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(float[][] distMatrix, boolean crossed){ //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 (!crossed) {
                                        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] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
                                        } 
                                } else {
                                        // We need to check this because it can happen when the 2 contact types (i/j) have overlapping atoms, e.g. ALL/BB
                                        // It is not strictly necessary, because distance in case i=j would be 0 (atom to itself). It's just to make sure that 
                                        // there wouldn't be rounding problems in comparing to 0.0 in get_graph in Pdb
                                        if (j_serial!=i_serial) { 
                                                distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
                                        }
                                }
                        }
                }

        }
        
        public void getDistancesToNeighborBox(Box nbBox ,float[][] distMatrix, boolean crossed){
                for (int i_serial:i_pointsInBox.keySet()){
                        for (int j_serial:nbBox.j_pointsInBox.keySet()){
                                if (!crossed) {
                                        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]==0.0f){ // i.e. if we haven't passed through this cell yet
                                                        distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
                                                }
                                        }
                                } else {
                                        distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
                                }
                        }
                }
        }
        
        // Beware, this returns only the size for i
        public int size() {
                return i_pointsInBox.size();
        }
        
}
Revision:	433
Committed:	Tue Nov 27 17:58:26 2007 UTC (16 years, 10 months ago) by duarte
Original Path:	*branches/aglappe-jung/proteinstructure/Box.java*
File size:	2476 byte(s)
Log Message:	Added more comments
Line	User	Rev	File contents
1	duarte	226	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	duarte	228	private TreeMap<Integer,Point3d> i_pointsInBox;
12			private TreeMap<Integer,Point3d> j_pointsInBox;
13	duarte	226
14			public Box(Point3i floor){
15			this.floor=floor;
16	duarte	228	i_pointsInBox = new TreeMap<Integer, Point3d>();
17			j_pointsInBox = new TreeMap<Integer, Point3d>();
18	duarte	226	}
19
20	duarte	228	public void put_i_Point(int serial, Point3d point){
21			i_pointsInBox.put(serial, point);
22	duarte	226	}
23
24	duarte	228	public void put_j_Point(int serial, Point3d point){
25			j_pointsInBox.put(serial, point);
26			}
27
28	duarte	421	public void getDistancesWithinBox(float[][] distMatrix, boolean crossed){ //we pass a reference to the distMatrix that we alter within this method
29	duarte	228	for (int i_serial:i_pointsInBox.keySet()) {
30			for (int j_serial:j_pointsInBox.keySet()) {
31	duarte	421	if (!crossed) {
32	duarte	228	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	duarte	282	distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
35	duarte	228	}
36			} else {
37	duarte	433	// We need to check this because it can happen when the 2 contact types (i/j) have overlapping atoms, e.g. ALL/BB
38			// It is not strictly necessary, because distance in case i=j would be 0 (atom to itself). It's just to make sure that
39			// there wouldn't be rounding problems in comparing to 0.0 in get_graph in Pdb
40			if (j_serial!=i_serial) {
41	duarte	421	distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial));
42			}
43	duarte	226	}
44			}
45			}
46
47			}
48
49	duarte	421	public void getDistancesToNeighborBox(Box nbBox ,float[][] distMatrix, boolean crossed){
50	duarte	228	for (int i_serial:i_pointsInBox.keySet()){
51			for (int j_serial:nbBox.j_pointsInBox.keySet()){
52	duarte	421	if (!crossed) {
53	duarte	228	if (j_serial>i_serial) {
54			// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
55	duarte	282	if (distMatrix[i_serial][j_serial]==0.0f){ // i.e. if we haven't passed through this cell yet
56			distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
57	duarte	228	}
58	duarte	226	}
59	duarte	228	} else {
60	duarte	282	distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial));
61	duarte	226	}
62			}
63			}
64			}
65
66	stehr	250	// Beware, this returns only the size for i
67			public int size() {
68			return i_pointsInBox.size();
69			}
70
71	duarte	226	}