Step 6 of 10: Menus

Menus: bringing it all together

You may have noticed by now that PhyloWidget has quite a few configuration parameters (many of which were shown off in the gallery in the first vignette). In order to fit all of the options into a small, widget-like space, PhyloWidget provides a densely-packed set of toolbar menus allowing access to most (but not all!) of its available settings. You've already seen the search component, but click below to activate the full toolbar: The toolbar menu should look and feel fairly similar to most modern toolbars, with a couple of exceptions. Under the "view" menu, you'll find a couple of different types of menu elements, including checkboxes and what we call "number scrollers":
  • Checkboxes: these items usually control an on/off configuration setting, such as whether or not to show branch lengths. Simply click to check or uncheck the item.
  • Number scrollers: these unique menu items are used to control a numerical parameter. The cursor should become an "up-down" pointer when the mouse is hovering above these menu items, and you can change the value by clicking and dragging. To reset the value to its default, double-click the menu item.

Power user tip: many of the toolbar items have keyboard shortcuts; these are displayed to the right of the menu item. You can run this command at any time from within PhyloWidget by typing the keyboard shortcut. The shortcut for 'Zoom to Full' can be especially handy.

Nearing the end

With the addition of the toolbar menu, we've finally reached the point where you have access to all of PhyloWidget's functionality. There is still information left to mention regarding the menu system and PhyloWidget's more advanced features (for example, why some of the options under the File menu are disabled), but if you were just looking to get a basic introduction to PhyloWidget's user interface elements, then congratulations—you're done!

Full disclosure

What good would any documentation be without a boring, comprehensive listing of toolbar menu items and descriptions? We wouldn't want to disappoint, so below you will find a complete listing, accompanied by a description for each item:

  • File, for loading and saving tree files and graphics
    • New Tree: deletes the current tree and replaces it with the default.
    • Load Tree, for tree input
      • From File: opens a file dialog to select a tree file to load.
      • Manual Input: opens a text box to manually type or paste in a tree.
    • Save Tree: opens a file dialog to output a Newick-formatted version of the current tree.
    • Export Image: opens a dialog for exporting the current tree to a variety of image formats (PDF, PNG, JPG, and TIFF are supported).
  • View, for changing rendering and display options
    • Zoom to Full: zooms in or out as necessary to cause the tree to fill the screen.
    • Renderer Type, for changing the renderer
      • Rectangular: the standard cladogram view.
      • Diagonal: the slanted cladogram view.
      • Circular: a circular representation of the tree.
    • Render Options, for changing parameters related to rendering
      • Minimum Text Size: the minimum text size at which to display node labels. Very low values cause the rendering to become sluggish.
      • Branch Length Scaling: how much to horizontally "stretch" the tree. Sometimes useful for trees with very small branch length values.
      • Stretch to Fit: causes the renderer to stretch the tree to fit the width of the window.
      • Show Clade Labels: if set, the renderer will display labels of non-leaf nodes, if they exist.
      • Antialias: if set, PhyloWidget will use a smoother, but much slower, rendering method, resulting in a cleaner-looking display.
    • Style, for changing the style of the drawn tree
      • Text Multiplier: how much to scale the node label text size. A value of 1 uses the default text size.
      • Text Angle: how much to rotate the node label text.
      • Node Size: how much to scale the node size. A value of 10 is equal to the height of the whole row.
      • Line Weight: how much to scale the line weight. A value of 10 is equal to the height of the whole row.
    • Show all Labels: causes ALL leaf labels to be shown, regardless of the minimum text size. If the tree is large, this setting will cause rendering to be very sluggish. Consider yourself warned!
    • Branch Lengths: whether or not to use branch length information. Not applicable for the diagonal renderer.
  • Tree, for performing operations on the tree structure
    • Mutator: a sub-menu for randomly mutating the current tree. The sub-menu items should be self-explanatory. This is not too useful for scientific purposes, but handy for testing the software.
    • Structure, for global operations on the tree structure.
      • Align all Leaves: changes the branch lengths of the tree so that all leaf nodes are aligned.
      • Flip Tree: reverses the order of the entire tree.
      • Auto-Sort Tree: causes the tree to become 'ladderized,' or sorted to a point where each node's children are sorted according to the number of vertices in their enclosed subtrees.
      • Remove 'Elbows': removes 'elbow vertices' from the tree, or vertices which have one parent and one child.
    • Annotation, for operations affecting the tree annotation (labels, etc.)
      • Enforce Unique Labels: enforces the uniqueness of node labels, automatically appending an ending (such as "#1") to duplicate nodes.
      • Ignore Annotations: whether or not to ignore the NHX annotations when displaying and saving the tree.
      • Load Google Images: triggers a Google image search, which will search and insert images from Google into the current tree. This is a BETA feature, but feedback is welcome!

Created with Processing.