JAL-4021 todo & fix FileFormat tests

diff --git a/src/jalview/ext/forester/io/PhyloXmlFile.java b/src/jalview/ext/forester/io/PhyloXmlFile.java
index 3cb3223..3d04fe5 100644 (file)
--- a/src/jalview/ext/forester/io/PhyloXmlFile.java
+++ b/src/jalview/ext/forester/io/PhyloXmlFile.java
@@ -21,7 +21,7 @@ public class PhyloXmlFile extends AlignFile
   @Override
   public String print(SequenceI[] seqs, boolean jvsuffix)
   {
-    // TODO Auto-generated method stub
+    // TODO JAL-4021 - not yet implemented
     return null;
   }
 

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 361d699..889ab1b 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -437,7 +437,7 @@ public enum FileFormat implements FileFormatI
   // }
   //
   // },
-  PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, true)
+  PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, false)
   {
 
     @Override
@@ -450,6 +450,7 @@ public enum FileFormat implements FileFormatI
     @Override
     public AlignmentFileWriterI getWriter(AlignmentI al)
     {
+      // TODO: JAL-4021
       // handle within Aptx?
       return null;
     }

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 27cfa5e..3d2c316 100644 (file)
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -78,7 +78,7 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetReadableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, PhyloXML]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -97,14 +97,14 @@ public class FileFormatsTest
   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, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, PhyloXML]";
     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, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, PhyloXML]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -113,7 +113,7 @@ public class FileFormatsTest
      */
     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, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, PhyloXML, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }