owl/trunk/testJUNGframework.java

import java.sql.SQLException;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;


import edu.uci.ics.jung.graph.util.EdgeType;
import edu.uci.ics.jung.graph.util.Pair;

import proteinstructure.*;


public class testJUNGframework {

        public static void main(String[] args) throws GraphFileFormatError, PdbLoadError, SQLException, PdbCodeNotFoundError {
                Pdb pdb = new PdbasePdb("7adh");
                pdb.load("A");
                
                RIGraph graph = pdb.get_graph("Ca", 8.0);
                RIGraph graph2 = pdb.get_graph("Ca/Cb", 8.0);
                //RIGraph graph = new FileRIGraph("/scratch/local/temp.graph");
                //RIGraph graph = new DbRIGraph("casp_decoys",9);
                //System.out.println(graph);
                System.out.println("#pdb code:"+graph.getPdbCode());
                System.out.println("#chain code:"+graph.getChainCode());
                System.out.println("#pdb chain code:"+graph.getPdbChainCode());
                System.out.println("#full length:"+graph.getFullLength());
                System.out.println("#obs length:"+graph.getObsLength());
                System.out.println("#ct:"+graph.getContactType());
                System.out.println("#cutoff:"+graph.getCutoff());
                System.out.println("#edge count:"+graph.getEdgeCount());
                System.out.println("#vertex count:"+graph.getVertexCount()); 

                // TEST getting atom weights and weights
                for (RIGEdge e:graph.getEdges()) {
                        Pair<RIGNode> pair = graph.getEndpoints(e);
                        System.out.println(pair.getFirst()+" "+pair.getSecond()+" atom w: "+e.getAtomWeight()+" w: "+e.getWeight() );
                }
                
                
                // TEST printing node information
                System.out.println("TEST printing node information");
                for (int ind:graph.getSerials()){
                        RIGNode n = graph.getNodeFromSerial(ind);
                        SecStrucElement sselem = n.getSecStrucElement();
                        char sstype = sselem==null?0:sselem.getType();
                        System.out.println("V"+n.getResidueSerial()+" "+n.getResidueType()+" "+sstype);
                        
                }               
                System.out.println();
                
                
                // TEST of neighbourhood methods
                System.out.println("TEST neighbor methods");
                HashMap<Pair<Integer>,Integer> cmNbhSizes = graph.getAllCommonNbhSizes();

                for (Pair<Integer> pair:cmNbhSizes.keySet()) {
                        //for (int j=170;j<=180;j++) {
                        if (pair.getFirst()==109 && pair.getSecond()>=170 && pair.getSecond()<=180) {
                                RIGNbhood nbh = graph.getNbhood(graph.getNodeFromSerial(pair.getSecond()));
                                System.out.println("nbhood of "+pair.getSecond()+": "+ nbh);
                                for (RIGNode nb:nbh.values()) {
                                        System.out.print(" "+nb);
                                }
                                System.out.println();

                                int size = cmNbhSizes.get(pair);
                                System.out.println("common neighbs for edge "+pair.getFirst()+", "+pair.getSecond()+": "+size);
                                RIGCommonNbhood cmNbh = graph.getCommonNbhood(graph.getNodeFromSerial(pair.getFirst()), graph.getNodeFromSerial(pair.getSecond()));
                                for (RIGNode nb:cmNbh.values()){
                                        System.out.print(" "+nb);
                                }
                                System.out.println();
                                System.out.println(cmNbh);
                        }
                }

                // TEST of evaluate prediction
                System.out.println("TEST eval prediction");
                PredEval pev = graph.evaluatePrediction(graph2);
                pev.print();
                
                // TEST of isDirected()
                System.out.println("TEST isDirected");
                if (graph.isDirected()) {
                        System.out.println("directed");
                }
                
                // TEST of Pair<Integer>, does it respect equals
                System.out.println("TEST Pair<Integer>");
                Pair<Integer> p1 = new Pair<Integer>(1,2);
                Pair<Integer> p2 = new Pair<Integer>(1,2);
                Set<Pair<Integer>> set = new HashSet<Pair<Integer>>();
                set.add(p1);
                set.add(p2);
                if (p1.equals(p2)) {
                        System.out.println("2 pairs are equal");
                }
                System.out.println(set);
                
                // TEST of degree methods and getSuccessorCount, getPredecessorCount, getNeighborCount
                // degree and neighbor counts are different when the graph has parallel edges (our graphs shouldn't have them anyway)
                System.out.println("TEST degree and neighbor count methods");
                // graph is undirected, graph2 is directed
                System.out.println("undirected graph: ");
                for (int serial=1;serial<=10;serial++){
                        RIGNode node = graph.getNodeFromSerial(serial);
                        System.out.println("node "+serial+": nbr count "+graph.getNeighborCount(node)+", predec count: "+graph.getPredecessorCount(node)+", successor count: "+graph.getSuccessorCount(node));
                        System.out.println("node "+serial+": degree "+graph.degree(node)+", in degree: "+graph.inDegree(node)+", out degree: "+graph.outDegree(node));
                }
                System.out.println("directed graph: ");
                for (int serial=1;serial<=10;serial++){
                        RIGNode node = graph2.getNodeFromSerial(serial);
                        System.out.println("node "+serial+": nbr count "+graph2.getNeighborCount(node)+", predec count: "+graph2.getPredecessorCount(node)+", successor count: "+graph2.getSuccessorCount(node));
                        System.out.println("node "+serial+": degree "+graph2.degree(node)+", in degree: "+graph2.inDegree(node)+", out degree: "+graph2.outDegree(node));
                }

                // TEST adding and getting directed/undirected edges
                System.out.println("TEST adding and getting directed/undirected edges: ");
                RIGraph g = new RIGraph("ABCD");
                EdgeType edgeType = EdgeType.UNDIRECTED;
                RIGNode n1 = g.getNodeFromSerial(1);
                RIGNode n2 = g.getNodeFromSerial(2);
                RIGNode n3 = g.getNodeFromSerial(3);
                g.addEdge(new RIGEdge(1), n1, n2, edgeType);
                g.addEdge(new RIGEdge(2), n2, n1, edgeType);
                g.addEdge(new RIGEdge(3), n1, n2, edgeType);
                g.addEdge(new RIGEdge(4), n1, n3, edgeType);
                for (RIGEdge e:g.getEdges()) {
                        System.out.println(g.getEndpoints(e).getFirst()+" "+g.getEndpoints(e).getSecond()+", w "+e.getAtomWeight());
                }
                System.out.println("vertex count: "+g.getVertexCount());
                System.out.println("edge count: "+g.getEdgeCount());
                System.out.println("edge w "+ g.findEdge(n3, n1).getAtomWeight());
                
                // TEST copying of RIGraph objects and restrictRange methods
                System.out.println("TEST copying of RIGraph objects");
                Pdb pdb1 = new PdbasePdb("1bxy");
                pdb1.load("A");
                Pdb pdb2 = new PdbasePdb("1sha");
                pdb2.load("A");
                RIGraph g1 = pdb1.get_graph("Ca", 8);
                RIGraph g2 = pdb2.get_graph("Ca", 8);
                System.out.println("g1: "+g1.getPdbCode()+" nodes: "+g1.getVertexCount()+" edges: "+g1.getEdgeCount());
                System.out.println("g2: "+g2.getPdbCode()+" nodes: "+g2.getVertexCount()+" edges: "+g2.getEdgeCount());
                RIGraph newgraph = g1.copy();
                System.out.println("new g: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
                newgraph = g2;
                System.out.println("new g reassigned to g2: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
                newgraph.restrictContactsToMaxRange(10);
                System.out.println("new g reassigned to g2, max range 10: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
                System.out.println("g1: "+g1.getPdbCode()+" nodes: "+g1.getVertexCount()+" edges: "+g1.getEdgeCount());
                
        }
        

}
Revision:	492
Committed:	Wed Jan 2 13:18:57 2008 UTC (16 years, 8 months ago) by duarte
File size:	6767 byte(s)
Log Message:	Copied the aglappe-jung branch into trunk.
Line	File contents
1	import java.sql.SQLException;
2	import java.util.HashMap;
3	import java.util.HashSet;
4	import java.util.Set;
5
6
7	import edu.uci.ics.jung.graph.util.EdgeType;
8	import edu.uci.ics.jung.graph.util.Pair;
9
10	import proteinstructure.*;
11
12
13	public class testJUNGframework {
14
15	public static void main(String[] args) throws GraphFileFormatError, PdbLoadError, SQLException, PdbCodeNotFoundError {
16	Pdb pdb = new PdbasePdb("7adh");
17	pdb.load("A");
18
19	RIGraph graph = pdb.get_graph("Ca", 8.0);
20	RIGraph graph2 = pdb.get_graph("Ca/Cb", 8.0);
21	//RIGraph graph = new FileRIGraph("/scratch/local/temp.graph");
22	//RIGraph graph = new DbRIGraph("casp_decoys",9);
23	//System.out.println(graph);
24	System.out.println("#pdb code:"+graph.getPdbCode());
25	System.out.println("#chain code:"+graph.getChainCode());
26	System.out.println("#pdb chain code:"+graph.getPdbChainCode());
27	System.out.println("#full length:"+graph.getFullLength());
28	System.out.println("#obs length:"+graph.getObsLength());
29	System.out.println("#ct:"+graph.getContactType());
30	System.out.println("#cutoff:"+graph.getCutoff());
31	System.out.println("#edge count:"+graph.getEdgeCount());
32	System.out.println("#vertex count:"+graph.getVertexCount());
33
34	// TEST getting atom weights and weights
35	for (RIGEdge e:graph.getEdges()) {
36	Pair<RIGNode> pair = graph.getEndpoints(e);
37	System.out.println(pair.getFirst()+" "+pair.getSecond()+" atom w: "+e.getAtomWeight()+" w: "+e.getWeight() );
38	}
39
40
41	// TEST printing node information
42	System.out.println("TEST printing node information");
43	for (int ind:graph.getSerials()){
44	RIGNode n = graph.getNodeFromSerial(ind);
45	SecStrucElement sselem = n.getSecStrucElement();
46	char sstype = sselem==null?0:sselem.getType();
47	System.out.println("V"+n.getResidueSerial()+" "+n.getResidueType()+" "+sstype);
48
49	}
50	System.out.println();
51
52
53	// TEST of neighbourhood methods
54	System.out.println("TEST neighbor methods");
55	HashMap<Pair<Integer>,Integer> cmNbhSizes = graph.getAllCommonNbhSizes();
56
57	for (Pair<Integer> pair:cmNbhSizes.keySet()) {
58	//for (int j=170;j<=180;j++) {
59	if (pair.getFirst()==109 && pair.getSecond()>=170 && pair.getSecond()<=180) {
60	RIGNbhood nbh = graph.getNbhood(graph.getNodeFromSerial(pair.getSecond()));
61	System.out.println("nbhood of "+pair.getSecond()+": "+ nbh);
62	for (RIGNode nb:nbh.values()) {
63	System.out.print(" "+nb);
64	}
65	System.out.println();
66
67	int size = cmNbhSizes.get(pair);
68	System.out.println("common neighbs for edge "+pair.getFirst()+", "+pair.getSecond()+": "+size);
69	RIGCommonNbhood cmNbh = graph.getCommonNbhood(graph.getNodeFromSerial(pair.getFirst()), graph.getNodeFromSerial(pair.getSecond()));
70	for (RIGNode nb:cmNbh.values()){
71	System.out.print(" "+nb);
72	}
73	System.out.println();
74	System.out.println(cmNbh);
75	}
76	}
77
78	// TEST of evaluate prediction
79	System.out.println("TEST eval prediction");
80	PredEval pev = graph.evaluatePrediction(graph2);
81	pev.print();
82
83	// TEST of isDirected()
84	System.out.println("TEST isDirected");
85	if (graph.isDirected()) {
86	System.out.println("directed");
87	}
88
89	// TEST of Pair<Integer>, does it respect equals
90	System.out.println("TEST Pair<Integer>");
91	Pair<Integer> p1 = new Pair<Integer>(1,2);
92	Pair<Integer> p2 = new Pair<Integer>(1,2);
93	Set<Pair<Integer>> set = new HashSet<Pair<Integer>>();
94	set.add(p1);
95	set.add(p2);
96	if (p1.equals(p2)) {
97	System.out.println("2 pairs are equal");
98	}
99	System.out.println(set);
100
101	// TEST of degree methods and getSuccessorCount, getPredecessorCount, getNeighborCount
102	// degree and neighbor counts are different when the graph has parallel edges (our graphs shouldn't have them anyway)
103	System.out.println("TEST degree and neighbor count methods");
104	// graph is undirected, graph2 is directed
105	System.out.println("undirected graph: ");
106	for (int serial=1;serial<=10;serial++){
107	RIGNode node = graph.getNodeFromSerial(serial);
108	System.out.println("node "+serial+": nbr count "+graph.getNeighborCount(node)+", predec count: "+graph.getPredecessorCount(node)+", successor count: "+graph.getSuccessorCount(node));
109	System.out.println("node "+serial+": degree "+graph.degree(node)+", in degree: "+graph.inDegree(node)+", out degree: "+graph.outDegree(node));
110	}
111	System.out.println("directed graph: ");
112	for (int serial=1;serial<=10;serial++){
113	RIGNode node = graph2.getNodeFromSerial(serial);
114	System.out.println("node "+serial+": nbr count "+graph2.getNeighborCount(node)+", predec count: "+graph2.getPredecessorCount(node)+", successor count: "+graph2.getSuccessorCount(node));
115	System.out.println("node "+serial+": degree "+graph2.degree(node)+", in degree: "+graph2.inDegree(node)+", out degree: "+graph2.outDegree(node));
116	}
117
118	// TEST adding and getting directed/undirected edges
119	System.out.println("TEST adding and getting directed/undirected edges: ");
120	RIGraph g = new RIGraph("ABCD");
121	EdgeType edgeType = EdgeType.UNDIRECTED;
122	RIGNode n1 = g.getNodeFromSerial(1);
123	RIGNode n2 = g.getNodeFromSerial(2);
124	RIGNode n3 = g.getNodeFromSerial(3);
125	g.addEdge(new RIGEdge(1), n1, n2, edgeType);
126	g.addEdge(new RIGEdge(2), n2, n1, edgeType);
127	g.addEdge(new RIGEdge(3), n1, n2, edgeType);
128	g.addEdge(new RIGEdge(4), n1, n3, edgeType);
129	for (RIGEdge e:g.getEdges()) {
130	System.out.println(g.getEndpoints(e).getFirst()+" "+g.getEndpoints(e).getSecond()+", w "+e.getAtomWeight());
131	}
132	System.out.println("vertex count: "+g.getVertexCount());
133	System.out.println("edge count: "+g.getEdgeCount());
134	System.out.println("edge w "+ g.findEdge(n3, n1).getAtomWeight());
135
136	// TEST copying of RIGraph objects and restrictRange methods
137	System.out.println("TEST copying of RIGraph objects");
138	Pdb pdb1 = new PdbasePdb("1bxy");
139	pdb1.load("A");
140	Pdb pdb2 = new PdbasePdb("1sha");
141	pdb2.load("A");
142	RIGraph g1 = pdb1.get_graph("Ca", 8);
143	RIGraph g2 = pdb2.get_graph("Ca", 8);
144	System.out.println("g1: "+g1.getPdbCode()+" nodes: "+g1.getVertexCount()+" edges: "+g1.getEdgeCount());
145	System.out.println("g2: "+g2.getPdbCode()+" nodes: "+g2.getVertexCount()+" edges: "+g2.getEdgeCount());
146	RIGraph newgraph = g1.copy();
147	System.out.println("new g: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
148	newgraph = g2;
149	System.out.println("new g reassigned to g2: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
150	newgraph.restrictContactsToMaxRange(10);
151	System.out.println("new g reassigned to g2, max range 10: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
152	System.out.println("g1: "+g1.getPdbCode()+" nodes: "+g1.getVertexCount()+" edges: "+g1.getEdgeCount());
153
154	}
155
156
157	}