Epic: VCell UI fixes

[jcschaff]

Motivation

• user interface bugs place VCell in a bad light - leading the user to judge the quality of the underlying product with suspicion.

Completion Criteria

• all VCell UI bugs that are likely to be encountered should be fixed or otherwise accommodated (e.g. remove functionality)
• all VCell UI enhancements implemented or moved to other Epics.

Tasks (bugs)

• Results Graphing Functions errors for Moving Boundary Simulations #146
• Copy and Paste does not paste multiple reactions #150
• Scan parameter menu does not automatically pop up on Macs #157
• Expand identification of catalysts with dashed line to situations where catalyst species is part of a gobal parameter #176
• Include species with D=0 in "Post Processing Stats Data" #179
• ODE solver selection menu - change default solver to "Autoselect IDA or CVODE" #183
• Identify issues with background and mapping in geometry editor #194
• Ensure go back to original location in Model pane after clicking within database pane #203
• Bug when creating geometry if change subdomain name error window pops up that is subsequently ingnored when name entered. #289
• Defining new Volume Spatial Process in Kinematics always associated with first listed volume Spatial Object #290
• Opening VCell brings prompt to save previously exported sim results. #304
• Local sim results window pops behind the main VCell window #429
• Orphaned shapes remain after deleting species / reactions. #574
• Orphaned metadata remains after deleting species / reactions with RDF annotations. #575
• Global parameters are not listed under the Kinetics tab of a Rule-based Reaction #611
• Movie files from surface view not opened by windows player #772
• Smart Copy/Paste Broken in 7.5 release #792
• Multiple stochastic runs are not displayed #832
• Bug reported: ArrayIndexOutOfBounds in FunctionRangeGenerator.getFunctionStatistics() #858
• Bug with sharing permissions dialog box #869
• Display of simulation results for spatial does not redraw properly when using auto scale at all times #898
• Curator access to database needs fixes, specifically to flags #936
• Local run Par Scan doesn't show full results #950
• Parameter Estimation Window retains old values when switching to a new application in a Biomodel #1024
• [ ]

Tasks (minor enhancements)

• Make molecular composition layout default in rule-based models #153
• Refine copy and paste for rule-based models #154
• Create annotation fields for Application elements #175
• Allow choice of concentrations or counts for observables and generated species for RBM #182
• Add right click to search reactions for Reaction Table under add a new reaction #184
• Allow assignment of .vcml files to open in VCell in macs #187
• When "Force Continuous" applied in spatial stochastic application, don't allow species to be displayed as number of particles #181
• Need warning when users enter circular expressions  #214
• Control Click does not work on Mac when adding states to molecules #219
• Add progress bar or hourglass to time plot to indicate something is happening #221
• Allow right click to paste into initial conditions #222
• Expand search to include annotations #223
• Revive SabioRK using their native search tools #224
• Allow other panes besides reaction diagram to tear off from main workspace #225
• Client Side Annotations Search #751
• Online Annotations Search Window #752
• Error Reports from Contact-Us improvements #835
• [ ]

Tasks (major enhancements)

• Implement new GUI design for spatial sim results viewer #191
• Field data needs update and better integration with geometry #648
• permit VCell client installation without admin privileges #805
• [ ]