compbio.runner

Class RunnerUtil

java.lang.Object

compbio.runner.RunnerUtil

public final class RunnerUtil
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.log4j.Logger	log

Constructor Summary

Constructors

Constructor and Description
RunnerUtil()

Method Summary

Modifier and Type	Method and Description
static <T> PresetManager<T>	getPresets(java.lang.Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
static Alignment	readClustalFile(java.lang.String workDirectory, java.lang.String clustFile)
static java.util.Map<java.lang.String,Score>	readJronnFile(java.lang.String workDirectory, java.lang.String clustFile)
static RNAStructScoreManager	readRNAStruct(java.lang.String workDirectory, java.lang.String structFile)
static void	writeClustalInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec, char gapChar)
static void	writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Methods inherited from class java.lang.Object

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

Field Detail

log

public static org.apache.log4j.Logger log

Constructor Detail

RunnerUtil

public RunnerUtil()

Method Detail

getSupportedOptions

public static <T> RunnerConfig<T> getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)

getPresets

public static <T> PresetManager<T> getPresets(java.lang.Class<? extends Executable<T>> clazz)

readClustalFile

public static final Alignment readClustalFile(java.lang.String workDirectory,
                                              java.lang.String clustFile)
                                       throws UnknownFileFormatException,
                                              java.io.IOException,
                                              java.io.FileNotFoundException,
                                              java.lang.NullPointerException

Throws:

UnknownFileFormatException

java.io.IOException

java.io.FileNotFoundException

java.lang.NullPointerException

readJronnFile

public static final java.util.Map<java.lang.String,Score> readJronnFile(java.lang.String workDirectory,
                                                                        java.lang.String clustFile)
                                                                 throws UnknownFileFormatException,
                                                                        java.io.IOException,
                                                                        java.io.FileNotFoundException,
                                                                        java.lang.NullPointerException

Throws:

UnknownFileFormatException

java.io.IOException

java.io.FileNotFoundException

java.lang.NullPointerException

writeInput

public static void writeInput(java.util.List<FastaSequence> sequences,
                              ConfiguredExecutable<?> exec)
                       throws JobSubmissionException

Throws:

JobSubmissionException

writeClustalInput

public static void writeClustalInput(java.util.List<FastaSequence> sequences,
                                     ConfiguredExecutable<?> exec,
                                     char gapChar)
                              throws JobSubmissionException

Throws:

JobSubmissionException

readRNAStruct

public static RNAStructScoreManager readRNAStruct(java.lang.String workDirectory,
                                                  java.lang.String structFile)
                                           throws java.io.IOException,
                                                  java.io.FileNotFoundException

Throws:

java.io.IOException

java.io.FileNotFoundException