JAL-3106 use .jvp as default

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 6d7042d..e94e1ce 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -12,13 +32,14 @@ public enum FileFormat implements FileFormatI
   Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new FastaFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new FastaFile();
     }
@@ -26,13 +47,14 @@ public enum FileFormat implements FileFormatI
   Pfam("PFAM", "pfam", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PfamFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PfamFile();
     }
@@ -40,13 +62,14 @@ public enum FileFormat implements FileFormatI
   Stockholm("Stockholm", "sto,stk", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new StockholmFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new StockholmFile(al);
     }
@@ -56,13 +79,14 @@ public enum FileFormat implements FileFormatI
   PIR("PIR", "pir", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PIRFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PIRFile();
     }
@@ -70,13 +94,14 @@ public enum FileFormat implements FileFormatI
   BLC("BLC", "BLC", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new BLCFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new BLCFile();
     }
@@ -84,13 +109,14 @@ public enum FileFormat implements FileFormatI
   AMSA("AMSA", "amsa", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new AMSAFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new AMSAFile(al);
     }
@@ -98,13 +124,14 @@ public enum FileFormat implements FileFormatI
   Html("HTML", "html", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new HtmlFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new HtmlFile();
     }
@@ -119,13 +146,14 @@ public enum FileFormat implements FileFormatI
   Rnaml("RNAML", "xml,rnaml", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new RnamlFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new RnamlFile();
     }
@@ -134,13 +162,14 @@ public enum FileFormat implements FileFormatI
   Json("JSON", "json", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new JSONFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JSONFile();
     }
@@ -155,13 +184,14 @@ public enum FileFormat implements FileFormatI
   Pileup("PileUp", "pileup", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PileUpfile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PileUpfile();
     }
@@ -170,13 +200,14 @@ public enum FileFormat implements FileFormatI
   MSF("MSF", "msf", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new MSFfile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new MSFfile();
     }
@@ -185,13 +216,14 @@ public enum FileFormat implements FileFormatI
   Clustal("Clustal", "aln", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new ClustalFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new ClustalFile();
     }
@@ -199,13 +231,14 @@ public enum FileFormat implements FileFormatI
   Phylip("PHYLIP", "phy", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PhylipFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PhylipFile();
     }
@@ -213,7 +246,8 @@ public enum FileFormat implements FileFormatI
   Jnet("JnetFile", "", false, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       JPredFile af = new JPredFile(source);
       af.removeNonSequences();
@@ -221,7 +255,7 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null; // todo is this called?
     }
@@ -230,21 +264,38 @@ public enum FileFormat implements FileFormatI
   Features("GFF or Jalview features", "gff2,gff3", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new FeaturesFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    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 AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       boolean isParseWithJMOL = StructureImportSettings
               .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
@@ -264,7 +315,7 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
@@ -278,13 +329,14 @@ public enum FileFormat implements FileFormatI
   MMCif("mmCIF", "cif", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new JmolParser(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
@@ -295,16 +347,17 @@ public enum FileFormat implements FileFormatI
       return true;
     }
   },
-  Jalview("Jalview", "jar,jvp", true, true)
+  Jalview("Jalview", "jvp, jar", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return null;
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null;
     }
@@ -314,6 +367,12 @@ public enum FileFormat implements FileFormatI
     {
       return false;
     }
+
+    @Override
+    public boolean isIdentifiable()
+    {
+      return false;
+    }
   };
 
   private boolean writable;
@@ -387,4 +446,14 @@ public enum FileFormat implements FileFormatI
   {
     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;
+  }
 }