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root/owl/trunk/testDeltaDistanceMap.java

#	Line 1 | Line 1
1		import proteinstructure.*;
2		import java.util.*;
3
4	+	import edu.uci.ics.jung.graph.util.Pair;
5	+
6		/**
7		* Calculate a matrix containing the element-wise differences between the distance maps of two proteins
8		* @author stehr
#	Line 19 | Line 21
21		String chainCode2 = "B";
22
23		System.out.println("Loading pdb objects...");
24	<	Pdb pdb1 = new PdbasePdb("12as", "B");
24	>	Pdb pdb1 = new PdbasePdb("12as");
25	>	pdb1.load("B");
26		assert(pdb1 != null);
27	<	Pdb pdb2 = new PdbasePdb("12as", "A");
27	>	Pdb pdb2 = new PdbasePdb("12as");
28	>	pdb2.load("A");
29		assert(pdb2 != null);
30
31		System.out.println("Calculating distance maps...");
32	<	HashMap<Edge,Double> distMap1 = pdb1.calculate_dist_matrix("Ca");
32	>	HashMap<Pair<Integer>,Double> distMap1 = pdb1.calculate_dist_matrix("Ca");
33		assert(distMap1 != null);
34	<	HashMap<Edge,Double> distMap2 = pdb2.calculate_dist_matrix("Ca");
34	>	HashMap<Pair<Integer>,Double> distMap2 = pdb2.calculate_dist_matrix("Ca");
35		assert(distMap2 != null);
36
37		System.out.println("Calculating difference distance map...");
38	<	HashMap<Edge,Double> diffDistMap = pdb1.getDiffDistMap("Ca", pdb2, "Ca");
38	>	HashMap<Pair<Integer>,Double> diffDistMap = pdb1.getDiffDistMap("Ca", pdb2, "Ca");
39		assert(diffDistMap != null);
40		assert(diffDistMap.size() == distMap1.size());
41		assert(diffDistMap.size() == distMap2.size());
#	Line 40 | Line 44
44		int mis = 0;
45		for(int i=1; i<=pdb1.getFullLength();i++) {
46		for(int j=1; j<i;j++) {
47	<	if(!diffDistMap.containsKey(new Edge(j,i))) {
47	>	if(!diffDistMap.containsKey(new Pair<Integer>(j,i))) {
48		//System.out.print("(" + i + "," + j + ") ");
49		mis++;
50		}
#	Line 48 | Line 52
52		}
53		System.out.println(mis);
54
55	<	Edge e = new Edge(27,30);
55	>	Pair<Integer> e = new Pair<Integer>(27,30);
56
57		double dist1 = distMap1.get(e);
58		double dist2 = distMap2.get(e);

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