compbio.runner
Class Util

java.lang.Object
  compbio.runner.Util

public final class Util
extends java.lang.Object

Field Summary

static java.lang.String

SPACE

Constructor Summary

Util()

Method Summary

static <T> LimitsManager<T>	getLimits(java.lang.Class<? extends Executable<T>> clazz) For now just assume that all parameters which came in needs setting it will be a client responsibility to prepare RunnerConfig object then
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 void	writeInput(java.util.List<FastaSequence> sequences, ConfiguredExecutable<?> exec)

Methods inherited from class java.lang.Object

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

Field Detail

SPACE

public static final java.lang.String SPACE

See Also:

Constant Field Values

Constructor Detail

Util

public Util()

Method Detail

getLimits

public static <T> LimitsManager<T> getLimits(java.lang.Class<? extends Executable<T>> clazz)

For now just assume that all parameters which came in needs setting it will be a client responsibility to prepare RunnerConfig object then

Parameters:

rconfig -

Returns:

public static List toOptionString(RunnerConfig rconfig) { String option = ""; List options = new ArrayList(); for (Parameter par : rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) { option = par.getOptionName(); } else { option = par.getOptionName() + "=" + par.getPossibleValues().get(0); } // separate options options.add(option); } return options; }

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

writeInput

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