edu.mssm.crover.tables.readers
Class DSSPTableReader

java.lang.Object
  |
  +--edu.mssm.crover.tables.readers.DSSPTableReader

public class DSSPTableReader

extends java.lang.Object

Reads a DSSP (W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637; http://www.sander.ebi.ac.uk/dssp) file. The most useful information holds in a table.

Constructor Summary

DSSPTableReader()

Method Summary

static int[]	addColumns(Table table, java.io.Reader schema) Build the schema for a DSSP file.
static void	addData(Table table, java.io.Reader data, int[] index)
java.lang.String	getDescription()
java.lang.String	getShortName()
static void	main(java.lang.String[] args)
static void	parseLine(Table t, java.lang.String line, int linenumber, int[] index)
static Table	read(java.io.Reader schema, java.io.InputStream data)
static Table	read(java.io.Reader schema, java.io.Reader data)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DSSPTableReader

public DSSPTableReader()

Method Detail

getShortName

public java.lang.String getShortName()

getDescription

public java.lang.String getDescription()

read

public static Table read(java.io.Reader schema,
                         java.io.InputStream data)
                  throws UnsupportedFormatException,
                         SyntaxErrorException

UnsupportedFormatException

SyntaxErrorException

read

public static Table read(java.io.Reader schema,
                         java.io.Reader data)
                  throws UnsupportedFormatException,
                         SyntaxErrorException

UnsupportedFormatException

SyntaxErrorException

addColumns

public static int[] addColumns(Table table,
                               java.io.Reader schema)
                        throws java.io.IOException,
                               SyntaxErrorException

Build the schema for a DSSP file. Nothing is read from the "schema" file. It is just ignored.

java.io.IOException

SyntaxErrorException

addData

public static void addData(Table table,
                           java.io.Reader data,
                           int[] index)
                    throws SyntaxErrorException,
                           java.io.IOException

SyntaxErrorException

java.io.IOException

parseLine

public static void parseLine(Table t,
                             java.lang.String line,
                             int linenumber,
                             int[] index)
                      throws SyntaxErrorException,
                             java.io.IOException

SyntaxErrorException

java.io.IOException

main

public static void main(java.lang.String[] args)