Uses of Class
org.biojava.nbio.alignment.io.StockholmStructure

Packages that use StockholmStructure

Package	Description
org.biojava.nbio.alignment.io

Uses of StockholmStructure in org.biojava.nbio.alignment.io

Methods in org.biojava.nbio.alignment.io that return StockholmStructure

Modifier and Type	Method and Description
StockholmStructure	StockholmFileParser.parse(InputStream inStream) parses InputStream and returns a the first contained alignment in a StockholmStructure object.
StockholmStructure	StockholmFileParser.parse(String filename) Parses a Stockholm file and returns a StockholmStructure object with its content. This function is meant to be used for single access to specific file and it closes the file after doing its assigned job.

Methods in org.biojava.nbio.alignment.io that return types with arguments of type StockholmStructure

Modifier and Type	Method and Description
List<StockholmStructure>	StockholmFileParser.parse(InputStream inStream, int max) parses an InputStream and returns at maximum max objects contained in that file. This method leaves the stream open for further calls of StockholmFileParser.parse(InputStream, int) (same function) or StockholmFileParser.parseNext(int).
List<StockholmStructure>	StockholmFileParser.parse(String filename, int max) Parses a Stockholm file and returns a StockholmStructure object with its content. This function doesn't close the file after doing its assigned job; to allow for further calls of StockholmFileParser.parseNext(int).
List<StockholmStructure>	StockholmFileParser.parseNext(int max) Tries to parse and return as maximum as max structures in the last used file or input stream. Please consider calling either StockholmFileParser.parse(InputStream), StockholmFileParser.parse(InputStream, int), or StockholmFileParser.parse(String, int) before calling this function.