Full package name: mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator Duty: File Coordinator (mesquite.lib.duties.FileCoordinator)
Module Explanation
Coordinates the reading, maintenance and linkages of files, which include Taxa, Trees, CharacterData, and other objects. This module is hired directly by the Mesquite trunk module.
Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70
Commands of Basic File Coordinator
getNumberOfDataSets
Explanation: Returns the total number of character data matrices stored in the project
getDataSets
Explanation: Returns a vector of the character data matrices stored in the project
writeProtect
Explanation: Sets the home file of the project so it is write protected
getNumberOfTaxas
Explanation: Returns the number of sets of taxa stored in the project
getTaxas
Explanation: Returns a vector of the sets of taxa stored in the project
getCharacterModel
Explanation: Returns a character model stored in the project
Parameters: [name of character model
timeSaved
Explanation: Reads from the file the time the file was last saved (used in IDSnapshot)
Parameters: [time in milliseconds]
linkFileExp
Explanation: Reads a file as linked to a current file, so that they can share information, with an explanation as to what link is for, for error reporting
Parameters: [fileDescriptionText][path to file][importer]
linkFile
Explanation: Reads a file as linked to a current file, so that they can share information
Parameters: [path to file][importer][failureText]
linkURL
Explanation: Reads a file at a URL as linked to a current file, so that they can share information
Parameters: [URL]
includeFile
Explanation: Reads a file and incorporates all of its information into the home file of the current project
Parameters: [path to file]
includeFileFuse
Explanation: Reads a file and incorporates all of its information into the home file of the current project
Parameters: [path to file]
revert
Explanation: Reverts to saved by closing ALL files without saving then opening the home file of project
getNEXUSFileForReading
Explanation: Opens a NEXUS file and returns it for reading
Parameters: [path to file]
getNEXUSFileBlock
Explanation: Opens a NEXUS file and returns the first block of a given type
Parameters: [block type][path to file]
includeURL
Explanation: Reads a file at a URL and incorporates all of its information into the home file of the current project
Parameters: [URL]
linkTreeFile
Explanation: Reads a tree file as linked to a current file, so that they can share information
Parameters: [path to file]
includeTreeFile
Explanation: Reads a tree file and incorporates all of its information into the home file of the current project
Parameters: [path to file]
newLinkedFile
Explanation: Create a new linked file
Parameters: [path to file]
showChart
Explanation: Brings a current chart window to the fore
Parameters: [number of chart window]
getAssistant
Explanation: Returns a reference to the file assistant module
Parameters: [name of module]
chartWizard
Explanation: Brings up the chart wizard
newAssistant
Explanation: Hires new file assistant module
Parameters: [name of module]
saveFiles
Explanation: Save all files in project
saveFile
Explanation: Saves file
Parameters: [number of file]
saveHomeFile
Explanation: Saves home file
Parameters: [number of file]
renameAndSaveFile
Explanation: Renames file
Parameters: [number of file]
saveFileAs
Explanation: Saves file as... to create a separate copy
Parameters: [number of file]
getInfo
Explanation: Gives information about the project
export
Explanation: Exports information to another format
saveLinkagesAs
Explanation: NOT FUNCTIONING
closeFile
Explanation: Closes file
Parameters: [number of file]
closeAllWindows
Explanation: Closes all tabs
showFileOnDisk
Explanation: Show file on disk
Parameters: [number of file]
closeFileByName
Explanation: Closes file
Parameters: [name of file]
closeProject
Explanation: Closes this project (which may consist of a single open file)
getPathToProject
Explanation: Returns path to this project
getHomeFileName
Explanation: Returns name of home file of this project
getProject
Explanation: Returns this project
getProjectID
Explanation: Returns identification number of this project
allToFront
Explanation: Brings all of the windows belonging to the project to the front.
end
Explanation: Not used; placed here to suppress warning that command "end" from Mesquite block not handled
