contextFold.app
Class PredictLib

java.lang.Object
  extended by contextFold.app.PredictLib

public class PredictLib
extends java.lang.Object

Produces secondary structure predictions for a library of RNA sequences, given in a FASTA format.

Usage (from the 'ContextFold' directory):
    "java -cp bin contextFold.app.PredictLib <arg1 name>:X1 <arg2 name>:X2 ...", where Xi is the value to assign for the i-th argument.

Usage examples:
    java -cp bin contextFold.app.PredictLib lib:C:/RNAdata/sequences.txt
    java -cp bin contextFold.app.PredictLib lib:C:/RNAdata/sequences.txt model:trained/StMedCoHigh.model out:predictions/sequences.pred

Required argument:
    lib - Path to a FASTA file, containing the input RNA strings.

Main optional arguments (use the 'man' argument for the complete list):
    man - Prints the usage manual.
    out - Path to the prediction output file (if not specified, a file with the same name as the input file and an the added '.pred' extension will be generated in the same directory as the input file).
    model - Specifies a scoring model (Default: trained/StHighCoHigh.model).
    validate - Validates prediction quality at the end of the run (Allowed values: yes, no (default)).
    echo - Prints progress notifications to screen (Allowed values: yes (default), no, splits, octCounts).
    maxLength - Maximum length of predicted sequences (Default: 2147483647, longer sequences are ignored).
    minLength - Minimum length of predicted sequences (Default: 0, shorter sequences are ignored).


Constructor Summary
PredictLib()
           
 
Method Summary
static void main(java.lang.String[] args)
           
static void predictAll(FeatureManager featureManager, java.lang.String outputPath, java.util.List<RNA> rnas)
           
static void predictAll(FeatureManager featureManager, java.lang.String outputPath, java.util.List<RNA> rnas, java.lang.String echoStr)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PredictLib

public PredictLib()
Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException
Throws:
java.io.IOException

predictAll

public static void predictAll(FeatureManager featureManager,
                              java.lang.String outputPath,
                              java.util.List<RNA> rnas)
                       throws java.io.IOException
Throws:
java.io.IOException

predictAll

public static void predictAll(FeatureManager featureManager,
                              java.lang.String outputPath,
                              java.util.List<RNA> rnas,
                              java.lang.String echoStr)
                       throws java.io.IOException
Throws:
java.io.IOException