CViT Files

==============================
CViT - Chromosome Viewing Tool
==============================

Ethalinda Cannon
ethy@a415software.com

1/12/13 - Release 1.2

CViT is a Perl script used to quickly generate images that show features on 
genomic sequence. It is intentionally simplistic and low-tech; there are 
limitless possibilities for how one might view such data and CViT is 
optimized for speed and ease of use over high-tech features.

Input is one or more files in GFF3 format.
(see http://www.sequenceontology.org/gff3.shtml)
One of these files must contain records describing one or more "chromosomes" 
(which could represent a psuedomolecule, BAC, contig, linkage group, any 
sort of contiguous stretch of DNA, or even a protein structure). These 
"chromosomes" are the backbone that the features are placed on.

Output is a PNG or SVG image.

CViT can be wrapped in other Perl scripts to extend its capability, or 
called by web pages to generate on-demand images. For example, BLAST 
hits can be displayed on a whole-genome view and displayed in a web 
browser.

Most aspects of the image can be modified without touching the code. 
See the ini file, config/cvit.ini.

Note that all names, types, and attributes in the GFF are case-sensitive.


Requirements:
-------------
Perl 5.8.8+

GD library (http://www.libgd.org)

Perl libraries:
  GD
  GD::Arrow
  GD::Image
  GD::Text
  GD::SVG
  SVG
  Config::IniFiles
  Data::Dumper


Files:
------
cvit.pl        - the main scripts
cvit.log       - tracks behavior and errors
config/        - contains one or more .ini files
documentation/ - how to use CViT
examples/      - examples of CViT use
fonts/         - contains truetype fonts
pkgs/
   ColorManager.pm  - manages colors
   ConfigManager.pm - manages the drawing options from .ini file
   CvitImage.pm     - holds base image
   CvitLib.pm       - library of general purpose functions
   errorlog.pm      - writes to cvit.log
   FontManager.pm   - manages fonts
   GFFManager.pm    - manages the GFF records
   GlyphCalc.pm     - calculates positions for all the glyphs
   GlyphDrawer.pm   - draws glyphs onto base image
rgb.txt        - list of possible colors

See config/cvit.ini and the examples for more information about how to use CViT.


Credits:
--------
CViT was designed and developed by Ethalinda and Steven Cannon. The icon was 
designed by Melanie Shaw.

********************************************************************************

Changelog:
----------
1.2    - Fixed bugs in coordinate systems with floating point values and placement of
         glyphs when chromosomes don't share the same start coordinate.
1.1    - Code clean-up, more and better error reporting, variable chromosome placement, 
         many bug fixes. Added support for SVG images.
1.0    - First stable release. Minor bug fixes. 'Measure' records can be 
         displayed as either ranges or positions. Value for 'measure' 
         records can be distance from chromosome as well as heatmap colors
         and histograms. Added web utility cvit-maker to distribution.
b2.0   - Made more consistent, added several drawing options, all options 
         in .ini file can be changed on the command line.
b1.3   - Improved ruler, including addition of fractional units (e.g. 
         Cytological McClintock units). Added ability to increase space to
         left or right of the chromosome set. Writes only one label if 
         multiple labeled glyphs are printed at one location. Bug fixes.
b1.2   - Added grayscale colors for heatmaps, better error reporting, many 
         bug fixes.
b1.1   - Truetype font support and better placement of text, features for 
         cytogentic maps, ruler can run backward
b1.0.1 - A few minor bug fixes. Added a legend image and file of feature 
         coordinates.
b1.0   - Initial SourceForge release