Main topics:

Visualize SAIs in editors.

OCCURRENCE
DESCRIPTION
Primary structure editor
Secondary structure editor
NOTES
EXAMPLES
WARNINGS
BUGS

OCCURRENCE

In sequence editors - primary editor (ARB_EDIT4) and secondary editor

DESCRIPTION

This function can be used to visualize SAIs (sequence associated information) in the primary structure and secondary structure editor windows.

Primary structure editor

Steps to use VISUALIZATION of SAIs in the primary structure editor:

Select SAI to be visualized from the SAI list (all SAIs present in the ARB database).
Select the color translation table (CTT) in the CTT list, if found. Or create one by pressing CREATE button. You can also copy the existing CTT and modify.
Once CTT is created, define desired colors (RANGE 0 to RANGE 9) for the respective characters in the selected SAI to paint as background of the sequence.
You can define the colors used in COLOR RANGE via 'PROPERTIES/CHANGE COLORS AND FONTS' menu.
Then, choose the visualization options. You can opt to visualize only MARKED species or ALL species in the primary editor.
Finally, be sure to check ENABLE VISUALIZATION check box.

If CTTs were defined for each existing/displayed SAIs in the primary editor, one can navigate through different SAIs in the editor and visualize the same instantly. To enable this feature, AUTOSELECT SAI should be enabled in 'Visualize SAI' window (VIEW->VISUALIZE SAIs menu).

Secondary structure editor

SAIs can also be visualized in the secondary structure editor.

To visualize SAI in secondary structure editor window, go to 'Properties' menu, click on 'Display options' sub-menu and select the 'Visualize SAI' check box.

You can also change the colors used to display SAIs by going to 'Properties/Change Colors and Fonts' menu in the secondary editor window.

NOTES

If SAIs are to be visualized in secondary structure editor window, one should select SAI, define CTT and check ENABLE VISUALIZATION check box in primary structure editor window using VISUALIZE SAI function (under VIEW menu in PRIMARY EDITOR). Additionally SAI visualization has to be enabled in ´SECEDIT display options´.

In order to retain the settings of CTT and associated SAIs, one should save the properties by going to 'Properties/Save properties' menu in primary editor.

Please note that the CTT definitions are stored in the local file (.arb_prop/edit4.arb) and deleting or modifying this file will lose all the information about CTT definitions used for visualization of SAIs for future sessions.