compbio.data.sequence

Class RNAStructReader

java.lang.Object

compbio.data.sequence.RNAStructReader

public class RNAStructReader
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static class	RNAStructReader.AlifoldLine
static class	RNAStructReader.AlifoldResult
(package private) static class	RNAStructReader.RNAOut

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static java.lang.String	alignmentP
(package private) static java.lang.String	bracket
(package private) static java.lang.String	centStructP
(package private) static java.lang.String	energyP
(package private) static java.lang.String	ensembleFreqP
(package private) static java.lang.String	floatP
(package private) static java.lang.String	freeEnergyP
(package private) static java.lang.String	freqP
(package private) static java.lang.String	justStructP
(package private) static java.lang.String	MEAStructP
(package private) static java.lang.String	mfeStructP
(package private) static java.lang.String	notData
(package private) static java.lang.String	ps
(package private) static java.lang.String	PStructP
(package private) static java.lang.String	s
(package private) static java.lang.String	seqP
(package private) static java.lang.String	stochBTStructP
(package private) static java.lang.String	structP

Constructor Summary

Constructors

Constructor and Description
RNAStructReader()

Method Summary

Modifier and Type	Method and Description
private static RNAStructReader.RNAOut	identify(java.lang.String token)
private static RNAStructReader.AlifoldLine	identifyLine(java.lang.String line)
static void	main(java.lang.String[] args)
static java.util.TreeSet<Score>	newEmptyScore(java.lang.Enum<?> res)
private static java.util.TreeSet<Score>	newSetScore(java.lang.Enum<?> res, java.util.List<java.lang.Float> scores)
static RNAStructScoreManager	readRNAStructStream(java.io.InputStream stdout)
static RNAStructScoreManager	readRNAStructStream(java.io.InputStream stdout, java.io.InputStream alifold)

Methods inherited from class java.lang.Object

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

Field Detail

s

static java.lang.String s

bracket

static java.lang.String bracket

notData

static java.lang.String notData

seqP

static java.lang.String seqP

structP

static java.lang.String structP

floatP

static java.lang.String floatP

energyP

static java.lang.String energyP

freqP

static java.lang.String freqP

ps

static java.lang.String ps

alignmentP

static java.lang.String alignmentP

mfeStructP

static java.lang.String mfeStructP

justStructP

static java.lang.String justStructP

stochBTStructP

static java.lang.String stochBTStructP

PStructP

static java.lang.String PStructP

centStructP

static java.lang.String centStructP

MEAStructP

static java.lang.String MEAStructP

freeEnergyP

static java.lang.String freeEnergyP

ensembleFreqP

static java.lang.String ensembleFreqP

Constructor Detail

RNAStructReader

public RNAStructReader()

Method Detail

readRNAStructStream

public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout)
                                                 throws java.io.IOException

Throws:

java.io.IOException

newSetScore

private static java.util.TreeSet<Score> newSetScore(java.lang.Enum<?> res,
                                                    java.util.List<java.lang.Float> scores)

newEmptyScore

public static java.util.TreeSet<Score> newEmptyScore(java.lang.Enum<?> res)

readRNAStructStream

public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout,
                                                        java.io.InputStream alifold)
                                                 throws java.io.IOException

Throws:

java.io.IOException

identify

private static RNAStructReader.RNAOut identify(java.lang.String token)

identifyLine

private static RNAStructReader.AlifoldLine identifyLine(java.lang.String line)

main

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