BioTech FYI Center - Resources

EMBOSS FAQ (Frequently Asked Questions)

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Q) Plotters and pen colours.
A) The hp drivers presume the pens are loaded as:- 

    SP1     black
    SP2     white
    SP3     red
    SP4     green
    SP5     blue
    SP6     cyan
    SP7     magenta
    SP8     yellow

Otherwise your output will have different colours.

Q) Browsing the Gnu site I came across libplot, libxmi and plot utils. Would these be a suitable replacement for PLPLOT?
A) So far they are still GPL rather than LGPL.

Robert Maier promised a while back to LGPL them but has not yet. Pity. Makes all the difference for linking in third party applications to EMBOSS.

Q) I am trying to compile PNG support into EMBOSS on our CTU Unix system. This requires the z, png and gd libraries, which are not on our system at the moment.
Does anyone know where I can get these libraries for either OSF or CTU Unix? All the references to them I have found on the web have been for Linux. Are these platform independent (so I can use the Linux libraries)? Or do I need specific versions for our unix version?

A) You should be able to compile them from the source on just about any Unix platform. 

  
http://www.info-zip.org/pub/infozip/zlib/
  
http://libpng.sourceforge.net/
  
http://www.boutell.com/gd/
Q) I get error messages when I try to display X11 on my PC. I am running the Hummingbird Exceed X11 emulator.
A) The Hummingbird Exceed X11 emulator (and maybe other systems) use the 'TrueColor' display by default.

You should change the configuration settings so that it uses 'PseudoColor'. In version 6.1 of Hummingbird Exceed, this is done by clicking on the Exceed section of the Windows 98 tool bar at the bottom of the screen. Select 'Tools', then 'Configuration', then Screen Definition. A window will appear.

In the 'Server Visual' popup menu on the left, select 'PseudoColor'. Click on 'OK'.

SECTION D - Data Files

Q) How do I use my own private data file?
A) You may wish to amend one of the standard EMBOSS data files. One of the data files you might wish to alter are the translation table files.

'transeq' has been written to only read in one of the standard translation files:

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EMBOSS FAQ (Frequently Asked Questions)