genoPlotR changes
=================

0.6.1 - 2011-03-30
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BUGFIX:
- Vignette contained non-ASCII characters
- Fixed an incoherent variable name in arrow_coord

0.6 - 2011-03-16
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NEW FEATURES:
- Added transparency support in apply_color_scheme, which is applied by
  default.
- Added a function, artemisColors(), that returns the colors as in Artemis.
- read_dna_seg_from_file can now read color or colour tags in genbank or embl
  files.
- Added experimental support for tree branches annotations.
BUGFIX:
- Further corrected a bug occuring when fixed_gap_length was set, and allowing
  comparisons with 0 rows.
- Fasta types were incorrectly guessed
NOTE: some of the features have been released in an intermediate version 0.5.9

0.5.8 - 2011-01-31
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NEW FEATURE:
- The plot area is now clipped, as a workaround to avoid comparisons that
  are too large.
BUGFIX:
- Corrected a bug occuring when fixed_gap_length was set

0.5.7 - 2010-12-16
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BUGFIX:
- Corrected as.dna_seg to prevent factors to slip in and fixed the gene_type
  verification.
NEW FEATURE:
- Changing the color of the dna_labels is possible (not for trees yet)

0.5.6 - 2010-10-04
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BUGFIX:
- Modified the feature parsing algorithm, features with an "_" inside (ex. 
  misc_feature) were parsed incorrectly.

0.5.5 - 2010-09-27
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NEW FEATURES:
- Added a new gene_type: lines (and the corresponding side_lines)
- Improved the example for gene_type

0.5.4 - 2010-09-15
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BUGFIX:
- Added some extra checks on mauve input data, and on dna_seg input data
  to avoid mysterious error messages

0.5.3 - 2010-09-08
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Article published in Bioinformatics, added a CITATION file.

0.5.2 - 2010-08-24
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NEW FEATURES:
- Added read_dna_seg_from_fasta, that can read a fasta file and return one
  segment of the corresponding length
- Added two arguments to plot_gene_map, to allow to define the minimum gap
  length and to allow to have fixed gap length but still automating the 
  placement of the whole segment.
BUGFIX:
- Corrected a bug that provoked errors in displaying subsegments that were 
  closer to each other than the gap length

0.5.1 - 2010-08-19
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BUGFIX:
- Added aliases in the documentation to avoid warnings when compiling

0.5   - 2010-06-14
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NEW FEATURES:
- New argument to plot_gene_map: n_scale_ticks, gives the approx. number of 
  ticks in the dna_seg_scales
- New argument to plot_gene_map: scale_cex, allows to change the size
  of the labels in dna_seg_scales
- New argument to plot_gene_map: dna_seg_label_cex, allows to change the 
  size of the labels in the tree or dna_seg_labels


0.4.1 - 2010-06-01
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BUGFIX:
- Added support for large phylogenetic trees. Given the mandatory use of
  enum.phylog to permute the trees to fit the labels with the dna_seg labels,
  big trees (requiring more than 1000 permutations) broke the program.
  Now either the tree is permutable, in the right order, or an error is
  thrown.

0.4   - 2010-04-19 
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NEW FEATURES:
- Add the multisegment support
- dna_scales, annotations on all the segments, 
- Generated new examples. 

0.3   - 2010-04-09
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NEW FEATURES:
- On plot_gene_maps, it is now possible to add automatic scale to any or 
  all dna_segments.
- It is possible (and recommended) to apply "global" color scheme at the 
  time of plotting (and not when parsing comparisons).
INTERNALS:
- Application of color schemes is now more rational
- Named every element and viewport, so its easier to navigate
- Removed dependancies to RColorBrewer

0.2   - 2010-01-11
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Initial commit to R-Forge