+
+ @Override
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat,
+ StructureImportSettings.TFType tempfacType) throws IOException
+ {
+ AlignmentI al = super.readFile(selectedFile, file, sourceType,
+ fileFormat, tempfacType);
+ return al;
+ }
+
+ @Override
+ public AlignmentI readFile(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ AlignmentI al = super.readFile(file, sourceType, fileFormat);
+ return al;
+ }
+
+ public AlignmentI readFile(File file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+ return al;
+ }
+
+ @Override
+ public AlignmentI readFromFile(FileParse source, FileFormatI format)
+ throws IOException
+ {
+ AlignmentI al = super.readFromFile(source, format);
+ return al;
+ }
+
+ /**
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
+ * @param format
+ * @param ap
+ * alignment panel originating the view
+ * @return String containing flat file
+ */
+ public String formatSequences(FileFormatI format, AlignmentViewPanel ap,
+ boolean selectedOnly)
+ {
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
+ }
+
+ public AlignmentI readFromFile(AlignmentFileReaderI source,
+ FileFormatI format) throws IOException
+ {
+ FileParse fp = new FileParse(source.getInFile(),
+ source.getDataSourceType());
+ return readFromFile(fp, format);
+ }
+