AtomParticuleStyle.cs

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namespace Molecule.View.DisplayAtom
{

    using UnityEngine;
    using System.Collections;
    using Molecule.Model;
    using Molecule.Control;
    using UI;
    public class AtomParticleStyle : IAtomStyle
    {
        public static ArrayList atomOrderList;
        public static ArrayList atomOrderListArray;

        private float[] scale=new float[7];


        public AtomParticleStyle()  
        {
            if(UIData.secondarystruct)
                MoleculeModel.p = new Particle[MoleculeModel.CaSplineList.Count];
            else
                MoleculeModel.p = new Particle[MoleculeModel.atomsLocationlist.Count];


            scale[0]=(MoleculeModel.carbonScale)/10;
            scale[1]=(MoleculeModel.nitrogenScale)/10;
            scale[2]=(MoleculeModel.oxygenScale)/10;
            scale[3]=(MoleculeModel.sulphurScale)/10;
            scale[4]=(MoleculeModel.phosphorusScale)/10;
            scale[5]=(MoleculeModel.hydrogenScale)/10;          
            scale[6]=(MoleculeModel.unknownScale)/10;   
        }


        public void DisplayAtoms(UIData.AtomType type_atom, bool force_display = false)
        {
            UIData.shadow = false;


            if(type_atom==UIData.AtomType.particleball) {
                ArrayList atomListByAxisOrder;                  
                
                if(UIData.secondarystruct)
                    atomListByAxisOrder=AtomListByAxisOrder(MoleculeModel.CaSplineList);
                else
                    atomListByAxisOrder=AtomListByAxisOrder(MoleculeModel.atomsLocationlist);

                DisplayAtomParticle(atomListByAxisOrder);
            }
            else if(type_atom==UIData.AtomType.particleballalphablend) {
                ArrayList atomListByAxisOrder;
                if(UIData.secondarystruct) {
                    atomListByAxisOrder=AtomListByAxisOrder(MoleculeModel.CaSplineList);
                }
                else {
                    atomListByAxisOrder=AtomListByAxisOrder(MoleculeModel.atomsLocationlist);
                }
                DisplayAtomParticle(atomListByAxisOrder);
            }

            GameObject shurikenParticleManagerObj = GameObject.FindGameObjectWithTag("ShurikenParticleManager");
            ShurikenParticleManager shManager = shurikenParticleManagerObj.GetComponent<ShurikenParticleManager>();
            shManager.Init();

            UIData.isParticlesInitialized = true;

        }
        
        

        private void DisplayAtomParticle(ArrayList atomsLocation) {
            Color c=new Color();
            Vector3 v=new Vector3();
                        
            int Number=atomsLocation.Count;
            
            for(int k=0;k<Number;k++) {
                int i = (int)(atomsLocation[k] as float[])[4];
                int order=1;
                
                float typenumber=(atomsLocation[k] as float[])[3];
                c = MoleculeModel.atomsColorList[i];
                switch ( (int) typenumber ) {
                    case 0: 
                            //c= (MoleculeModel.carbonColor.color);
                            v=new Vector3(1.7f*scale[0],1.7f*scale[0],1.7f*scale[0]);
                            break;
                    case 1:
                            //c= (MoleculeModel.nitrogenColor.color);
                            v=new Vector3(1.55f*scale[1],1.55f*scale[1],1.55f*scale[1]);
                            break;
                    case 2:
                            //c= (MoleculeModel.oxygenColor.color);
                            v=new Vector3(1.52f*scale[2],1.52f*scale[2],1.52f*scale[2]);
                            break;
                    case 3:
                            //c= (MoleculeModel.sulphurColor.color);
                            v=new Vector3(2.27f*scale[3],2.27f*scale[3],2.27f*scale[3]);
                            break;
                    case 4:
                            //c= (MoleculeModel.phosphorusColor.color); 
                            v=new Vector3(1.18f*scale[4],1.18f*scale[4],1.18f*scale[4]);
                            break;
                    case 5:
                            //c= (MoleculeModel.hydrogenColor.color);
                            v=new Vector3(1.2f*scale[5],1.2f*scale[5],1.2f*scale[5]);
                            break;
                    default:
                            //c= (MoleculeModel.unknownColor.color);
                            v=new Vector3(1.0f*scale[6],1.0f*scale[6],1.0f*scale[6]);
                            break;
                }
                CreateParticleBall(i,k,atomsLocation,c,v,order);
            }

        }

        private void CreateParticleBall(int type,int start,ArrayList atomLocationalist,Color c,Vector3 v,int order) {       
//          Debug.Log("CreateParticleBall"+start);
            float[]  fLocation=atomLocationalist[start] as float[];
            Vector3 location=new Vector3(fLocation[0],fLocation[1],fLocation[2]);
            MoleculeModel.p[start].position=location;
            MoleculeModel.p[start].size=(float)(v[0]);
            MoleculeModel.p[start].color=c;
            MoleculeModel.p[start].energy=1000;
        }

//      private ArrayList AtomListByAxisOrder(ArrayList alist)
        public ArrayList AtomListByAxisOrder(IList alist) {
            // Debug.Log("Entering :: AtomListByAxisOrder");
            ArrayList atomListByOrder=new ArrayList();

            for(int i=0;i<alist.Count;i++) {
                float typenumber=0f;
                string  type;
                if(UIData.secondarystruct)
                    type = (MoleculeModel.CaSplineTypeList[i] as AtomModel).type;
                else
                    type = (MoleculeModel.atomsTypelist[i] as AtomModel).type;

                switch(type) {
                        case "C": 
                                typenumber=0f;
                                break;
                        case "N":
                                typenumber=1f;
                                break;
                        case "O":
                                typenumber=2f;
                                break;
                        case "S":
                                typenumber=3f;
                                break;
                        case "P":
                                typenumber=4f;
                                break;
                        case "H":
                                typenumber=5f;
                                break;
                        default:
                                typenumber=6f;
                                break;
                    }
                float[] atom=new float[5];
                atom[0]=(alist[i] as float[])[0];
                atom[1]=(alist[i] as float[])[1];
                atom[2]=(alist[i] as float[])[2];
                atom[3]=typenumber;
                atom[4]=i;
                atomListByOrder.Add(atom);
            }
//          atomListByOrder=alist;//if we write like this directly, it will change the order of alist.
            atomListByOrder.Sort(new StructComparer());
            
            return atomListByOrder;
        }

    }
}