compbio.runner
Class Util

java.lang.Object
  compbio.runner.Util

public final class Util
extends Object

Field Summary

static org.apache.log4j.Logger	log
static String	SPACE

Constructor Summary

Util()

Method Summary

static <T> PresetManager<T>	getPresets(Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	getSupportedOptions(Class<? extends Executable<T>> clazz)
static Alignment	readClustalFile(String workDirectory, String clustFile)
static Map<String,Score>	readJronnFile(String workDirectory, String clustFile)
static void	writeInput(List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Methods inherited from class java.lang.Object

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

Field Detail

log

public static org.apache.log4j.Logger log

SPACE

public static final String SPACE

See Also:

Constant Field Values

Constructor Detail

Util

public Util()

Method Detail

getSupportedOptions

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

getPresets

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

readClustalFile

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

Throws:

UnknownFileFormatException

IOException

FileNotFoundException

NullPointerException

readJronnFile

public static final Map<String,Score> readJronnFile(String workDirectory,
                                                    String clustFile)
                                             throws UnknownFileFormatException,
                                                    IOException,
                                                    FileNotFoundException,
                                                    NullPointerException

Throws:

UnknownFileFormatException

IOException

FileNotFoundException

NullPointerException

writeInput

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

Throws:

JobSubmissionException