First Steps - Screen Layout
This page is intended to provide as much information about
the different components of the Bluejay screen as possible.
Main Menu Bar
The main menu (as shown below) is the application's main control
center. From here you can do most of the usual tasks of any application.
Under each Menu Item, you can find:
- Program - Drawing Prefs,
Network Prefs, Memory Prefs, Parsing Prefs, Storage Prefs, Diagnostics,
Upgrade, Exit
- Edit - Undo Action, Repeat
Action
- Session - Login,
Resume..., Destroy, Enter Edit Mode (Note: enabled only upon successful
internet / server connection)
- Bookmarks - Various
preset bookmarks.
- Document
- New, Open, Close, Rename / Reposition, Destroy, Make Snapshot Copy,
Create Milestone, Revert to Milestone, Abandon Changes, Print, Export,
Convert Image to SVG, View Raw Data
- View - Pie Chart, Two Frame,
Six Frame, Text, No Tab, Shape Tab, Orientation Tab
- Selection - Copy, Paste,
Cut, All, All Peers, None, Inverse
- Query - Define, Refine,
Perform Latest
- Help - Help Browser,
Quick Start, Program Identity (About)
Although, at first glance, one might think that this menu is
"disorganized" or "non-standard," much thought was put into
it and it's justification / explanation is as follows:
"On the far left is the topic of broadest scope: the program.
Moving to the right, with diminishing scope as we go, is first
the Session, then the document, then the pieces that comprise the document.
In descending order of importance are the four aspects of each component:
Their properties, views of them, functions that operate on them and their
access to the 'outside world.' "
- Alan Cooper's About Face - The
Essentials of User Interface Design
Note: Items "greyed-out" are either not available in your current view / contents or are not yet implemented.
Navigation Toolbar / Address Bar
Like a typical web browser, the back, forward, refresh
and bookmark buttons
are there for navigation purposes. Also, the address bar
functions as expected, taking in a web or file address for viewing.
On the right side of the Address Bar, is the mechanism
for zooming in and out of the main screen's contents:
- The plus (+) and minus (-) signs on
the outer edges of the Zooming tool allow for incremental zooming
- The number window is user-editable,
for fine-tuned zoom adjustment.
- The down-arrow allows for zoom selection
from a series of predefined zoom percentages.
Main Screen
This part of the application is the main "viewing window" where
information is graphically displayed.
Context Tree
The context tree displays or hides information provided by
the document in the main window.
How to Use the Context Tree:
The context tree displays the general structure of the document's XML.
It does not represent all of the data element instances, but what kinds
of elements are nested inside what others. By disabling a checkbox,
the data in the document fitting that nesting structure will not be considered
for painting. For example, disabling classification data elements
inside genes in AGAVE will cause genes to not be coloured according to their
classification data. In another example, bibliographic information
could be excluded from the display of a GenBank record by disabling the
references data element in the context tree. Be sure to hit "Apply"
in the top right corner of the tree to have the data masking take effect.
These types of view changes are distinct from disabling items in the Legend
because they do not simple toggle the appearance of elements fitting a biological
category, but cause a relayout of the graphic that ignores a data type altogether
(i.e. it will not appear in the legend).
Tabbed Panel
The tabbed panel consists of several components in itself and
are explained below:
Legend
The different identified genetic components are color coded
for ease of access to information. The legend serves to decode
the coding scheme.
Navigation
A base-pair "go-to" navigation feature that allows the user to specify exactly
which base pair in a particular sequence they would like to move to.
To be used for navigation through the document.
Notes
A basic text-input box for the user to add notes concerning
this document. Further feature explanation as it becomes available.
Execution Information Bar
As in a standard browser, this component gives information
as to the current state of the application and it's processing of information.
Progress Bar
Signifies the progress of the execution task at hand. (See
above, right side).
Document Rating Bar
Five yellow stars indicate relevance of the current document to the task
at hand (includes quality, etc.).
Five stars = most relevant. Selected by the user for
system feedback by clicking on the right most star for the appropriate
relevancy level.
