TODO/FIXME items in Gorgon code

shadowwalkersb commented 9 years ago

[ ] TODO <--------- FIX THIS (last paramater) Gorgon/FlexibleFittingEngine.h#L163
[ ] TODO Also normalize the sheet capacity here? GraphMatch/WongMatch15ConstrainedNoFuture.h#L1320
[ ] TODO Ask Matt if I correctly handled cases where apix_x != apix_y or apix_x != apix_z ProteinMorph/SSEHunter.h#L773
[ ] TODO check if the cast for mapSize is the way to go ProteinMorph/SSEHunter.h#L620
[ ] TODO Consider case where this voxel may have already been visited but with a longer path GraphMatch/SkeletonReader.h#L882
[ ] TODO Finish coding SetGeometryScores ProteinMorph/SSEHunter.h#L79
[ ] TODO Finish coding the geometry score portion of this function ProteinMorph/SSEHunter.h#L66
[ ] TODO finish this function ProteinMorph/SSEHunter.h#L376
[ ] TODO fix GraphMatch/SSECorrespondenceResult.h#L86
[ ] TODO Fix patthernLength and baseLength for sheet-to-sheet case. GraphMatch/WongMatch15ConstrainedNoFuture.h#L437
[ ] TODO Fix this: GraphMatch/Matcher6.h#L259
[ ] TODO Fix, has bug. But getting closer. GraphMatch/WongMatch15ConstrainedNoFuture.h#L480
[ ] TODO Fix! Gorgon/SSECorrespondenceEngine.h#L133
[ ] TODO Fix! 0 not acceptable! Gorgon/SSECorrespondenceEngine.h#L123
[ ] TODO If a vertex is part of both the sheet skeleton and the helix skeleton, typeCost = 0; ProteinMorph/SSEHunter.h#L240
[ ] TODO In EMAN1 the maximum distance is sqrt(3*4 ProteinMorph/SSEHunter.h#L220
[ ] TODO Is this the same as testing if it's in the sheet skeleton ProteinMorph/SSEHunter.h#L241
[ ] TODO looks like the following line just returns a single corner for the helix GraphMatch/StandardGraph.h#L349
[ ] TODO looks like the following line just returns a single corner for the helix GraphMatch/StandardGraph.h#L360
[ ] TODO Make it work with helices ProteinMorph/SSEHunter.h#L873
[ ] TODO Make this better!! GraphMatch/Matcher7.h#L253
[ ] TODO Make this more accurate GraphMatch/LedaMatch.h#L78
[ ] TODO Make this more accurate GraphMatch/Matcher6.h#L98
[ ] TODO Make this more accurate GraphMatch/Matcher7.h#L108
[ ] TODO Make this more accurate GraphMatch/VFInexact.h#L94
[ ] TODO Make this more accurate GraphMatch/VFMatch.h#L86
[ ] TODO Make this more accurate GraphMatch/WongMatch.h#L104
[ ] TODO Make this more accurate GraphMatch/WongMatch15.h#L109
[ ] TODO Make this more accurate GraphMatch/WongMatch15Constrained.h#L110
[ ] TODO Make this more accurate GraphMatch/WongMatch15ConstrainedOnlyA.h#L109
[ ] TODO Make this more accurate GraphMatch/WongMatch15Ordered.h#L107
[ ] TODO Make this more accurate GraphMatch/WongMatch2.h#L125
[ ] TODO Make this more accurate GraphMatch/WongMatchMissing.h#L100
[ ] TODO Make this more accurate GraphMatch/WongMatchMissing15.h#L105
[ ] TODO Make this more accurate GraphMatch/WongMatchMissing15Linked.h#L109
[ ] TODO possibly implement mouse picking using ray intersection Gorgon/CAlphaRenderer.h#L214
[ ] TODO possibly implement mouse picking using ray intersection Gorgon/CAlphaRenderer.h#L329
[ ] TODO possibly implement mouse picking using ray intersection Gorgon/CAlphaRenderer.h#L1014
[ ] TODO possibly implement mouse picking using ray intersection Gorgon/CAlphaRenderer.h#L1093
[ ] TODO possibly implement mouse picking using ray intersection Gorgon/CAlphaRenderer.h#L1383
[ ] TODO read file by small chunks, combine in one large string ExternalLibraries/alglib/ap.h#L1081
[ ] TODO Remove this arbitrary weight! GraphMatch/WongMatch15ConstrainedNoFuture.h#L575
[ ] TODO Scale the sheet size by the geometric scale factor to make units match GraphMatch/SkeletonReader.h#L349
[ ] TODO TEST ProteinMorph/SSEHunter.h#L600
[ ] TODO TEST ProteinMorph/SSEHunter.h#L747
[ ] TODO TEST ProteinMorph/SSEHunter.h#L766
[ ] TODO Test this function!!!! ProteinMorph/SSEHunter.h#L659
[ ] TODO test whether in the helix skeleton ProteinMorph/SSEHunter.h#L243
[ ] TODO throw an exception ProteinMorph/SSEHunter.h#L409
[ ] XXX test for "small" instead ProteinMorph/CurveDeformer.h#L512

/src_py

[ ] TODO: check on whether the current match is a helix or a strand Gorgon/src_py/calpha_structure_editor.py#L1085
[ ] TODO: Move this color changing code somewhere else Gorgon/src_py/sse_helix_correspondence_finder_form.py#L1062
[ ] TODO: only count strands that are different. every sheet must be the same color! Gorgon/src_py/sse_helix_correspondence_finder_form.py#L951
[ ] TODO: figure out how to handle orphan strands Gorgon/src_py/seq_model/Chain.py#L888
[ ] TODO: Mike this raises an error!; Gorgon/src_py/sse_helix_correspondence_finder_form.py#L791
[ ] TODO: This method can be refactored using the chain.secels dictionary... this would stop the need to search for previous and next helices.. Gorgon/src_py/calpha_flexible_fitting_form.py#L504
[ ] TODO: make sure this will not eventually overwrite chain IDs from a PDB file that doesn't start at A. Gorgon/src_py/seq_model/Chain.py#L335
[ ] TODO: Add a test for input of *.seq files Gorgon/src_py/seq_model/SeqModelTests.py#L205
[ ] TODO: find a more elegant way than dividing radius by the apix_X to fix the scaling problem Gorgon/src_py/calpha_structure_editor.py#L125
[ ] TODO: We need to figure out how to handle this exception Gorgon/src_py/seq_model/Chain.py#L106
[ ] TODO:We might want to modify this to use any unused numbers (after a rename) Gorgon/src_py/seq_model/Chain.py#L102
[ ] TODO: Put a error message here telling the user that the save failed Gorgon/src_py/volume_sse_builder_form.py#L63
[ ] TODO: perhaps we should change this behavior, in case someone modified a chain object then imported a PDB with a chain of the same name Gorgon/src_py/seq_model/Chain.py#L59

/cc PR #106

shadowwalkersb commented 9 years ago

@GorgonCryoEM/developers There are some (!) TODO comments in the code. They are listed in the description above. Every item has a description and a link which should take you directly to the line where the item is. Can check the ones that have been fixed and are not relevant any more?

shadowwalkersb commented 7 years ago

Dropping.

GorgonCryoEM / Gorgon

TODO/FIXME items in Gorgon code #62