X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileFormat.java;h=889ab1b5a3adace6d3f33dee85258edbe7011c02;hb=556647d95b0a68273fce9ade5ff97f1de9292b2c;hp=a7113f637bd2ca03625026c2c8328e30050c8a86;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index a7113f6..889ab1b 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -1,33 +1,47 @@
+/*
+ * 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;
-import java.util.HashMap;
-import java.util.Map;
-
 public enum FileFormat implements FileFormatI
 {
-  Fasta("FASTA", "fa, fasta, mfa, fastq", true, true)
+  Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new FastaFile(inFile, sourceType);
-    }
-
-    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new FastaFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new FastaFile();
     }
@@ -35,44 +49,31 @@ public enum FileFormat implements FileFormatI
   Pfam("PFAM", "pfam", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new PfamFile(inFile, sourceType);
-    }
-
-    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new PfamFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PfamFile();
     }
   },
-  Stockholm("STH", "sto,stk", true, true)
+  Stockholm("Stockholm", "sto,stk", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new StockholmFile(inFile, sourceType);
-    }
-    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new StockholmFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
-      return new StockholmFile();
+      return new StockholmFile(al);
     }
 
   },
@@ -80,20 +81,14 @@ public enum FileFormat implements FileFormatI
   PIR("PIR", "pir", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new PIRFile(inFile, sourceType);
-    }
-    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new PIRFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PIRFile();
     }
@@ -101,39 +96,44 @@ public enum FileFormat implements FileFormatI
   BLC("BLC", "BLC", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new BLCFile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new BLCFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new BLCFile();
     }
   },
-  Html("HTML", "html", true, false)
+  AMSA("AMSA", "amsa", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
-      return new HtmlFile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+      return new AMSAFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new AMSAFile(al);
+    }
+  },
+  Html("HTML", "html", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new HtmlFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new HtmlFile();
     }
@@ -148,40 +148,30 @@ public enum FileFormat implements FileFormatI
   Rnaml("RNAML", "xml,rnaml", true, false)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new RnamlFile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new RnamlFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new RnamlFile();
     }
 
   },
-  Json("JSON","json", true, true)
+  Json("JSON", "json", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new JSONFile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new JSONFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JSONFile();
     }
@@ -193,22 +183,17 @@ public enum FileFormat implements FileFormatI
     }
 
   },
-  Pileup("PileUp", "?", false, false)
+  Pileup("PileUp", "pileup", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new PileUpfile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new PileUpfile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PileUpfile();
     }
@@ -217,40 +202,30 @@ public enum FileFormat implements FileFormatI
   MSF("MSF", "msf", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new MSFfile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new MSFfile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new MSFfile();
     }
 
   },
-  Clustal("CLUSTAL", "aln", true, true)
+  Clustal("Clustal", "aln", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new ClustalFile(inFile, sourceType);
-    }    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new ClustalFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new ClustalFile();
     }
@@ -258,38 +233,53 @@ public enum FileFormat implements FileFormatI
   Phylip("PHYLIP", "phy", true, true)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
-      return new PhylipFile(inFile, sourceType);
+      return new PhylipFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new PhylipFile();
+    }
+  },
+  GenBank("GenBank Flatfile", "gb, gbk", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
-      return new PhylipFile(source);
+      return new GenBankFile(source, "GenBank");
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
-      return new PhylipFile();
+      return null;
     }
   },
-  Jnet("JnetFile", "", false, false)
+  Embl("ENA Flatfile", "txt", true, false)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
-      JPredFile af = new JPredFile(inFile, sourceType);
-      af.removeNonSequences();
-      return af;
+      // Always assume we import from EMBL for now
+      return new EmblFlatFile(source, DBRefSource.EMBL);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
+  Jnet("JnetFile", "", false, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       JPredFile af = new JPredFile(source);
@@ -298,84 +288,58 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null; // todo is this called?
     }
 
   },
-  Features("GFF or Jalview features", "gff2,gff3", false, false)
+  Features("GFF or Jalview features", "gff2,gff3", true, false)
   {
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
-    {
-      return new FeaturesFile(true, inFile, sourceType);
-    }
-
-    @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       return new FeaturesFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new FeaturesFile();
     }
   },
-  PDB("PDB", "", false, false)
+  ScoreMatrix("Substitution matrix", "", false, false)
   {
-
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
-      // TODO obtain config value from preference settings.
-      // Set value to 'true' to test PDB processing with Jmol: JAL-1213
-      boolean isParseWithJMOL = StructureImportSettings
-              .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
-      if (isParseWithJMOL)
-      {
-        return new JmolParser(
-                StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isProcessSecondaryStructure(),
-                StructureImportSettings.isExternalSecondaryStructure(),
-                inFile,
-                sourceType);
-      }
-      else
-      {
-        StructureImportSettings.setShowSeqFeatures(true);
-        return new MCview.PDBfile(
-                StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isProcessSecondaryStructure(),
-                StructureImportSettings.isExternalSecondaryStructure(),
-                inFile,
-                sourceType);
-      }
+      return new ScoreMatrixFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
+  PDB("PDB", "pdb,ent", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
       boolean isParseWithJMOL = StructureImportSettings
               .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
       if (isParseWithJMOL)
       {
-        return new JmolParser(
-                StructureImportSettings.isVisibleChainAnnotation(),
-                StructureImportSettings.isProcessSecondaryStructure(),
-                StructureImportSettings.isExternalSecondaryStructure(),
-                source);
+        return new JmolParser(source);
       }
       else
       {
         StructureImportSettings.setShowSeqFeatures(true);
-        return new MCview.PDBfile(
+        return new mc_view.PDBfile(
                 StructureImportSettings.isVisibleChainAnnotation(),
                 StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),
@@ -384,79 +348,126 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
-  },
-  MMCif("mmCIF", "cif", false, false)
-  {
 
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
+    public boolean isStructureFile()
     {
-      return new JmolParser(
-              StructureImportSettings.isVisibleChainAnnotation(),
-              StructureImportSettings.isProcessSecondaryStructure(),
-              StructureImportSettings.isExternalSecondaryStructure(),
-              inFile, sourceType);
+      return true;
     }
-
+  },
+  MMCif("mmCIF", "cif", true, false)
+  {
     @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public AlignmentFileReaderI getReader(FileParse source)
             throws IOException
     {
-      return new JmolParser(
-              StructureImportSettings.isVisibleChainAnnotation(),
-              StructureImportSettings.isProcessSecondaryStructure(),
-              StructureImportSettings.isExternalSecondaryStructure(),
-              source);
+      return new JmolParser(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
+
+    @Override
+    public boolean isStructureFile()
+    {
+      return true;
+    }
   },
-  Jalview("Jalview", "jar,jvp", true, false)
+  Jalview("Jalview", "jvp, jar", true, true)
   {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return null;
+    }
 
     @Override
-    public AlignmentFileI getAlignmentFile(String inFile,
-            DataSourceType sourceType) throws IOException
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null;
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile(FileParse source)
+    public boolean isTextFormat()
+    {
+      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 null;
+      return new PhyloXmlFile(source);
     }
 
     @Override
-    public AlignmentFileI getAlignmentFile()
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
+      // TODO: JAL-4021
+      // handle within Aptx?
       return null;
     }
-  };
 
-  /**
-   * A lookup map of enums by upper-cased name
-   */
-  private static Map<String, FileFormat> names;
-  static
-  {
-    names = new HashMap<String, FileFormat>();
-    for (FileFormat format : FileFormat.values())
+    @Override
+    public boolean isTextFormat()
     {
-      names.put(format.toString().toUpperCase(), format);
+      return true;
     }
-  }
 
+    @Override
+    public boolean isTreeFile()
+    {
+      return true;
+    }
+
+  };
   private boolean writable;
 
   private boolean readable;
@@ -472,27 +483,6 @@ public enum FileFormat implements FileFormatI
   }
 
   @Override
-  public String getShortDescription()
-  {
-    return toString();
-  }
-
-  /**
-   * Returns the file format with the given name, or null if format is null or
-   * invalid. Unlike valueOf(), this is not case-sensitive, to be kind to
-   * writers of javascript.
-   * 
-   * @param format
-   * @return
-   */
-  public static FileFormatI forName(String format)
-  {
-    // or could store format.getShortDescription().toUpperCase()
-    // in order to decouple 'given name' from enum name
-    return format == null ? null : names.get(format.toUpperCase());
-  }
-
-  @Override
   public boolean isReadable()
   {
     return readable;
@@ -511,7 +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)
@@ -527,4 +520,42 @@ public enum FileFormat implements FileFormatI
   {
     return extensions;
   }
+
+  /**
+   * Answers the display name of the file format (as for example shown in menu
+   * options). This name should not be locale (language) dependent.
+   */
+  @Override
+  public String getName()
+  {
+    return name;
+  }
+
+  @Override
+  public boolean isTextFormat()
+  {
+    return true;
+  }
+
+  @Override
+  public boolean isStructureFile()
+  {
+    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;
+  }
 }