branches/aglappe-jung/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 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");
                RIGraph g1 = new PdbasePdb("1bxy","A").get_graph("Ca", 8);
                RIGraph g2 = new PdbasePdb("1sha","A").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:	424
Committed:	Fri Nov 23 14:21:33 2007 UTC (16 years, 11 months ago) by duarte
File size:	6693 byte(s)
Log Message:	Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
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			// TEST of isDirected()
81			System.out.println("TEST isDirected");
82			if (graph.isDirected()) {
83			System.out.println("directed");
84			}
85
86			// TEST of Pair<Integer>, does it respect equals
87			System.out.println("TEST Pair<Integer>");
88			Pair<Integer> p1 = new Pair<Integer>(1,2);
89			Pair<Integer> p2 = new Pair<Integer>(1,2);
90			Set<Pair<Integer>> set = new HashSet<Pair<Integer>>();
91			set.add(p1);
92			set.add(p2);
93			if (p1.equals(p2)) {
94			System.out.println("2 pairs are equal");
95			}
96			System.out.println(set);
97
98	duarte	424	// TEST of degree methods and getSuccessorCount, getPredecessorCount, getNeighborCount
99			// degree and neighbor counts are different when the graph has parallel edges (our graphs shouldn't have them anyway)
100			System.out.println("TEST degree and neighbor count methods");
101	duarte	420	// graph is undirected, graph2 is directed
102			System.out.println("undirected graph: ");
103			for (int serial=1;serial<=10;serial++){
104			RIGNode node = graph.getNodeFromSerial(serial);
105	duarte	424	System.out.println("node "+serial+": nbr count "+graph.getNeighborCount(node)+", predec count: "+graph.getPredecessorCount(node)+", successor count: "+graph.getSuccessorCount(node));
106			System.out.println("node "+serial+": degree "+graph.degree(node)+", in degree: "+graph.inDegree(node)+", out degree: "+graph.outDegree(node));
107	duarte	420	}
108			System.out.println("directed graph: ");
109			for (int serial=1;serial<=10;serial++){
110			RIGNode node = graph2.getNodeFromSerial(serial);
111	duarte	424	System.out.println("node "+serial+": nbr count "+graph2.getNeighborCount(node)+", predec count: "+graph2.getPredecessorCount(node)+", successor count: "+graph2.getSuccessorCount(node));
112			System.out.println("node "+serial+": degree "+graph2.degree(node)+", in degree: "+graph2.inDegree(node)+", out degree: "+graph2.outDegree(node));
113	duarte	420	}
114
115	duarte	423	// TEST adding and getting directed/undirected edges
116			System.out.println("TEST adding and getting directed/undirected edges: ");
117	duarte	420	RIGraph g = new RIGraph("ABCD");
118	duarte	421	EdgeType edgeType = EdgeType.UNDIRECTED;
119	duarte	420	RIGNode n1 = g.getNodeFromSerial(1);
120			RIGNode n2 = g.getNodeFromSerial(2);
121	duarte	421	RIGNode n3 = g.getNodeFromSerial(3);
122	duarte	420	g.addEdge(new RIGEdge(1), n1, n2, edgeType);
123			g.addEdge(new RIGEdge(2), n2, n1, edgeType);
124			g.addEdge(new RIGEdge(3), n1, n2, edgeType);
125	duarte	421	g.addEdge(new RIGEdge(4), n1, n3, edgeType);
126	duarte	420	for (RIGEdge e:g.getEdges()) {
127			System.out.println(g.getEndpoints(e).getFirst()+" "+g.getEndpoints(e).getSecond()+", w "+e.getAtomWeight());
128			}
129			System.out.println("vertex count: "+g.getVertexCount());
130			System.out.println("edge count: "+g.getEdgeCount());
131	duarte	421	System.out.println("edge w "+ g.findEdge(n3, n1).getAtomWeight());
132	duarte	423
133			// TEST copying of RIGraph objects and restrictRange methods
134			System.out.println("TEST copying of RIGraph objects");
135			RIGraph g1 = new PdbasePdb("1bxy","A").get_graph("Ca", 8);
136			RIGraph g2 = new PdbasePdb("1sha","A").get_graph("Ca", 8);
137			System.out.println("g1: "+g1.getPdbCode()+" nodes: "+g1.getVertexCount()+" edges: "+g1.getEdgeCount());
138			System.out.println("g2: "+g2.getPdbCode()+" nodes: "+g2.getVertexCount()+" edges: "+g2.getEdgeCount());
139			RIGraph newgraph = g1.copy();
140			System.out.println("new g: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
141			newgraph = g2;
142			System.out.println("new g reassigned to g2: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
143			newgraph.restrictContactsToMaxRange(10);
144			System.out.println("new g reassigned to g2, max range 10: "+newgraph.getPdbCode()+" nodes: "+newgraph.getVertexCount()+" edges: "+newgraph.getEdgeCount());
145			System.out.println("g1: "+g1.getPdbCode()+" nodes: "+g1.getVertexCount()+" edges: "+g1.getEdgeCount());
146
147	duarte	420	}
148
149
150			}