tags/aglappe-0.9.3/testJUNGframework.java

import java.io.FileNotFoundException;
import java.io.IOException;
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 FileNotFoundException, IOException, GraphFileFormatError, PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError, GraphIdNotFoundError {
                Pdb pdb = new PdbasePdb("7adh", "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<RIGNode>,Integer> cmNbhSizes = graph.getAllCommonNbhSizes();
                int i = 109;
                for (int j=170;j<=180;j++) {
                        RIGNbhood nbh = graph.getNbhood(graph.getNodeFromSerial(j));
                        System.out.println("nbhood of "+j+": "+ nbh);
                        for (RIGNode nb:nbh.values()) {
                                System.out.print(" "+nb);
                        }
                        System.out.println();
                        int size = cmNbhSizes.get(new Pair<RIGNode>(graph.getNodeFromSerial(i),graph.getNodeFromSerial(j)));
                        System.out.println("common neighbs for edge "+i+", "+j+": "+size);
                        RIGCommonNbhood cmNbh = graph.getCommonNbhood(graph.getNodeFromSerial(i), graph.getNodeFromSerial(j));
                        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 range restrict methods
                System.out.println();
                System.out.println("TEST restrict methods");
                System.out.println("num contacts full range: "+graph.getEdgeCount());
                graph.restrictContactsToMaxRange(10);
                System.out.println("num contacts max range 10: "+graph.getEdgeCount());
                
                
                // 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 getSuccessorCount, getPredecessorCount, getNeighborCount
                System.out.println("TEST degree methods: getNeighborCount, getSuccessorCount, getPredecessorCount");
                // 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("degree for node "+serial+": "+graph.getNeighborCount(node)+", indegree: "+graph.getPredecessorCount(node)+", outdegree: "+graph.getSuccessorCount(node));
                }
                System.out.println("directed graph: ");
                for (int serial=1;serial<=10;serial++){
                        RIGNode node = graph2.getNodeFromSerial(serial);
                        System.out.println("degree for node "+serial+": "+graph2.getNeighborCount(node)+", indegree: "+graph2.getPredecessorCount(node)+", outdegree: "+graph2.getSuccessorCount(node));
                }

                // TEST adding and getting undirected edges
                System.out.println("TEST adding and getting 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());
        }
        

}
Revision:	421
Committed:	Thu Nov 22 19:42:11 2007 UTC (16 years, 11 months ago) by duarte
Original Path:	*branches/aglappe-jung/testJUNGframework.java*
File size:	5478 byte(s)
Log Message:	Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff)) Loads of better comments
Line	File contents
1	import java.io.FileNotFoundException;
2	import java.io.IOException;
3	import java.sql.SQLException;
4	import java.util.HashMap;
5	import java.util.HashSet;
6	import java.util.Set;
7
8
9	import edu.uci.ics.jung.graph.util.EdgeType;
10	import edu.uci.ics.jung.graph.util.Pair;
11
12	import proteinstructure.*;
13
14
15	public class testJUNGframework {
16
17	public static void main(String[] args) throws FileNotFoundException, IOException, GraphFileFormatError, PdbaseInconsistencyError, PdbCodeNotFoundError, SQLException, PdbChainCodeNotFoundError, GraphIdNotFoundError {
18	Pdb pdb = new PdbasePdb("7adh", "A");
19
20	RIGraph graph = pdb.get_graph("Ca", 8.0);
21	RIGraph graph2 = pdb.get_graph("Ca/Cb", 8.0);
22	//RIGraph graph = new FileRIGraph("/scratch/local/temp.graph");
23	//RIGraph graph = new DbRIGraph("casp_decoys",9);
24	//System.out.println(graph);
25	System.out.println("#pdb code:"+graph.getPdbCode());
26	System.out.println("#chain code:"+graph.getChainCode());
27	System.out.println("#pdb chain code:"+graph.getPdbChainCode());
28	System.out.println("#full length:"+graph.getFullLength());
29	System.out.println("#obs length:"+graph.getObsLength());
30	System.out.println("#ct:"+graph.getContactType());
31	System.out.println("#cutoff:"+graph.getCutoff());
32	System.out.println("#edge count:"+graph.getEdgeCount());
33	System.out.println("#vertex count:"+graph.getVertexCount());
34
35	// TEST getting atom weights and weights
36	for (RIGEdge e:graph.getEdges()) {
37	Pair<RIGNode> pair = graph.getEndpoints(e);
38	System.out.println(pair.getFirst()+" "+pair.getSecond()+" atom w: "+e.getAtomWeight()+" w: "+e.getWeight() );
39	}
40
41
42	// TEST printing node information
43	System.out.println("TEST printing node information");
44	for (int ind:graph.getSerials()){
45	RIGNode n = graph.getNodeFromSerial(ind);
46	SecStrucElement sselem = n.getSecStrucElement();
47	char sstype = sselem==null?0:sselem.getType();
48	System.out.println("V"+n.getResidueSerial()+" "+n.getResidueType()+" "+sstype);
49
50	}
51	System.out.println();
52
53
54	// TEST of neighbourhood methods
55	System.out.println("TEST neighbor methods");
56	HashMap<Pair<RIGNode>,Integer> cmNbhSizes = graph.getAllCommonNbhSizes();
57	int i = 109;
58	for (int j=170;j<=180;j++) {
59	RIGNbhood nbh = graph.getNbhood(graph.getNodeFromSerial(j));
60	System.out.println("nbhood of "+j+": "+ nbh);
61	for (RIGNode nb:nbh.values()) {
62	System.out.print(" "+nb);
63	}
64	System.out.println();
65	int size = cmNbhSizes.get(new Pair<RIGNode>(graph.getNodeFromSerial(i),graph.getNodeFromSerial(j)));
66	System.out.println("common neighbs for edge "+i+", "+j+": "+size);
67	RIGCommonNbhood cmNbh = graph.getCommonNbhood(graph.getNodeFromSerial(i), graph.getNodeFromSerial(j));
68	for (RIGNode nb:cmNbh.values()){
69	System.out.print(" "+nb);
70	}
71	System.out.println();
72	System.out.println(cmNbh);
73	}
74
75	// TEST of evaluate prediction
76	System.out.println("TEST eval prediction");
77	PredEval pev = graph.evaluatePrediction(graph2);
78	pev.print();
79
80
81	// TEST of range restrict methods
82	System.out.println();
83	System.out.println("TEST restrict methods");
84	System.out.println("num contacts full range: "+graph.getEdgeCount());
85	graph.restrictContactsToMaxRange(10);
86	System.out.println("num contacts max range 10: "+graph.getEdgeCount());
87
88
89
90	// TEST of isDirected()
91	System.out.println("TEST isDirected");
92	if (graph.isDirected()) {
93	System.out.println("directed");
94	}
95
96	// TEST of Pair<Integer>, does it respect equals
97	System.out.println("TEST Pair<Integer>");
98	Pair<Integer> p1 = new Pair<Integer>(1,2);
99	Pair<Integer> p2 = new Pair<Integer>(1,2);
100	Set<Pair<Integer>> set = new HashSet<Pair<Integer>>();
101	set.add(p1);
102	set.add(p2);
103	if (p1.equals(p2)) {
104	System.out.println("2 pairs are equal");
105	}
106	System.out.println(set);
107
108	// TEST of getSuccessorCount, getPredecessorCount, getNeighborCount
109	System.out.println("TEST degree methods: getNeighborCount, getSuccessorCount, getPredecessorCount");
110	// graph is undirected, graph2 is directed
111	System.out.println("undirected graph: ");
112	for (int serial=1;serial<=10;serial++){
113	RIGNode node = graph.getNodeFromSerial(serial);
114	System.out.println("degree for node "+serial+": "+graph.getNeighborCount(node)+", indegree: "+graph.getPredecessorCount(node)+", outdegree: "+graph.getSuccessorCount(node));
115	}
116	System.out.println("directed graph: ");
117	for (int serial=1;serial<=10;serial++){
118	RIGNode node = graph2.getNodeFromSerial(serial);
119	System.out.println("degree for node "+serial+": "+graph2.getNeighborCount(node)+", indegree: "+graph2.getPredecessorCount(node)+", outdegree: "+graph2.getSuccessorCount(node));
120	}
121
122	// TEST adding and getting undirected edges
123	System.out.println("TEST adding and getting undirected edges: ");
124	RIGraph g = new RIGraph("ABCD");
125	EdgeType edgeType = EdgeType.UNDIRECTED;
126	RIGNode n1 = g.getNodeFromSerial(1);
127	RIGNode n2 = g.getNodeFromSerial(2);
128	RIGNode n3 = g.getNodeFromSerial(3);
129	g.addEdge(new RIGEdge(1), n1, n2, edgeType);
130	g.addEdge(new RIGEdge(2), n2, n1, edgeType);
131	g.addEdge(new RIGEdge(3), n1, n2, edgeType);
132	g.addEdge(new RIGEdge(4), n1, n3, edgeType);
133	for (RIGEdge e:g.getEdges()) {
134	System.out.println(g.getEndpoints(e).getFirst()+" "+g.getEndpoints(e).getSecond()+", w "+e.getAtomWeight());
135	}
136	System.out.println("vertex count: "+g.getVertexCount());
137	System.out.println("edge count: "+g.getEdgeCount());
138	System.out.println("edge w "+ g.findEdge(n3, n1).getAtomWeight());
139	}
140
141
142	}