Module: Tree Window

Full package name: mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker
Duty: Tree Window Maker (mesquite.lib.duties.TreeWindowMaker)

Module Explanation

Makes a basic tree window, which contains a tool palette. Hires assistants for the tree window (e.g., Trace Character).

Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70

Menu items of Tree Window

Tree Source

Commands of Tree Window

getTaxa
- Explanation: Returns the block of taxa associated with this tree window
show
- Explanation: Displays the tree window
suppressEPCResponse
- Explanation: Suppresses responding to parameters changed.
desuppressEPCResponse
- Explanation: Suppresses responding to parameters changed.
desuppressEPCResponseNORESET
- Explanation: Suppresses responding to parameters changed.
setTree
- Explanation: Sets the tree in the window to the description passed
- Parameters: [standard tree description]
setEditMode
- Explanation: Sets the mode to that of With Trees To Edit By Hand
setTreeSourceEditMode
- Explanation: Sets the source of trees for edit mode
setTreeSource
- Explanation: Sets the source of trees
- Parameters: [name of tree source module]
makeTreeWindow
- Explanation: Constructs a tree window referring to a block of taxa, or returns the existing window if this module has already made one.
- Parameters: [number of block of taxa, 0 based]
getTreeDrawCoordinator
- Explanation: Returns the tree draw coordinating module
getTreeWindow
- Explanation: Returns the tree window
getTree
- Explanation: Returns the tree
treeEdited
- Explanation: Sets the tree as having been edited (thus showing it as "untitled"
newAssistant
- Explanation: Hires a tree display assistant module
- Parameters: [name of assistant module]
newWindowAssistant
- Explanation: Hires a tree window assistant module
- Parameters: [name of assistant module]
logLastResultString
- Explanation: Logs last result string
getLastResultString
- Explanation: Returns last result string
getLastResult
- Explanation: Returns last MesquiteNumber result
newAssistant
- Explanation: Hires a tree display assistant module
- Parameters: [name of assistant module]
getInfoPanel
- Explanation: Returns the tree info panel
getAsTable
- Explanation: Returns analyses at nodes as a table
showAsTable
- Explanation: Shows analyses at nodes as a table
showTaxon
- Explanation: Shows taxon
- Parameters: [id of taxa block][number of taxon]
selectTaxon
- Explanation: Selects taxon
- Parameters: [number of taxon]
legendsToHome
- Explanation: Puts legends in default position
getTreeDrawCoordinator
- Explanation: Returns the tree draw coordinating module
forceRepaint
- Explanation: Forces a repaint
newWindowAssistant
- Explanation: Hires a tree window assistant module
- Parameters: [name of assistant module]
getTree
- Explanation: Returns the tree
bringToFront
- Explanation: Brings the graphics of an assistant module to the front
- Parameters: [number of assistant module among TreeDisplayDrawnExtra owners]
closeDisplayAssistant
- Explanation: Closes an assistant module
- Parameters: [number of assistant module]
saveMacroDisplayAssistant
- Explanation: Saves a macro to redo the analysis of an assistant module
- Parameters: [number of assistant module]
treeEdited
- Explanation: Sets the tree as having been edited (e.g. so that it can be treated as "untitled")
queryEditedTreeMode
- Explanation: Sets the tree to that described by the string passed
- Parameters: [Parenthesis notation string of tree]
setTree
- Explanation: Sets the tree to that described by the string passed
- Parameters: [Parenthesis notation string of tree]
showRecentEdited
- Explanation: Sets the tree to a recently edited tree
- Parameters: [number of edited tree]
recoverLastEditedTree
- Explanation: Recovers the last edited tree
showWindow
- Explanation: Shows the window
setTreeAnnotation
- Explanation: Sets the annotation for the current tree
- Parameters: [Annotation for tree in window]
getNumTrees
- Explanation: Returns the number of trees
getTreeNumber
- Explanation: Returns the current tree number
setTreeNumber
- Explanation: Sets the tree to be the i'th one from the current tree source
- Parameters: [number of tree to be shown]
chooseTree
- Explanation: Present a dialog box to choose a tree from the current tree source
storeTreeAs
- Explanation: Stores the current tree as a new stored tree in a tree block
storeTreeAsOther
- Explanation: Stores the current tree as a new stored tree in another tree block
storeTree
- Explanation: Stores the current tree back into the original stored tree from which it came
getTreeVector
- Explanation: Gets tree vector being shown.
nextTree
- Explanation: Goes to the next tree in the tree source. THIS RUNS ON GUI THREAD.
previousTree
- Explanation: Goes to the previous tree in the tree source. THIS RUNS ON GUI THREAD.
stepThroughTrees
- Explanation: Steps through the trees.
goToNextTree
- Explanation: Goes to the next tree in the tree source.
undo
- Explanation: Undoes the previous tree change
copyTree
- Explanation: Copies a description of the tree
Paste
- Explanation: Pastes a description of the tree
alterBranchLengths
- Explanation: Hires a module to alter or transform branch lengths
- Parameters: [name of module]
alterTree
- Explanation: Hires a module to alter the tree
- Parameters: [name of module]
toggleInfoPanel
- Explanation: Toggles whether the info panel is on
togglePrintName
- Explanation: Toggles whether to add the name of the tree when printing
useSuggestedSize
- Explanation: (For old scripts only) Requests that the tree is drawn to a default (suggested) size
toggleSizeToFit
- Explanation: (For old scripts only) Sets whether or not the tree is drawn so as to fit within the window, or so as to fit within a scrollable pane
- Parameters: [on or off to indicate whether constrained to window]
sizeDrawing
- Explanation: (For old scripts only) Sets the size of the drawing pane area (and implicitly sets to fixed size)
- Parameters: [width in pixels of drawing area] [height in pixels of drawing area]
setOrigin
- Explanation: (For old scripts only) Sets the origin for the scrolling area
- Parameters: [origin x] [origin y]
scale
- Explanation: Sets zoom scale
- Parameters: [log base 2 of scale]
setDrawingSizeMode
- Explanation: Sets the drawing size mode
- Parameters: [mode] [width in pixels of drawing area] [height in pixels of drawing area] [x origin] [y origin]
toggleLegendFloat
- Explanation: When Size to Window is false, brings legends into view
toggleTextOnTree
- Explanation: In Text version of window, controls whether extras like trace character show their information directly on a tree or as a list of nodes
setSize
- Explanation: Sets size of tree window
- Parameters: [width in pixels of window] [height in pixels of window]
setTool
- Explanation: Sets the current tool
- Parameters: [name of tool]
rootAlongBranch
- Explanation: Root current tree along branch
- Parameters: [branch number]
moveBranch
- Explanation: Move one branch onto another
- Parameters: [branch being moved] [branch onto which first will be attached]
exchangeBranches
- Explanation: Exchange two branches
- Parameters: [first branch number] [second branch number]
magnifyClade
- Explanation: Magnify clade descendant from node
- Parameters: [node number]
zoomBT
- Explanation: Zoom image
- Parameters: [branch][x][y]
zoom
- Explanation: Zoom image
- Parameters: [x][y]
zoomReset
- Explanation: Resets zoom scale to normal
toggleRerootLadderize
- Explanation: Toggles whether or not to ladderize after rerooting
zoomOptions
- Explanation: Show popup for options for zoom
- Parameters: [x][y]
rerootOptions
- Explanation: Show popup for options for reroot
- Parameters: [x][y]
ladderize
- Explanation: Ladderizes the clade
- Parameters: [branch number]
focalLadderize
- Explanation: Ladderizes the clade with focal taxon at left or right
- Parameters: [taoxn number]
collapseBranch
- Explanation: Collapse branch to yield polytomy
- Parameters: [branch number]
collapseAll
- Explanation: Collapse all internal branches in clade descendant from node
- Parameters: [node number]
drawAsTriangle
- Explanation: Draw clade descendant from node compactly as a triangle
- Parameters: [node number]
cutClade
- Explanation: Cut clade descendant from node
- Parameters: [node number]
cutSelectedTaxa
- Explanation: Cuts selected taxa from the tree
showTaxaList
- Explanation: Shows the list of taxa
undo
- Explanation: Undoes the previous change in the window
setToPreviousTool
- Explanation: Sets the tool to the previous tool.
showSnapshot
- Explanation: Shows the commands needed to put window and its modules into their current states
text
- Explanation: Put text version of window into log
selectTree
- Explanation: Selects tree
- Parameters: [number of tree][id of tree block]
touchTaxon
- Explanation: Touches taxon (selects it and shows it if possible)
- Parameters: [number of taxon][id of taxa block]
selectCharacter
- Explanation: Selects character
- Parameters: [number of character][id of character matrix]