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()
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SPACE
public static final java.lang.String SPACE
- See Also:
- Constant Field Values
Util
public Util()
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)