mesquite.align.lib
Class AlignScoreForTaxonGen

java.lang.Object
  mesquite.lib.MenuOwner
      mesquite.lib.EmployerEmployee
          mesquite.lib.MesquiteModule
              mesquite.lib.duties.NumberForTaxon
                  mesquite.align.lib.AlignScoreForTaxonGen

All Implemented Interfaces:

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

public abstract class AlignScoreForTaxonGen
extends NumberForTaxon

Field Summary

protected PairwiseAligner	aligner
protected int	alphabetLength
protected MesquiteInteger	comparisonTaxon
protected Taxa	currentTaxa
protected MatrixSourceCoord	matrixSourceTask
protected MCharactersDistribution	observedStates

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

AlignScoreForTaxonGen()

Method Summary

void	calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString)
java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandChecker checker) A request for the MesquiteModule to perform a command.
void	employeeParametersChanged(MesquiteModule employee, MesquiteModule source, Notification notification) Generated by an employee calling its parametersChanged method.
void	employeeQuit(MesquiteModule employee) Generated by an employee who quit.
protected abstract void	getAlignmentScore(DNAData data, MCategoricalDistribution observedStates, int it1, int it2, MesquiteNumber score)
CompatibilityTest	getCompatibilityTest() Returns CompatibilityTest so other modules know if this is compatible with some object.
java.lang.String	getExplanation() returns an explanation of what the module does.
java.lang.String	getParameters() returns current parameters, for logging etc..
abstract java.lang.String	getScoreName()
Snapshot	getSnapshot(MesquiteFile file) Return Mesquite commands that will put the module (approximately) back into its current state.
void	initAligner()
void	initialize(Taxa taxa) Called to provoke any necessary initialization.
boolean	isSubstantive() returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module
int[][]	modifyAlignmentCosts(int[][] defaultSubs) Override if one wishes to modify the alignment costs away from the default.
boolean	queryReferenceTaxon()
boolean	requestPrimaryChoice() returns whether this module is requesting to appear as a primary choice
boolean	startJob(java.lang.String arguments, java.lang.Object condition, boolean hiredByName) startJob is called automatically when an employee is hired.

Methods inherited from class mesquite.lib.duties.NumberForTaxon

calculateNumber, calculateNumberInContext, getDutyClass, getDutyName, getNameOfValueCalculated, initialize, returnsMultipleValues

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, echoStringToFile, employeeOutputInvalid, employerWithWindow, endJob, fileAboutToBeWritten, fileDirtiedByCommand, fileElementAdded, fileReadIn, finalize, findNEXUSBlock, getAppletInfo, getAuthors, getAutoSaveMacros, getBrowserManualPath, getBrowserPanel, getBuildDate, getBuildVersion, getCitation, getCommandPagePath, getDateReleased, getDefaultModule, getDocsPath, getExpectedPath, getFunctionIconPath, getHireSubchoice, getHTMLExplanation, getID, getIfLastEmployee, getKeywords, getManualPath, getMesquiteVersion, getModuleInfo, getName, getNameAndParameters, getNameForMenuItem, getNexusBlockTest, getNexusCommands, getNexusCommandTest, getPackageImagesPath, getPackageIntroModule, getPackagePath, getParametersChangedNotifier, getPath, getPermanentIDString, getProject, getRootImageDirectoryPath, getRootPath, getShortClassName, getShortClassName, getSizedRootImageFilePath, getSubfunctions, getSubfunctionsVector, getURLString, getUserChooseable, getVersion, getVersionInt, getVersionOfFirstRelease, getVeryShortName, getXMLPrefsVersion, iQuit, iQuit, isCorrectRootTag, isPrerelease, 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, respondToPaging, returningPage, saveLastResult, saveLastResult, saveLastResult, saveLastResult, saveLastResultString, saveLastResultString, setAutoSaveMacros, setProject, setToLastEmployee, showCitation, showHTMLSnippet, showLogWindow, showLogWindow, showManual, showMe, showWebPage, showWebPage, sorry, 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

Methods inherited from interface mesquite.lib.duties.NumberForItem

accumulateParameters, getName, getNameAndParameters

Field Detail

matrixSourceTask

protected MatrixSourceCoord matrixSourceTask

currentTaxa

protected Taxa currentTaxa

observedStates

protected MCharactersDistribution observedStates

aligner

protected PairwiseAligner aligner

alphabetLength

protected int alphabetLength

comparisonTaxon

protected MesquiteInteger comparisonTaxon

Constructor Detail

AlignScoreForTaxonGen

public AlignScoreForTaxonGen()

Method Detail

startJob

public boolean startJob(java.lang.String arguments,
                        java.lang.Object condition,
                        boolean hiredByName)

Description copied from class: MesquiteModule

startJob is called automatically when an employee is hired. The parameter scripting indicates if the hiring occurs in the context of automated scripting (e.g., on reading a Mesquite block of a NEXUS file). The module can limit user interface calls (e.g. dialog boxes) when scripting occurs.

The MesquiteModule should override this method, to add code to initialize things it needs, and to hire relevant necessary employees. startJob must return true if the module was successfully started; false otherwise. Thus, if the module needs a data matrix but the file has none, it returns false and the hiring process is undone.

Most modules will ignore the arguments and condition.

Specified by:

startJob in class MesquiteModule

getSnapshot

public Snapshot getSnapshot(MesquiteFile file)

Description copied from class: MesquiteModule

Return Mesquite commands that will put the module (approximately) back into its current state. Used so that on file save, a Mesquite block can be saved that will return the user more or less to previous state.

Overrides:

getSnapshot in class MesquiteModule

employeeQuit

public void employeeQuit(MesquiteModule employee)

Generated by an employee who quit. The MesquiteModule should act accordingly.

Overrides:

employeeQuit in class MesquiteModule

modifyAlignmentCosts

public int[][] modifyAlignmentCosts(int[][] defaultSubs)

Override if one wishes to modify the alignment costs away from the default.

initAligner

public void initAligner()

requestPrimaryChoice

public boolean requestPrimaryChoice()

returns whether this module is requesting to appear as a primary choice

Overrides:

requestPrimaryChoice in class MesquiteModule

initialize

public void initialize(Taxa taxa)

Called to provoke any necessary initialization. This helps prevent the module's intialization queries to the user from happening at inopportune times (e.g., while a long chart calculation is in mid-progress)

Specified by:

initialize in class NumberForTaxon

calculateNumber

public void calculateNumber(Taxon taxon,
                            MesquiteNumber result,
                            MesquiteString resultString)

Specified by:

calculateNumber in class NumberForTaxon

getAlignmentScore

protected abstract void getAlignmentScore(DNAData data,
                                          MCategoricalDistribution observedStates,
                                          int it1,
                                          int it2,
                                          MesquiteNumber score)

queryReferenceTaxon

public boolean queryReferenceTaxon()

doCommand

public java.lang.Object doCommand(java.lang.String commandName,
                                  java.lang.String arguments,
                                  CommandChecker checker)

Description copied from class: MesquiteModule

A request for the MesquiteModule to perform a command. It is passed two strings, the name of the command and the arguments. This should be overridden by any module that wants to respond to a command.

Specified by:

doCommand in interface Commandable

Overrides:

doCommand in class MesquiteModule

getCompatibilityTest

public CompatibilityTest getCompatibilityTest()

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

Overrides:

getCompatibilityTest in class MesquiteModule

employeeParametersChanged

public void employeeParametersChanged(MesquiteModule employee,
                                      MesquiteModule source,
                                      Notification notification)

Description copied from class: MesquiteModule

Generated by an employee calling its parametersChanged method. The MesquiteModule should act accordingly, for instance, asking the employee to do a recalculation.

Overrides:

employeeParametersChanged in class MesquiteModule

getScoreName

public abstract java.lang.String getScoreName()

isSubstantive

public boolean isSubstantive()

Description copied from class: MesquiteModule

returns whether this module does substantive calculations affecting analysis results, or only a graphical/UI/input-output module

Overrides:

isSubstantive in class MesquiteModule

getParameters

public java.lang.String getParameters()

Description copied from class: MesquiteModule

returns current parameters, for logging etc..

Specified by:

getParameters in interface NumberForItem

Overrides:

getParameters in class MesquiteModule

getExplanation

public java.lang.String getExplanation()

returns an explanation of what the module does.

Specified by:

getExplanation in interface Explainable

Overrides:

getExplanation in class MesquiteModule