There are two ArkDB application routes which allow users to select and draw maps. The ArkDB Simple Maps Interface and ArkDB Species navigation paths, both allow users to draw maps in the ArkDB Map Drawing Application.

The maps provide a variety of map functions through the use of simple mouse-click operations and on-screen context menus.

Marker labels are displayed - and those that are not (initally at least) are represented as a blue dash. However hovering the mouse over a label or a blue dash will display marker name, and its start, middle, and end position.

Map relationships are displayed as blue lines, drawn between matching markers on adjacent maps.

What to do here:

Map focus:

When the mouse is over a map, the map draws a faint grey box border. This indicates that the map has focus and is the map currently recieving attention by the user

Map movement:

Any map can be dragged and repositioned by clicking the map with the left mouse button, and holding the left button down whilst moving the mouse

Note: if a map is moved to a position which overlaps another map, then any map relationship lines between these maps will not be drawn until the maps are separated i.e. the grey box around a map must not overlap with any other map

Maps are drawn according to their start and end locations, and marker locations are displayed at relevant regular intervals on the map. Where the density of markers in a given map region might clutter the initial map display - then only the blue marker notches denote the marker locations. That is, not all marker labels may be displayed when any map is drawn initially.

However is possible to "Zoom" into a region of interest in order to expand it, allowing a more detailed display of marker labels in that region.

What to do here:

Activate the map context menu by a right mouse click on the map

Select, and click on, the yellow highlighted 'Zoom Map...'

A Dialog Box is presented requesting a Start and End range. This range allows the user to indicate the "Zoom" region of interest.

What to do here:

Enter the 'Start Range' and 'End Range' values into the Dialog Box

Note: these values must not be less than or greater than the minmum start or maximum end values for the map

Click 'OK'

The map is redrawn, and the region displayed is now the "Zoom" region. This visual expansion allows a greater level of map detail to be displayed between this new Start and End range.

What to do here:

Repeat the 'Zoom Map...' operation as and if necessary until the region of interest displays the required level of detail

Marker display allows a user to determine which marker names will be displayed for a given map. In this way, either a single map marker - or all map markers - can be displayed.

What to do here:

Activate the map context menu by a right mouse click on the map

Select, and click on, the yellow highlighted 'Marker Display Option...'

A menu lists all of the markers for the map. Those which show as highlighted marker names in the list, represent those which are currently displayed on the map itself. The non-highlighted marker names, are not currently displayed on the map.

What to do here:

To select a single marker to be displayed on the map, select it by clicking on the marker name using the left mouse button

or:-

To select a contiguous group of markers from the list, the user should click the first marker using the left mouse button, similtaneously holding down the Shift button on the keyboard, and click on a second marker (one which is either further up or further down the list). All markers between the first and second marker will be selected

or:-

To pick a number of markers individually, click on seperate markers using the left mouse button whilst similtaneously holding down the Ctrl key on the keyboard

Click 'OK'

The user selected markers from the list are displayed on the map.

The user deselected markers from the list are no longer displayed on the map.

What to do here:

Repeat the 'Marker Display Option...' operation as necessary so that only the marker names of interest are displayed on the map

Maps can be drawn such that their vertical and horizontal orientations are reversed. Vertical flip has the effect of turning the map "upside down". Horizontal flip has the effect of drawing the map "back to front".

What to do here:

Activate the map context menu by a right mouse click on the map

Select and click on the yellow highlighted 'Flip Map Vertically'

or:-

Select and click on the yellow highlighted 'Flip Map Horizontally'

The map is redrawn with its vertical or horizontal orientation reversed according to whether "Flip Map Vertically" or "Flip Map Horizontally" was selected.

What to do here:

Flip the maps until a desired map orientation or layout is achieved

These options both act to remove map information from the display. Either partially in the case of 'Toggle Title', which removes the map title details from the top of the map ie Map Name, Sex, Species and Chromosome. Or entirely in the case of 'Remove Map' which results in the complete removal of the map from the display.

The former switches Map Title "on and off" (hence "toggle"). The latter is a one way operation, that is once a map is removed it can't be redisplayed - unless as a result of subsequent ArkDB map selection and redraw.

What to do here:

Remove maps or map titles from the display as appropriate

When more than one map is drawn, and a marker on one map has the same ArkDB accession number as a marker on the adjacent map, then a blue relationship line is drawn between them.

What to do here:

Nothing

Relationship lines are drawn automatically by the map drawing application when it determines that there are equivalent ArkDB marker accessions on adjacent maps

Its possible to more clearly highlight any identical marker accessions in adjacent maps.

In this way, markers of interest can be made to stand out from other adjacent markers on the same map.

What to do here:

Position the cursor on the blue relationship line

Click on the left mouse button

The related markers are now displayed in purple text, and if the marker label was previously undisplayed , it is now displayed

Its possible that markers on adjacent maps may have the same marker label or name, but not the same ArkDB accession. There is a way to highlight these "same label" markers in any adjacent maps.

What to do here:

Click the right mouse button on the map panel (the map panel is the white area in which the maps are drawn)

The map panel context menu is displayed

Click on 'Display Relationship For Identical Labels'

Relationship lines are drawn in red to indicate that the relationship which is being highlighted is joining markers with the "same label".

What to do here:

Note: in this way its possible to toggle between the kind of relationship lines which join adjacent markers. As before:

Click the right mouse button on the map panel

The map panel context menu is displayed

Click on 'Display Relationship For Identical Labels'

...relationship lines will now be redrawn in blue, denoting the relationship is now identifying identical marker accessions, rather than labels

When the mouse is placed over a marker name, a yellow higlighted marker detail window pops up (hovers) displaying marker start, middle and end position. The user can click on this to display further marker details.

What to do here:

Double mouse click for marker details

If the user chose to display marker details for a map, then the relevant details are displayed. These details include:

Note: related maps are ArkDB maps, containing the same marker accession or label. One or more of these Maps can be selected by clicking on the Checkbox for each related Map. When such maps are drawn side by side, then any marker relationships are visible by virtue of the relationship lines which join the common marker(s).

What to do here:

Click on the Checkbox for each Map

or:-

Click on the 'Select All Maps' button to Checkbox all related Maps

Click the 'Draw Maps' button