Map View preferences

This preferences pane is used to configure some aspects of the Map View window.

Shadowing

A shadow is placed behind all symbols.

Smart Layout

When Smart Layout is enabled the normal automatic above/below settings for Map feature layout are overridden as follows:

A test is made to see if the Smart Layout algorithm should be activated. To be activated, the sequence should have at least an average of the value in the window (default 50) features present on each line. The calculation counts the number of lines and divide by the number of VISIBLE features to determine if Smart Layout should be activated.
Labels are turned off (they may already be off from the other Map Preference Pane setting, but this makes sure they are).
The algorithm should first check to see if any CDS or gene features are present with "automatic" layout (i.e. that have "above", "below" or "above or below" layouts).
As the layout code loops through the visible features with auto-layout, instead of trying to layout to avoid colliding with other features, it assigns a specific level to each feature.
CDS features with "Above or below sequence line" are assigned to level +1 if they are on the plus strand or -2 if they are on the complementary strand. CDS "above" features are always assigned to +1 and CDS "below" features are always assigned to -2.
gene features with "Above or below sequence line" are assigned to level +3 if they are on the plus strand or -4 if they are on the complementary strand. gene "above" features are always assigned to +3 and gene "below" features are always assigned to -4. If there were no automatic CDS features then the gene feature levels are decreased by 2 to +1 and -2.
All "other" features are assigned to levels +5 and -6 using the same above/below/above or below logic above. If there are no CDS features, the levels are dropped by 2. If there are no gene features the levels are dropped by 2.

Anti Aliasing

Anti Aliasing is a technique where the jagged edges of lines and other symbols, produced by pixels are smoothed with the addition of grey pixels. The eye then perceives a smoother line.

Overview Size

This controls the size of the overview that shows the entire sequence and the location shown in the main window.

Graphics Height

This controls the height of symbols shown on each level,

Maximum Levels

Enable Label Hiding

For large feature rich sequences hiding labels will improve the performance and show a cleaner Map.