TreeDyn User's Manual
TreeDyn Tutorial Identification - Querying leaf labels
Abstract

The tutorial deals with the "Find panel", basicaly how to locating leaves on a tree knowing its name : you select a name from a list and the corresponding graphical item is hightlight. But the TreeDyn "Find panel" has much more features. This tutorial will teach you how to use patterns on leaves names, helping you to detect clusters, it may be usefull if the leaves names integrate knowledge throught a given code. We will explore the graphical operations of TreeDyn for higthlighting items, either in exlusive or inclusive maner. All these processes will also be apllied on multiple trees, teaching you how to use the tree targetting system of TreeDyn. Finally we will see Alternagraphics, that is to say how to make tree graphicals animations. Follow this tutorial step by step, the differents section are not independants.


Table of contents
Table of contents:

Data:
Data set #1 Newick

Conventions:
  • M1 = Left Mouse Button
  • M3 = Right Mouse Button
  • CM = Contextual Menu with M3

Opening a tree
  • Download and open this tree (Main TreeDyn Panel / File menu / Open command)

    • Get ready with the "Find Panel"

  • Main TreeDyn Panel / View menu / "Find panel"
  • "Operation" menu. The "Operation" menu let you select a highlighting operation. By default, this operation is set to "Leaf Foreground Color".
  • "Reset" menu. The Reset menu enable you a manual or an automatic itinitialisation of graphicals variables between each find process
  • "Tree(s) Target" menu. The "Tree(s) Target" menu let you target the tree(s) you want to explore, whatever their including window
  • "Case sensitive" checkbox. If Case sensitive checkbox is check on, the find process will be case sensitive : the pattern a* will not match A*
  • "Update" button. If you open tree(s) after the activation of the find panel, the update button will update the leaves list
  • "Filter" entry. The filter entry let you enter filters on leaves list, for instance if you want to see only the leaves beginning with the letter A, enter the pattern A*. Note that the find process will not be activated
  • "Leaves" List. the leaves list is the list of all the leaves names from all the tree(s) currently open within a TreeDyn session. Don't forget to update this list with the update button. If you double-clic on a leave name, a Find process will be launched: it will higligth the graphical item corresponding to the selected leave, using the current operation (see "Operation" menu) for the targetted tree(s) (see "Tree(s) target" menu)
  • "Find" entry. The Find entry is the main find entry for exploring tree(s). You can use pattern here : the key A* will higlight the graphical items corresponding to the leaves name beginning with an A, knowing the current operation and the targetted tree(s)
  • "History" List. all the find keywords you use are list here : either leaves names or patterns. Select an item from this list and the find process will be reactivated.
  • "Clear History" button. This control will clear the history list
  • "Alternagraphics" button. Alternagraphics enable you the making of Find animations using a selected list of Find Keywords keeps from the history list.

    • Looking for a leave
  • Find panel/"Operation" menu: select the "Leaf Foreground Color"
  • Find panel/"Tree(s) Target" menu: check on the tree "tree"
  • Find panel/"Update" menu: M1
  • Find panel/Leaves listbox: double-M1 on several leave names and look at the tree, each selected leaves names is highlight in red (use the tree canvas scrollbar if necessary).
  • Main TreeDyn Panel / View menu / Parameters panel (Color/Font/...): Color tab, select another color than the previous red one
  • Find panel/Leaves listbox: select leaves, look at the tree. The higlitht operation now use the new color. Depending on the TreeDyn operation you have selected, you may have to specify some modalities from the parameters panel (color but also text, symbols, font and so on)
    • Exlusive/Inclusive queries
  • the queries from the previous step are said to be Inclusive, that is to say a find process do not remove previous queries. In our example, as you select more and more leaves names from the Find listbox, there is more and more leaves with a red (or another color) Foreground color on the tree. Each process is additive. You keep results from previous searches.
  • Find panel/Operation: select the "Leaf Background color"
  • Find panel/Leaves listbox: select a leave (double-M1), look at the tree. The corresponding leave have now a new background color
  • Find panel/"Reset" menu: check on the "Leaf Background color" in the "Graphical variables to reset" section of the menu. Moreover, check on "Automatic Reset" option (same menu).
  • Find panel/Leaves listbox: select a leave (double-M1). Look at the tree: all the leaves with a hightlight foreground color are still here, but the new background color have switch to the last selected leave. The find process is said to be "Exclusive on Leaves Background color". Each time you select a leave from the find panel, all previous Leaves background colors are removed before the launched of the research.
  • Find panel/"Reset" menu: check on "select all" option "Graphical variables to reset" section of the menu
  • Find panel/Leaves listbox: select leaves. All graphical variable are initialize from a find process to another.
    • Highlighting leaves using patterns
  • Find panel/Operation menu: select the "Node Foreground Color"
  • Main TreeDyn Panel / View menu / Parameters panel (Color/Font/...): Color tab, select red color
  • Find panel/"Tree(s) Target" menu: check on the tree "Tree"
  • Find panel/"Case sensitive" checkbox: check on
  • Find panel/Find entry: enter the pattern A* and return: look at the tree. The find process have hightlight the foreground color of subtrees in red where all the corresponding leaves have a name begining with a "A"

    The following special sequences may appear in pattern:
    • * Matches any sequence of characters in string, including a null string.
    • ? Matches any single character in string.
    • [chars] Matches any character in the set given by chars. If a sequence of the form x-y appears in chars, then any character between x and y, inclusive, will match. {[A-z]} matches '_' when matching case-sensitively ('_' falls between the 'Z' and 'a'), with nocase this is considered like {[A-Za-z]} .
    • \x Matches the single character x. This provides a way of avoiding the special interpretation of the characters *?[]\ in pattern.
    It may be useful to put in leaves names some code related to characteristics and then using find patterns ans seing clusters

    • Exploring TreeDyn operations
  • Set up a Find session, use either leaves names or patterns and try several TreeDyn graphical operations from the "operation menu", for instance:
  • Leaf Illustration (columns) pattern A* Color blue (see below)
  • Leaf Annotate (columns) pattern C* Color red
  • Node Illustration (link) pattern A* Color green
  • Node Annotate pattern A*J* Color purple

    • Targetting several trees
  • All the Find operations can be applied on one or several trees, whatever their window(s). The only thing you have to do for working on multiple trees, is to use the TreeDyn targetting system. There is 3 ways to use it :
    1. Find panel / Tree(s) Target menu. This cascade menu is ordering trees by their corresponding window. Check on the trees you want to explore with Find sessions. You can select/unselect all the trees of a given window, and finally select all the trees of the current TreeDyn seesion, whatever their window (the option "Select All" a the menu root)
    2. Main TreeDyn panel / View menu / Tree panel. This panel list all the trees of the current session. Use the update button for seeing a complete list. The trees are classify by their corresponding window. Note that one window may contains several trees. For targetting a tree, simply check on its corresponding checkbox. When you do that a box will flash around the tree. If the checkbow is off the tree will not be explore by the Find process. You can target/untarget all the trees of a given window by using the "select all" / "unselect all" buttons respectively.
    3. you can target a tree or a set of trees by using contextual menus. For instance Canvas CM, Navigation menu, the command "Target Trees (exclusif)" will set tree target list to all the tree of the current window (previous targeted trees will be removed). The command "Target Trees (inclusif)" will add all the trees of the window to the tree target list. Finaly, the command "UnTarget Trees" will remove all the trees of the current window from the tree target list.
    • Alternagraphics
  • Find panel/Operation menu: select the "Leaf Foreground Color"
  • Main TreeDyn Panel / View menu / Parameters panel (Color/Font/...): Color tab, select red color
  • Find panel/"Tree(s) Target" menu: check on the tree "Tree"
  • Find panel/"Case sensitive" checkbox: check on
  • Clear the history listbox using the "Clear History" button
  • Find panel/Find entry: query the tree using thepatterns "A*", "B*", "C*", "S*" and "X*"
  • Activate the "Alternagraphics" panel ("Alternagraphics" button)
  • when activated, the Alternagraphics window list all the Find keywords from the Find panel history listbox. You can select/unselect all these keywords by using the "Select All" / "Unselect All" buttons, or by M1 the items themself
  • the operation menu let you select the operation which will be used for alternagraphics session
  • the manual mode let you query the tree with patterns in a manual step by step process with "Next" or "Previous" buttons
  • the automatic mode query all the selected Find keywords automatically. You can specify the number of loops the process will do. The time laps entry, in milliseconds, is the time between each queries of a given loop. When these parameters are set M1 the "Query" button. You can stop the process using the stop button, which will stop at the end of the current loop