mesquite.categ.lib
Class CategDataMatcher

java.lang.Object
  mesquite.lib.MenuOwner
      mesquite.lib.EmployerEmployee
          mesquite.lib.MesquiteModule
              mesquite.lib.duties.DataMatcher
                  mesquite.categ.lib.CategDataMatcher

All Implemented Interfaces:

Commandable, Doomable, Explainable, FileDirtier, FunctionExplainable, HNode, Identifiable, Listable, Logger, MesquiteListener, Showable

Direct Known Subclasses:

AlignMatch

public abstract class CategDataMatcher
extends DataMatcher

Field Summary

Fields inherited from class mesquite.lib.duties.DataMatcher

data, state, table

Fields inherited from class mesquite.lib.MesquiteModule

author, browserString, checkMethodsAtStartup, hiredAsDefaultInScripting, lastResult, lastResultString, logWindow, mesquiteDirectory, mesquiteDirectoryPath, mesquiteTrunk, moduleInfo, prefsDirectory, proj, textEdgeCompensationHeight, textEdgeCompensationWidth, totalFinalized, userDirectory

Fields inherited from class mesquite.lib.EmployerEmployee

employees, employer, startupBailOut, stringPos, suppressHireQueries, totalCreated, totalDisposed, useOtherChoices

Fields inherited from class mesquite.lib.MenuOwner

considerPriorities, doomed, MAXPRIORITY, menuCompositionTime, menuCompositionTime1, menuCompositionTime2, menuCompositionTime2a, menuCompositionTime2b, menuCompositionTime2c, menuCompositionTime3, menuCompositionTime4, menuCompositionTime5, menuCompositionTime6, menuCompositionTime7, menuCompositionTime8, menuCompositionTime9, menuTracing, module, parser

Fields inherited from interface mesquite.lib.MesquiteListener

ANNOTATION_ADDED, ANNOTATION_CHANGED, ANNOTATION_DELETED, ASSOCIATED_CHANGED, BRANCHES_REARRANGED, BRANCHLENGTHS_CHANGED, COMMAND_CANCELLED, DATA_CHANGED, ELEMENT_CHANGED, ITEMS_ADDED, NAMES_CHANGED, OBJECT_DESTROYED, PARTS_ADDED, PARTS_CHANGED, PARTS_DELETED, PARTS_MOVED, SELECTION_CHANGED, TAXA_SUBSTITUTED, TEXTFIELD_EDITED, UNKNOWN, VALUE_CHANGED

Fields inherited from interface mesquite.lib.HNode

MOUSEDOWN, MOUSEEXIT, MOUSEMOVE

Constructor Summary

CategDataMatcher()

Method Summary

double	getApproximateWorstMatchValue(CharacterState[] csOriginalArray) Returns the approximate value of the worst possible match.
abstract double	getApproximateWorstMatchValue(long[] originalArray)
double	getBestMatchValue(CharacterState[] csOriginalArray) Returns the value of the best possible match.
abstract double	getBestMatchValue(long[] originalArray)
CompatibilityTest	getCompatibilityTest() Returns CompatibilityTest so other modules know if this is compatible with some object.
double	sequenceMatch(CharacterState[] csOriginalArray, CharacterState[] csCandidateArray) Returns the match of the two CharacterState arrays
double	sequenceMatch(CharacterState[] csOriginalArray, int candidateTaxon, int candidateStartChar, MesquiteInteger candidateEndChar) Returns whether candidate stretch of matrix, in taxon candidateTaxon, starting at candidateStartChar, ending at candidateEndChar, matches the data passed in the CharacterState array csOriginalArray.
abstract double	sequenceMatch(long[] originalArray, int candidateTaxon, int candidateStartChar, MesquiteInteger candidateEndChar)
abstract double	sequenceMatch(long[] originalArray, long[] candidateArray)

Methods inherited from class mesquite.lib.duties.DataMatcher

getBestMatchValue, getDutyClass, getDutyName, getHigherIsBetter, getWorstMatchValue, prepare, requiresApplicable, sequenceMatch, sequenceMatch, setTableAndData

Methods inherited from class mesquite.lib.MesquiteModule

accumulateParameters, addNEXUSBlock, alert, alert, anySubstantivePrereleases, broadCastAssignedID, changed, classFieldChanged, clearLastResult, clearResultAndLastResult, compatibleWithSystem, containerOfModule, createSupportDirectory, deleteSupportDirectory, discreetAlert, discreetAlert, dispose, disposing, doCommand, echoStringToFile, employeeOutputInvalid, employeeParametersChanged, employeeQuit, employerWithWindow, endJob, fileAboutToBeWritten, fileDirtiedByCommand, fileElementAdded, fileReadIn, finalize, findNEXUSBlock, getAppletInfo, getAuthors, getAutoSaveMacros, getBrowserManualPath, getBrowserPanel, getBuildDate, getBuildVersion, getCitation, getCommandPagePath, getDateReleased, getDefaultModule, getDocsPath, getExpectedPath, getExplanation, getFunctionIconPath, getHireSubchoice, getHTMLExplanation, getID, getIfLastEmployee, getKeywords, getManualPath, getMesquiteVersion, getModuleInfo, getName, getNameAndParameters, getNameForMenuItem, getNexusBlockTest, getNexusCommands, getNexusCommandTest, getPackageImagesPath, getPackageIntroModule, getPackagePath, getParameters, getParametersChangedNotifier, getPath, getPermanentIDString, getProject, getRootImageDirectoryPath, getRootPath, getShortClassName, getShortClassName, getSizedRootImageFilePath, getSnapshot, getSubfunctions, getSubfunctionsVector, getURLString, getUserChooseable, getVersion, getVersionInt, getVersionOfFirstRelease, getVeryShortName, getXMLPrefsVersion, iQuit, iQuit, isCorrectRootTag, isPrerelease, isSubstantive, listEmployeeParameters, listEmployees, loadPreferences, log, log, logln, logln, loglnNoEcho, logNoEcho, makeCommand, mesquiteStartup, nameIsInstanceOf, nameMatches, offHold, okToDispose, onHold, outputInvalid, pageModule, panelGoAway, parametersChanged, parametersChanged, parseFullXMLDocument, permanentIDExists, preparePreferencesForFile, preparePreferencesForXML, processPreferencesFromFile, processPreferencesFromXML, processSingleXMLPreference, projectEstablished, quittingConditions, readNexusBlock, readNexusCommand, readUnrecognizedCommand, registerSubfunction, removeNEXUSBlock, removePaging, reportProfiling, requestPrimaryChoice, respondToPaging, returningPage, saveLastResult, saveLastResult, saveLastResult, saveLastResult, saveLastResultString, saveLastResultString, setAutoSaveMacros, setProject, setToLastEmployee, showCitation, showHTMLSnippet, showLogWindow, showLogWindow, showManual, showMe, showWebPage, showWebPage, sorry, startJob, startProfiling, storePreferences, superStartJob, supportDirectoryPath, toString, URLinPackageIntro, windowGoAway, writeNexusCommands, xmlPrefsVersionMustMatch

Methods inherited from class mesquite.lib.EmployerEmployee

canHireMoreThanOnce, closeDownAllEmployees, decrementEmployeeBrowserRefreshSuppression, deferBranchPriority, employeeOfWhichEmployee, findCharacterDataEditor, findCharacterDataEditorRec, findElementManager, findEmployee, findEmployee, findEmployeeNeed, findEmployeeWithDuty, findEmployeeWithDuty, findEmployeeWithIDNumber, findEmployeeWithName, findEmployeeWithName, findEmployeeWithName, findEmployeeWithPermanentID, findEmployerWithDuty, findImmediateEmployeeWithDuty, findModelCurator, findModelCuratorRec, findModules, findModulesWithDuty, findNearestColleagueWithDuty, findNearestColleagueWithName, findNearestModuleWithDuty, findNextEmployeeWithDuty, fireEmployee, getClonableEmployeeCommand, getEmployeeNeeds, getEmployeeNeedsVector, getEmployeeReference, getEmployeeVector, getEmployer, getEmployerPath, getExplanationByWhichHired, getFileCoordinator, getHColor, getHDaughters, getHImage, getHiredAs, getHiringCommand, getHiringCondition, getHMother, getHShow, getImmediateEmployeesWithDuty, getNextEmployeeWithDuty, getNumberOfEmployees, getNumSupplements, getSearchableAsModule, getSupplementName, getTypeName, hireAllCompatibleEmployees, hireAllEmployees, hireAllOtherCompatibleEmployees, hireAllOtherEmployees, hireCompatibleEmployee, hireEmployee, hireEmployeeFromModuleInfo, hireNamedEmployee, hireNamedEmployee, hireNamedEmployee, hNodeAction, hSupplementTouched, incrementEmployeeBrowserRefreshSuppression, instantiateEmployee, instantiateModule, internalStartUp, isEmployerOf, isMacroAnchor, isPriorityFixed, listEmployees, listNeeds, makeEmployeeVector, moduleActiveWord, moveEmployeeToFront, numCompatibleModulesAvailable, numModulesAvailable, purposeOfEmployee, queryChooseModule, refreshBrowser, registerEmployeeNeed, registerEmployeeNeed, replaceCompatibleEmployee, replaceEmployee, replaceEmployeeWithNext, setHiringCommand, setPriorityFixed, setShowHiringPath, whatIsMyPurpose

Methods inherited from class mesquite.lib.MenuOwner

addAuxiliaryMenu, addCheckMenuItem, addCheckMenuItemToSubmenu, addItemToSubmenu, addItemToSubmenu, addLineToSubmenu, addMenuItem, addMenuItem, addMenuItem, addMenuLine, addModuleMenuItems, addSubmenu, addSubmenu, addSubmenu, addSubmenu, addSubmenu, checkMISVector, composeMenuBar, decrementMenuResetSuppression, defineMenus, deleteAllMenuItems, deleteMenuItem, destroyMenu, disposeMenuSpecifications, doom, findMenuAmongEmployers, getContainingMenuSpec, getMenu, getMenuItemSpecs, getMenuResetSuppression, getModuleWindow, getUseMenubar, incrementMenuResetSuppression, isDoomed, makeMenu, needsMenu, recomposeWindowsMenu, resetAllMenuBars, resetAllWindowsMenus, resetContainingMenuBar, setMenuResetSuppression, setMenuToUse, setModule, setModuleWindow, setUndoMenuItemEnabled, setUseMenubar, showPopUp, zeroMenuResetSuppression

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

CategDataMatcher

public CategDataMatcher()

Method Detail

sequenceMatch

public double sequenceMatch(CharacterState[] csOriginalArray,
                            int candidateTaxon,
                            int candidateStartChar,
                            MesquiteInteger candidateEndChar)

Description copied from class: DataMatcher

Returns whether candidate stretch of matrix, in taxon candidateTaxon, starting at candidateStartChar, ending at candidateEndChar, matches the data passed in the CharacterState array csOriginalArray. Note that while candidateStartChar is fixed, candidateEndChar is not, and the length of the potential matching region iis determined by the module, and the chosen end character is to be returned in candidateEndChar.

Specified by:

sequenceMatch in class DataMatcher

sequenceMatch

public double sequenceMatch(CharacterState[] csOriginalArray,
                            CharacterState[] csCandidateArray)

Returns the match of the two CharacterState arrays

Specified by:

sequenceMatch in class DataMatcher

getBestMatchValue

public double getBestMatchValue(CharacterState[] csOriginalArray)

Description copied from class: DataMatcher

Returns the value of the best possible match. Should be overridden by subclasses if they can calculate the value.

Specified by:

getBestMatchValue in class DataMatcher

getApproximateWorstMatchValue

public double getApproximateWorstMatchValue(CharacterState[] csOriginalArray)

Description copied from class: DataMatcher

Returns the approximate value of the worst possible match. Should be overridden by subclasses if they can calculate the value.

Specified by:

getApproximateWorstMatchValue in class DataMatcher

getBestMatchValue

public abstract double getBestMatchValue(long[] originalArray)

getApproximateWorstMatchValue

public abstract double getApproximateWorstMatchValue(long[] originalArray)

sequenceMatch

public abstract double sequenceMatch(long[] originalArray,
                                     long[] candidateArray)

sequenceMatch

public abstract double sequenceMatch(long[] originalArray,
                                     int candidateTaxon,
                                     int candidateStartChar,
                                     MesquiteInteger candidateEndChar)

getCompatibilityTest

public CompatibilityTest getCompatibilityTest()

Description copied from class: MesquiteModule

Returns CompatibilityTest so other modules know if this is compatible with some object.

Overrides:

getCompatibilityTest in class MesquiteModule