JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,

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

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 6d7042d..5a95a9e 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -12,13 +12,14 @@ 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 +27,14 @@ 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 +42,14 @@ 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 +59,14 @@ 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 +74,14 @@ 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 +89,14 @@ 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 +104,14 @@ 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 +126,14 @@ 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 +142,14 @@ 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 +164,14 @@ 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 +180,14 @@ 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 +196,14 @@ 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 +211,14 @@ 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 +226,8 @@ 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 +235,7 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null; // todo is this called?
     }
@@ -230,13 +244,14 @@ 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();
     }
@@ -244,7 +259,8 @@ public enum FileFormat implements FileFormatI
   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 +280,7 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
@@ -278,13 +294,14 @@ 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?
     }
@@ -298,13 +315,14 @@ public enum FileFormat implements FileFormatI
   Jalview("Jalview", "jar,jvp", 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;
     }