mesquite.align.lib
Class AlignMatch

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

All Implemented Interfaces:

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

public abstract class AlignMatch
extends CategDataMatcher

Field Summary

protected MesquiteSubmenuSpec

mss

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

AlignMatch()

Method Summary

java.lang.Object	doCommand(java.lang.String commandName, java.lang.String arguments, CommandChecker checker) A request for the MesquiteModule to perform a command.
double	getApproximateWorstMatchValue(long[] originalArray)
double	getBestMatchValue(long[] originalArray)
boolean	getHigherIsBetter() Returns whether or not better matches have higher values or not.
Snapshot	getSnapshot(MesquiteFile file) Return Mesquite commands that will put the module (approximately) back into its current state.
abstract long[]	getTransformedCandidateArray(long[] candidateArray)
protected void	initAligner()
int[][]	modifyAlignmentCosts(int[][] defaultSubs) Override if one wishes to modify the alignment costs away from the default.
double	sequenceMatch(long[] originalArray, int candidateTaxon, int candidateStartChar, MesquiteInteger candidateEndChar) Returns whether candidate stretch of matrix matches the data contained in the long array
double	sequenceMatch(long[] originalArray, long[] candidateArray) Returns the match of the two long arrays
void	setTableAndData(MesquiteTable table, CharacterData data)
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.categ.lib.CategDataMatcher

getApproximateWorstMatchValue, getBestMatchValue, getCompatibilityTest, sequenceMatch, sequenceMatch

Methods inherited from class mesquite.lib.duties.DataMatcher

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

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, 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, 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, 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

Field Detail

mss

protected MesquiteSubmenuSpec mss

Constructor Detail

AlignMatch

public AlignMatch()

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

modifyAlignmentCosts

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

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

initAligner

protected void initAligner()

setTableAndData

public void setTableAndData(MesquiteTable table,
                            CharacterData data)

Overrides:

setTableAndData in class DataMatcher

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

getHigherIsBetter

public boolean getHigherIsBetter()

Returns whether or not better matches have higher values or not.

Overrides:

getHigherIsBetter in class DataMatcher

sequenceMatch

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

Returns the match of the two long arrays

Specified by:

sequenceMatch in class CategDataMatcher

getBestMatchValue

public double getBestMatchValue(long[] originalArray)

Specified by:

getBestMatchValue in class CategDataMatcher

getApproximateWorstMatchValue

public double getApproximateWorstMatchValue(long[] originalArray)

Specified by:

getApproximateWorstMatchValue in class CategDataMatcher

sequenceMatch

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

Returns whether candidate stretch of matrix matches the data contained in the long array

Specified by:

sequenceMatch in class CategDataMatcher

getTransformedCandidateArray

public abstract long[] getTransformedCandidateArray(long[] candidateArray)

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