FileFormatI further tweaks, clean compile

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 04d68e8..e0a607b 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -78,58 +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", "PHYLIP", "JSON",
-      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", "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" };
+  // 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",
-      "PHYLIP", "JSON" };
+  // 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", "phy", "json", "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",
-      "PHYLIP", "JSON", "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()
   {
@@ -148,19 +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();
   }
 
@@ -224,29 +227,28 @@ public class AppletFormatAdapter
       {
         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);
+      // 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 '"
-              + fileFormat
-              + "' reader.\n" + e);
+              + fileFormat + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
@@ -666,8 +668,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        FileFormatI idformat = new IdentifyFile().identify(file,
-                protocol);
+        FileFormatI idformat = new IdentifyFile().identify(file, protocol);
         if (idformat == null)
         {
           if (debug)