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> pointsInBox;
        
        public Box(Point3i floor){
                this.floor=floor;
                pointsInBox = new TreeMap<Integer, Point3d>(); 
        }
        
        public void putPoint(int serial, Point3d point){
                pointsInBox.put(serial, point);
        }

        public void getDistancesWithinBox(double[][] distMatrix){ //we pass a reference to the distMatrix that we alter within this method
                for (int i_serial:pointsInBox.keySet()) {
                        for (int j_serial:pointsInBox.keySet()) {
                                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] = pointsInBox.get(i_serial).distance(pointsInBox.get(j_serial));
                                }
                        }
                }

        }
        
        public void getDistancesToNeighborBox(Box nbBox ,double[][] distMatrix){
                for (int i_serial:pointsInBox.keySet()){
                        for (int j_serial:nbBox.pointsInBox.keySet()){
                                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] = pointsInBox.get(i_serial).distance(nbBox.pointsInBox.get(j_serial));
                                        }
                                }
                        }
                }
        }
        
}
Revision:	226
Committed:	Fri Jul 6 13:43:30 2007 UTC (17 years, 2 months ago) by duarte
File size:	1420 byte(s)
Log Message:	First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used. Using javax.vectormath objects for the vectors (distance method also from that) Using TreeMap for get_coords_for_ct
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			private TreeMap<Integer,Point3d> pointsInBox;
12
13			public Box(Point3i floor){
14			this.floor=floor;
15			pointsInBox = new TreeMap<Integer, Point3d>();
16			}
17
18			public void putPoint(int serial, Point3d point){
19			pointsInBox.put(serial, point);
20			}
21
22			public void getDistancesWithinBox(double[][] distMatrix){ //we pass a reference to the distMatrix that we alter within this method
23			for (int i_serial:pointsInBox.keySet()) {
24			for (int j_serial:pointsInBox.keySet()) {
25			if (j_serial>i_serial){
26			// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
27			distMatrix[i_serial][j_serial] = pointsInBox.get(i_serial).distance(pointsInBox.get(j_serial));
28			}
29			}
30			}
31
32			}
33
34			public void getDistancesToNeighborBox(Box nbBox ,double[][] distMatrix){
35			for (int i_serial:pointsInBox.keySet()){
36			for (int j_serial:nbBox.pointsInBox.keySet()){
37			if (j_serial>i_serial){
38			// this only works if previously we have made sure that atom serials are sequential from 0 to MAXATOMSERIAL
39			if (distMatrix[i_serial][j_serial]==0.0){ // i.e. if we haven't passed through this cell yet
40			distMatrix[i_serial][j_serial] = pointsInBox.get(i_serial).distance(nbBox.pointsInBox.get(j_serial));
41			}
42			}
43			}
44			}
45			}
46
47			}