reverting FileFormat; moving BSMLFile and related FileFormat to unused

for now.

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index df76c61..cb61740 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -29,21 +29,6 @@ import java.io.IOException;
 
 public enum FileFormat implements FileFormatI
 {
-  BSML("BSML", "bbb", true, false)
-  {
-    @Override
-    public AlignmentFileReaderI getReader(FileParse source)
-            throws IOException
-    {
-      return new BSMLFile(source);
-    }
-
-    @Override
-    public AlignmentFileWriterI getWriter(AlignmentI al)
-    {
-      return null;
-    }
-  },
   Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
   {
     @Override

diff --git a/src/jalview/io/BSMLFile.java b/unused/BSMLFile.java
similarity index 100%
rename from src/jalview/io/BSMLFile.java
rename to unused/BSMLFile.java

diff --git a/unused/FileFormat.java b/unused/FileFormat.java
new file mode 100644 (file)
index 0000000..df76c61
--- /dev/null
+++ b/unused/FileFormat.java
@@ -0,0 +1,474 @@
+/*
+ * 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 jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
+
+import java.io.IOException;
+
+public enum FileFormat implements FileFormatI
+{
+  BSML("BSML", "bbb", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new BSMLFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+  },
+  Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new FastaFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new FastaFile();
+    }
+  },
+  Pfam("PFAM", "pfam", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new PfamFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new PfamFile();
+    }
+  },
+  Stockholm("Stockholm", "sto,stk", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new StockholmFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new StockholmFile(al);
+    }
+
+  },
+
+  PIR("PIR", "pir", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new PIRFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new PIRFile();
+    }
+  },
+  BLC("BLC", "BLC", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new BLCFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new BLCFile();
+    }
+  },
+  AMSA("AMSA", "amsa", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      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 AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new HtmlFile();
+    }
+
+    @Override
+    public boolean isComplexAlignFile()
+    {
+      return true;
+    }
+
+  },
+  Rnaml("RNAML", "xml,rnaml", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new RnamlFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new RnamlFile();
+    }
+
+  },
+  Json("JSON", "json", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new JSONFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new JSONFile();
+    }
+
+    @Override
+    public boolean isComplexAlignFile()
+    {
+      return true;
+    }
+
+  },
+  Pileup("PileUp", "pileup", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new PileUpfile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new PileUpfile();
+    }
+
+  },
+  MSF("MSF", "msf", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new MSFfile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new MSFfile();
+    }
+
+  },
+  Clustal("Clustal", "aln", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new ClustalFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new ClustalFile();
+    }
+  },
+  Phylip("PHYLIP", "phy", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new PhylipFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new PhylipFile();
+    }
+  },
+  Jnet("JnetFile", "", false, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      JPredFile af = new JPredFile(source);
+      af.removeNonSequences();
+      return af;
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null; // todo is this called?
+    }
+
+  },
+  Features("GFF or Jalview features", "gff2,gff3", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new FeaturesFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      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
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      boolean isParseWithJMOL = StructureImportSettings
+              .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
+      if (isParseWithJMOL)
+      {
+        return new JmolParser(source);
+      }
+      else
+      {
+        StructureImportSettings.setShowSeqFeatures(true);
+        return new mc_view.PDBfile(
+                StructureImportSettings.isVisibleChainAnnotation(),
+                StructureImportSettings.isProcessSecondaryStructure(),
+                StructureImportSettings.isExternalSecondaryStructure(),
+                source);
+      }
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new JmolParser(); // todo or null?
+    }
+
+    @Override
+    public boolean isStructureFile()
+    {
+      return true;
+    }
+  },
+  MMCif("mmCIF", "cif", true, false)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new JmolParser(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new JmolParser(); // todo or null?
+    }
+
+    @Override
+    public boolean isStructureFile()
+    {
+      return true;
+    }
+  },
+  Jalview("Jalview", "jvp, jar", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return null;
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return null;
+    }
+
+    @Override
+    public boolean isTextFormat()
+    {
+      return false;
+    }
+
+    @Override
+    public boolean isIdentifiable()
+    {
+      return true;
+    }
+  };
+
+  private boolean writable;
+
+  private boolean readable;
+
+  private String extensions;
+
+  private String name;
+
+  @Override
+  public boolean isComplexAlignFile()
+  {
+    return false;
+  }
+
+  @Override
+  public boolean isReadable()
+  {
+    return readable;
+  }
+
+  @Override
+  public boolean isWritable()
+  {
+    return writable;
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param shortName
+   * @param extensions
+   *          comma-separated list of file extensions associated with the format
+   * @param isReadable
+   * @param isWritable
+   */
+  private FileFormat(String shortName, String extensions,
+          boolean isReadable, boolean isWritable)
+  {
+    this.name = shortName;
+    this.extensions = extensions;
+    this.readable = isReadable;
+    this.writable = isWritable;
+  }
+
+  @Override
+  public String getExtensions()
+  {
+    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;
+  }
+
+  /**
+   * 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;
+  }
+}