- public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar,jvp",
- "sto,stk", "xml,rnaml" }; // ".blast"
+ // 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" };