package org.catacomb.numeric.difnet;
   
   import org.catacomb.report.E;
   
   
   
   public class CellPoint {
      public int activeType;
      public int geometricalType;
  
      public double x;
      public double y;
      public double z;
      public double r;
  
      public CellPoint[] nbr;
      public int nnbr;
  
  
      // temporary variables for indexing a structure from a given starting pt;
      public int index;
      public int parentIndex;
  
      // temporary work variables
      public int iwork;
      public boolean umark;  // user marked points;
      public boolean wmark;  // own working marks;
      public boolean dead;   // marking prior to removal
      public int wcount;     // for counting contacts when tracing loops
  
  
      // x and y positions when part of a dendrogram, set by MLC
      public double dgx;
      public double dgy;
  
  
      public String name;  // not sure about this POSERR;
  
      public CellPoint() {
          nbr = new CellPoint[6];
          nnbr = 0;
          dead = false;
          umark = false;
          wmark = false;
      }
  
  
      public CellPoint(double x, double y, double z, double r,
                       int gtype, int atype) {
          this();
          this.x = x;
          this.y = y;
          this.z = z;
          this.r = r;
          this.geometricalType = (gtype < 0 ? 0 : gtype);
          this.activeType = (atype < 0 ? 0 : atype);
      }
  
  
      public CellPoint makeCopy() {
          return new CellPoint(x, y, z, r, geometricalType, activeType);
      }
  
  
      public void setWork(int iw) {
          iwork = iw;
      }
      public int getWork() {
          return iwork;
      }
  
  
      public String toString() {
          return ("zyzr: " + x + " " + y + " " + z + " " + r + " nnbr=" + nnbr);
      }
  
  
      public void setPosition(double[] a) {
          x = a[0];
          y = a[1];
          z = a[2];
          if (a.length >= 3) {
              r = a[3];
          }
      }
  
  
      public void locateBetween(CellPoint cpa, CellPoint cpb, double f) {
          double wf = 1. - f;
          x = f * cpb.x + wf * cpa.x;
          y = f * cpb.y + wf * cpa.y;
          z = f * cpb.z + wf * cpa.z;
          r = f * cpb.r + wf * cpa.r;
      }
  
  
  
     public void addNeighbor(CellPoint cpn) {
         if (nnbr >= nbr.length) {
             CellPoint[] pn = new CellPoint[2*nnbr];
             for (int i = 0; i < nnbr; i++) {
                 pn[i] = nbr[i];
             }
             nbr = pn;
         }
         nbr[nnbr++] = cpn;
     }
 
 
     public void removeNeighbor(CellPoint cp) {
         int ii = -1;
         for (int i = 0; i < nnbr; i++) {
             if (nbr[i] == cp) {
                 ii = i;
             }
         }
         if (ii >= 0) {
             for (int i = ii; i < nnbr-1; i++) {
                 nbr[i] = nbr[i+1];
             }
             nnbr--;
         }
     }
 
 
     public void replaceNeighbor(CellPoint cp, CellPoint cr) {
 
         int ii = -1;
         for (int i = 0; i < nnbr; i++) {
             if (nbr[i] == cp) {
                 ii = i;
             }
         }
         if (ii >= 0) {
             nbr[ii] = cr;
         } else {
             E.error(" (replaceNeighbor) couldnt find nbr " + cp +
                     " in nbrs list of " + this);
         }
     }
 
 
     public boolean hasNeighbor(CellPoint cp) {
         boolean hn = false;
         for (int i = 0; i < nnbr; i++) {
             if (nbr[i] == cp) {
                 hn = true;
             }
         }
         return hn;
     }
 
 
     public void removeDeadNeighbors() {
         for (int i = nnbr-1; i >= 0; i--) {
             if (nbr[i].dead) {
                 removeNeighbor(nbr[i]);
             }
         }
     }
 
 
     public double distanceTo(CellPoint cp) {
         double dx = x - cp.x;
         double dy = y - cp.y;
         double dz = z - cp.z;
         return Math.sqrt(dx*dx + dy*dy + dz*dz);
     }
 
 
     public void movePerp(CellPoint ca, CellPoint cb, double dperp) {
         double dx = cb.x - ca.x;
         double dy = cb.y - ca.y;
         double f = Math.sqrt(dx*dx + dy*dy);
         dx /= f;
         dy /= f;
         x += dperp * dy;
         y -= dperp * dx;
     }
 
 
 }