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Preserve internalized substrates and custom data in Cell::convert_to_cell_definition function #307

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drbergman
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  • Add line to preserve internalized substrates after copying the entire phenotype
  • Add code to preserve custom data marked as conserved
  • store conserved boolean when reading in xml

…_cell_definition` function

* Add line to preserve internalized substrates after copying the entire phenotype
* Add code to preserve custom data marked as conserved
* store conserved boolean when reading in xml
MathCancer added a commit that referenced this pull request Oct 14, 2024
Changed defaults in BioFVM Basic Agents so that cells ingest not just cell volume, but also internalized substrates by default.

This is in response to Issue #307
MathCancer added a commit that referenced this pull request Oct 14, 2024
In response to Issue #307, cells by default ingest 100% of internalized substrates when eating another cell.
MathCancer added a commit that referenced this pull request Oct 14, 2024
In response to Issue #307, cells by default ingest 100% of conserved custom variables when eating another cell.
MathCancer added a commit that referenced this pull request Oct 14, 2024
In response to Issue #307, cells by default ingest 100% of internalized substrates when eating another cell.

(Note that the values for std::vector<bool> fraction_tranferred_when_ingested in Basic_Agent is *overwritten* by constructors in the cell Phenotype, so we have ot do it there.)
@MathCancer MathCancer merged commit ee154ee into MathCancer:development Oct 15, 2024
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@drbergman drbergman deleted the fix-internalized-substrates branch November 8, 2024 21:34
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