X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=74fd4224d6da25c5e743eac892d330f4da40e826;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=2243a5c9f6ed034f8d8d158d9b54aa19abf5cc7a;hpb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2243a5c..74fd422 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -27,8 +27,9 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
-import jalview.util.MessageManager;
 
 import java.io.File;
 import java.io.IOException;
@@ -48,14 +49,6 @@ public class AppletFormatAdapter
 {
   private AlignmentViewPanel viewpanel;
 
-  public static String FILE = "File";
-
-  public static String URL = "URL";
-
-  public static String PASTE = "Paste";
-
-  public static String CLASSLOADER = "ClassLoader";
-
   /**
    * add jalview-derived non-secondary structure annotation from PDB structure
    */
@@ -71,7 +64,7 @@ public class AppletFormatAdapter
    */
   boolean serviceSecondaryStruct = false;
 
-  private AlignFile alignFile = null;
+  private AlignmentFileI alignFile = null;
 
   String inFile;
 
@@ -85,58 +78,59 @@ public class AppletFormatAdapter
   /**
    * List of valid format strings used in the isValidFormat method
    */
-  public static final String[] READABLE_FORMATS = new String[] { "BLC",
-      "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
-      "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
-      IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
+  // public static final String[] READABLE_FORMATS = new String[] { "BLC",
+  // "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
+  // "JnetFile", "RNAML", "PHYLIP", "JSON",
+  // IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
 
   /**
    * List of readable format file extensions by application in order
    * corresponding to READABLE_FNAMES
    */
-  public static final String[] READABLE_EXTENSIONS = new String[] {
-      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
-      ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT, "cif" };
-
-  /**
-   * List of readable formats by application in order corresponding to
-   * READABLE_EXTENSIONS
-   */
-  public static final String[] READABLE_FNAMES = new String[] { "Fasta",
-      "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
-      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
-      "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
+  // public static final String[] READABLE_EXTENSIONS = new String[] {
+  // "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  // "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp",
+  // "html", "cif" };
+
+  //
+  // /**
+  // * List of readable formats by application in order corresponding to
+  // * READABLE_EXTENSIONS
+  // */
+  // public static final String[] READABLE_FNAMES = new String[] { "Fasta",
+  // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
+  // "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
+  // "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
    * method
    */
-  public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
-      "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
-      PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
+  // public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
+  // "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
+  // "PHYLIP", "JSON" };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * that are writable by the application.
    */
-  public static final String[] WRITABLE_EXTENSIONS = new String[] {
-      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
+  // public static final String[] WRITABLE_EXTENSIONS = new String[] {
+  // "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  // "sto,stk", "phy", "json", "jvp" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
-  public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
-      "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
-      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
+  // public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
+  // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP",
+  // "JSON", "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
   // TODO: make these messages dynamic
   public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
-          + prettyPrint(READABLE_FORMATS);
+          + prettyPrint(FileFormat.getReadableFormats());
 
   public AppletFormatAdapter()
   {
@@ -155,19 +149,21 @@ public class AppletFormatAdapter
   }
 
   /**
-   *
-   * @param els
-   * @return grammatically correct(ish) list consisting of els elements.
+   * Formats a grammatically correct(ish) list consisting of the given objects
+   * 
+   * @param things
+   * @return
    */
-  public static String prettyPrint(String[] els)
+  public static String prettyPrint(List<? extends Object> things)
   {
     StringBuffer list = new StringBuffer();
-    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
+    for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
     {
-      list.append(els[i]);
+      list.append(things.get(i).toString());
       list.append(", ");
     }
-    list.append(" and " + els[els.length - 1] + ".");
+    // could i18n 'and' here
+    list.append(" and " + things.get(things.size() - 1).toString() + ".");
     return list.toString();
   }
 
@@ -182,115 +178,34 @@ public class AppletFormatAdapter
   }
 
   /**
-   * check that this format is valid for reading
-   *
-   * @param format
-   *          a format string to be compared with READABLE_FORMATS
-   * @return true if format is readable
-   */
-  public static final boolean isValidFormat(String format)
-  {
-    return isValidFormat(format, false);
-  }
-
-  /**
-   * validate format is valid for IO
-   *
-   * @param format
-   *          a format string to be compared with either READABLE_FORMATS or
-   *          WRITEABLE_FORMATS
-   * @param forwriting
-   *          when true, format is checked for containment in WRITEABLE_FORMATS
-   * @return true if format is valid
-   */
-  public static final boolean isValidFormat(String format,
-          boolean forwriting)
-  {
-    if (format == null)
-    {
-      return false;
-    }
-    boolean valid = false;
-    String[] format_list = (forwriting) ? WRITEABLE_FORMATS
-            : READABLE_FORMATS;
-    for (String element : format_list)
-    {
-      if (element.equalsIgnoreCase(format))
-      {
-        return true;
-      }
-    }
-
-    return valid;
-  }
-
-  /**
    * Constructs the correct filetype parser for a characterised datasource
    *
    * @param inFile
    *          data/data location
-   * @param type
+   * @param sourceType
    *          type of datasource
-   * @param format
-   *          File format of data provided by datasource
+   * @param fileFormat
    *
-   * @return DOCUMENT ME!
+   * @return
    */
-  public AlignmentI readFile(String inFile, String type, String format)
-          throws java.io.IOException
+  public AlignmentI readFile(String file, DataSourceType sourceType,
+          FileFormatI fileFormat) throws IOException
   {
-    // TODO: generalise mapping between format string and io. class instances
-    // using Constructor.invoke reflection
-    this.inFile = inFile;
+    this.inFile = file;
     try
     {
-      if (format.equals("FASTA"))
-      {
-        alignFile = new FastaFile(inFile, type);
-      }
-      else if (format.equals("MSF"))
+      if (FileFormat.PDB.equals(fileFormat)
+              || FileFormat.MMCif.equals(fileFormat))
       {
-        alignFile = new MSFfile(inFile, type);
-      }
-      else if (format.equals("PileUp"))
-      {
-        alignFile = new PileUpfile(inFile, type);
-      }
-      else if (format.equals("CLUSTAL"))
-      {
-        alignFile = new ClustalFile(inFile, type);
-      }
-      else if (format.equals("BLC"))
-      {
-        alignFile = new BLCFile(inFile, type);
-      }
-      else if (format.equals("PIR"))
-      {
-        alignFile = new PIRFile(inFile, type);
-      }
-      else if (format.equals("PFAM"))
-      {
-        alignFile = new PfamFile(inFile, type);
-      }
-      else if (format.equals("JnetFile"))
-      {
-        alignFile = new JPredFile(inFile, type);
-        ((JPredFile) alignFile).removeNonSequences();
-      }
-      else if (format.equals("PDB"))
-      {
-        // TODO obtain config value from preference settings.
-        // Set value to 'true' to test PDB processing with Jmol: JAL-1213
         boolean isParseWithJMOL = StructureImportSettings
-                .getDefaultPDBFileParser()
-                .equals(StructureImportSettings.StructureParser.JMOL_PARSER);
+                .getDefaultPDBFileParser().equalsIgnoreCase(
+                        StructureImportSettings.StructureParser.JMOL_PARSER
+                                .toString());
         if (isParseWithJMOL)
         {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  type);
+          alignFile = new JmolParser(inFile,                  sourceType);
         }
         else
         {
@@ -299,85 +214,70 @@ public class AppletFormatAdapter
           StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  type);
+                  sourceType);
         }
-        ((StructureFile) alignFile).setDbRefType(format);
-      }
-      else if (format.equals("mmCIF"))
-      {
-        StructureImportSettings.addSettings(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
-        ((StructureFile) alignFile).setDbRefType(format);
+        ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
+                .equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
-      else if (format.equals("STH"))
-      {
-        alignFile = new StockholmFile(inFile, type);
-      }
-      else if (format.equals("SimpleBLAST"))
-      {
-        alignFile = new SimpleBlastFile(inFile, type);
-      }
-      else if (format.equals(PhylipFile.FILE_DESC))
-      {
-        alignFile = new PhylipFile(inFile, type);
-      }
-      else if (format.equals(JSONFile.FILE_DESC))
-      {
-        alignFile = new JSONFile(inFile, type);
-      }
-      else if (format.equals(HtmlFile.FILE_DESC))
-      {
-        alignFile = new HtmlFile(inFile, type);
-      }
-      else if (format.equals("RNAML"))
-      {
-        alignFile = new RnamlFile(inFile, type);
-      }
-      else if (format.equals(IdentifyFile.FeaturesFile))
+      else
       {
-        alignFile = new FeaturesFile(true, inFile, type);
-      }
-      return buildAlignmentFrom(alignFile);
+        alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+      }
+      // new FastaFile(inFile, sourceType);
+      // new MSFfile(inFile, sourceType);
+      // new PileUpfile(inFile, sourceType);
+      // new ClustalFile(inFile, sourceType);
+      // new BLCFile(inFile, sourceType);
+      // new PIRFile(inFile, sourceType);
+      // new PfamFile(inFile, sourceType);
+      // alignFile = new JPredFile(inFile, sourceType);
+      // ((JPredFile) alignFile).removeNonSequences();
+      // new StockholmFile(inFile, sourceType);
+      // new SimpleBlastFile(inFile, sourceType);
+      // new PhylipFile(inFile, sourceType);
+      // new JSONFile(inFile, sourceType);
+      // new HtmlFile(inFile, sourceType);
+      // new RnamlFile(inFile, sourceType);
+      // alignFile = new FeaturesFile(true, inFile, sourceType);
+      return buildAlignmentFromFile();
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format
-              + "' reader.\n" + e);
+      System.err.println("Failed to read alignment using the '"
+              + fileFormat + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
-        throw new java.io.IOException(e.getMessage());
+        throw new IOException(e.getMessage());
       }
 
       // Finally test if the user has pasted just the sequence, no id
-      if (type.equalsIgnoreCase("Paste"))
+      if (sourceType == DataSourceType.PASTE)
       {
         try
         {
           // Possible sequence is just residues with no label
-          alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-          return buildAlignmentFrom(alignFile);
+          alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+                  DataSourceType.PASTE);
+          return buildAlignmentFromFile();
 
         } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
-            throw new java.io.IOException(e.getMessage());
+            throw new IOException(e.getMessage());
           }
 
           ex.printStackTrace();
         }
       }
-      if (format.equalsIgnoreCase("HTML"))
+      if (FileFormat.Html.equals(fileFormat))
       {
         throw new IOException(e.getMessage());
       }
-      // If we get to this stage, the format was not supported
-      throw new java.io.IOException(SUPPORTED_FORMATS);
     }
+    throw new FileFormatException(SUPPORTED_FORMATS);
   }
 
   /**
@@ -388,53 +288,16 @@ public class AppletFormatAdapter
    * @param format
    *          File format of data that will be provided by datasource
    *
-   * @return DOCUMENT ME!
+   * @return
    */
-  public AlignmentI readFromFile(FileParse source, String format)
-          throws java.io.IOException
+  public AlignmentI readFromFile(FileParse source, FileFormatI format)
+          throws IOException
   {
-    // TODO: generalise mapping between format string and io. class instances
-    // using Constructor.invoke reflection
-    // This is exactly the same as the readFile method except we substitute
-    // 'inFile, type' with 'source'
     this.inFile = source.getInFile();
-    String type = source.type;
+    DataSourceType type = source.dataSourceType;
     try
     {
-      if (format.equals("FASTA"))
-      {
-        alignFile = new FastaFile(source);
-      }
-      else if (format.equals("MSF"))
-      {
-        alignFile = new MSFfile(source);
-      }
-      else if (format.equals("PileUp"))
-      {
-        alignFile = new PileUpfile(source);
-      }
-      else if (format.equals("CLUSTAL"))
-      {
-        alignFile = new ClustalFile(source);
-      }
-      else if (format.equals("BLC"))
-      {
-        alignFile = new BLCFile(source);
-      }
-      else if (format.equals("PIR"))
-      {
-        alignFile = new PIRFile(source);
-      }
-      else if (format.equals("PFAM"))
-      {
-        alignFile = new PfamFile(source);
-      }
-      else if (format.equals("JnetFile"))
-      {
-        alignFile = new JPredFile(source);
-        ((JPredFile) alignFile).removeNonSequences();
-      }
-      else if (format.equals("PDB"))
+      if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
       {
         // TODO obtain config value from preference settings
         boolean isParseWithJMOL = false;
@@ -442,8 +305,7 @@ public class AppletFormatAdapter
         {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, source);
+          alignFile = new JmolParser(source);
         }
         else
         {
@@ -453,44 +315,12 @@ public class AppletFormatAdapter
         }
         ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
-      else if (format.equals("mmCIF"))
-      {
-        StructureImportSettings.addSettings(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct);
-        alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
-                localSecondaryStruct, serviceSecondaryStruct, source);
-        ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
-      }
-      else if (format.equals("STH"))
-      {
-        alignFile = new StockholmFile(source);
-      }
-      else if (format.equals("RNAML"))
-      {
-        alignFile = new RnamlFile(source);
-      }
-      else if (format.equals("SimpleBLAST"))
-      {
-        alignFile = new SimpleBlastFile(source);
-      }
-      else if (format.equals(PhylipFile.FILE_DESC))
-      {
-        alignFile = new PhylipFile(source);
-      }
-      else if (format.equals(IdentifyFile.FeaturesFile))
-      {
-        alignFile = new FeaturesFile(inFile, type);
-      }
-      else if (format.equals(JSONFile.FILE_DESC))
-      {
-        alignFile = new JSONFile(source);
-      }
-      else if (format.equals(HtmlFile.FILE_DESC))
+      else
       {
-        alignFile = new HtmlFile(source);
+        alignFile = format.getAlignmentFile(source);
       }
 
-      return buildAlignmentFrom(alignFile);
+      return buildAlignmentFromFile();
 
     } catch (Exception e)
     {
@@ -501,23 +331,24 @@ public class AppletFormatAdapter
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
-        throw new java.io.IOException(e.getMessage());
+        throw new FileFormatException(e.getMessage());
       }
 
       // Finally test if the user has pasted just the sequence, no id
-      if (type.equalsIgnoreCase("Paste"))
+      if (type == DataSourceType.PASTE)
       {
         try
         {
           // Possible sequence is just residues with no label
-          alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-          return buildAlignmentFrom(alignFile);
+          alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+                  DataSourceType.PASTE);
+          return buildAlignmentFromFile();
 
         } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
-            throw new java.io.IOException(e.getMessage());
+            throw new IOException(e.getMessage());
           }
 
           ex.printStackTrace();
@@ -525,7 +356,7 @@ public class AppletFormatAdapter
       }
 
       // If we get to this stage, the format was not supported
-      throw new java.io.IOException(SUPPORTED_FORMATS);
+      throw new FileFormatException(SUPPORTED_FORMATS);
     }
   }
 
@@ -533,10 +364,9 @@ public class AppletFormatAdapter
    * boilerplate method to handle data from an AlignFile and construct a new
    * alignment or import to an existing alignment
    * 
-   * @param alignFile2
    * @return AlignmentI instance ready to pass to a UI constructor
    */
-  private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
+  private AlignmentI buildAlignmentFromFile()
   {
     // Standard boilerplate for creating alignment from parser
     // alignFile.configureForView(viewpanel);
@@ -559,7 +389,7 @@ public class AppletFormatAdapter
    * @param selectedOnly
    * @return flatfile in a string
    */
-  public String formatSequences(String format, boolean jvsuffix,
+  public String formatSequences(FileFormatI format, boolean jvsuffix,
           AlignmentViewPanel ap, boolean selectedOnly)
   {
 
@@ -595,86 +425,31 @@ public class AppletFormatAdapter
    *
    * @return alignment flat file contents
    */
-  public String formatSequences(String format, AlignmentI alignment,
+  public String formatSequences(FileFormatI format, AlignmentI alignment,
           boolean jvsuffix)
   {
     try
     {
-      AlignFile afile = null;
-      if (format.equalsIgnoreCase("FASTA"))
-      {
-        afile = new FastaFile();
-      }
-      else if (format.equalsIgnoreCase("MSF"))
-      {
-        afile = new MSFfile();
-      }
-      else if (format.equalsIgnoreCase("PileUp"))
-      {
-        afile = new PileUpfile();
-      }
-      else if (format.equalsIgnoreCase("CLUSTAL"))
-      {
-        afile = new ClustalFile();
-      }
-      else if (format.equalsIgnoreCase("BLC"))
-      {
-        afile = new BLCFile();
-      }
-      else if (format.equalsIgnoreCase("PIR"))
-      {
-        afile = new PIRFile();
-      }
-      else if (format.equalsIgnoreCase("PFAM"))
-      {
-        afile = new PfamFile();
-      }
-      else if (format.equalsIgnoreCase("STH"))
-      {
-        afile = new StockholmFile(alignment);
-      }
-      else if (format.equalsIgnoreCase("AMSA"))
-      {
-        afile = new AMSAFile(alignment);
-      }
-      else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
-      {
-        afile = new PhylipFile();
-      }
-      else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
-      {
-        afile = new JSONFile();
-      }
-      else if (format.equalsIgnoreCase("RNAML"))
-      {
-        afile = new RnamlFile();
-      }
-
-      else
-      {
-        throw new Exception(
-                MessageManager
-                        .getString("error.implementation_error_unknown_file_format_string"));
-      }
+      AlignmentFileI afile = format.getAlignmentFile(alignment);
 
       afile.setNewlineString(newline);
-      afile.addJVSuffix(jvsuffix);
       afile.setExportSettings(exportSettings);
       afile.configureForView(viewpanel);
 
       // check whether we were given a specific alignment to export, rather than
       // the one in the viewpanel
+      SequenceI[] seqs = null;
       if (viewpanel == null || viewpanel.getAlignment() == null
               || viewpanel.getAlignment() != alignment)
       {
-        afile.setSeqs(alignment.getSequencesArray());
+        seqs = alignment.getSequencesArray();
       }
       else
       {
-        afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+        seqs = viewpanel.getAlignment().getSequencesArray();
       }
 
-      String afileresp = afile.print();
+      String afileresp = afile.print(seqs, jvsuffix);
       if (afile.hasWarningMessage())
       {
         System.err.println("Warning raised when writing as " + format
@@ -691,14 +466,14 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public static String checkProtocol(String file)
+  public static DataSourceType checkProtocol(String file)
   {
-    String protocol = FILE;
+    DataSourceType protocol = DataSourceType.FILE;
     String ft = file.toLowerCase().trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
-      protocol = URL;
+      protocol = DataSourceType.URL;
     }
     return protocol;
   }
@@ -719,8 +494,10 @@ public class AppletFormatAdapter
           System.gc();
           long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
-          AlignmentI al = afa.readFile(args[i], FILE,
-                  new IdentifyFile().identify(args[i], FILE));
+          AlignmentI al = afa
+                  .readFile(args[i], DataSourceType.FILE,
+                          new IdentifyFile().identify(args[i],
+                                  DataSourceType.FILE));
           t1 += System.currentTimeMillis();
           System.gc();
           memf += r.totalMemory() - r.freeMemory();
@@ -731,7 +508,7 @@ public class AppletFormatAdapter
             try
             {
               System.out.println(new AppletFormatAdapter().formatSequences(
-                      "FASTA", al, true));
+                      FileFormat.Fasta, al, true));
             } catch (Exception e)
             {
               System.err
@@ -770,16 +547,17 @@ public class AppletFormatAdapter
    * @param format
    * @return protocol that yields the data parsable as the given type
    */
-  public static String resolveProtocol(String file, String format)
+  public static DataSourceType resolveProtocol(String file,
+          FileFormatI format)
   {
     return resolveProtocol(file, format, false);
   }
 
-  public static String resolveProtocol(String file, String format,
-          boolean debug)
+  public static DataSourceType resolveProtocol(String file,
+          FileFormatI format, boolean debug)
   {
     // TODO: test thoroughly!
-    String protocol = null;
+    DataSourceType protocol = null;
     if (debug)
     {
       System.out.println("resolving datasource started with:\n>>file\n"
@@ -803,10 +581,9 @@ public class AppletFormatAdapter
         System.err.println("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
       }
-      ;
       if (rtn)
       {
-        protocol = AppletFormatAdapter.CLASSLOADER;
+        protocol = DataSourceType.CLASSLOADER;
       }
 
     } catch (Exception ex)
@@ -817,12 +594,12 @@ public class AppletFormatAdapter
 
     if (file.indexOf("://") > -1)
     {
-      protocol = AppletFormatAdapter.URL;
+      protocol = DataSourceType.URL;
     }
     else
     {
       // skipping codebase prepend check.
-      protocol = AppletFormatAdapter.FILE;
+      protocol = DataSourceType.FILE;
     }
     FileParse fp = null;
     try
@@ -858,7 +635,7 @@ public class AppletFormatAdapter
       {
         System.out.println("Accessing as paste.");
       }
-      protocol = AppletFormatAdapter.PASTE;
+      protocol = DataSourceType.PASTE;
       fp = null;
       try
       {
@@ -878,7 +655,7 @@ public class AppletFormatAdapter
     {
       return null;
     }
-    if (format == null || format.length() == 0)
+    if (format == null)
     {
       return protocol;
     }
@@ -886,8 +663,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        String idformat = new jalview.io.IdentifyFile().identify(file,
-                protocol);
+        FileFormatI idformat = new IdentifyFile().identify(file, protocol);
         if (idformat == null)
         {
           if (debug)
@@ -926,20 +702,13 @@ public class AppletFormatAdapter
           System.err.println("File deemed not accessible via " + protocol);
           e.printStackTrace();
         }
-        ;
-
       }
     }
     return null;
   }
 
-  public AlignFile getAlignFile()
+  public AlignmentFileI getAlignFile()
   {
     return alignFile;
   }
-
-  public void setAlignFile(AlignFile alignFile)
-  {
-    this.alignFile = alignFile;
-  }
 }