.. _PhysiCell_java_VirusMacrophage_Epithelial_java:

Epitelial.java
==============

.. role:: raw-html(raw)
   :format: html

.. raw:: html

   <style>
   pre {
      white-space: pre-wrap !important;       /* Сохраняет пробелы, но разрешает перенос */
      word-wrap: break-word !important;       /* Переносит длинные слова */
      overflow-wrap: break-word !important;   /* Альтернатива для совместимости */
      hyphens: auto !important;               /* Перенос с тире */
   }
   </style>

.. code-block:: console

    import ru.biosoft.physicell.biofvm.Microenvironment;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.core.CellFunctions.UpdatePhenotype;
    import ru.biosoft.physicell.core.Phenotype;

    public class Epithelial extends UpdatePhenotype
    {
        @Override
        public void execute(Cell pCell, Phenotype phenotype, double dt)
        {
            // bookkeeping
            Microenvironment microenvironment = pCell.getMicroenvironment();
            int nVirus = microenvironment.findDensityIndex( "virus" );
            int nInterferon = microenvironment.findDensityIndex( "interferon" );

            // compare against viral load. Should I commit apoptosis? 
            double virus = phenotype.molecular.internSubstrates[nVirus];
            if( virus >= pCell.customData.get( "burst_virion_count" ) )
            {
                pCell.lyseCell(); // start_death( apoptosis_model_index );
                pCell.functions.updatePhenotype = null;
                return;
            }

            // replicate virus particles inside me 
            if( virus >= pCell.customData.get( "min_virion_count" ) )
            {
                double new_virus = pCell.customData.get( "viral_replication_rate" ) * dt;
                phenotype.molecular.internSubstrates[nVirus] += new_virus;
            }

            if( virus >= pCell.customData.get( "virion_threshold_for_interferon" ) )
            {
                phenotype.secretion.secretionRates[nInterferon] = pCell.customData.get( "max_interferon_secretion_rate" );
            }
        }
    }