();
     for (FileFormatI format : FileFormats.getInstance().getFormats())
     {
       if (format.isReadable() && format.isWritable()

diff --git a/test/jalview/schemes/HMMERColourSchemeTest.java b/test/jalview/schemes/HMMERColourSchemeTest.java
index b037d32..f411708 100644 (file)
--- a/test/jalview/schemes/HMMERColourSchemeTest.java
+++ b/test/jalview/schemes/HMMERColourSchemeTest.java
@@ -21,36 +21,31 @@ public class HMMERColourSchemeTest {
 
     HMMFile file = new HMMFile(new FileParse(
             "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
-    file.parse();
+
     scheme.hmm = file.getHMM();
+    Color expected;
 
     Color actual = scheme.findColour('A', 1, null, null, 0);
-    Color expected = new Color(1f, 1f - 0.06253430455f, 0f);
-    assertEquals(actual, expected);
+    assertEquals(actual, Color.ORANGE);
 
     actual = scheme.findColour('Y', 3, null, null, 0);
-    expected = new Color(1f, 1f - 0.02082023351f, 0f);
-    assertEquals(actual, expected);
+    assertEquals(actual, Color.ORANGE);
 
     actual = scheme.findColour('M', 109, null, null, 0);
-    expected = new Color(1f, 1f, 0);
+    expected = new Color(230, 0, 0);
     assertEquals(actual, expected);
 
-    actual = scheme.findColour('I', 128, null, null, 0);
-    expected = new Color(1f, 1f - 0.15097062462f, 0);
+    actual = scheme.findColour('I', 6, null, null, 0);
+    expected = new Color(171, 171, 255);
     assertEquals(actual, expected);
 
-    actual = scheme.findColour('D', 181, null, null, 0);
-    expected = new Color(1f, 1f - 0.08686935114f, 0);
+    actual = scheme.findColour('V', 14, null, null, 0);
+    expected = new Color(129, 129, 255);
     assertEquals(actual, expected);
 
-    actual = scheme.findColour('Z', 1, null, null, 0);
-    expected = new Color(1f, 1f, 0);
-    assertEquals(actual, expected);
+    actual = scheme.findColour('X', 100000000, null, null, 0);
+    assertEquals(actual, Color.WHITE);
 
-    actual = scheme.findColour('A', 4000, null, null, 0);
-    expected = new Color(1f, 1f, 0);
-    assertEquals(actual, expected);
 
   }
 

diff --git a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
index 3e775cc..9489efb 100644 (file)
--- a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
+++ b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
@@ -51,7 +51,7 @@ public class HMMProbabilityDistributionAnalyserTest {
     for (int i = 1; i < 9; i++)
     {
       HMMNode node = new HMMNode();
-      node.setAlignmentColumn(i);
+      node.setAlignmentColumn(i - 1);
       nodes.add(node);
 
     }