compbio.runner
Class Util
java.lang.Object
compbio.runner.Util
public final class Util
- extends java.lang.Object
Field Summary |
static org.apache.log4j.Logger |
log
|
static java.lang.String |
SPACE
|
Constructor Summary |
Util()
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
log
public static org.apache.log4j.Logger log
SPACE
public static final java.lang.String SPACE
- See Also:
- Constant Field Values
Util
public Util()
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