org.proteinshader.structure.io
Interface StructureReader

All Known Implementing Classes:

PDBStructureReader

public interface StructureReader

StructureReader provides an interface for reading a protein structure from a file.

In this first version of the program, the StructureReader interface has only one concrete implementation, PDBStructureReader, which expects a PDB formatted text file. Future versions of the program will likely also have an XMLStructureReader and an MMCIFStructureReader for reading PDBML/XML and mmCIF formats, respectively.

Method Summary

List<String>	getBadLines() Returns a list with any bad lines that were found the last time readStructure() was called.
Structure	readStructure(File file) Reads a protein structure from a file and returns a Structure object.
Structure	readStructure(String filename) Reads a protein structure from a file and returns a Structure object.

Method Detail

readStructure

Structure readStructure(String filename)
                        throws StructureReaderException

Reads a protein structure from a file and returns a Structure object. A StructureReaderException will be thrown if a problem occurs.

Parameters:

filename - the full name of the file to read.

Returns:

The newly created Structure.

Throws:

StructureReaderException - if an IO error occurs.

readStructure

Structure readStructure(File file)
                        throws StructureReaderException

Reads a protein structure from a file and returns a Structure object. A StructureReaderException will be thrown if a problem occurs.

Parameters:

file - the file to read.

Returns:

The newly created Structure.

Throws:

StructureReaderException - if an IO error occurs.

getBadLines

List<String> getBadLines()

Returns a list with any bad lines that were found the last time readStructure() was called.

Returns:

A list of invalid lines from a PDB formatted file.