The following image illustrates the main components of the CINEMA user interface, the CINEMA Control window and an Alignment View window. The CINEMA control window is, as its name suggests, the main hub of the CINEMA application, whilst Alignment Views are used to display (and support interaction with) individual alignments. The CINEMA control window manages information about an alignment, e.g. its sequence groups, motifs and annotations; it is also context-sensitive: it will update itself to display information pertinent to the currently active alignment. Alignment Views are discussed in detail in the next section.

The central tool in CINEMA is the alignment view, a powerful and flexible interface for visualising and editing a
multiple sequence alignment. With an alignment view, it is possible to:

• Navigate an alignment in a fast, simple and intuitive manner
• Visualise an alignment at different levels-of-detail
• Open multiple views onto a single alignment, each capable of showing different regions of the alignment, at different levels of detail and
  with different residue colour-schemes
• Edit an alignment directly using the mouse
• Open different alignments, each in their own view, for side-by-side comparison.

An alignment view consists of four regions, as illustrated in the following image:

1. The sequence alignment itself, which fills the main central region of the view.
2. The sequence labels, to the left of the sequences. The sequence labels give an identifying name for each sequence (usually the database ID or
   accession), and illustrate any sequence groupings that have been assigned.
3. The regions above and below the alignment, which can house a variety of tools and visual aids. In the image, both
   regions are showing a numerical key, illustrating the start and end indices of the section of the alignment currently on display. The
   bottom region also houses a consensus sequence, coloured to show the degree of conservation.
4. The toolbar, providing fast access to the different interaction modes, zoom controls, adding sequences, etc.

In general, a multiple sequence alignment will be considerably larger in area than the view onto it; only small sub-sections of such an alignment will thus be visible at a time. The alignment view offers a number of simple methods for navigating a large alignment, so that different sections of it can be displayed.

Scroll bars

Scroll bars are provided at the bottom and right edges of the alignment view window when necessary, and allow the current view to be scrolled left/right or up/down in the standard manner using the mouse.

Keyboard navigation

The alignment may also be navigated using a number of keyboard short-cuts:

• The cursor keys can be used to move the current view left or right a residue position at a time, and up or down a sequence at a time.
• The Home and End keys move the view to the beginning and end of the alignment respectively, without changing the vertical position of the view in any way. Holding down the control key while pressing Home or End moves the view to the top-left or bottom-right edges of the alignment.
• The Page Up and Page Down keys move the view up or down, by the number of sequences that fill the height of the current view window (a 'page' of sequences). Holding down the control key while pressing Page Up or Page Down moves the view directly to the top or bottom of the alignment.

Mouse-based navigation

If present, the mouse-wheel may be used as a short-cut for some of the alignment navigation described above. There are 3 possible mouse-wheel navigation modes:

• Mouse-wheel alone scrolls the alignment up/down on a per-sequence basis, or, when all sequences are currently displayed, scrolls the alignment left/right on a per-residue basis.
• Mouse-wheel & Ctrl key scrolls the alignment right/left a screen-width at a time.
• Mouse-wheel & Shift key zooms the view in/out, in the same manner as the free zoom control.

It is also possible to freely pan around the alignment area with the mouse, by holding down the space bar and clicking and dragging with the left hand mouse button

While working with a sequence alignment, it may be desirable to visualise it at different levels of detail, providing, for example:

• A general overview of the entire alignment.
• A close-up view onto a specific section of the alignment for detailed editing.

CINEMA allows an alignment to be visualised at a wide range of different levels of detail, and provides a simple, intuitive method for switching between these levels using interactive 'zoom' controls. There are three basic zoom controls on the main tool bar:

• Zoom in will move the view 'closer' to the alignment, increasing the level-of-detail but decreasing the effective size of the area being visualised.
• Zoom out will move the view 'further away' from the alignment, decreasing the level-of-detail and increasing the effective size of the area being visualised.
• Free zoom provides an intuitive technique for selecting the desired level of detail using a mouse-operated slider.

It is also possible to freely zoom into/out from an alignment by holding down the shift key whilst scrolling the mouse wheel.

It is possible to have several alignment views open onto the same alignment, allowing:

• Different regions of the same alignment to be visualised simultaneously, at different levels-of-detail if required.
• Different regions of the same alignment to be edited without the need to repeatedly shift the view between each region.

In order to create a new view onto the current alignment, select the icon from the main toolbar, or the New view window option

from the View menu.

Active region highlighting

When there are two or more view windows open for the same alignment, CINEMA can provide a visual cue that illustrates if, and where, the region of the alignment shown in the current view coincides with the regions shown in the other views. All views, except that which is currently active, are dimmed slightly, with only the regions of the alignment coinciding with that displayed in the active view shown at full intensity. The following image illustrates this behaviour:

Active region highlighting is turned off by default, as it can cause CINEMA to run slowly on some less powerful computers. To turn this feature on, see the section on Customising CINEMA.

Currently, CINEMA computes its consensus according to the the modal residue at each "column" of the alignment (where a column is the same gapped residue position on each sequence.) The default consensus sequence is coloured according to the degree of conservation of each column of the alignment: the more conserved a column is, the lighter its corresponding residue on the consensus sequence, and vice-versa. For the columns that are 100% conserved, the residue symbol at that column is also drawn. The following images illustrates the basic consensus sequence:

Showing and hiding the consensus sequences

A consensus sequence is only automatically shown in an Alignment View if the alignment contains more than one sequence. It is possible to hide (and, if necessary re-show) the consensus sequence at any point:

• To hide a consensus sequence, right-click on its label and chose Hide consensus from the context menu.
• To re-show a hidden consensus sequence, choose Show consensus from the View menu, on the main CINEMA menu bar.

Configuring the look of the consensus sequence

It is possible to change the way the consensus sequence looks, for example to show only 100% conserved residues, or to colour the consensus sequence using the standard residue colours, instead of the default monochrome. Changing the look of the consensus sequence is achieved by right-clicking on the consensus sequence label and selecting the appropriate option from the context menu. The following images illustrates some of the alternatives currently available:

Drawing the consensus sequence as a graph

It is also possible to draw the consensus sequence as a graph, as illustrated in the following image:

To draw the consensus as a graph, first right-click on the consensus sequence label to open the consensus context menu; next, open the Draw consensus as... sub-menu, and finally select the Graph option. To have the consensus drawn as a sequence again, choose Sequence from the Draw consensus as... sub-menu.

If the mouse pointer is positioned over the alignment area or the sequence labels, and the 't' key pressed, a 'tool-tip' will be displayed providing information about that particular region of the alignment:

If the mouse pointer is over the alignment, the tool-tip displays:

• The sequence the pointer is currently over.
• The particular residue of that sequence the pointer is over.
• The actual position of this residue along the sequence.
• The relative position of the residue along the sequence, i.e. ignoring any gaps.

If the pointer is over a sequence label, the tool-tip displays the full sequence identification information, along with any other description data available for that sequence.

Automatic alignment tips

If desired, CINEMA can display alignment tips automatically, whenever the mouse pointer is left idle for a few seconds over the alignment or label areas. To turn automatic alignment tips on, see the section on Customising CINEMA.

Most operations that can be performed on a sequence alignment are accessed via the context menu, which appears when the right hand mouse button is clicked in an alignment view window. The context menu adapts to the current task: the options it displays will depend upon which region of the alignment view the mouse was clicked in and what operation the user was performing when the mouse was clicked.

It is important that the user becomes familiar with the context menu, as many of CINEMA's functions are only accessible through it.