programminglife2015 / lifetiles Goto Github PK

Init JavaFX. Draw basic screen components such as menu and panels. Make Tree visualization panel and Graph visualization panel.

Buckets contain the references to the DNA strains at some index. Because of the strain subset selection feature, these buckets need to be cached due to performance.

Currently SequenceGenerator does this, but it has to traverse the graph. To avoid this, sequences can be generated when parsing directly (and put into the graph object).

This makes part of (long) tiles without text. Letter spacing or size needs to be adjusted.

Visualize nodes and edges in a TileMap

In modena.bss of JavaFX these warnings get thrown. These need to be fixed.

Navigate in the TileMap (move left and right) and make basic (non-semantic) zooming possible

For the sake of modularity, the package structure needs to be refactored. An example of this:

├── nl.tudelft.lifetiles
│   ├── graph
│   │   ├── model
│   │   ├── view
│   │   ├── controller
│   ├── tree
│   │   ├── model
│   │   ├── view
│   │   ├── controller
│   ├── strains
│   │   ├── model
│   │   ├── view
│   │   ├── controller

Insert empty nodes based on relative coordinates.

Mock-ups to illustrate our problem solution.

Make navigation possible in the tree

Product Vision must be delivered 30-4-2015

nl.tudelft.lifetiles.core.controller.ViewController is not thread-safe but used in different JavaFX threads.

Parse the given Node and Edges files.

Create the Node and Edges datastructure. Find appropriate library and create specific implementation

The package structure has become a mess again.

• nl.tudelft.lifetiles.graph.models.sequence should be merged into nl.tudelft.lifetiles.sequence.
• The graph and tile classes should be merged.
• Make the plural package names (i.e. models) singular.

The horizontal scroll-bar now is the fully zoomed out version of the graph. On that scroll-bar, a rectangle is placed, indicating the area of the graph currently displayed in the graph view. Inspired on the scroll-bar of PyDev (http://i.stack.imgur.com/4cIgU.png).

Loop over the data and use inversed dijkstra, maximum distance.

Is SequenceSegment.endVar overhead by SequenceSegment.startVar + SequenceSegment.contentVar.getLength()?

align horizontal based on relative coordinates

Architecture Design must be delivered 30-4-2015

Currently it is only able to parse files located in the build path, this is undesired.

Currently it uses the singleton ViewController for communication between controllers. By decentralizing the controller communication, this can be refactored into a more MVC adhering structure. It will also improve performance, since ViewController is very slow.

The parser throws a NullPointerException whenever the file to parse is not found. This, among other exception handling kinks, need to be improved so that these error messages eventually can be properly displayed to the user.

When the user clicks on a specific tile, the graph view should only display the strains containing the strains "passing through" that tile and update the sunburst diagram accordingly.

Parse the given Newick files. Find appropriate libary

See pull request #58

Currently the main view does not scale vertically properly; it is fixed. The panes need to be fixed so that they scale in the right way. The sequence & tree views ought to have a fixed height, but the graph view should scale vertically too.

Parser returns wrong data, not sequences but segment coordinates, must be looked at. Add test and solve.

Initialize SunburstJ library and display the standard static parsed Newick file

Data view(er) is too ambiguous, Sequence viewer is a more clear definition.

Parsing the 100_strains data set causes a stack-overflow. This can possible be resolved by https://github.com/ProgrammingLife5/LifeTiles/issues/22 .

Currently the user isn't informed of an error, the program just terminates or silently throws an exception. This isn't desired behaviour.

In the interface, the user should be able to import all the required files from the menu.

Save a location of the sequence inside the graph viewer to the bookmarks so that the user can find that location back easily.