The Main Window is where most of the user interface resides. The major functional areas are shown below. Each of these panels can be resized by clicking and dragging its divider bar.
Click on an area to learn more:

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The toolbar is a place to find the most commonly used functions in Juxta. From left to right, these functions are:
Open Comparison Set—Loads a comparison set from a previously saved .jxt file.
Save Comparison Set—Saves the current comparison set to a .jxt file.
Add Document—Imports a new document into the comparison set (see Add Document Dialog).
Remove Document—Removes the currently selected document from the comparison set.
Edit Bibliographic Information—Edit the bibliographic information of the currently selected document (see Bibliographic Info Dialog).
Find Text—Opens the Find Text Dialog for finding text in the currently selected document (see Find Dialog).
Open Collation Histogram—Opens the Collation Histogram (see Collation Histogram Dialog).
Generate Critical Apparatus—Generates a critical apparatus for the currently selected document (see Generate Critical Apparatus Dialog).
Toggle Location Markers—Toggles location marker display in the Document Panel for lines (or stanzas if these are marked).
Re-Collate—Documents are collated automatically when a new document is added or removed from the Comparison Set. This is only needed if you want to change the options, such as ignoring punctuation.
Search Text In Files—Type in the input box and click on the icon to do a search of a particular term or terms in all documents in the comparison set. Note that you can see a list of recently searched for terms by clicking the triangle just to the right of the input box.

The Comparison Explorer displays all documents in the current comparison set. These documents are automatically collated against one another.
Documents can be added or removed from the list by using the Add Document and Remove Document buttons on the toolbar. The display name of a document can be modified by editing its “short name” field in the Bibliographic Info Dialog.
The document highlighted in green is the current base document, from which comparisons are made. Each of the documents has a meter to the right indicating its degree of difference from the base document. Placing the mouse pointer over a given document reveals this value expressed as a number.
To the left of the document name is a checkbox. Deselecting this checkbox temporarily excludes the document from the collation results. This exclusion is applied throughout the rest of Juxta's computations and outputs. For example, excluded documents do not appear in the critical apparatus output.

The Document Panel can display the results of an entire collation or it can zoom in on a specific comparison between two texts. To facilitate this, the Document Panel has two modes: Heat Map View and Comparison View. These modes can be toggled with the tabs at the bottom of the panel.
Line numbering and other markings can be summoned by clicking on the “Toggle Location Marks” button on the toolbar.
When the Heat Map View is selected, Juxta displays a collation against the current base text. The current base text is the text highlighted in green in the Comparison Explorer to the left of the Document Panel.
The text is color coded to indicate the degree of variance evident at any particular area of the text. Lighter shades of blue indicate that fewer witness vary from the base text at this location. The darker the shade of blue, the more witnesses differ at this location.
Clicking on the text itself reveals all variants for a particular location. The variants display in the right hand margin of the text as depicted below:

When such variations are displayed one can add critical annotations. The operation is initiated by mousing over the witness label (displayed in green) and clicking the grayed-out star that appears on mouse over. This will display an “Edit Note” box where the annotation is entered. The note appears in the Secondary Panel below the Document Panel.
When an editorial note has been entered about a specific variant, the grayed-out star is displayed in bold ( ) and remains on display if the comparison set is saved.
There are four types of differences reported by Juxta. As the image illustration above shows, they are marked with the following glyphs:
—Indicates a difference between base and witness text at this location.
—Indicates that there is text present at this location in the witness text where there is no such text present in the base text.
—Indicates that there is text present in the base text that is not present at this location in the witness text.
—Indicates there there is a move defined.
If the user clicks on a difference when in Annotation Mode the Edit Note dialog will appear.
The Comparison View allows for side-by-side inspection of two texts. While the Heat Map View permits the user to view the status of the base text relative to all of the other texts in the collation, the Comparison View focuses on just two texts at a time. As the user scrolls through the comparison, the two texts are kept in step with one another. The user can easily flip back and forth between the Heat Map View and the Comparison View by selecting a highlighted difference from either text. Line numbering and other markings can be summoned in this view by clicking on the “Toggle Location Marks” button on the toolbar.
Here is the toolbar in the comparison panel:

The two drop-down controls allow you to choose any of the texts for the left and right sides. The lock icon between the drop-down controls toggles between having the two texts scroll together and having the text each have a scroll bar so they can be scrolled independently. The icon on the upper right side is the Move command. It is enabled when there is a selection made in both texts.

The Secondary Panel houses supporting information relevant to the document or documents currently being displayed in the Document Panel. The Secondary Panel has four modes: Notes View, Image View, Moves View, and Search View. These modes can be selected by clicking on the tabs at the bottom of the panel.
The Notes View is a table of the annotations that the user has recorded for this comparison set. For each annotation, the following columns of information are displayed:
Base Text—The base text for the difference this note marks.
Witness Text—The witness text for the difference this note marks.
Lemma—The text heading that heads the list of variants.
Notes—The text of the annotation itself.
The Notes View also has a toolbar containing the Document Tracking Mode Button and the Delete Note Button. When the Document Tracking Mode Button is depressed (which is the default behavior) the Document Panel automatically repositions to display text corresponding to the currently selected note. The Delete Note Button deletes the currently selected note or notes. Double clicking on a note in the Notes View brings up the Edit Note Dialog for the selected note.
The Image View displays an image associated with the text presently in the Document Panel. The image can be zoomed using the buttons on the toolbar below the image area. The image can be panned by pointing to it with the mouse, holding down the mouse button, and moving the mouse while holding the button. Images are associated with location markers or milestones in the process of importing a document in XML format (described below).
The Moves View shows the location of each move that has been created in the comparison set. To see a move, click on it and it will appear in the Document View. To delete a move, click on it and click on the "Remove Selected View" icon on the bottom of the Moves View.
The Search View shows the results of the last search. Click on a search item and it will be shown in the Document View. The "Highlight All Search Results" icon on the bottom of this view toggles whether all the matches are highlighted in the Document View.