Week 3 Report:
1. Finished Xref comparison of DataNodes using BidgeDB IDMapperStack. This IDMapperStack is made available to the comparison plugin through SwingEngine.getGdbManager().getCurrentGdb();. The IdMapperStack stacks all the available IDMappers and provides a common handle for Id mappping. The comparison now requires the user to first select a biological database (Data->Select Gene/Metabolite Database), so that the IDMapperStack has got atleast one IDMapper to start with.
2. Yet to finish Line comparison.
3. UI layout for "Results Pane" modified to accommodate DataNode-comparison results and Line-comparison results in their own separate JTables. For ow the results under Line-comparison would be the same as DataNode-comparison results as Line-comparison is still in progress.
4. The pathway loading and comparing now happen inside a separate background thread using the SwingWorker class. Hence a progress dialog would pop-up during the loading period. Followed the example from SwingEngine.openPathway().
5. Fixed bugs related to highlighting PathwayElements, window re-size events, KeyListener events for the "results" Panel's JTables' rows.
6. Documented most of the source code and refactored code. I will be doing this on a regular basis as mentioned in the previous blog post.
7. Need to discuss:
a. what would be next after finishing Line comparison.
b. Is "comparison pop-up window" the way forward or showing pathway comparison inside PathVisio's main panel better ?
Please feel free to put down any comments regarding the plugin or its code.
Below are the screenshots of Pathway-comparison plug-in:
regards,
Praveen Kumar
1. Finished Xref comparison of DataNodes using BidgeDB IDMapperStack. This IDMapperStack is made available to the comparison plugin through SwingEngine.getGdbManager().getCurrentGdb();. The IdMapperStack stacks all the available IDMappers and provides a common handle for Id mappping. The comparison now requires the user to first select a biological database (Data->Select Gene/Metabolite Database), so that the IDMapperStack has got atleast one IDMapper to start with.
2. Yet to finish Line comparison.
3. UI layout for "Results Pane" modified to accommodate DataNode-comparison results and Line-comparison results in their own separate JTables. For ow the results under Line-comparison would be the same as DataNode-comparison results as Line-comparison is still in progress.
4. The pathway loading and comparing now happen inside a separate background thread using the SwingWorker class. Hence a progress dialog would pop-up during the loading period. Followed the example from SwingEngine.openPathway().
5. Fixed bugs related to highlighting PathwayElements, window re-size events, KeyListener events for the "results" Panel's JTables' rows.
7. Need to discuss:
a. what would be next after finishing Line comparison.
b. Is "comparison pop-up window" the way forward or showing pathway comparison inside PathVisio's main panel better ?
Please feel free to put down any comments regarding the plugin or its code.
Below are the screenshots of Pathway-comparison plug-in:
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| Progress Dialog pops up when "Compare" is clicked |
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| Comparing two different pathways and no match is found. Note: Line Comparison is not yet ready |
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| Comparing the same pathway for lack of two similar pathways. Hence all the DataNodes with Xrefs are highlighted in both the pathways. |
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| Highlighting a match ( PathwayElement i.e DataNode found in both of the pathways) by clicking on a row in the results. Each row corresponds to a match |
regards,
Praveen Kumar
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