trunk/proteinstructure/Graph.java

package proteinstructure;

import java.io.FileOutputStream;
import java.io.PrintStream;
import java.io.IOException;
import java.util.TreeMap;
import java.util.HashMap;

/**
 * A residue interaction graph derived from a single chain pdb protein structure
 * 
 * @author              Jose Duarte
 * Class:               Graph
 * Package:             proteinstructure
 */
public class Graph {

        public final static String GRAPHFILEFORMATVERSION = "1.0";
        
        public EdgeSet contacts; // we keep it public to be able to re-reference the object directly (getContacts() copies it)
        
        protected TreeMap<Integer,String> nodes; // nodes is a TreeMap of residue serials to residue types (3 letter code)
        protected String sequence;                              // the full sequence (with unobserved residues and non-standard aas ='X')
        protected String pdbCode;
        protected String chainCode;
        protected String pdbChainCode;
        protected double cutoff;
        protected String ct;                                    // the contact type
        protected boolean directed;
        
        // fullLength is length of full sequence or:
        // -if sequence not provided (when reading from db): length of everything except possible unobserved residues at end of chain
        // -if sequence and nodes not provided (when reading from file and sequence field missing): length except possible unobserved residues at end of chain and possible nodes without contacts at end of chain
        protected int fullLength; 
        protected int obsLength;  // length without unobserved, non standard aas 
        
        protected int numContacts;
        
        protected boolean modified;
        
        public Graph() {
                
        }
                
        /**
         * Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
         * Must also pass contact type, cutoff, pdbCode and chainCode
         * @param contacts
         * @param nodes
         * @param sequence
         * @param cutoff
         * @param ct
         * @param pdbCode
         * @param chainCode
         */
        protected Graph (EdgeSet contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String pdbCode, String chainCode, String pdbChainCode) {
                this.contacts=contacts;
                this.cutoff=cutoff;
                this.nodes=nodes;
                this.sequence=sequence;
                this.pdbCode=pdbCode;
                this.chainCode=chainCode;
                this.pdbChainCode=pdbChainCode;
                this.ct=ct;
                this.fullLength=sequence.length();
                this.obsLength=nodes.size();
                this.numContacts=contacts.size();
                this.modified=false;
                this.directed=false;
                if (ct.contains("/")){
                        directed=true;
                }
                
                assert(this.pdbCode.equals(this.pdbCode.toLowerCase()));                                // pdb codes should be always lower case 
                assert(this.pdbChainCode.equals(this.pdbChainCode.toUpperCase()));              // pdb chain codes should be always upper case
        }
        

        //TODO implement (from python) write_graph_to_db, do we really need it here??
                
        public void write_graph_to_file (String outfile) throws IOException {
                PrintStream Out = new PrintStream(new FileOutputStream(outfile));
                Out.println("#AGLAPPE GRAPH FILE ver: "+GRAPHFILEFORMATVERSION);
                Out.println("#SEQUENCE: "+sequence);
                Out.println("#PDB: "+pdbCode);
                Out.println("#PDB CHAIN CODE: "+pdbChainCode);
                Out.println("#CHAIN: "+chainCode);
                Out.println("#CT: "+ct);
                Out.println("#CUTOFF: "+cutoff);
                for (Edge pair:contacts){
                        int i_resser=pair.i;
                        int j_resser=pair.j;
                        Out.println(i_resser+"\t"+j_resser);
                }
                Out.close();            
        }
        
        /**
         * Gets list of contacts as a new EdgeSet (deep copied)
         * 
         */
        public EdgeSet getContacts(){
                EdgeSet newContacts = new EdgeSet();
                for (Edge cont:contacts){
                        newContacts.add(new Edge(cont.i,cont.j));
                }
                return newContacts;
        }
        
        /**
         * Gets TreeMap of nodes, deep copying  
         * 
         */
        public TreeMap<Integer,String> getNodes(){
                TreeMap<Integer,String> newNodes = new TreeMap<Integer,String>();
                for (int resser:nodes.keySet()){
                        newNodes.put(resser, nodes.get(resser));
                }
                return newNodes;
        }
        
        /**
         * Deep copies this Graph object returning new one
         * @return
         */
        public Graph copy(){
                return new Graph(getContacts(),getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);           
        }
        
        /**
         * Gets a reference to this Graph deep copying contacts but re-referencing nodes
         * @return
         */
        public Graph copyKeepingNodes(){
                return new Graph(getContacts(),nodes,sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);                
        }       
        
        /**
         * Returns an int matrix with 1s for contacts and 0s for non contacts, i.e. the contact map
         * In non-crossed cases this should give us the upper half matrix (contacts are only j>i)
         * In crossed cases this gives us a full matrix (contacts are both j>i and i>j since they are directed)
         * @return
         */
        public int[][] getIntMatrix(){
                // this initialises the matrix to 0 (i.e. no contact)
                int[][] cm = new int[fullLength][fullLength];
                // we put a 1 for all given contacts
                for (Edge cont:contacts){
                        int i_resser = cont.i;
                        int j_resser = cont.j;
                        cm[i_resser-1][j_resser-1]=1;
                }
                return cm;
        }

        /**
         * Gets a node's residue type given the residue serial
         * @param resser
         * @return
         */
        public String getResType(int resser){
                return nodes.get(resser);
        }
        
        /**
         * Gets node neighbourhood given a residue serial
         * @param resser
         * @return
         */
        public NodeNbh getNodeNbh(int resser){
                NodeNbh nbh = new NodeNbh(resser, getResType(resser));
                //this could be implemented using the contact map matrix and scanning through 1 column/row
                //it would be just slightly faster, here we do 2*numContacts iterations, using matrix would be only fullLength iterations
                //however we would then have the overhead of creating the matrix
                for (Edge cont:contacts){
                        if (cont.i==resser) nbh.put(cont.j, nodes.get(cont.j));
                        if (cont.j==resser) nbh.put(cont.i, nodes.get(cont.i));
                }
                return nbh;
        }
        
        /**
         * Gets edge neighbourhood (common neighbourhood) given a residue serial pair
         * @param i_resser
         * @param j_resser
         * @return
         */
        public EdgeNbh getEdgeNbh(int i_resser, int j_resser){
                EdgeNbh nbh = new EdgeNbh(i_resser, getResType(i_resser), j_resser, getResType(j_resser));
                NodeNbh i_nbhd = getNodeNbh(i_resser);
                NodeNbh j_nbhd = getNodeNbh(j_resser);
                if (j_nbhd.size()>=i_nbhd.size()) { //with this we will be slightly faster, always iterating through smallest TreeMap
                        for (int resser:i_nbhd.keySet()) {
                                if (j_nbhd.containsKey(resser)) nbh.put(resser, i_nbhd.get(resser));
                        }
                } else {
                        for (int resser:j_nbhd.keySet()) {
                                if (i_nbhd.containsKey(resser)) nbh.put(resser, j_nbhd.get(resser));                    
                        }
                }
                return nbh;
        }
        
        /**
         * Gets 2nd shell node neighbourhood
         * @param resser
         */
        public NodeNbh get2ndshellNodeNbh(int resser){
                // first we create a NodeNbh object for the second shell, central residue is given resser
                NodeNbh nbh2ndshell = new NodeNbh(resser,getResType(resser));
                // we get 1st neighbourhood
                NodeNbh nbh = this.getNodeNbh(resser);
                for (int nb:nbh.keySet()){
                        NodeNbh nbh2 = this.getNodeNbh(nb); // for each first neighbour we take its neighbourhood
                        for (int nb2:nbh2.keySet()){
                                if (nb2!=resser && !nbh.containsKey(nb2)){ // if the 2nd neighbour nb2 is not the given resser or is not a 1st neighbour
                                        nbh2ndshell.put(nb2, getResType(nb2));
                                }
                        }
                }
                return nbh2ndshell;
        }
        
        public void addEdge(Edge cont){
                contacts.add(cont); // contacts is a TreeSet and thus takes care of duplicates
                int oldNumContacts = numContacts;
                numContacts=getNumContacts();
                // if number of contacts changed that means we actually added a new contact and thus we modified the graph
                if (numContacts!=oldNumContacts) modified=true;
                
        }
        
        public void delEdge(Edge cont){
                contacts.remove(cont);
                numContacts--;
                modified=true;
        }
        
        public void restrictContactsToMaxRange(int range){
                EdgeSet edgesToDelete = new EdgeSet();
                for (Edge cont:contacts){
                        if (cont.getRange()>range) edgesToDelete.add(cont);
                }
                for (Edge cont:edgesToDelete){
                        delEdge(cont);
                }
        }
        
        public void restrictContactsToMinRange(int range){
                EdgeSet edgesToDelete = new EdgeSet();
                for (Edge cont:contacts){
                        if (cont.getRange()<range) edgesToDelete.add(cont);
                }
                for (Edge cont:edgesToDelete){
                        delEdge(cont);
                }
        }

        /**
         * Returns a HashMap with all edge neighbourhood sizes (if they are >0) for each cell in the contact map
         * @return
         */
        public HashMap<Edge,Integer> getAllEdgeNbhSizes() {
                HashMap<Edge,Integer> sizes = new HashMap<Edge, Integer>();
                if (!directed) {
                        for (int i=1; i<fullLength;i++){
                                for (int j=i+1; j<fullLength;j++){
                                        int size = getEdgeNbh(i, j).size();
                                        if (size>0)     sizes.put(new Edge(i,j), size);
                                }
                        }                       
                } else {
                        for (int i=1; i<fullLength;i++){
                                for (int j=1; j<fullLength;j++){
                                        if (i!=j){
                                                int size = getEdgeNbh(i, j).size();
                                                if (size>0) sizes.put(new Edge(i,j), size);
                                        }
                                }
                        }
                }
                return sizes;
        }

        //TODO not sure what kind of return we want, for now is a HashMap with three graph objects 
        public HashMap<String,Graph> compare(Graph other) throws Exception{
                //first check that other has same sequence than this, otherwise throw exception
                if (!this.sequence.equals(other.sequence)){
                        //TODO throw specific exception
                        throw new Exception("Sequence of 2 graphs to compare differ, can't compare them.");
                }
                EdgeSet common = new EdgeSet();
                EdgeSet onlythis = new EdgeSet();
                EdgeSet onlyother = new EdgeSet();
                for (Edge cont:this.contacts){
                        if (other.contacts.contains(cont)) {
                                common.add(cont);
                        } else{
                                onlythis.add(cont);
                        }
                }
                for (Edge cont:other.contacts){
                        if (!this.contacts.contains(cont)){
                                onlyother.add(cont);
                        }
                }
                Graph commongraph = new Graph (common,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
                Graph onlythisgraph = new Graph (onlythis,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
                Graph onlyothergraph = new Graph (onlyother,getNodes(),sequence,cutoff,ct,other.pdbCode,other.chainCode,other.pdbChainCode);
                HashMap<String,Graph> result = new HashMap<String,Graph>();
                result.put("common", commongraph);
                result.put("onlythis", onlythisgraph);
                result.put("onlyother",onlyothergraph);
                return result;
        }
        
        public boolean isModified(){
                return modified;
        }
        
        public boolean isDirected(){
                return directed;
        }
        
        public String getPdbCode() {
                return pdbCode;
        }
        
        public String getPdbChainCode(){
                return pdbChainCode;
        }
        
        public String getChainCode(){
                return chainCode;
        }
        
        public String getSequence(){
                return sequence;
        }
        
        public int getFullLength(){
                return fullLength;
        }
        
        public int getObsLength(){
                return obsLength;
        }
        
        public int getNumContacts(){
                // in theory we could return just numContacts, because we have taken care of updating it every time contacts changed
                // however we call directly contacts.size() as I feel is safer
                return contacts.size(); 
        }
        
        public String getContactType() {
                return ct;
        }
        
        public double getCutoff(){
                return cutoff;
        }
}
Revision:	234
Committed:	Tue Jul 10 14:14:58 2007 UTC (17 years, 7 months ago) by duarte
File size:	10826 byte(s)
Log Message:	Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
Line	File contents
1	package proteinstructure;
2
3	import java.io.FileOutputStream;
4	import java.io.PrintStream;
5	import java.io.IOException;
6	import java.util.TreeMap;
7	import java.util.HashMap;
8
9	/**
10	* A residue interaction graph derived from a single chain pdb protein structure
11	*
12	* @author Jose Duarte
13	* Class: Graph
14	* Package: proteinstructure
15	*/
16	public class Graph {
17
18	public final static String GRAPHFILEFORMATVERSION = "1.0";
19
20	public EdgeSet contacts; // we keep it public to be able to re-reference the object directly (getContacts() copies it)
21
22	protected TreeMap<Integer,String> nodes; // nodes is a TreeMap of residue serials to residue types (3 letter code)
23	protected String sequence; // the full sequence (with unobserved residues and non-standard aas ='X')
24	protected String pdbCode;
25	protected String chainCode;
26	protected String pdbChainCode;
27	protected double cutoff;
28	protected String ct; // the contact type
29	protected boolean directed;
30
31	// fullLength is length of full sequence or:
32	// -if sequence not provided (when reading from db): length of everything except possible unobserved residues at end of chain
33	// -if sequence and nodes not provided (when reading from file and sequence field missing): length except possible unobserved residues at end of chain and possible nodes without contacts at end of chain
34	protected int fullLength;
35	protected int obsLength; // length without unobserved, non standard aas
36
37	protected int numContacts;
38
39	protected boolean modified;
40
41	public Graph() {
42
43	}
44
45	/**
46	* Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
47	* Must also pass contact type, cutoff, pdbCode and chainCode
48	* @param contacts
49	* @param nodes
50	* @param sequence
51	* @param cutoff
52	* @param ct
53	* @param pdbCode
54	* @param chainCode
55	*/
56	protected Graph (EdgeSet contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String pdbCode, String chainCode, String pdbChainCode) {
57	this.contacts=contacts;
58	this.cutoff=cutoff;
59	this.nodes=nodes;
60	this.sequence=sequence;
61	this.pdbCode=pdbCode;
62	this.chainCode=chainCode;
63	this.pdbChainCode=pdbChainCode;
64	this.ct=ct;
65	this.fullLength=sequence.length();
66	this.obsLength=nodes.size();
67	this.numContacts=contacts.size();
68	this.modified=false;
69	this.directed=false;
70	if (ct.contains("/")){
71	directed=true;
72	}
73
74	assert(this.pdbCode.equals(this.pdbCode.toLowerCase())); // pdb codes should be always lower case
75	assert(this.pdbChainCode.equals(this.pdbChainCode.toUpperCase())); // pdb chain codes should be always upper case
76	}
77
78
79	//TODO implement (from python) write_graph_to_db, do we really need it here??
80
81	public void write_graph_to_file (String outfile) throws IOException {
82	PrintStream Out = new PrintStream(new FileOutputStream(outfile));
83	Out.println("#AGLAPPE GRAPH FILE ver: "+GRAPHFILEFORMATVERSION);
84	Out.println("#SEQUENCE: "+sequence);
85	Out.println("#PDB: "+pdbCode);
86	Out.println("#PDB CHAIN CODE: "+pdbChainCode);
87	Out.println("#CHAIN: "+chainCode);
88	Out.println("#CT: "+ct);
89	Out.println("#CUTOFF: "+cutoff);
90	for (Edge pair:contacts){
91	int i_resser=pair.i;
92	int j_resser=pair.j;
93	Out.println(i_resser+"\t"+j_resser);
94	}
95	Out.close();
96	}
97
98	/**
99	* Gets list of contacts as a new EdgeSet (deep copied)
100	*
101	*/
102	public EdgeSet getContacts(){
103	EdgeSet newContacts = new EdgeSet();
104	for (Edge cont:contacts){
105	newContacts.add(new Edge(cont.i,cont.j));
106	}
107	return newContacts;
108	}
109
110	/**
111	* Gets TreeMap of nodes, deep copying
112	*
113	*/
114	public TreeMap<Integer,String> getNodes(){
115	TreeMap<Integer,String> newNodes = new TreeMap<Integer,String>();
116	for (int resser:nodes.keySet()){
117	newNodes.put(resser, nodes.get(resser));
118	}
119	return newNodes;
120	}
121
122	/**
123	* Deep copies this Graph object returning new one
124	* @return
125	*/
126	public Graph copy(){
127	return new Graph(getContacts(),getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
128	}
129
130	/**
131	* Gets a reference to this Graph deep copying contacts but re-referencing nodes
132	* @return
133	*/
134	public Graph copyKeepingNodes(){
135	return new Graph(getContacts(),nodes,sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
136	}
137
138	/**
139	* Returns an int matrix with 1s for contacts and 0s for non contacts, i.e. the contact map
140	* In non-crossed cases this should give us the upper half matrix (contacts are only j>i)
141	* In crossed cases this gives us a full matrix (contacts are both j>i and i>j since they are directed)
142	* @return
143	*/
144	public int[][] getIntMatrix(){
145	// this initialises the matrix to 0 (i.e. no contact)
146	int[][] cm = new int[fullLength][fullLength];
147	// we put a 1 for all given contacts
148	for (Edge cont:contacts){
149	int i_resser = cont.i;
150	int j_resser = cont.j;
151	cm[i_resser-1][j_resser-1]=1;
152	}
153	return cm;
154	}
155
156	/**
157	* Gets a node's residue type given the residue serial
158	* @param resser
159	* @return
160	*/
161	public String getResType(int resser){
162	return nodes.get(resser);
163	}
164
165	/**
166	* Gets node neighbourhood given a residue serial
167	* @param resser
168	* @return
169	*/
170	public NodeNbh getNodeNbh(int resser){
171	NodeNbh nbh = new NodeNbh(resser, getResType(resser));
172	//this could be implemented using the contact map matrix and scanning through 1 column/row
173	//it would be just slightly faster, here we do 2*numContacts iterations, using matrix would be only fullLength iterations
174	//however we would then have the overhead of creating the matrix
175	for (Edge cont:contacts){
176	if (cont.i==resser) nbh.put(cont.j, nodes.get(cont.j));
177	if (cont.j==resser) nbh.put(cont.i, nodes.get(cont.i));
178	}
179	return nbh;
180	}
181
182	/**
183	* Gets edge neighbourhood (common neighbourhood) given a residue serial pair
184	* @param i_resser
185	* @param j_resser
186	* @return
187	*/
188	public EdgeNbh getEdgeNbh(int i_resser, int j_resser){
189	EdgeNbh nbh = new EdgeNbh(i_resser, getResType(i_resser), j_resser, getResType(j_resser));
190	NodeNbh i_nbhd = getNodeNbh(i_resser);
191	NodeNbh j_nbhd = getNodeNbh(j_resser);
192	if (j_nbhd.size()>=i_nbhd.size()) { //with this we will be slightly faster, always iterating through smallest TreeMap
193	for (int resser:i_nbhd.keySet()) {
194	if (j_nbhd.containsKey(resser)) nbh.put(resser, i_nbhd.get(resser));
195	}
196	} else {
197	for (int resser:j_nbhd.keySet()) {
198	if (i_nbhd.containsKey(resser)) nbh.put(resser, j_nbhd.get(resser));
199	}
200	}
201	return nbh;
202	}
203
204	/**
205	* Gets 2nd shell node neighbourhood
206	* @param resser
207	*/
208	public NodeNbh get2ndshellNodeNbh(int resser){
209	// first we create a NodeNbh object for the second shell, central residue is given resser
210	NodeNbh nbh2ndshell = new NodeNbh(resser,getResType(resser));
211	// we get 1st neighbourhood
212	NodeNbh nbh = this.getNodeNbh(resser);
213	for (int nb:nbh.keySet()){
214	NodeNbh nbh2 = this.getNodeNbh(nb); // for each first neighbour we take its neighbourhood
215	for (int nb2:nbh2.keySet()){
216	if (nb2!=resser && !nbh.containsKey(nb2)){ // if the 2nd neighbour nb2 is not the given resser or is not a 1st neighbour
217	nbh2ndshell.put(nb2, getResType(nb2));
218	}
219	}
220	}
221	return nbh2ndshell;
222	}
223
224	public void addEdge(Edge cont){
225	contacts.add(cont); // contacts is a TreeSet and thus takes care of duplicates
226	int oldNumContacts = numContacts;
227	numContacts=getNumContacts();
228	// if number of contacts changed that means we actually added a new contact and thus we modified the graph
229	if (numContacts!=oldNumContacts) modified=true;
230
231	}
232
233	public void delEdge(Edge cont){
234	contacts.remove(cont);
235	numContacts--;
236	modified=true;
237	}
238
239	public void restrictContactsToMaxRange(int range){
240	EdgeSet edgesToDelete = new EdgeSet();
241	for (Edge cont:contacts){
242	if (cont.getRange()>range) edgesToDelete.add(cont);
243	}
244	for (Edge cont:edgesToDelete){
245	delEdge(cont);
246	}
247	}
248
249	public void restrictContactsToMinRange(int range){
250	EdgeSet edgesToDelete = new EdgeSet();
251	for (Edge cont:contacts){
252	if (cont.getRange()<range) edgesToDelete.add(cont);
253	}
254	for (Edge cont:edgesToDelete){
255	delEdge(cont);
256	}
257	}
258
259	/**
260	* Returns a HashMap with all edge neighbourhood sizes (if they are >0) for each cell in the contact map
261	* @return
262	*/
263	public HashMap<Edge,Integer> getAllEdgeNbhSizes() {
264	HashMap<Edge,Integer> sizes = new HashMap<Edge, Integer>();
265	if (!directed) {
266	for (int i=1; i<fullLength;i++){
267	for (int j=i+1; j<fullLength;j++){
268	int size = getEdgeNbh(i, j).size();
269	if (size>0) sizes.put(new Edge(i,j), size);
270	}
271	}
272	} else {
273	for (int i=1; i<fullLength;i++){
274	for (int j=1; j<fullLength;j++){
275	if (i!=j){
276	int size = getEdgeNbh(i, j).size();
277	if (size>0) sizes.put(new Edge(i,j), size);
278	}
279	}
280	}
281	}
282	return sizes;
283	}
284
285	//TODO not sure what kind of return we want, for now is a HashMap with three graph objects
286	public HashMap<String,Graph> compare(Graph other) throws Exception{
287	//first check that other has same sequence than this, otherwise throw exception
288	if (!this.sequence.equals(other.sequence)){
289	//TODO throw specific exception
290	throw new Exception("Sequence of 2 graphs to compare differ, can't compare them.");
291	}
292	EdgeSet common = new EdgeSet();
293	EdgeSet onlythis = new EdgeSet();
294	EdgeSet onlyother = new EdgeSet();
295	for (Edge cont:this.contacts){
296	if (other.contacts.contains(cont)) {
297	common.add(cont);
298	} else{
299	onlythis.add(cont);
300	}
301	}
302	for (Edge cont:other.contacts){
303	if (!this.contacts.contains(cont)){
304	onlyother.add(cont);
305	}
306	}
307	Graph commongraph = new Graph (common,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
308	Graph onlythisgraph = new Graph (onlythis,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
309	Graph onlyothergraph = new Graph (onlyother,getNodes(),sequence,cutoff,ct,other.pdbCode,other.chainCode,other.pdbChainCode);
310	HashMap<String,Graph> result = new HashMap<String,Graph>();
311	result.put("common", commongraph);
312	result.put("onlythis", onlythisgraph);
313	result.put("onlyother",onlyothergraph);
314	return result;
315	}
316
317	public boolean isModified(){
318	return modified;
319	}
320
321	public boolean isDirected(){
322	return directed;
323	}
324
325	public String getPdbCode() {
326	return pdbCode;
327	}
328
329	public String getPdbChainCode(){
330	return pdbChainCode;
331	}
332
333	public String getChainCode(){
334	return chainCode;
335	}
336
337	public String getSequence(){
338	return sequence;
339	}
340
341	public int getFullLength(){
342	return fullLength;
343	}
344
345	public int getObsLength(){
346	return obsLength;
347	}
348
349	public int getNumContacts(){
350	// in theory we could return just numContacts, because we have taken care of updating it every time contacts changed
351	// however we call directly contacts.size() as I feel is safer
352	return contacts.size();
353	}
354
355	public String getContactType() {
356	return ct;
357	}
358
359	public double getCutoff(){
360	return cutoff;
361	}
362	}