owl/trunk/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.DIRECTED;
                RIGNode n1 = g.getNodeFromSerial(1);
                RIGNode n2 = g.getNodeFromSerial(2);
                g.addEdge(new RIGEdge(1), n1, n2, edgeType);
                g.addEdge(new RIGEdge(2), n2, n1, edgeType);
                g.addEdge(new RIGEdge(3), n1, n2, 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(n1, n2).getAtomWeight());
        }
        

}
Revision:	420
Committed:	Thu Nov 22 17:27:44 2007 UTC (16 years, 10 months ago) by duarte
Original Path:	*branches/aglappe-jung/testJUNGframework.java*
File size:	5390 byte(s)
Log Message:	First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Line	User	Rev	File contents
1	duarte	420	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.DIRECTED;
126			RIGNode n1 = g.getNodeFromSerial(1);
127			RIGNode n2 = g.getNodeFromSerial(2);
128			g.addEdge(new RIGEdge(1), n1, n2, edgeType);
129			g.addEdge(new RIGEdge(2), n2, n1, edgeType);
130			g.addEdge(new RIGEdge(3), n1, n2, edgeType);
131			for (RIGEdge e:g.getEdges()) {
132			System.out.println(g.getEndpoints(e).getFirst()+" "+g.getEndpoints(e).getSecond()+", w "+e.getAtomWeight());
133			}
134			System.out.println("vertex count: "+g.getVertexCount());
135			System.out.println("edge count: "+g.getEdgeCount());
136			System.out.println("edge w "+ g.findEdge(n1, n2).getAtomWeight());
137			}
138
139
140			}