source: branches/tree/HELP_SOURCE/source/visualizeSAI.hlp

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

#Please insert subtopic references  (line starts with keyword SUB)
SUB     accessibility_sai.hlp
SUB     e4.hlp
SUB     arb_secedit.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           Visualize SAIs in editors.

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.

SECTION    Primary structure editor

            Steps to use VISUALIZATION of SAIs in the 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 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).

SECTION    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 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