LowHangingFruit
From PathVisio Wiki
Here we list some tasks that are low-priority, but should be fairly easy to implement and a great way to get to know the project. Send an email to martijn.vaniersel (at) bigcat.unimaas.nl if you're interested in taking up one of these tasks.
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Insert genes dialog
Create a dialog window that lets you paste a number of gene identifiers, and lets you select a database. When you press an OK button, these gene identifiers are turned into a stack of geneproduct objects on the pathway, which can then subsequently be edited manually. The goal of this is to have a quick way to get started with a new pathway from a list of identifiers.
Advanced pathway search
The search panel lets you search a directory of gpml files for a single symbol or gene ID. It would be really great if the program lets you search for multiple search terms at the same time. For example, entering "P53 MDM2" will search for pathways containing both symbols, and "P53 OR MDM2" will search for either term. Further improvements could be fuzzy matching to be forgiving of misspellings, and indexing to speed up the search.
Advanced edit options
- Snap line angles (to steps of 45 degrees)
- Move objects by arrow keys
- Snap to grid
Where to start looking?
For snap to angles and grid, you probably need to make a modification to the vMoveBy method in the Handle class.
Magnifier glass
It would be cool if you could use your mouse cursor as a magnifier glass to look at a pathway in more detail. Imagine that when you go over a gene of your pathway, you would see it magnified in a tooltip, or the sidepanel. This could be very useful for studying expression data with many variables, when your genebox is divided in a lot of little boxes and you need to look more closely. Or if your pathway is very large, you could zoom out to get a birds-eye-view and move your mose over the regions of interest, which are then shown in more detail in the magnifier panel.
Where to start looking?
To create a magnifier panel, you could add a new tabfolder to the side panel, hook into the MouseMove events of the pathway and draw the pathway with a different zoom level on the Graphics2D object of the magnifier sidepanel.
Generic color-sets
Currently you have to re-create your color-sets for every new dataset. It could be useful to enable users to save the color-set criteria to a file which can be loaded on another dataset. Because column names (aka samples, conditions) may vary between datasets, a user interface should be available to couple the stored column names to the column names in the new dataset on loading the criteria file.
Done or work in progress
Object Alignment toolbar
Create a toolbar that appears in edit mode with the following buttons
- a button to set the x center of all selected items to the mean x center
- idem for y center
- a button to set the left side of all selected items to the lowest x coordinate
- idem for top side
- idem for right side
- idem for bottom side
- a button to expand the width of all currently selected items to the maximum width
- idem for height
See also: bug #84
Group ID's
The GPML now is able to store GroupID's. Create a user-interface for this Grouping function.
