compbio.runner

Class Util

java.lang.Object

compbio.runner.Util

public final class Util
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.log4j.Logger	log
private static compbio.util.PropertyHelper	ph
static java.lang.String	SPACE

Constructor Summary

Constructors

Constructor and Description
Util()

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 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

ph

private static final compbio.util.PropertyHelper ph

SPACE

public static final java.lang.String SPACE

See Also:

Constant Field Values

Constructor Detail

Util

public Util()

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