The main screen has three portions; the menubar, the output window and the error window. Of these, the output and error windows are identical except for the data that appears within them. Here we describe the general operation of the output window only, although the details apply to the error window too.
The output window consists of a text window with a bunch of labels and buttons
above it. At the top left we have the window name followed by a colon. After
the colon the name of the current output file will be shown in blue italic
letters. All new output appearing in this window will also be sent to this
file. Initially no output file is specified and this label is blank (as can be
seen in the error window). Using the "Redirect" menu located at the top right
of the window a new file can be opened, or an existing one closed (in which
case output is no longer sent to the specified file). The output and error
windows may both have redirection files, at the same time.
The "Scroll on output" check button toggles whether the window should
automatically scroll whenever new output appears to ensure this output is
visible. The default (as seen in the illustration) state is to
scroll. The "Clear" button removes all output from the window.
Each command, when run, adds a title to the output window. This
contains the current time together with the command name. Output for
this command then appears beneath this header. In the illustration the
output from three commands is visible. Of these the "edit contig"
command produce no output, but still has a header.
Pressing the right button with the cursor above a piece of output
(either in its header or the text beneath it) will pop up a menu of
operations. This operation is not valid for the error window. The
commands are:
Deletes this text from the output window
Sends this text to a specified file
Sends this text to a specified list
Starts up a specified command and sends this text to the input of the
command. Any output from the command is added back to the output
window. Any errors from the command appear in the output window.
Currently this allows commands to run for up to five seconds, and
terminates the command if it has taken longer. To start longer running
applications add an ampersand (&) after the command name.
The text in the error window has a different format to the output
window. Instead of large portions of text separated by headers, each
item in the error window consists of a single line containing the
date, the name of the function producing the error, and a brief
description of the error. Many error messages will be displayed in
their own dialogue boxes (eg not having write access to a file) and
hence will not appear in the error window. Each time an error message
is added the bell is rung.
Note that currently output added to the output or error windows does
not appear until the function producing the output has stopped. This
is particularly noticable within long running functions such as
assembly where nothing appears to be happening (except perhaps for the
bell ringing occasionally when failed readings are listed in the error
window). It is planned for this behaviour to be changed in the future
to reveal output whilst it is being created.
![[picture]](interface.output.gif.html)
(Click for full size image)
Remove
Output to disk
Output to list
Output to command
This page is maintained by
James Bonfield.
Last generated on 29 April 1996.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/interface_8.html