ZMap Design Documentation


Pages Under Construction

The documentation pages are being re-organised and updated.

Some old files are held in ZMap/web and will be moved into ZMap/doc on a gradual basis. The ZMap/Web directory will be maintained during this process as some build scripts depend on it and as the files are in the CVS it provides a backup. Some other files that have been deleted from ZMap/doc have been copied to ~mh17/zmap/doc.old and ~mh17/zmap/web.old until they get transferred to the new CVS directory tree.

As files get added or copied or converted they will hopefully get added to this contents page, which is intended to be in alpha order. As the number of files increase then we'll add some nice <div>s to put them in pretty columns.

NOTE: broken links

Due to a re-organisation and a directory rename many of the files contain broken links to the old directory. The build script has been modifed to fix these, but it would be better to fix each link in the source html at some point, Design_notes/ needs to be changed into Design/.

Contents
How it works About these pages

Application Callbacks
Configuration files Sequence config
Column Bumping
Coordinate systems and configuration
Container Featureset FToIHash
Featuresets Config Column Ordering
Features search
Focus/ highlight items
Featuresets and Styles and Glyphs
Styles (Global)
pipeServer Config
Threads
All about Views
Requests and ideas Masking EST's with mRNA's
Feature Notepad
Otterlace interface Show Evidence
RNAseq
BAM file data (short reads)
Standalone Operation
SQLite configuration
Server & featureset configuration
Screenshots
GFF (file) based Zmap
Column Groups
FooCanvas Loose Ends (Dec 2012)
Performance Canvas Tweaks
New Model Canvas
Density Plots Config
SequenceFeature LocusFeature
FooCanvas
Performance
Optimising
New Window
Containers Post implementation
Screen Refresh
User Docs Running Zmap
Styles
Config
Unfinished Buisness

Things to fix

Here's a list of suspicious bits of code encountered while looking for something else