Acedb user guide: giface

(From the programmer's point of view, it is more like xace, but with gif-images as its graphics output mode instead of interactive X11-windows.)

A lot of improvements have been made to the general user-friendliness of giface since version 4.8. Since this version is still in development and may not be officially released. Comments are included about the restrictions of giface version 4.7 and earlier.

You run giface just like tace, with the database directory as a command line argument, or set as the ACEDB environment variable. There is a new single new command added to the standard tace menu, "gif". This opens up a separate menu, with prompt "acedb-gif> ". In this menu you can issue the following commands:

(command options inside [brackets] are optional, the vertical bar '|' indicates a choice of possible options, words in italics are values specified by the user.)

Commands

dimensions [-D displaytype] x y

This sets the dimensions in pixels of the image that subsequent command will create. The default sizes for all or only a specified displaytype will be reset.
Note on version 4.7 and earlier : no -D option available - only the sizes for displays of type GMAP, FMAP and PMAP will be affected. For multiple dimension changes to take effect you had to quit and re-enter the gif sub-menu.

display [-D displaytype] [-view view] [class key]

Graphic display of the current (or the specified object). An object is defined by its class and its key (the object's name).
This is the same action that xace would perform when double-clicking on the object when its listed in the KeySet window.
The default display mode is the standard Tree Display (e.g. for Author objects) or a graphical map display (e.g. for sequence objects). The -D option can be used to change the default display type. The argument displaytype can be one of display types listed in wspec/options.wrm, where the default type for each class is defined. Typically you would use -D TREE to force the textual display or -D GMAP for Map objects, -D FMAP for Sequence objects or -D PMAP for Clone objects.
The -view options works for map displays of type GMAP and allows the user to specify the view object to be used to configure the GMAP display. The argument view is a valid name of a View object, which contain column definitions.

gifdump filename

Saves the active graph as a gif-image. The extension ".gif" is added if filename, doesn't already have that suffix. Other information about clickable objects on the graph is written to filename.boxes (if filename has no ".gif" suffix) or basename.boxes (where basename is the filename argument with the ".gif" suffix). The format of the .boxes file is explained below.
This command is typically used after the display or map command.
If filename is not an absolute pathname (starting with '/') the file will be created in current working directory.
Note on version 4.7 and earlier : You should always specify an absolute pathname, and the extensions .gif and .boxes are always added to the filename.

psdump filename

Saves the active graph as postscript. The extension ".ps" is added if filename, doesn't already have that suffix. This command is typically used after the display or map command.
If filename is not an absolute pathname (starting with '/') the file will be created in current working directory.
Note on version 4.7 and earlier : You should always specify an absolute pathname, and the extensions .ps is not added and should be provided in the filename argument by hand.

map map [-view view] [-coords x1 x2] [-hideheader] [-whole]

Set up a map display of the object map. The optional -view options has the function as for the display command. To zoom to a specific section of the map use the -coords option with the coordinate arguments x1 and x2 or the -whole option to show the entire map in one image.
If the image is used for a Web display, it may be useful to use -hideheader to blank out the buttons in the top row that you would usually see in this display in xace.
This command doesn't create an image file straight away, use the command gifdump to write out the result image.

pmap [-clone name] | [-contig name coord]

Create a physical map display for clones and contigs. Use the command gifdump or psdump to write out the result image.

seqget [sequence [-coords x1 x2]]

Sets active sequence for further seq- operations. The following seq- commands are issued in the same command line, e.g.
seqget bK714B7 ; seqactions -hide_header ; seqdisplay -visible_coords 10000 40000

seqactions [-dna] [-gf_features] [-hide_header] [-rev_comp]

Change parameters on the active sequence display.

seqcolumns {-on name} {-off name} [-list]

Changes column settings on active sequence display. Multiple -on ... or -off ... options can be specified. The column names are not case-sensitive, and names containing spaces have to be "quoted".
The names of available columns can be listed with the -list option. The columns are listed left to right with a '+' or '-' sign denoting whether they're switched on or off.
Note on version 4.7 and earlier : column names are case-sensitive and the -list option isn't available.

seqdisplay [-visible_coords v1 v2]

Creates the actual display for the active sequence. This is typically the last command in a sequence of commands starting with seqget. The image of the active graph can be written out using the gifdump or psdump function (see there).

seqfeatures [-file fname] [-version 1|2] [-list] [-source source(s)] [-feature feature(s)]

Writes out sequence features from the current sequence. The arguments for -source and -feature are '|' separated lists. It operates over the region specified by the -coords in the previous seqget command.

seqdna [-file fname]

Writes out the DNA sequence of the current sequence. It operates over the region specified by the -coords in the previous seqget command.

pepget protein | peptide [-coords x1 x2]

Sets current protein for further pep- operations on the same line.

pepseq [-file fname]

Exports current peptide sequence.

pepalign [-file fname]

Exports homols of current peptide sequence.

makemaps -gmap | -pmap | -cmap | -alpha | -all | -seqmap file | -seqclonemap file

makes cached maps and sorted class keysets

quit

This returns to the standard tace menu.

.boxes file format

The file is a set of lines :

boxnum x1 y1 x2 y2 class:name extra_text

The boxnum is probably irrelevant to external people. x1,y1,x2,y2 are the bounding box coordinates. The first 'class:name' specifies the object in the box. The extra text is variable information that can be added by the specific display. Often it contains information that can be used for mouseover type behavior. There may be no extra text.

Example

Unix-prompt: giface ~wormpub/acedb/ace4/cam
acedb> gif
acedb-gif> dim 600 480
acedb-gif> map Sequence-III -view MAP-sequence
acedb-gif> gifdump /tmp/seqIII
...
acedb-gif> quit
// 0 Active Objects 
acedb> quit

// A bientot 

Unix-prompt: 

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last edited: May 1999