trunk/proteinstructure/Graph.java

package proteinstructure;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.TreeMap;


public class Graph {

        ArrayList<Contact> contacts;
        TreeMap<Integer,String> nodes;
        String sequence;
        String accode;
        String chain;
        double cutoff;
        String ct;
        boolean directed;
        
        public Graph (ArrayList<Contact> contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String accode, String chain) {
                this.contacts=contacts;
                this.cutoff=cutoff;
                this.nodes=nodes;
                this.sequence=sequence;
                this.accode=accode;
                this.chain=chain;
                this.ct=ct;
                directed=false;
                if (ct.contains("/")){
                        directed=true;
                }
        }

        //TODO implement (from python) constructors for reading from file and db
        //TODO implement (from python) read_contacts_from_file
        //TODO implement (from python) read_contacts_from_db
        //TODO implement (from python) write_graph_to_db
        
        public void write_contacts_to_file (String outfile) throws IOException {
                PrintStream Out = new PrintStream(new FileOutputStream(outfile));
                for (Contact pair:contacts){
                        int i_resser=pair.i;
                        int j_resser=pair.j;
                        Out.println(i_resser+"\t"+j_resser);
                }
                Out.close();            
        }
        
        public ContactMap getCM() {
                // residues is the map from residue nums to residue types used in ContactMap class, i.e. it is the same as Pdb.resser2restype or Graph.nodes
                TreeMap<Integer,String> residues = new TreeMap<Integer,String>();
                // we copy residues from nodes (deep copy) 
                for (int node:nodes.keySet()){
                        residues.put(node, nodes.get(node));
                }
                // check if we are in directed or undirected case. If undirected we fill the opposite contacts to pass a full list of contacts to ContactMap (which contains full matrix)
                ArrayList<Contact> contacts2pass = new ArrayList<Contact>();
                if (directed){
                        contacts2pass=contacts;
                } else {
                        for (Contact cont:contacts){
                                int i_resser = cont.i;
                                int j_resser = cont.j;
                                contacts2pass.add(new Contact(i_resser,j_resser));
                                contacts2pass.add(new Contact(j_resser,i_resser));
                        }
                }
                // construct the ContactMap object and return it
                ContactMap cm = new ContactMap(contacts2pass,residues,sequence);
                return cm;
                
        }
        
}
Revision:	129
Committed:	Thu May 10 13:12:32 2007 UTC (17 years, 9 months ago) by duarte
File size:	2243 byte(s)
Log Message:	NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed Passing more data from Pdb to Graph in get_graph New constructor in ContactMap
Line	User	Rev	File contents
1	duarte	123	package proteinstructure;
2			import java.io.FileOutputStream;
3			import java.io.PrintStream;
4			import java.io.IOException;
5			import java.util.ArrayList;
6	duarte	129	import java.util.TreeMap;
7	duarte	123
8
9			public class Graph {
10
11			ArrayList<Contact> contacts;
12	duarte	129	TreeMap<Integer,String> nodes;
13			String sequence;
14			String accode;
15			String chain;
16	duarte	123	double cutoff;
17			String ct;
18	duarte	129	boolean directed;
19	duarte	123
20	duarte	129	public Graph (ArrayList<Contact> contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String accode, String chain) {
21	duarte	123	this.contacts=contacts;
22			this.cutoff=cutoff;
23	duarte	129	this.nodes=nodes;
24			this.sequence=sequence;
25			this.accode=accode;
26			this.chain=chain;
27	duarte	123	this.ct=ct;
28	duarte	129	directed=false;
29			if (ct.contains("/")){
30			directed=true;
31			}
32	duarte	123	}
33	duarte	129
34			//TODO implement (from python) constructors for reading from file and db
35			//TODO implement (from python) read_contacts_from_file
36			//TODO implement (from python) read_contacts_from_db
37			//TODO implement (from python) write_graph_to_db
38	duarte	123
39			public void write_contacts_to_file (String outfile) throws IOException {
40			PrintStream Out = new PrintStream(new FileOutputStream(outfile));
41			for (Contact pair:contacts){
42			int i_resser=pair.i;
43			int j_resser=pair.j;
44			Out.println(i_resser+"\t"+j_resser);
45			}
46			Out.close();
47			}
48	duarte	129
49			public ContactMap getCM() {
50			// residues is the map from residue nums to residue types used in ContactMap class, i.e. it is the same as Pdb.resser2restype or Graph.nodes
51			TreeMap<Integer,String> residues = new TreeMap<Integer,String>();
52			// we copy residues from nodes (deep copy)
53			for (int node:nodes.keySet()){
54			residues.put(node, nodes.get(node));
55			}
56			// check if we are in directed or undirected case. If undirected we fill the opposite contacts to pass a full list of contacts to ContactMap (which contains full matrix)
57			ArrayList<Contact> contacts2pass = new ArrayList<Contact>();
58			if (directed){
59			contacts2pass=contacts;
60			} else {
61			for (Contact cont:contacts){
62			int i_resser = cont.i;
63			int j_resser = cont.j;
64			contacts2pass.add(new Contact(i_resser,j_resser));
65			contacts2pass.add(new Contact(j_resser,i_resser));
66			}
67			}
68			// construct the ContactMap object and return it
69			ContactMap cm = new ContactMap(contacts2pass,residues,sequence);
70			return cm;
71
72			}
73
74	duarte	123	}