statalign.postprocess.utils
Class RNAalifold

java.lang.Object
  statalign.postprocess.utils.RNAalifold

public class RNAalifold
extends java.lang.Object

Given an alignment of sequence this class shells to the RNAalifold appropriately and returns a RNAalifold secondary structure prediction.

Field Summary

static java.lang.String

executable

Constructor Summary

RNAalifold()

Method Summary

static boolean	checkRNAalifold()
static RNAalifoldResult	fold(java.util.List<java.lang.String> sequences, java.util.List<java.lang.String> sequenceNames, java.lang.String arguments)
static RNAalifoldResult	fold(java.util.List<java.lang.String> sequences, java.util.List<java.lang.String> sequenceNames, java.lang.String arguments, boolean noErrorMessages)
static RNAalifoldResult	fold(java.util.List<java.lang.String> sequences, java.util.List<java.lang.String> sequenceNames, java.lang.String arguments, boolean useMatrix, boolean noErrorMessages)
static double[][]	loadBasePairProbMatrix(java.io.File basePairFile, int length)
static java.lang.String	loadDotBracketStructure(java.io.File alifoldOut)
static void	main(java.lang.String[] args)
static void	saveClustalW(java.util.List<java.lang.String> sequences, java.util.List<java.lang.String> sequenceNames, java.io.File outFile)

Methods inherited from class java.lang.Object

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

Field Detail

executable

public static java.lang.String executable

Constructor Detail

RNAalifold

public RNAalifold()

Method Detail

checkRNAalifold

public static boolean checkRNAalifold()

fold

public static RNAalifoldResult fold(java.util.List<java.lang.String> sequences,
                                    java.util.List<java.lang.String> sequenceNames,
                                    java.lang.String arguments)
                             throws java.lang.Exception

Throws:

java.lang.Exception

fold

public static RNAalifoldResult fold(java.util.List<java.lang.String> sequences,
                                    java.util.List<java.lang.String> sequenceNames,
                                    java.lang.String arguments,
                                    boolean noErrorMessages)
                             throws java.lang.Exception

Throws:

java.lang.Exception

fold

public static RNAalifoldResult fold(java.util.List<java.lang.String> sequences,
                                    java.util.List<java.lang.String> sequenceNames,
                                    java.lang.String arguments,
                                    boolean useMatrix,
                                    boolean noErrorMessages)
                             throws java.lang.Exception

Throws:

java.lang.Exception

saveClustalW

public static void saveClustalW(java.util.List<java.lang.String> sequences,
                                java.util.List<java.lang.String> sequenceNames,
                                java.io.File outFile)

loadDotBracketStructure

public static java.lang.String loadDotBracketStructure(java.io.File alifoldOut)

loadBasePairProbMatrix

public static double[][] loadBasePairProbMatrix(java.io.File basePairFile,
                                                int length)

main

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