source: trunk

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Diff Rev Age Author Log Message
(edit) @256   11 years j TODO updated
(edit) @255   11 years j Added PTMs field to peptides in protein
(edit) @254   11 years j Deleted tasks that are done
(edit) @253   11 years j Changed font for protein sequence
(edit) @252   11 years j Better exception handling for formatted protein sequence coverage
(edit) @251   11 years j Added CSS class to show peptides in protein
(edit) @250   11 years j Added text wrapping to protein sequence in the view
(edit) @249   11 years j Injected covered sequence into protein template
(edit) @248   11 years j Added formatted protein sequence coverage to protein view
(edit) @247   11 years j Restored ZEO configuration
(edit) @246   11 years j Separated coverage method into setting the coverage sequence and the …
(edit) @245   11 years j Fixed protein sequence coverage calculation
(edit) @244   11 years j Removed 'PPMs' label from MME field in templates
(edit) @243   11 years j Fixed Calculation of MME
(edit) @242   11 years j Updated TODO
(edit) @241   11 years j Fixed display for non-quantified proteins
(edit) @240   11 years j Fixed PSM view for PSMs which don't have quantitation
(edit) @239   11 years j TODO updated after first user feedback
(edit) @238   11 years j Deactivated ZEO until I get proper sorting
(edit) @237   11 years j Add finish message when building
(edit) @236   11 years j Better formatting of building times
(edit) @235   11 years j Update max_score for proteins when building
(edit) @234   11 years j Updated TODO to reflect proper architecture for efficient cataloging, …
(edit) @233   11 years j Added indexing by path and max_score
(edit) @232   11 years j Commented out catalog search for proteins, to be implemented later
(edit) @231   11 years j Don't track minimal dataset
(edit) @230   11 years j Don't track anything in db
(edit) @229   11 years j Indexing maximum score of each peptide in a catalog
(edit) @228   11 years j Added zeo.conf to use zeo with the application
(edit) @227   11 years j Updated dependencies in order to use ZEO
(edit) @226   11 years j Cosmetic changes
(edit) @225   11 years j TODO revamped
(edit) @224   11 years j Added score filter form to experiment template
(edit) @223   11 years j Fixed protein batch
(edit) @222   11 years j Removed awful function to filter proteins by maximum score and instead …
(edit) @221   11 years j Assign maximum protein score to the object instead of returning
(edit) @220   11 years j Included max_score in Peptide instantiation
(edit) @219   11 years j Added function to protein model to get the maximum score of all the …
(edit) @218   11 years j Quick and dirty filtering of proteins by maximum score of its petides
(edit) @217   11 years j Better arrangment of imports for views
(edit) @216   11 years j Experiment view filters by maximum score of all the peptides …
(edit) @215   11 years j Removed completed tasks from TODO
(edit) @214   11 years j Updated protein template to show protein ratios
(edit) @213   11 years j Better rounding of numbers for PSM data
(edit) @212   11 years j Added update method for protein ratios, update of psm ratios done …
(edit) @211   11 years j TODO updated
(edit) @210   11 years j Added calculation of quant ratios at for psms, updated template to …
(edit) @209   11 years j Parsing XIC integration for MsQuant?
(edit) @208   11 years j TODO updated
(edit) @207   11 years j Added a line to show the PSM scan in the XICs
(edit) @206   11 years j Removed few tasks from TODO
(edit) @205   11 years j Added drawing of scans taken for quantitation in psm template
(edit) @204   11 years j Added method to PSM to check whether it was quantified, updated …
(edit) @203   11 years j Added method to peptide to check if it has any peptides quantified, …
(edit) @202   11 years j Fixed points and lines for XIC and spectrum plots
(edit) @201   11 years j More tasks after naive XIC drawing
(edit) @200   11 years j Added canvas plotting of XIC
(edit) @199   11 years j JSON coordinates for XIC plotting accessible from psm view
(edit) @198   11 years j Minor cosmetic changes
(edit) @197   11 years j TODO updated: more granular tasks for quantitation
(edit) @196   11 years j Added function to find out psm id by spectrum id and completed MsQuant?
(edit) @195   11 years j Fixed bug that was assigning psm_refs to spectra wrongly
(edit) @194   11 years j Added psm references to spectrum and updated mascot parser
(edit) @193   11 years j Added repoze.catalog to distribute dependencies
(edit) @192   11 years j Added MsQuant? parser to appmaker
(edit) @191   11 years j Itergroup like parsing iterator for MsQuant? parser. It alternates …
(edit) @190   11 years j Deleted sequence parsing for MsQuant? output (not possible to parse …
(edit) @189   11 years j Explained modification position issue with MsQuant? output in TODO.
(edit) @188   11 years j Obtaining spec id from msquant files
(edit) @187   11 years j Parsing msquant psm data
(edit) @186   11 years j Added dummy msquant module to parse msquant output, added the msquant …
(edit) @185   11 years j Removed brackets from the formatted peptide sequence
(edit) @184   11 years j Deleted unnecessary folders variable in appmaker
(edit) @183   11 years j TODO updated
(edit) @182   11 years j Readable URLs for psms and peptide models
(edit) @181   11 years j Updated templates to show MME
(edit) @180   11 years j Calculate MME for all Psms
(edit) @179   11 years j Renamed functions to update proteins and peptides
(edit) @178   11 years j TODO updated
(edit) @177   11 years j 1 px width for peaks in spectrum graph
(edit) @176   11 years j Better xs limits for spectrum graph
(edit) @175   11 years j Added flot.js resource and drawing the spectra from psm view
(edit) @174   11 years j Proper JSON output of MS/MS peaks for PSM view
(edit) @173   11 years j Added psm view with its template and link from peptide view
(edit) @172   11 years j TODO updated
(edit) @171   11 years j Parsing MS/MS peaks
(edit) @170   11 years j TODO updated
(edit) @169   11 years j Added peptide template
(edit) @168   11 years j Added psm view, template and links from peptive view
(edit) @167   11 years j Renamed views like Python functions
(edit) @166   11 years j Added link to home to the master template
(edit) @165   11 years j TODO updated
(edit) @164   11 years j Added protein sequence formatting and updated protein template to show …
(edit) @163   11 years j Updated protein template to show number of PSMs and score
(edit) @162   11 years j Added method to update the maximum score of the psms of a peptide
(edit) @161   11 years j TODO updated
(edit) @160   11 years j Coverage is stored as a protein attribute, added sorting by coverage too
(edit) @159   11 years j Added naked_seq attribute constructor to peptide and sequence coverage …
(edit) @158   11 years j TODO updated
(edit) @157   11 years j Storing psms and peptide counts as attributes of peptides and proteins …
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