.. _PhysiCell_java_Worm_WormRule_java:

WormRule.java
=============

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.. code-block:: console

    import ru.biosoft.physicell.biofvm.Microenvironment;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.core.CellFunctions.CustomCellRule;
    import ru.biosoft.physicell.core.Model;
    import ru.biosoft.physicell.core.Phenotype;
    import ru.biosoft.physicell.core.standard.Chemotaxis;
    import ru.biosoft.physicell.core.CellFunctions.UpdateMigrationBias;
    import ru.biosoft.physicell.biofvm.VectorUtil;

    public class WormRule extends CustomCellRule
    {
        private Model model;
        private boolean isInit = false;

        public void init(Model model)
        {
            this.model = model;
            isInit = true;
        }

        @Override
        public void execute(Cell pCell, Phenotype phenotype, double dt)
        {
            if (!isInit)
                init(pCell.getModel());

            // bookkeeping 
            Microenvironment m = pCell.getMicroenvironment();
            int nSignal = m.findDensityIndex( "signal" );

            // look for cells to form attachments, if 0 attachments
            int number_of_attachments = pCell.state.numberAttachedCells();
            if( number_of_attachments == 0 )
            {
                for( Cell neighbor : pCell.nearby_interacting_cells() )
                {
                    if( neighbor.state.numberAttachedCells() < neighbor.customData.get( "max_attachments" ) )
                    {
                        Cell.attachcCells( neighbor, pCell );
                        number_of_attachments++;
                    }
                    if( number_of_attachments > pCell.customData.get( "max_attachments" ) )
                        break;
                }
            }

            if( number_of_attachments == 0 )
            {
                pCell.functions.updateMigration = new Chemotaxis();
            }
            else if( number_of_attachments == 1 ) // if 1 attachment, do some logic  
            {
                // constant expression in end cells 
                pCell.customData.set( "head", pCell.customData.get( "head_initial" ) );

                // am I the head? 
                boolean head = false;
                if( pCell.customData.get( "head" ) > pCell.state.attachedCells.iterator().next().customData.get( "head" ) )
                    head = true;

                //            if( head )
                pCell.functions.updateMigration = head ? new HeadMigration( model ) : new TailMigration( model );
                //            else
                //                pCell.functions.updateMigration = new TailMigration( model );

                phenotype.secretion.secretionRates[nSignal] = 100;
            }
            else if( number_of_attachments > 1 ) // if 2 or more attachments, use middle 
            {
                pCell.functions.updateMigration = new MiddleMigration( model );
                phenotype.secretion.secretionRates[nSignal] = 1;
            }
        }

    public class HeadMigration extends Chemotaxis
    {
        private int direction;
        private double speed;
        private double bias;
        private double persistenceTime;

        public HeadMigration(Model model)
        {
            direction = model.getParameterInt( "head_migration_direction" );
            speed = model.getParameterDouble( "head_migration_speed" );
            bias = model.getParameterDouble( "head_migration_bias" );
            persistenceTime = model.getParameterDouble( "head_migration_persistence" );
        }

        @Override
        public void execute(Cell pCell, Phenotype phenotype, double dt)
        {
            phenotype.motility.chemotaxisDirection = direction;
            phenotype.motility.migrationSpeed = speed;
            phenotype.motility.migrationBias = bias;
            phenotype.motility.persistenceTime = persistenceTime;
            // use this for fun rotational paths 
            /*
            double r = norm( pCell.position ) + 1e-16; 
            phenotype.motility.migration_bias_direction[0] = - pCell.position[1] / r; 
            phenotype.motility.migration_bias_direction[1] = pCell.position[0] / r; 
            
            normalize( &(phenotype.motility.migration_bias_direction) ); 
            return; 
            */
            super.execute( pCell, phenotype, dt );
        }
    }

    public class MiddleMigration extends UpdateMigrationBias
    {
        double speed;

        public MiddleMigration(Model model)
        {
            speed = model.getParameterDouble( "middle_migration_speed" );
        }

        public void execute(Cell pCell, Phenotype phenotype, double dt)
        {
            // get velocity from "Upstream" 
            Cell headCell = null;
            for( Cell cell : pCell.state.attachedCells )
            {
                if( headCell == null || cell.customData.get( "head" ) > headCell.customData.get( "head" ) )
                    headCell = cell;
            }
            phenotype.motility.migrationSpeed = speed;
            phenotype.motility.migrationBiasDirection = headCell.phenotype.motility.migrationBiasDirection;
            VectorUtil.normalize( phenotype.motility.migrationBiasDirection );
        }
    }

    public class TailMigration extends Chemotaxis
    {
        private int direction;
        private double speed;
        private double bias;
        private double persistenceTime;

        public TailMigration(Model model)
        {
            direction = model.getParameterInt( "tail_migration_direction" );
            speed = model.getParameterDouble( "tail_migration_speed" );
            bias = model.getParameterDouble( "tail_migration_bias" );
            persistenceTime = model.getParameterDouble( "tail_migration_persistence" );
        }

        @Override
        public void execute(Cell pCell, Phenotype phenotype, double dt)
        {
            phenotype.motility.chemotaxisDirection = direction;
            phenotype.motility.migrationSpeed = speed;
            phenotype.motility.migrationBias = bias;
            phenotype.motility.persistenceTime = persistenceTime;
            super.execute( pCell, phenotype, dt );
        }
    }

    }