.. _PhysiCell_java_VirusMacrophage_Macrophage_java:

Macrophage.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 java.util.ArrayList;
    import java.util.List;

    import ru.biosoft.physicell.biofvm.CartesianMesh;
    import ru.biosoft.physicell.biofvm.Microenvironment;
    import ru.biosoft.physicell.biofvm.VectorUtil;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.core.CellContainer;
    import ru.biosoft.physicell.core.CellDefinition;
    import ru.biosoft.physicell.core.CellFunctions.UpdatePhenotype;
    import ru.biosoft.physicell.core.Phenotype;

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

            CellDefinition pMacrophage = pCell.getModel().getCellDefinition( "macrophage" );

            // digest virus particles inside me 
            double implicitEulerConstant = ( 1.0 + dt * pCell.customData.get( "virus_digestion_rate" ) );
            phenotype.molecular.internSubstrates[nVirus] /= implicitEulerConstant;

            // check for contact with a cell
            List<Cell> neighbors = get_possible_neighbors( pCell );
            for( Cell neighbor : neighbors )
            {
                if( neighbor != pCell && neighbor.type != pMacrophage.type )
                {
                    double dist = VectorUtil.dist( neighbor.position, pCell.position );
                    double maxDistance = 1.1 * ( pCell.phenotype.geometry.radius + neighbor.phenotype.geometry.radius );

                    // if it is not a macrophage, test for viral load if high viral load, eat it. 
                    if( neighbor.phenotype.molecular.internSubstrates[nVirus] > pCell.customData.get( "min_virion_detection_threshold" )
                            && dist < maxDistance )
                    {
                        pCell.ingestCell( neighbor );
                    }
                }
            }
        }

        public String display()
        {
            return "Ingests infected cells.";
        }

        public List<Cell> get_possible_neighbors(Cell pCell)
        {
            int mechanicsVoxelIndex = pCell.get_current_mechanics_voxel_index();
            CellContainer container = pCell.get_container();
            CartesianMesh mesh = container.mesh;
            List<Cell> neighbors = new ArrayList<>( container.agentGrid.get( mechanicsVoxelIndex ) );

            for( int neighborVoxel : mesh.moore_connected_voxel_indices[mechanicsVoxelIndex] )
            {
                if( !Cell.isNeighborVoxel( pCell,
                        mesh.voxels[mechanicsVoxelIndex].center, mesh.voxels[neighborVoxel].center, neighborVoxel ) )
                    continue;
                neighbors.addAll( container.agentGrid.get( neighborVoxel ) );
            }
            return neighbors;
        }
    }