Version 1.0 of CMap has been released.
You can get the new version from SourceForge,
Highlights of this release are:
- Ribbon option for correspondences
- New Feature Glyphs
- A dot-plot view
- An image_only URL parameter allowing a CMap image to be embedded in
- Easier install with directory guessing
- API better documented for writing custom scripts to load data
If you have any questions, please let me know.
For anyone who installed the release candidate, simply download the new
release and run "perl Build.PL; ./Build; sudo ./Build install". No
updates to the database or config files are needed.
If you are updating from version 0.16, see the documentation in the
upgrade/ directory included in the package.
Thanks to everyone who has helped make CMap better through questions,
comments, testing and code.
Full change list below.
- Added three new feature glyphs: heatmap, i_beam and bar.
- Added a feature that will stack comparative maps in real time.
- Added a dot-plot view.
- Added a ribbon glyph for correspondences
- Added the unused feature types into the legend, colored grey with a little +
box which will add them to the display.
- Added an image_only parameter that will cause CMap to only return the html
tag pointing to the image.
- Added the ability to define additional buttons in the config file that will
be displayed only when certain criteria are met. These buttons will change
parameters in the menu and submit.
- Added the ability to define the default species that a new user will have
selected in the opening menu. This will not override the information in a
- Added a button for the user to hide the legend (Hide the Legend).
- Added the ability inside each map type configuration to define the
feature_default_display value for individual feature types when displayed on
maps of that type.
- Added a display/ignore option for individual evidence types
(evidence_default_display) which is similar to the feature_default_display
option for features.
- Added a unit granularity for a map type to allow for math with the correct
- Added color2 option to the banding glyph.
- Added a third overlap color to the banding glyph.
- Added the ability to add custom colors to feature glyphs which are outside
the pre-decided set.
- Added start and stop parameters to View Feature on Map view.
- Added the feature_modification_code option to the feature_type definition in
the config file which allows code that will modify the look of a feature.
- A network install script is included that will download and install CMap and
all it's pre-requisites. It is based on the GBrowse script
- More robust install options such as directory guessing which was borrowed
- Modified the installer to ask the user if they want to change the options
individually rather than making them learn an archaic flag system.
- Modified the installer to also allow installing a demo.
- Removed Bio::Perl from the base requirements.
- Deleting objects will also delete their xrefs.
- Increased speed of importing correspondences.
- Tightened up security.
- Modified the internal link generation to only use relative links.
- Changed the word "Crop" to "Show only" for the map arrow pop-ups because it
- Modified the saved link interface to make it a little more user friendly.
- Modified the feature_details page for clarity.
- Changed the order of the Feature Types in the legend to reflect the order of
the drawing lanes.
- Removed some of the legend when in clean view.
- Modified the behavior for a comparative map that no longer has
correspondences displayed. Now it will keep the map unless the "Eliminate
Orphans" button is pressed.
- Modified the interface slightly to create a row of buttons for Dotplot,
Eliminate Orphans and New Reference Maps.
- Wrote a document, CMAP_API.pod, explaining the CMap API.
- Modified code to make the API more consistant.
- Made changes to allow the ViewFeatureOnMap module to return only the image
tag when passed the image_only parameter in its redirect.
- Hides the stacked maps that don't have any correspondences due to reference
map truncation (as well as hide any subsequent maps that only have corrs to
- In the initial menu, added a check to see if any maps are selected and
popping up a warning if not.
- Wrote a document briefly explaining the support scripts.
- In the cmap_admin.pl script, added an "all" option for deleting maps from a
- In the cmap_admin.pl script, added a "delete features" option.
- In the cmap_admin.pl script, added the ability to purge all the caches on a
machine from different datasources at once.
- In the cmap_admin.pl script, added the ability to narrow the delete duplicate
correspondence method to a single map set.
- In the cmap_create_stacked_maps.pl script, attributes are created for each
contig feature that reports the number of correspondences to each reference
- In the cmap_create_stacked_maps.pl script, an xref is created to link back to
the original map.
- In the cmap_create_stacked_maps.pl script, maps are sorted and displayed
based on the number of correspondences to each reference maps.
- In the cmap_create_stacked_maps.pl script, added a correspondence cutoff.
- In the cmap_create_stacked_maps.pl script, added the ability to import the
alignments in a file rather than relying on a correspondence voting
- In the cmap_create_stacked_maps.pl script, added the ability to only use
correspondences with specific evidence types to create the order and
orientation of the stacked maps.
- In the cmap_create_stacked_maps.pl script, the script will now report errors
and die if stack maps don't have any corrs to the reference map they are
- The new cmap_examine_attribute.pl script looks in the database for a
specified attribute that the administrator wants on every object of the
specified type (map set, feature, etc).
- The new cmap_data_diagnostics.pl script crawls the database to ensure the
CMap data is okay.
- Fixed bug where CMap would trust the user-supplied start and stop of the map
instead of checking their validity.
- Fixed a bug where a slot would stay stacked even after it was unchecked.
- Fixed bug in heatmap legend creation.
- Fixed a flaw in the tick mark logic. Rather than rounding the location
string of the tick mark, it now places the tick marks at reasonably rounded
- Fixed issues with importing correspondences: Multiple imports were being
ignored because they were being deleted after the first one.
- Fixed issues with importing correspondences: If a feature_acc was missing in
the db, it would create corrs with ALL the features in the db
- Fixed a problem where CMap drew maps as if they were truncated when they were
- Fixed problem where duplicate correspondences could be made where two
features had the same name and the same aliases.
- Fixed problem with the stacked maps being drawn into the legend.
- Fixed an issue where if you hit enter when in a text box, it would submit as
if the dot-plot button was clicked. Now it submits as though the redraw was
- Fixed an API problem where update_feature() couldn't update a start or stop
- Fixed problem with the session id being cached during a whole page cache
causing use of a common session. This causes CMap to fail when the session
expires and potentially gets confused when multiple people are changing the
- Fixed problem in the feature details page where corrs with multiple evidences
were being displayed twice.
- Fixed a problem to allow the attribute_value of attributes to be "0".