statalign.io.input.plugins
Class PDBReader

java.lang.Object
  statalign.io.input.DataReader
      statalign.io.input.plugins.PDBReader

public class PDBReader
extends DataReader

Field Summary

static java.util.HashMap<java.lang.String,java.lang.String>	mp13
java.util.HashMap<java.lang.String,java.lang.String>	mp31

Constructor Summary

PDBReader()

Method Summary

java.lang.String	oneLetter(java.lang.String threeLetter)
ProteinSkeletons	read(java.io.Reader reader)
java.util.List<java.lang.String>	supportedExtensions() DataReader plugins must override this to return a list of supported file extensions.
static void	writePDB(double[][][] coors, java.lang.String[] seqs, java.lang.String[] names, java.io.FileWriter fw)

Methods inherited from class statalign.io.input.DataReader

read, read, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

mp31

public java.util.HashMap<java.lang.String,java.lang.String> mp31

mp13

public static java.util.HashMap<java.lang.String,java.lang.String> mp13

Constructor Detail

PDBReader

public PDBReader()

Method Detail

supportedExtensions

public java.util.List<java.lang.String> supportedExtensions()

Description copied from class: DataReader

DataReader plugins must override this to return a list of supported file extensions.

Specified by:

supportedExtensions in class DataReader

Returns:

a list of all lower case file extensions supported by this plugin

read

public ProteinSkeletons read(java.io.Reader reader)
                      throws java.io.IOException

Specified by:

read in class DataReader

Throws:

java.io.IOException

writePDB

public static void writePDB(double[][][] coors,
                            java.lang.String[] seqs,
                            java.lang.String[] names,
                            java.io.FileWriter fw)
                     throws java.io.IOException

Throws:

java.io.IOException

oneLetter

public java.lang.String oneLetter(java.lang.String threeLetter)