contextFold.app
Class Predict
java.lang.Object
contextFold.app.Predict
public class Predict
- extends java.lang.Object
Produces secondary structure predictions for RNA sequences.
Usage (from the 'ContextFold' directory):
    "java -cp bin contextFold.app.Predict <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.Predict in:C:/RNAdata/sequences.txt
    java -cp bin contextFold.app.Predict in:AAGGCCUUGGGGAAGGCCUU
    java -cp bin contextFold.app.Predict in:C:/RNAdata/sequences.txt
model:trained/StMedCoHigh.model out:predictions/sequences.pred
Required argument:
    in - Either a single RNA string, or a path to a file that contains 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).
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 output,
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 |
Predict
public Predict()
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 output,
java.util.List<RNA> rnas,
java.lang.String echoStr)
throws java.io.IOException
- Throws:
java.io.IOException