#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     accessibility_sai.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		Visualization of Sequence Associated Information (SAI) in Primary and Secondary Editors.

OCCURRENCE	In Sequence Editors - Primary Editor (ARB_EDIT4) and Secondary Editor

DESCRIPTION

            This function can be used to Visualize Sequence Associated Information (SAI)
            in the Primary Structure and Secondary Structure Editor windows.

            Steps to use VISUALIZATION of SAIs in Primary Structure Editor:

               1. Select SAI to be visualized from the SAI list (all SAIs present in the
               ARB Database).

               2. 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.

               3. 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.

               4. You can define the colors used in COLOR RANGE
               via 'PROPERTIES/CHANGE COLORS AND FONTS' menu.

               5. Then, choose the visualization options. You can opt to visualize only
               MARKED species or ALL species in the primary editor.

               6. Finally, be sure to check ENABLE VISUALIZATION check box.

            If Color Translation Tables 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).

            Sequence Associated Information can also be visualized in Secondary Structure
            Editor.

               To Visualize SAI in Secondary Structure editor window - Go to PROPERTIES
               menu, click on CHANGE DISPLAY 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 LINK{sec_display.hlp}.

            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.

	    See also LINK{e4_background_priority.hlp}.

EXAMPLES	None

WARNINGS	None

BUGS		No bugs known
