A B C D E F G H I J L M N O P R S T U V W X

S

SETTING_ASKTOVERIFYSETTINGS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_ASKTOVERIFYSETTINGS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_ASKTOVERIFYSETTINGS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_BANJOSEED - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_BANJOSEED_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_BANJOSEED_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_BESTNETWORKSARE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_BESTNETWORKSARE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_BESTNETWORKSARE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CMDARG_SETTINGSDIRECTORY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CMDARG_SETTINGSDIRECTORY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CMDARG_SETTINGSFILENAME - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CMDARG_SETTINGSFILENAME_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CMDARG_SETTINGSFILENAME_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COMPUTECONSENSUSGRAPH - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COMPUTECONSENSUSGRAPH_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COMPUTECONSENSUSGRAPH_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COMPUTEINFLUENCESCORES - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COMPUTEINFLUENCESCORES_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COMPUTEINFLUENCESCORES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COOLINGFACTOR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COOLINGFACTOR_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_COOLINGFACTOR_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CREATEDOTOUTPUT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CREATEDOTOUTPUT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CREATEDOTOUTPUT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CYCLECHECKERCHOICE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CYCLECHECKERCHOICE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_CYCLECHECKERCHOICE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DATAREPORT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DATASET - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DATASET_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DATASET_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DBNMANDATORYIDENTITYLAGS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DBNMANDATORYIDENTITYLAGS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DBNMANDATORYIDENTITYLAGS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DBNMANDATORYIDENTITYLAGS_NONE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DECIDERCHOICE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DECIDERCHOICE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DECIDERCHOICE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEFAULTMAXPARENTCOUNT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEFAULTMAXPARENTCOUNT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEFAULTMAXPARENTCOUNT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEFAULT_DEBUGINFO - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEFAULT_THREADS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEPREC_NUMBEROFINTERMEDIATEPROGRESSREPORTS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DEPREC_WRITETOFILEINTERVAL - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONEXCEPTIONS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONEXCEPTIONS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONEXCEPTIONS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONEXCEPTIONS_NONE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONPOLICY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONPOLICY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONPOLICY_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISCRETIZATIONREPORT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYCONSENSUSGRAPHASHTML - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYCONSENSUSGRAPHASHTML_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYCONSENSUSGRAPHASHTML_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYDEBUGINFO - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYDEBUGINFO_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYDEBUGINFO_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYMEMORYINFO - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYMEMORYINFO_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYMEMORYINFO_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYSTATISTICS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYSTATISTICS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYSTATISTICS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYSTRUCTURES - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYSTRUCTURES_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DISPLAYSTRUCTURES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DOTFILEEXTENSION - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DOTFILEEXTENSION_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DOTFILEEXTENSION_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DOTGRAPHICSFORMAT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DOTGRAPHICSFORMAT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_DOTGRAPHICSFORMAT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_EQUIVALENTSAMPLESIZE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_EQUIVALENTSAMPLESIZE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_EQUIVALENTSAMPLESIZE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_ERRORDIRECTORY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_ERRORDIRECTORY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_ERRORFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_EVALUATORCHOICE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_EVALUATORCHOICE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_EVALUATORCHOICE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORCONSENSUSGRAPH - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORCONSENSUSGRAPH_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORCONSENSUSGRAPH_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORTOPGRAPH - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORTOPGRAPHSASHTML - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORTOPGRAPHSASHTML_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORTOPGRAPHSASHTML_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORTOPGRAPH_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEFORTOPGRAPH_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEPREFIXFORTHREADS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEPREFIXFORTHREADS_DEFAULT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEPREFIXFORTHREADS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILENAMEPREFIXFORTHREADS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILEREPORTINGINTERVAL - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILEREPORTINGINTERVAL_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FILEREPORTINGINTERVAL_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FULLPATHTODOTEXECUTABLE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FULLPATHTODOTEXECUTABLE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_FULLPATHTODOTEXECUTABLE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_HTMLFILEEXTENSION - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_HTMLFILEEXTENSION_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_HTMLFILEEXTENSION_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INITIALSTRUCTUREFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INITIALSTRUCTUREFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INITIALSTRUCTUREFILE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INITIALTEMPERATURE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INITIALTEMPERATURE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INITIALTEMPERATURE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INPUTDIRECTORY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INPUTDIRECTORY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_INPUTDIRECTORY_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXACCEPTEDNETWORKSBEFORECOOLING - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXACCEPTEDNETWORKSBEFORECOOLING_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXACCEPTEDNETWORKSBEFORECOOLING_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXMARKOVLAG - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXMARKOVLAG_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXMARKOVLAG_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPARENTCOUNT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPARENTCOUNTFORRESTART - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPARENTCOUNTFORRESTART_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPARENTCOUNTFORRESTART_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPARENTCOUNT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPARENTCOUNT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKSBEFORECOOLING - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKSBEFORECOOLING_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKSBEFORECOOLING_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKSBEFORERESTART - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKSBEFORERESTART_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKSBEFORERESTART_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXPROPOSEDNETWORKS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXRESTARTS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXRESTARTS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXRESTARTS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXSEARCHTIME - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXSEARCHTIME_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXSEARCHTIME_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MAXTHREADS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINACCEPTEDNETWORKSBEFOREREANNEALING - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINACCEPTEDNETWORKSBEFOREREANNEALING_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINACCEPTEDNETWORKSBEFOREREANNEALING_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINMARKOVLAG - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINMARKOVLAG_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINMARKOVLAG_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINNETWORKSBEFORECHECKING - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINNETWORKSBEFORECHECKING_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINNETWORKSBEFORECHECKING_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINPROPOSEDNETWORKSAFTERHIGHSCORE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINPROPOSEDNETWORKSAFTERHIGHSCORE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINPROPOSEDNETWORKSAFTERHIGHSCORE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINPROPOSEDNETWORKSBEFORERESTART - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINPROPOSEDNETWORKSBEFORERESTART_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MINPROPOSEDNETWORKSBEFORERESTART_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MUSTBEPRESENTEDGESFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MUSTBEPRESENTEDGESFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MUSTBEPRESENTEDGESFILE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MUSTNOTBEPRESENTEDGESFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MUSTNOTBEPRESENTEDGESFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_MUSTNOTBEPRESENTEDGESFILE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_NBEST - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_NBEST_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_NBEST_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_NOTES - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_NOTES_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_NOTES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONCOUNT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONCOUNT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONCOUNT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILES_OMIT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILES_USED_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OBSERVATIONSFILE_WILDCARD_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OUTPUTDIRECTORY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OUTPUTDIRECTORY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_OUTPUTDIRECTORY_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PRECOMPUTE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PRECOMPUTE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PRECOMPUTE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PROJECT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PROJECT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PROJECT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PROPOSERCHOICE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PROPOSERCHOICE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_PROPOSERCHOICE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_REANNEALINGTEMPERATURE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_REANNEALINGTEMPERATURE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_REANNEALINGTEMPERATURE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_REPORTFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_REPORTFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_REPORTFILE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_RESTARTWITHRANDOMNETWORK - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_RESTARTWITHRANDOMNETWORK_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_RESTARTWITHRANDOMNETWORK_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SCREENREPORTINGINTERVAL - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SCREENREPORTINGINTERVAL_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SCREENREPORTINGINTERVAL_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SEARCHERCHOICE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SEARCHERCHOICE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SEARCHERCHOICE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_STATISTICDEFAULT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_STATISTICSCHOICE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_STATISTICSCHOICE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_STATISTICSCHOICE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SUMMARYFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_SUMMARYFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_THREADS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_THREADS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_THREADS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_TIMESTAMPSTRINGFORFILES - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_TIMESTAMPSTRINGFORFILES_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_TIMESTAMPSTRINGFORFILES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_TRACKINGFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_TRACKINGFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_USECACHE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_USECACHE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_USECACHE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_USER - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_USER_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_USER_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARCOUNT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARCOUNT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARCOUNT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARIABLENAMES - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARIABLENAMES_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARIABLENAMES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARIABLESAREINROWS - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARIABLESAREINROWS_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_VARIABLESAREINROWS_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLINPUTDIRECTORY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLINPUTDIRECTORY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLINPUTDIRECTORY_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLINPUTFILES - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLINPUTFILES_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLINPUTFILES_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLOUTPUTDIRECTORY - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLOUTPUTDIRECTORY_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLOUTPUTDIRECTORY_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLREPORTFILE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLREPORTFILE_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLREPORTFILE_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLSETTINGSTOEXPORT - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLSETTINGSTOEXPORT_DESCR - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
SETTING_XMLSETTINGSTOEXPORT_DISP - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
Searcher - class edu.duke.cs.banjo.learner.Searcher.
Combines common code shared by the different searcher implementations.
Searcher(Settings) - Constructor for class edu.duke.cs.banjo.learner.Searcher
Constructor for instantiating the objects shared between searcher implementations.
Searcher.HighScoreSetUpdater - class edu.duke.cs.banjo.learner.Searcher.HighScoreSetUpdater.
Base class of inner classes for updating the score info for a search.
Searcher.HighScoreSetUpdater() - Constructor for class edu.duke.cs.banjo.learner.Searcher.HighScoreSetUpdater
 
Searcher.SearchExecuter - class edu.duke.cs.banjo.learner.Searcher.SearchExecuter.
Base class of inner classes for executing a search.
Searcher.SearchExecuter() - Constructor for class edu.duke.cs.banjo.learner.Searcher.SearchExecuter
 
Searcher.SearchMultipleTerminator - class edu.duke.cs.banjo.learner.Searcher.SearchMultipleTerminator.
Subclass class of inner classes for terminating a search using possibly multiple criteria.
Searcher.SearchMultipleTerminator() - Constructor for class edu.duke.cs.banjo.learner.Searcher.SearchMultipleTerminator
 
Searcher.SearchTerminator - class edu.duke.cs.banjo.learner.Searcher.SearchTerminator.
Base class of inner classes for terminating a search.
Searcher.SearchTerminator() - Constructor for class edu.duke.cs.banjo.learner.Searcher.SearchTerminator
 
SearcherGreedy - class edu.duke.cs.banjo.learner.SearcherGreedy.
Implements a greedy search.
SearcherGreedy(Settings) - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy
Constructor for the greedy searcher implementation.
SearcherGreedy.BasicHighScoreSetUpdater - class edu.duke.cs.banjo.learner.SearcherGreedy.BasicHighScoreSetUpdater.
Inner class for tracking a set of N-best (N>1) scoring networks.
SearcherGreedy.BasicHighScoreSetUpdater() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.BasicHighScoreSetUpdater
 
SearcherGreedy.DoubleTerminator - class edu.duke.cs.banjo.learner.SearcherGreedy.DoubleTerminator.
Inner class for terminating a search with 2 termination criteria.
SearcherGreedy.DoubleTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.DoubleTerminator
 
SearcherGreedy.GlobalSearchExecuter - class edu.duke.cs.banjo.learner.SearcherGreedy.GlobalSearchExecuter.
Inner class for executing a search based on a set of local changes.
SearcherGreedy.GlobalSearchExecuter() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.GlobalSearchExecuter
 
SearcherGreedy.IterationsTerminator - class edu.duke.cs.banjo.learner.SearcherGreedy.IterationsTerminator.
Inner class for terminating a search based on a limit on the number of iterations.
SearcherGreedy.IterationsTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.IterationsTerminator
 
SearcherGreedy.LocalSearchExecuter - class edu.duke.cs.banjo.learner.SearcherGreedy.LocalSearchExecuter.
Inner class for executing a search based on a single local change.
SearcherGreedy.LocalSearchExecuter() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.LocalSearchExecuter
 
SearcherGreedy.RestartsTerminator - class edu.duke.cs.banjo.learner.SearcherGreedy.RestartsTerminator.
Inner class for terminating a search based on a limit on the number of restarts.
SearcherGreedy.RestartsTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.RestartsTerminator
 
SearcherGreedy.SingleHighScoreUpdater - class edu.duke.cs.banjo.learner.SearcherGreedy.SingleHighScoreUpdater.
Inner class for tracking a single high-scoring network
SearcherGreedy.SingleHighScoreUpdater() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.SingleHighScoreUpdater
 
SearcherGreedy.SingleTerminator - class edu.duke.cs.banjo.learner.SearcherGreedy.SingleTerminator.
Inner class for terminating a search with 1 termination criterion.
SearcherGreedy.SingleTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.SingleTerminator
 
SearcherGreedy.TimeTerminator - class edu.duke.cs.banjo.learner.SearcherGreedy.TimeTerminator.
Inner class for terminating a search based on a limit on the search time.
SearcherGreedy.TimeTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.TimeTerminator
 
SearcherGreedy.TripleTerminator - class edu.duke.cs.banjo.learner.SearcherGreedy.TripleTerminator.
Inner class for terminating a search with 3 termination criteria.
SearcherGreedy.TripleTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherGreedy.TripleTerminator
 
SearcherI - interface edu.duke.cs.banjo.learner.SearcherI.
Documents the interface for creating a searcher implementation.
SearcherSimAnneal - class edu.duke.cs.banjo.learner.SearcherSimAnneal.
Implements a simulated annealing-based search.
SearcherSimAnneal(Settings) - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal
Constructor for the simulated annealing searcher implementation.
SearcherSimAnneal.BasicHighScoreSetUpdater - class edu.duke.cs.banjo.learner.SearcherSimAnneal.BasicHighScoreSetUpdater.
Inner class for tracking a set of N-best (N>1) scoring networks.
SearcherSimAnneal.BasicHighScoreSetUpdater() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.BasicHighScoreSetUpdater
 
SearcherSimAnneal.DoubleTerminator - class edu.duke.cs.banjo.learner.SearcherSimAnneal.DoubleTerminator.
Inner class for terminating a search with 2 termination criteria.
SearcherSimAnneal.DoubleTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.DoubleTerminator
 
SearcherSimAnneal.GlobalSearchExecuter - class edu.duke.cs.banjo.learner.SearcherSimAnneal.GlobalSearchExecuter.
Inner class for executing a search based on a set of local changes.
SearcherSimAnneal.GlobalSearchExecuter() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.GlobalSearchExecuter
 
SearcherSimAnneal.IterationsTerminator - class edu.duke.cs.banjo.learner.SearcherSimAnneal.IterationsTerminator.
Inner class for terminating a search based on a limit on the number of iterations.
SearcherSimAnneal.IterationsTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.IterationsTerminator
 
SearcherSimAnneal.LocalSearchExecuter - class edu.duke.cs.banjo.learner.SearcherSimAnneal.LocalSearchExecuter.
 
SearcherSimAnneal.LocalSearchExecuter() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.LocalSearchExecuter
 
SearcherSimAnneal.RestartsTerminator - class edu.duke.cs.banjo.learner.SearcherSimAnneal.RestartsTerminator.
Inner class for terminating a search based on a limit on the number of restarts.
SearcherSimAnneal.RestartsTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.RestartsTerminator
 
SearcherSimAnneal.SingleHighScoreUpdater - class edu.duke.cs.banjo.learner.SearcherSimAnneal.SingleHighScoreUpdater.
Inner class for tracking a single high-scoring network
SearcherSimAnneal.SingleHighScoreUpdater() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.SingleHighScoreUpdater
 
SearcherSimAnneal.SingleTerminator - class edu.duke.cs.banjo.learner.SearcherSimAnneal.SingleTerminator.
Inner class for terminating a search with 1 termination criterion.
SearcherSimAnneal.SingleTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.SingleTerminator
 
SearcherSimAnneal.TimeTerminator - class edu.duke.cs.banjo.learner.SearcherSimAnneal.TimeTerminator.
Inner class for terminating a search based on a limit on the search time.
SearcherSimAnneal.TimeTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.TimeTerminator
 
SearcherSimAnneal.TripleTerminator - class edu.duke.cs.banjo.learner.SearcherSimAnneal.TripleTerminator.
Inner class for terminating a search with 3 termination criteria.
SearcherSimAnneal.TripleTerminator() - Constructor for class edu.duke.cs.banjo.learner.SearcherSimAnneal.TripleTerminator
 
SearcherSkip - class edu.duke.cs.banjo.learner.SearcherSkip.
This searcher is only setting up as much of the bayesnet structures as is necessary to prepare for the post-processing, without actually having to go through a search.
SearcherSkip(Settings) - Constructor for class edu.duke.cs.banjo.learner.SearcherSkip
 
SettingItem - class edu.duke.cs.banjo.data.settings.SettingItem.
Holds an individual setting that is loaded into Banjo.
SettingItem(String, String, String) - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem
 
SettingItem(SettingItem) - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem
Constructor based on an existing settingItem.
SettingItem.DataTypeValidator - class edu.duke.cs.banjo.data.settings.SettingItem.DataTypeValidator.
 
SettingItem.DataTypeValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.DataTypeValidator
 
SettingItem.DiscretizationExceptionsValidator - class edu.duke.cs.banjo.data.settings.SettingItem.DiscretizationExceptionsValidator.
 
SettingItem.DiscretizationExceptionsValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.DiscretizationExceptionsValidator
 
SettingItem.DiscretizationPolicyValidator - class edu.duke.cs.banjo.data.settings.SettingItem.DiscretizationPolicyValidator.
 
SettingItem.DiscretizationPolicyValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.DiscretizationPolicyValidator
 
SettingItem.DoubleValidator - class edu.duke.cs.banjo.data.settings.SettingItem.DoubleValidator.
 
SettingItem.DoubleValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.DoubleValidator
 
SettingItem.FileValidator - class edu.duke.cs.banjo.data.settings.SettingItem.FileValidator.
 
SettingItem.FileValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.FileValidator
 
SettingItem.IntegerListValidator - class edu.duke.cs.banjo.data.settings.SettingItem.IntegerListValidator.
 
SettingItem.IntegerListValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.IntegerListValidator
 
SettingItem.IntegerValidator - class edu.duke.cs.banjo.data.settings.SettingItem.IntegerValidator.
 
SettingItem.IntegerValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.IntegerValidator
 
SettingItem.LongValidator - class edu.duke.cs.banjo.data.settings.SettingItem.LongValidator.
 
SettingItem.LongValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.LongValidator
 
SettingItem.PathValidator - class edu.duke.cs.banjo.data.settings.SettingItem.PathValidator.
 
SettingItem.PathValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.PathValidator
 
SettingItem.StringValidator - class edu.duke.cs.banjo.data.settings.SettingItem.StringValidator.
 
SettingItem.StringValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.StringValidator
 
SettingItem.TimeStampValidator - class edu.duke.cs.banjo.data.settings.SettingItem.TimeStampValidator.
 
SettingItem.TimeStampValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.TimeStampValidator
 
SettingItem.TimeValidator - class edu.duke.cs.banjo.data.settings.SettingItem.TimeValidator.
 
SettingItem.TimeValidator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.TimeValidator
 
SettingItem.Validator - class edu.duke.cs.banjo.data.settings.SettingItem.Validator.
 
SettingItem.Validator() - Constructor for class edu.duke.cs.banjo.data.settings.SettingItem.Validator
 
Settings - class edu.duke.cs.banjo.data.settings.Settings.
Manages the initial, validated, and dynamically updated parameters that are used by the various search algorithms.
Settings() - Constructor for class edu.duke.cs.banjo.data.settings.Settings
Basic constructor that simply sets up the internal data for the settings object.
Settings(Settings) - Constructor for class edu.duke.cs.banjo.data.settings.Settings
Constructor based on an existing settings.
Settings(Settings, int) - Constructor for class edu.duke.cs.banjo.data.settings.Settings
Constructor based on an existing settings.
StringUtil - class edu.duke.cs.banjo.utility.StringUtil.
Contains a collection of general purpose string-related code.
StringUtil() - Constructor for class edu.duke.cs.banjo.utility.StringUtil
(Empty) constructor for static StringUtil class.
scoreDiff - Variable in class edu.duke.cs.banjo.learner.components.EvaluatorBDe
 
scoreDiff - Variable in class edu.duke.cs.banjo.utility.InfluenceScorer
 
screenReportInterval - Variable in class edu.duke.cs.banjo.learner.Searcher
 
screenReportTimeDelta - Variable in class edu.duke.cs.banjo.learner.Searcher
 
searchExecuter - Variable in class edu.duke.cs.banjo.learner.Searcher
 
searchLoopIndex - Variable in class edu.duke.cs.banjo.bayesnet.BayesNetStructure
 
searchLoopsRemaining - Variable in class edu.duke.cs.banjo.learner.SearcherGreedy.IterationsTerminator
 
searchLoopsRemaining - Variable in class edu.duke.cs.banjo.learner.SearcherSimAnneal.IterationsTerminator
 
searchTerminator - Variable in class edu.duke.cs.banjo.learner.Searcher
 
searcher - Variable in class edu.duke.cs.banjo.application.BanjoThreadHandler
 
searcherStatistics - Variable in class edu.duke.cs.banjo.learner.Searcher
 
searcherStats - Variable in class edu.duke.cs.banjo.learner.Searcher
 
selectorChangeTypeCount - Variable in class edu.duke.cs.banjo.learner.components.Proposer.EdgeSelector
 
serialVersionUID - Static variable in class edu.duke.cs.banjo.utility.BanjoException
 
setBanjoSeed(long) - Method in class edu.duke.cs.banjo.data.settings.Settings
 
setBanjoSeed(long) - Method in class edu.duke.cs.banjo.utility.BanjoRandomNumber
 
setChangeStatus(int) - Method in class edu.duke.cs.banjo.bayesnet.BayesNetChange
 
setChangeStatus(int) - Method in interface edu.duke.cs.banjo.bayesnet.BayesNetChangeI
The status of a BayesNetChange may change over the search process.
setCurrentParents(EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.bayesnet.BayesNetManager
 
setCurrentParents(EdgesWithCachedStatisticsI) - Method in interface edu.duke.cs.banjo.bayesnet.BayesNetManagerI
 
setCurrentScore(double) - Method in class edu.duke.cs.banjo.learner.components.Decider
 
setCurrentScore(double) - Method in interface edu.duke.cs.banjo.learner.components.DeciderI
Sets the score of the current network.
setCycleAtNode(int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
setDefaultValueUsed(boolean) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setDocumentLocator(Locator) - Method in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
setDynamicProcessParameter(String, String) - Method in class edu.duke.cs.banjo.data.settings.Settings
Sets the dynamic process parameter to the supplied value.
setEntry(int, int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArray
 
setEntry(int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
setEntry(int, int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
setEntry(int, int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrix
 
setEntry(int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
setEntry(int, int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
setEntry(int, int, int, int) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesI
 
setEntry(int, int, int) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
setEntry(int, int, int, int) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
setHighScoreStructureSet(TreeSet) - Method in class edu.duke.cs.banjo.data.settings.Settings
 
setItemNameFormattedForDisplay(String) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setItemValueAsLoaded(String) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setItemValueValidated(String) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setMatrix(int[]) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArray
 
setMatrix(int[][][]) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrix
 
setMessage(String) - Method in class edu.duke.cs.banjo.utility.BanjoException
 
setNBestMax(long) - Method in class edu.duke.cs.banjo.utility.NBestProcessor
 
setNetworkScore(double) - Method in class edu.duke.cs.banjo.bayesnet.BayesNetStructure
 
setNetworkScore(double) - Method in interface edu.duke.cs.banjo.bayesnet.BayesNetStructureI
 
setNetworkStructure(EdgesI) - Method in class edu.duke.cs.banjo.bayesnet.BayesNetStructure
 
setNetworkStructure(EdgesI) - Method in interface edu.duke.cs.banjo.bayesnet.BayesNetStructureI
 
setObjItemInfo(Object) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setObjItemValue(Object) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setObservationDataPoints(int[]) - Method in class edu.duke.cs.banjo.data.observations.ObservationsAsArray
 
setObservationDataPoints(int[][][]) - Method in class edu.duke.cs.banjo.data.observations.ObservationsAsMatrix
 
setObservationValue(int, int, int, int) - Method in class edu.duke.cs.banjo.data.observations.ObservationsAsArray
 
setObservationValue(int, int, int, int) - Method in class edu.duke.cs.banjo.data.observations.ObservationsAsMatrix
 
setObservationValue(int, int, int, int) - Method in interface edu.duke.cs.banjo.data.observations.ObservationsI
 
setObservations(ObservationsI) - Method in class edu.duke.cs.banjo.data.settings.Settings
 
setProcessData(Settings) - Static method in class edu.duke.cs.banjo.utility.StringUtil
Provides access to the (main) settings.
setStrRawObservationDataPoints(String[][]) - Method in class edu.duke.cs.banjo.data.observations.PreprocessedObservations
 
setToCombinedMatrices(EdgesWithCachedStatisticsI, EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
setToCombinedMatrices(EdgesWithCachedStatisticsI, EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
setToCombinedMatrices(EdgesWithCachedStatisticsI, EdgesWithCachedStatisticsI) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
setTraceFileName(int, String) - Method in class edu.duke.cs.banjo.utility.FileUtil
 
setValidSetting(boolean) - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
setValidatedProcessParameter(String, String) - Method in class edu.duke.cs.banjo.data.settings.Settings
Sets the validated process parameter (setting) to the supplied value.
setVariableNames(String[]) - Method in class edu.duke.cs.banjo.data.observations.ObservationsAsArray
 
setVariableNames(String[]) - Method in class edu.duke.cs.banjo.data.observations.ObservationsAsMatrix
 
setVariableNames(String[]) - Method in interface edu.duke.cs.banjo.data.observations.ObservationsI
 
settingName - Variable in class edu.duke.cs.banjo.utility.BanjoError
 
settings - Variable in class edu.duke.cs.banjo.application.Banjo
 
settings - Variable in class edu.duke.cs.banjo.application.BanjoThreadHandler
 
settings - Variable in class edu.duke.cs.banjo.utility.FileUtil
 
settings - Variable in class edu.duke.cs.banjo.utility.NBestProcessor
 
settings - Variable in class edu.duke.cs.banjo.utility.PostProcessor
 
settings - Variable in class edu.duke.cs.banjo.utility.PreProcessor
 
settings - Variable in class edu.duke.cs.banjo.utility.XMLProcessor
 
settingsUsedInThread - Variable in class edu.duke.cs.banjo.application.Banjo
 
setupFile(FileWriter, OutputStreamWriter, PrintWriter, String) - Method in class edu.duke.cs.banjo.utility.FileUtil
 
setupSearch() - Method in class edu.duke.cs.banjo.learner.SearcherGreedy
Set up the search, and compile various pieces of info about the search, to be used by the recorder.
setupSearch() - Method in class edu.duke.cs.banjo.learner.SearcherSimAnneal
Set up the search, and compile various pieces of info about the search, to be used by the recorder.
setupSearch() - Method in class edu.duke.cs.banjo.learner.SearcherSkip
 
sharedArgs - Variable in class edu.duke.cs.banjo.application.Banjo
 
sizeAfter - Variable in class edu.duke.cs.banjo.learner.SearcherGreedy.BasicHighScoreSetUpdater
 
sizeAfter - Variable in class edu.duke.cs.banjo.learner.SearcherSimAnneal.BasicHighScoreSetUpdater
 
sizeBefore - Variable in class edu.duke.cs.banjo.learner.SearcherGreedy.BasicHighScoreSetUpdater
 
sizeBefore - Variable in class edu.duke.cs.banjo.learner.SearcherSimAnneal.BasicHighScoreSetUpdater
 
sizeOfListOfChanges() - Method in class edu.duke.cs.banjo.learner.Searcher.SearchExecuter
 
sizeOfListOfChanges() - Method in class edu.duke.cs.banjo.learner.SearcherGreedy.GlobalSearchExecuter
 
sizeOfListOfChanges() - Method in class edu.duke.cs.banjo.learner.SearcherGreedy.LocalSearchExecuter
 
sizeOfListOfChanges() - Method in class edu.duke.cs.banjo.learner.SearcherSimAnneal.GlobalSearchExecuter
 
sizeOfListOfChanges() - Method in class edu.duke.cs.banjo.learner.SearcherSimAnneal.LocalSearchExecuter
 
skippedEntity(String) - Method in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
specifiedObservationCount - Variable in class edu.duke.cs.banjo.data.observations.Observations
 
startDocument() - Method in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
startElement(String, String, String, Attributes) - Method in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
startPrefixMapping(String, String) - Method in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
startTime - Variable in class edu.duke.cs.banjo.learner.Searcher
 
statisticsBuffer - Variable in class edu.duke.cs.banjo.learner.components.Recorder
 
storedArgs - Variable in class edu.duke.cs.banjo.application.BanjoThreadHandler
 
strBanjoSettings - Variable in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
strDbnMandatoryIdentityLags - Variable in class edu.duke.cs.banjo.bayesnet.BayesNetManager
 
strHeader - Static variable in class edu.duke.cs.banjo.learner.components.Recorder
 
strNetworkScore - Variable in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
strNetworkStructure - Variable in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
strOriginalDataPoints - Variable in class edu.duke.cs.banjo.data.observations.DataPreparer
 
strRawObservationDataPoints - Variable in class edu.duke.cs.banjo.data.observations.PreprocessedObservations
 
streamWriter - Variable in class edu.duke.cs.banjo.utility.FileUtil
 
structureSelector - Variable in class edu.duke.cs.banjo.learner.components.Proposer
 
subtractMatrix(EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
subtractMatrix(EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
subtractMatrix(EdgesWithCachedStatisticsI) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.Proposer.StructureSelector
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.Proposer
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves.EdgesAsMatrixSelector
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves.multipleMovesStructureSelector
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves
 
suggestBayesNetChange(BayesNetManagerI) - Method in interface edu.duke.cs.banjo.learner.components.ProposerI
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerRandomLocalMove.EdgesAsArraySelector
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerRandomLocalMove.EdgesAsMatrixSelector
 
suggestBayesNetChange(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerRandomLocalMove
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.Proposer.StructureSelector
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves.EdgesAsArraySelector
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves.EdgesAsMatrixSelector
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves.multipleMovesStructureSelector
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerAllLocalMoves
 
suggestBayesNetChanges(BayesNetManagerI) - Method in interface edu.duke.cs.banjo.learner.components.ProposerI
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerRandomLocalMove.EdgesAsArraySelector
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerRandomLocalMove.EdgesAsMatrixSelector
 
suggestBayesNetChanges(BayesNetManagerI) - Method in class edu.duke.cs.banjo.learner.components.ProposerRandomLocalMove
 
suggestedBayesNetChange - Variable in class edu.duke.cs.banjo.learner.Searcher
 
suggestedChangeList - Variable in class edu.duke.cs.banjo.learner.Searcher
 
summaryBuffer - Variable in class edu.duke.cs.banjo.learner.components.Recorder
 

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