Todo
Add lots more tests for algorithms.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 6.)
Todo
Re-factor the Entrez model to something more elegant. It’s sort of a mess.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 10.)
Todo
Cython sliding window and accumulating sliding window.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 15.)
Todo
Make shovel file modular or switch to something else.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 19.)
Todo
Beautify created DMGs with all the bells and whistles.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 23.)
Todo
When searching again on the Entrez view, or computing again on the Results view, stale data is left in the forms. They should be clear when a new search/analysis is performed.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 27.)
Todo
Rename file_loaded event to something that makes more sense.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 33.)
Todo
Loading a file or a sequence from Entrez should prompt if overwriting a sequence currently typed in.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 37.)
Todo
Handle no Internet on the Entrez view.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 42.)
Todo
Switch assert mock calls to Gray’s new style.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 46.)
Todo
Throttle calls to ESpell.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 50.)
Todo
Refactor error shower code as shown in the Presenter First paper.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 54.)
Todo
Measure speed of algorithm. Decided to add a “Timing” tab which gets populated in the same way as Results when compute_islands is called. We will compose the SeqInputModel with a TimingModel. The SeqInputModel calls a setter on the TimingModel which then sends the information to the TimingView. The timing view will list the algorithms run. The algorithms which are run can be chosen from a multiple select box within the SeqInputModel. The timings will initially be graphed using a bar graph for single runs, and then be changed to a box plot for multiple runs of the same algorithm.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 58.)
Todo
Decrease the cyclomatic complexity of the Python accumulator algorithm.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 71.)
Todo
Refine global sequence text edit to have an auto-zoom.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 75.)
Todo
C-based extension model implementing sliding window.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 79.)
Todo
Refine global sequence text edit with numbered lines, better format, etc.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 83.)
Todo
In the open file dialog, the dialog should remember the directory last visited. To do this between opens, use a variable. To do this between runs (better), store it in a QSettings instance.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 88.)
Todo
Figure out why flake8>1.5 is not working with NOQA comments. For now we are just staying at flake8==1.5.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 94.)
Todo
Tabbed interface for sequence files.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 99.)
Todo
Analysis run history.
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 103.)
Todo
Load fasta sequence from file
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 107.)
Todo
Perform “client-side” validation for the Sequence box:
(The original entry is located in /var/build/user_builds/cpg-islands/checkouts/latest/docs/source/todo.rst, line 111.)
Todo
Add lots more tests for algorithms.
Todo
Re-factor the Entrez model to something more elegant. It’s sort of a mess.
Todo
Cython sliding window and accumulating sliding window.
Todo
Make shovel file modular or switch to something else.
Todo
Beautify created DMGs with all the bells and whistles.
Todo
When searching again on the Entrez view, or computing again on the Results view, stale data is left in the forms. They should be clear when a new search/analysis is performed.
Todo
Rename file_loaded event to something that makes more sense.
Todo
Loading a file or a sequence from Entrez should prompt if overwriting a sequence currently typed in.
Todo
Handle no Internet on the Entrez view.
Todo
Switch assert mock calls to Gray’s new style.
Todo
Throttle calls to ESpell.
Todo
Refactor error shower code as shown in the Presenter First paper.
Todo
Measure speed of algorithm. Decided to add a “Timing” tab which gets populated in the same way as Results when compute_islands is called. We will compose the SeqInputModel with a TimingModel. The SeqInputModel calls a setter on the TimingModel which then sends the information to the TimingView. The timing view will list the algorithms run. The algorithms which are run can be chosen from a multiple select box within the SeqInputModel. The timings will initially be graphed using a bar graph for single runs, and then be changed to a box plot for multiple runs of the same algorithm.
Todo
Decrease the cyclomatic complexity of the Python accumulator algorithm.
Todo
Refine global sequence text edit to have an auto-zoom.
Todo
C-based extension model implementing sliding window.
Todo
Refine global sequence text edit with numbered lines, better format, etc.
Todo
In the open file dialog, the dialog should remember the directory last visited. To do this between opens, use a variable. To do this between runs (better), store it in a QSettings instance.
Todo
Figure out why flake8>1.5 is not working with NOQA comments. For now we are just staying at flake8==1.5.
Todo
Tabbed interface for sequence files.
Todo
Analysis run history.
Todo
Load fasta sequence from file
Todo
Perform “client-side” validation for the Sequence box: