helix.graph.program.isofun
Class IsofunOptions

java.lang.Object
  extended by helix.graph.util.CommandLine
      extended by helix.graph.algo.c3part.C3PartOptions
          extended by helix.graph.program.isofun.IsofunOptions

public class IsofunOptions
extends C3PartOptions


Field Summary
 String algoName
           
 boolean check
           
 boolean cleanup
           
 List<Integer> deltaEps
           
 List<Integer> deltaGap
           
 boolean memdog
           
 boolean reportGaps
           
 boolean reportOGs
           
 boolean tandem
           
 int tandemMinFrac
           
 int tandemMinSize
           
 
Fields inherited from class helix.graph.algo.c3part.C3PartOptions
ALLPATH_LOOKAHEAD, CC_AGGREGATOR, ccDenseMode, ccDensity, CENTER_AGGREGATOR, CLIQUE_AGGREGATOR, colors, compressor, concthresh, debug, deltaShuf, DENSE_AGGREGATOR, DENSE_MODE_ABSOLUTE, DENSE_MODE_QUANTILE, DENSE_MODE_RELATIVE, FULLCOLOR_LOOKAHEAD, GLOBAL_OPTIMIZER, IDENT_COMPRESSOR, INCOLOR_COMPRESSOR, INSET_COMPRESSOR, INSETCOLOR_COMPRESSOR, ismulti, LOCAL_OPTIMIZER, logger, lookaheadName, maxstar, mincore, mineltsize, minsize, nbproc, NO_COMPRESSOR, NO_OPTIMIZER, nodeAggregatorName, ONEWAYPATH_LOOKAHEAD, OPTIMIZER_MODE_MAX, OPTIMIZER_MODE_MIN, optimizerMode, optimizerName, TREE_AGGREGATOR, TWOWAYPATH_LOOKAHEAD, USER_OPTIMIZER, userColors, verbose
 
Constructor Summary
IsofunOptions(String[] args)
           
 
Method Summary
static C3PartAlgo getAlgoForName(String name, Graph graph)
          get proper algorithm from name
 void parse()
          override parse to further check user options.
 void set_algo(List<String> args)
          new stubs
 void set_check(List<String> args)
           
 void set_cleanup(List<String> args)
           
 void set_deltaeps(List<String> args)
           
 void set_deltagap(List<String> args)
           
 void set_memdog(List<String> args)
           
 void set_reportgaps(List<String> args)
           
 void set_reportogs(List<String> args)
           
 void set_tandem(List<String> args)
           
 
Methods inherited from class helix.graph.algo.c3part.C3PartOptions
set_aggregator, set_colors, set_compressor, set_debug, set_deltashuf, set_help, set_ismulti, set_lookahead, set_maxstar, set_mincore, set_mineltsize, set_minsize, set_nbproc, set_optimizer, set_verbose
 
Methods inherited from class helix.graph.util.CommandLine
addOption, boolToString, getCommand, getNonOptionArguments, getOption, getUsage, isSetByUser, setUsage, stringToBool, stringToInt
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

algoName

public String algoName

check

public boolean check

cleanup

public boolean cleanup

tandem

public boolean tandem

tandemMinSize

public int tandemMinSize

tandemMinFrac

public int tandemMinFrac

reportGaps

public boolean reportGaps

memdog

public boolean memdog

deltaGap

public List<Integer> deltaGap

deltaEps

public List<Integer> deltaEps

reportOGs

public boolean reportOGs
Constructor Detail

IsofunOptions

public IsofunOptions(String[] args)
Method Detail

getAlgoForName

public static C3PartAlgo getAlgoForName(String name,
                                        Graph graph)
get proper algorithm from name


parse

public void parse()
           throws CommandLineException
override parse to further check user options. note: further checking may also be done in the setOptions method for each algo.

Overrides:
parse in class CommandLine
Throws:
CommandLineException

set_algo

public void set_algo(List<String> args)
new stubs


set_check

public void set_check(List<String> args)

set_cleanup

public void set_cleanup(List<String> args)

set_tandem

public void set_tandem(List<String> args)

set_reportgaps

public void set_reportgaps(List<String> args)

set_reportogs

public void set_reportogs(List<String> args)

set_memdog

public void set_memdog(List<String> args)

set_deltagap

public void set_deltagap(List<String> args)

set_deltaeps

public void set_deltaeps(List<String> args)