JAL-4021 todo & fix FileFormat tests

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 5a95a9e..889ab1b 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -1,12 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
+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;
 
-import java.io.IOException;
-
 public enum FileFormat implements FileFormatI
 {
   Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
@@ -223,6 +245,37 @@ public enum FileFormat implements FileFormatI
       return new PhylipFile();
     }
   },
+  GenBank("GenBank Flatfile", "gb, gbk", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new GenBankFile(source, "GenBank");
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
+  Embl("ENA Flatfile", "txt", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      // Always assume we import from EMBL for now
+      return new EmblFlatFile(source, DBRefSource.EMBL);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
   Jnet("JnetFile", "", false, false)
   {
     @Override
@@ -256,6 +309,21 @@ public enum FileFormat implements FileFormatI
       return new FeaturesFile();
     }
   },
+  ScoreMatrix("Substitution matrix", "", false, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new ScoreMatrixFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
   PDB("PDB", "pdb,ent", true, false)
   {
     @Override
@@ -271,7 +339,7 @@ public enum FileFormat implements FileFormatI
       else
       {
         StructureImportSettings.setShowSeqFeatures(true);
-        return new MCview.PDBfile(
+        return new mc_view.PDBfile(
                 StructureImportSettings.isVisibleChainAnnotation(),
                 StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
@@ -312,7 +380,7 @@ public enum FileFormat implements FileFormatI
       return true;
     }
   },
-  Jalview("Jalview", "jar,jvp", true, true)
+  Jalview("Jalview", "jvp, jar", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -332,8 +400,74 @@ public enum FileFormat implements FileFormatI
     {
       return false;
     }
-  };
 
+    @Override
+    public boolean isIdentifiable()
+    {
+      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, false)
+  {
+
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new PhyloXmlFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      // TODO: JAL-4021
+      // handle within Aptx?
+      return null;
+    }
+
+    @Override
+    public boolean isTextFormat()
+    {
+      return true;
+    }
+
+    @Override
+    public boolean isTreeFile()
+    {
+      return true;
+    }
+
+  };
   private boolean writable;
 
   private boolean readable;
@@ -367,7 +501,10 @@ public enum FileFormat implements FileFormatI
    * @param extensions
    *          comma-separated list of file extensions associated with the format
    * @param isReadable
+   *          - can be recognised by IdentifyFile and imported with the given
+   *          reader
    * @param isWritable
+   *          - can be exported with the returned writer
    */
   private FileFormat(String shortName, String extensions,
           boolean isReadable, boolean isWritable)
@@ -405,4 +542,20 @@ 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
+   * override this method to return false.
+   */
+  public boolean isIdentifiable()
+  {
+    return true;
+  }
 }