Resolve "add support for modifications and states in sbml export/import"

Closes #572 (closed)

Support for modifications is implemented using SpeciesType features from multi package.

@marek.ostaszewski If you want me to implement it using Binding Sites from multi package please let me know how the data structures inside sbml should look like.

added 28 commits

• 2ef3b3a4 - suppoerted sbml packages in export are configurable
• a4ac9479 - javadoc added
• 7b958814 - basic test for parsing multi
• 179d6fc5 - export contains list of species type for multi package
• d99ec5db - export types contains structural state feature
• 325bae8e - unit test to check import export of structural state
• 75755533 - SBML Model is passed to converter instead of SBML Layout
• 842e8541 - JavaDoc added
• f9e55b64 - layout is no longer passed as an argument - it's always taken from the model
• e9ffb42c - species type contains list of all structural state values in the proper feature
• 399e0c4c - multi species type is exported
• a1c5b4a7 - export of species includes structural state proeprty
• 6fbe9845 - export refactored (it doesn't take layout is a constructor parameter anymore)
• 81538328 - exportElement doesn't take sbmlModel as a parameter
• a12c4ce9 - fix for https://github.com/sbmlteam/jsbml/issues/158 bug
• df26fb65 - parsing type from species type SBO term added
• 9e8db41b - parsing of structural state added
• 804e3371 - test cases from CBML multi specification
• aefaa1d7 - not supported kinetcs attributes are not passed into our model
• 9e5f374c - unused variable removed
• 29c25fc9 - export/import of position to compartment implemented
• cd164f44 - method providing species type id extracted
• a3fdae90 - method to obtain id of structural state feature extracted
• fdf3237e - method to extract id of position to compartment feature extracted
• ff3c5cb0 - unit tests for checking if sbml with multi examples (from specification) are parseable
• 79cbd71a - acceptance test for import export featers into multi
• e1bf8b03 - export with MULTI property separates species wth different structural state
• 24e9d06d - adding modification residues is class dependent (there is no possibil;ity to add…

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added 1 commit

• 1e393c97 - method signature fixed

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added 1 commit

• 885711cd - logger changed to transient property

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added 6 commits

• 293aa8d1 - serialization issue - logger should be a static field
• e819e032 - species types and species feature are created when necessary
• 173407fe - unused field removed from db
• b04fef5d - layout also layout modification residues if present and without layout
• a123fb58 - basic export of modificationrediues implemented
• 9b038127 - unit test do't run on file that is currently nor parsable by jsbml

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added 5 commits

• c6cf8c95 - removing unused imports
• 225dbf0e - debug removed
• e4b86014 - export/import of model notes added
• 84a716b5 - with null notes there is fallback to empty string
• 95da6a9d - model notes are empty string by default

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added 27 commits

• 0ae6f67e - model notes by default are empty string
• 5e75d645 - unit test checking if export of our custom properties is supported
• 8fbe61c3 - code responsible for import/export of multi properties unified
• 08c10511 - missing file
• bc2f74f3 - export/import of synonyms implemented
• e4fb0167 - featureValues extracted to common function
• 3724bc1a - export import of element symbol property added
• 87c9c660 - import/export of element full name added
• aa10c2d2 - import/export of element formula implemented
• 9713e553 - import export of element abbreviation implemented
• f67b3a38 - import/export of element former symbols implemented
• 24c1f8bb - export/import of homodimer property implemented
• 2e3ca9ce - import/export of hypothetical implemented
• 3f760694 - export/import of charge implemented
• d6c79df3 - unit test refactor
• 24efbac9 - export of modification residues in aliases contains info about alias reference id
• 61ad8af9 - export/import of activity proerty implemented
• d2d249d4 - position to compartment differentiate species if multi package is enabled
• ef0a3d1c - unused comment removed
• ee3aaf7b - export of font size implemented
• 08d7d7db - export of position to compartment uses proper names
• 1f093f89 - export of initial concentration added
• 24dce33c - complexes with different content are considered as different SBML entities if multi is enabled
• 9707e0b1 - when exporting with multi different activity creates different species
• c2746565 - different set of annotations create different SBML species
• bc441004 - different dimer creates different species in multi
• d6b56659 - more info when different due to class type difference

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added 3 commits

• e9f7817c - JavaDoc added
• a1f642ab - apache commons-text added to replace deprecated escapeXml functionality
• dc5b9db3 - imports organized

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unmarked as a Work In Progress

changed the description

enabled an automatic merge when the pipeline for dc5b9db3 succeeds

merged

mentioned in commit b59a2c90