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

0.8.11 - 2021-01-05
-------------------
Small fix:
- Replaced calls to order() on data.frames by do.call(order, list=...) to comply
  with the latest R developments.

0.8.10 - 2020-12-10
-------------------
Small fix:
- Removed calls to cairo_pdf(), replaced with standard pdf()

0.8.9 - 2019-01-16
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Fixing colors in the examples: col is now mapping to "col" and not to "fill",
and affects the example data (which has "col").

0.8.8 - 2018-02-21
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Small fix:
- pkg/man/genoPlotR-package.Rd had to be modified not to be unsynched with
  DESCRIPTION

0.8.7 - 2017-11-06
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Small bug fixes:
- Changed CITATION to comply with as.person() requirements
- Corrected a line too long in dna_segs.Rd
- Corrected broken links in the vignette

0.8.6 - 2017-05-15
------------------
Previous version created warnings with R 3.4.0. Removed the inst/doc
folder on R-forge. Package back on CRAN.

0.8.3 - 2015-07-02
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Adapting the package to new CRAN guidelines:
- Imports instead of Depends (imported packages)
- Cleaned up DESCRIPTION, updated email address
- Restored some functions on the webpage

0.8.2 - 2013-12-19
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Adapting the package to new CRAN guidelines:
- Moved vignette from inst/doc/ to vignettes/
- Reduced examples in plot_gene_map to get under 5s checking time

0.8.1 - 2012-11-19
------------------
BUGFIXES:
- Fixed a bug in read_mauve_backbone where the reference genome could be set
  to anything. Added check for that.
- Fixed a bug in apply_color_schemes and the main function, to prevent 
  comparisons with 0 rows to crash the program.

0.8 - 2012-06-21
----------------
NEW FEATURE:
- Comparisons that overlap xlims are now included and trimmed inside 
  xlims
BUGFIXES:
- Automatic horizontal placement of dna_segs had some error in certain
  conditions
- Reading artemis colors could not be overriden
- Error handling when reading null tables

0.7.1 - 2011-05-04
------------------
NEW FEATURE:
- A scale can be added to the tree (argument tree_scale)
BUGFIX:
- Arguments ylim (of seg_plot objects) were not taken into account 
  when plotting

0.7 - 2011-04-18
----------------
NEW FEATURES:
- It is now possible to plot user-defined graphs on top of each dna_seg,
  using the graphical functions of grid or user-defined ones. See
  seg_plot functions and argument in plot_gene_maps
- Added a function, auto_annotate, to create smart annotations from genbank
  or embl files.
- Added the possibility to use user-defined graphical functions to plot
  genes.
- Extra fields (tags) can be parsed from genbank and embl files.
BUGFIX:
- The last line of the features was not read in genbank and embl files

0.6.1 - 2011-03-30
------------------
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
------------------
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
------------------
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
------------------
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
------------------
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
------------------
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
------------------
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
------------------
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 
------------------
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
------------------
Initial commit to R-Forge