| 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(float[][] 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] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial)); |
| 35 |
} |
| 36 |
} else { |
| 37 |
distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(j_pointsInBox.get(j_serial)); |
| 38 |
} |
| 39 |
} |
| 40 |
} |
| 41 |
|
| 42 |
} |
| 43 |
|
| 44 |
public void getDistancesToNeighborBox(Box nbBox ,float[][] 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]==0.0f){ // i.e. if we haven't passed through this cell yet |
| 51 |
distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial)); |
| 52 |
} |
| 53 |
} |
| 54 |
} else { |
| 55 |
distMatrix[i_serial][j_serial] = (float)i_pointsInBox.get(i_serial).distance(nbBox.j_pointsInBox.get(j_serial)); |
| 56 |
} |
| 57 |
} |
| 58 |
} |
| 59 |
} |
| 60 |
|
| 61 |
// Beware, this returns only the size for i |
| 62 |
public int size() { |
| 63 |
return i_pointsInBox.size(); |
| 64 |
} |
| 65 |
|
| 66 |
} |
