Alignment Header Definition Files

Sequence alignments shown in Multalign Viewer may include header lines. For example, a Conservation line is shown by default.

Arbitrary, user-defined header lines may also be shown. New header contents can be loaded from an external header definition file (Headers... Load in the Multalign Viewer menu), while existing header contents can be saved to the same type of file (Headers... Save in the Multalign Viewer menu). Loading values for a header with the same name as an existing header will create an additional header line, not replace the values in the existing header line.


A hash symbol # at the beginning of a line signifies a comment.

Control lines indicate header name and type:

name: header_name
style: data_type
The header_name is a character string and the data_type can be character, numeric, or symbol. Both lines are optional. If the name line is omitted, the header will be listed as (no name) in the Headers menu. If the style line is omitted, it will be guessed from the first data value, as described below.

data_type header_value
character single character
symbol one of the following:
  • circle
  • diamond
  • square
  • star
numeric any numerical value

Header values are given in data lines of the form:

where alignment_pos is an integer position in the alignment. Data lines can be in any order, and not every position in the alignment must be represented in the file. Positions with no value will be blank in the header line. Control lines and comments can be interspersed with data lines. However, if multiple headers are defined in the same file, the name control line should precede all other lines for the corresponding header.

If the style is not specified, it will be assumed character if the header_value in the first data line is a single character, symbol if it matches a known symbol name, otherwise numeric.

Numeric header values are mapped to histogram bar heights in the range 0-1 for display, but the original input values will be used for residue attributes and written out when header contents are saved.

The color is optional but can be specified as either of the following:

A single header definition file can incorporate both kinds of color specifications, as well as lines without color specifications. Default colors are used for data without color specifications: black for character values, black outlines for symbol values, dark gray for the histogram bars corresponding to numeric values.

UCSF Computer Graphics Laboratory / August 2010