+ public static String PASTE = "Paste";
+
+ public static String CLASSLOADER = "ClassLoader";
+
+ /**
+ * add jalview-derived non-secondary structure annotation from PDB structure
+ */
+ boolean annotFromStructure = false;
+
+ /**
+ * add secondary structure from PDB data with built-in algorithms
+ */
+ boolean localSecondaryStruct = false;
+
+ /**
+ * process PDB data with web services
+ */
+ boolean serviceSecondaryStruct = false;
+
+ private AlignFile alignFile = null;
+
+ String inFile;
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ private AlignExportSettingI exportSettings;
+
+ /**
+ * 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" };
+
+ /**
+ * 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" };
+
+ /**
+ * 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 };
+
+ /**
+ * 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" };
+
+ /**
+ * 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" };