3 import jalview.datamodel.AlignmentI;
5 import java.io.IOException;
7 public interface FileFormatI
10 AlignmentFileI getAlignmentFile(String inFile, DataSourceType sourceType)
13 // TODO can we get rid of one of these methods?
14 AlignmentFileI getAlignmentFile(FileParse source) throws IOException;
16 AlignmentFileI getAlignmentFile(AlignmentI al);
18 AlignmentFileI getAlignmentFile();
20 boolean isComplexAlignFile();
23 * Returns a comma-separated list of file extensions associated with the
28 String getExtensions();
31 * Answers true if the format is one that Jalview can read. This implies that
32 * the format provides implementations for getAlignmentFile(FileParse) and
33 * getAlignmentFile(String, DataSourceType) which parse the data source for
41 * Answers true if the format is one that Jalview can write. This implies that
42 * the object returned by getAlignmentFile provides an implementation of the
50 * Answers true if the format is one that Jalview can output as text, e.g. to
55 boolean isTextFormat();
58 * Answers true if the file format is one that provides a 3D structure
62 boolean isStructureFile();