Map

The map provides a schematic visualization of loaded data. The map allows the scaling of the loaded region.

In the map area, features are used to be displayed. Each level is shown on its own line. To the left of the map, names of levels are located. For each nucleotide sequence, feature levels with the forward orientation are above and ones with the backward orientation - below the grey line representing a sequence.

New levels can be created either automatically as a result of operation with sequence (e.g., Tools>Motif search), or manually. To create new layout level manually, use the "New feature level" dialog.

On the map, the current cursor position is shown as a vertical line, which is also referred as "navigation line". To fix a certain position on the map, hold the Ctrl key along with left mouse button and then replace the cursor to required position. For replacing of previously fixed line, hold the Ctrl key and place the mouse cursor over the line. When the cursor occurs precisely over the line, it changes to shape, and then holding the left mouse button move the line to desired position. To remove previously fixed line, move it to the area with layers names.

Mouse right button click on a feature calls out the feature pop-up menu:

• Edit feature - call out the "Edit feature" dialog for editing feature data.
• Copy feature - copy selected feature.
• Delete feature - delete selected feature.
• Fit to view - "stretch" the image of the selected feature for all width of the map.
• Add to parent feature - If a feature is not a part of any other one, then in it's pop-up menu the "Add to parent feature" command appears. This command calls out the "Select parent" dialog, where the appropriate "parent" feature can be chosen. As a parent feature, any operon that lays in the same layer and overlaps the original feature can be used. If feature does not overlap any "operon" type one, the "No suitable parent found" message box will appear.
• Remove from parent - If a feature is already a part of any other one, then in it's pop-up menu the "Remove from parent" command appears. For example, CDS that is a part of an operon has in it's pop-up menu the this command.

The grey line represents a sequence. In the left map part, the levels names are represented. To set on/off the level representation on the map, use the checkbox near the level name in the List of sequences.

Feature display parameters can be specified in the "Edit feature"dialog. To select a feature, click on it. Selecting a feature causes the appropriate feature name to be highlighted in the "List of sequences" as well as the corresponding sequence to be highlighted on the "Sequence view" panel. If the clicked feature belongs to "CDS" type, the appropriate nucleotide and aminoacid sequences are highlighted on "Sequence view panel"; if the clicked feature belongs to some other type, only nucleotide sequence is highlighted. If multiple features are located at the same map point, click mouse to switch between them. Depending on the cursor position, the pop-up hint with the following information appears:

• List of features that overlap each other in the current position in the current layer (if cursor points to the feature);
• List of features that overlap each other in the current position in all layers (if cursor points to the grey layer that represents a sequence).

Features are used to be represented as color rectangles. User may change feature attributes in "Edit feature" dialog.

The cursor position on the map is displayed in the status line.

On mouse clicking on a feature, the sequences in Sequence view panel are being shifted in such a way that allows to display the feature location on the nucleotide sequence and feature name is highlighted in the List of sequences.

Holding the "Shift" key allows to change the map scaling by mouse. The scaling occurs from the map center.

Using the Graphic navigation bar an approximate length of displayed region can be assigned. The Precise navigation bar provides the ability to set the exact borders of region to be displayed.