JAL-1953 2.11.2 with Archeopteryx!

[jalview.git] / src / jalview / io / FileFormat.java

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index b701963..361d699 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -25,6 +25,7 @@ import java.io.IOException;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
+import jalview.ext.forester.io.PhyloXmlFile;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 
@@ -405,8 +406,67 @@ public enum FileFormat implements FileFormatI
     {
       return true;
     }
-  };
+  },
+  // Nexus("Nexus", "nex,nexus,nx,tre", true, true)
+  // {
+  //
+  // @Override
+  // public AlignmentFileReaderI getReader(FileParse source)
+  // throws IOException
+  // {
+  // return new NexusFile(source);
+  // }
+  //
+  // @Override
+  // public AlignmentFileWriterI getWriter(AlignmentI al)
+  // {
+  // // handle within Aptx?
+  // return null;
+  // }
+  //
+  // @Override
+  // public boolean isTextFormat()
+  // {
+  // return true;
+  // }
+  //
+  // @Override
+  // public boolean isTreeFile()
+  // {
+  // return true;
+  // }
+  //
+  // },
+  PhyloXML("PhyloXML", "phyloxml,phylo.xml,pxml", true, true)
+  {
+
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new PhyloXmlFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      // handle within Aptx?
+      return null;
+    }
+
+    @Override
+    public boolean isTextFormat()
+    {
+      return true;
+    }
+
+    @Override
+    public boolean isTreeFile()
+    {
+      return true;
+    }
 
+  };
   private boolean writable;
 
   private boolean readable;
@@ -482,6 +542,12 @@ public enum FileFormat implements FileFormatI
     return false;
   }
 
+  @Override
+  public boolean isTreeFile()
+  {
+    return false;
+  }
+
   /**
    * By default, answers true, indicating the format is one that can be
    * identified by IdentifyFile. Formats that cannot be identified should