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)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.