trunk/proteinstructure/Box.java

package proteinstructure;

import java.util.TreeMap;
import javax.vecmath.Point3d;
import javax.vecmath.Point3i;

public class Box {
        
        Point3i floor;
        
        private TreeMap<Integer,Point3d> i_pointsInBox;
        private TreeMap<Integer,Point3d> j_pointsInBox;
        
        public Box(Point3i floor){
                this.floor=floor;
                i_pointsInBox = new TreeMap<Integer, Point3d>();
                j_pointsInBox = new TreeMap<Integer, Point3d>();
        }
        
        public void put_i_Point(int serial, Point3d point){
                i_pointsInBox.put(serial, point);
        }

        public void put_j_Point(int serial, Point3d point){
                j_pointsInBox.put(serial, point);
        }

        public void getDistancesWithinBox(double[][] distMatrix, boolean directed){ //we pass a reference to the distMatrix that we alter within this method
                for (int i_serial:i_pointsInBox.keySet()) {
                        for (int j_serial:j_pointsInBox.keySet()) {
                                if (!directed) {
                                        if (j_serial>i_serial) { 
                                                // this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
                                                distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
                                        } 
                                } else {
                                        distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
                                }
                        }
                }

        }
        
        public void getDistancesToNeighborBox(Box nbBox ,double[][] distMatrix, boolean directed){
                for (int i_serial:i_pointsInBox.keySet()){
                        for (int j_serial:nbBox.j_pointsInBox.keySet()){
                                if (!directed) {
                                        if (j_serial>i_serial) {
                                                // this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
                                                if (distMatrix[i_serial][j_serial]==0.0){ // i.e. if we haven't passed through this cell yet
                                                        distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
                                                }
                                        }
                                } else {
                                        distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
                                }
                        }
                }
        }
        
}
Revision:	228
Committed:	Mon Jul 9 14:32:47 2007 UTC (17 years, 3 months ago) by duarte
File size:	1983 byte(s)
Log Message:	Now can do crossed contacts also with geometric hashing Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)
Line	File contents
1	package proteinstructure;
2
3	import java.util.TreeMap;
4	import javax.vecmath.Point3d;
5	import javax.vecmath.Point3i;
6
7	public class Box {
8
9	Point3i floor;
10
11	private TreeMap<Integer,Point3d> i_pointsInBox;
12	private TreeMap<Integer,Point3d> j_pointsInBox;
13
14	public Box(Point3i floor){
15	this.floor=floor;
16	i_pointsInBox = new TreeMap<Integer, Point3d>();
17	j_pointsInBox = new TreeMap<Integer, Point3d>();
18	}
19
20	public void put_i_Point(int serial, Point3d point){
21	i_pointsInBox.put(serial, point);
22	}
23
24	public void put_j_Point(int serial, Point3d point){
25	j_pointsInBox.put(serial, point);
26	}
27
28	public void getDistancesWithinBox(double[][] distMatrix, boolean directed){ //we pass a reference to the distMatrix that we alter within this method
29	for (int i_serial:i_pointsInBox.keySet()) {
30	for (int j_serial:j_pointsInBox.keySet()) {
31	if (!directed) {
32	if (j_serial>i_serial) {
33	// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
34	distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
35	}
36	} else {
37	distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
38	}
39	}
40	}
41
42	}
43
44	public void getDistancesToNeighborBox(Box nbBox ,double[][] distMatrix, boolean directed){
45	for (int i_serial:i_pointsInBox.keySet()){
46	for (int j_serial:nbBox.j_pointsInBox.keySet()){
47	if (!directed) {
48	if (j_serial>i_serial) {
49	// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
50	if (distMatrix[i_serial][j_serial]==0.0){ // i.e. if we haven't passed through this cell yet
51	distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
52	}
53	}
54	} else {
55	distMatrix[i_serial][j_serial] = i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
56	}
57	}
58	}
59	}
60
61	}