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
         */
        public 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){
                if (!directed && cont.i>cont.j){
                        // we invert in case of undirected and i>j because in undirected we have only the half of the matrix j>i
                        // if we added an edge i>j it could happen that the edge was already there but inverted and wouldn't be detected as a duplicate
                        cont = new Edge(cont.j,cont.i); 
                }
                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){
                if (!directed && cont.i>cont.j){
                        // we invert in case of undirected and i>j because in undirected we have only the half of the matrix j>i
                        // if we try to delete an edge i>j it won't be there, we have to invert it and then try to delete
                        cont = new Edge(cont.j,cont.i); 
                }
                contacts.remove(cont);
                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 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;
        }
        
        public boolean containsContact(Edge cont){
                // be careful with order, this checks strictly whether the cont.i, cont.j is given, strictly in that order!
                // in undirected case contacts are stored only in 1 direction (j>i) and thus if wrong order given it won't be found 
                return contacts.contains(cont);
        }
        
        public void resetContacts(){
                this.contacts = new EdgeSet();
        }
}
Revision:	252
Committed:	Thu Aug 9 10:37:14 2007 UTC (17 years, 6 months ago) by duarte
File size:	11994 byte(s)
Log Message:	Made constructor public
Line	User	Rev	File contents
1	duarte	123	package proteinstructure;
2	duarte	191
3	duarte	123	import java.io.FileOutputStream;
4			import java.io.PrintStream;
5			import java.io.IOException;
6	duarte	129	import java.util.TreeMap;
7	duarte	189	import java.util.HashMap;
8	duarte	123
9	duarte	207	/**
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	duarte	123	public class Graph {
17
18	duarte	144	public final static String GRAPHFILEFORMATVERSION = "1.0";
19	duarte	206
20	duarte	234	public EdgeSet contacts; // we keep it public to be able to re-reference the object directly (getContacts() copies it)
21	duarte	123
22	duarte	207	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	duarte	208	protected String pdbChainCode;
27	duarte	207	protected double cutoff;
28			protected String ct; // the contact type
29	duarte	208	protected boolean directed;
30	duarte	207
31	duarte	159	// 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	duarte	207	protected int fullLength;
35			protected int obsLength; // length without unobserved, non standard aas
36	duarte	159
37	duarte	207	protected int numContacts;
38	duarte	159
39	duarte	207	protected boolean modified;
40	duarte	175
41	duarte	207	public Graph() {
42
43			}
44
45	duarte	134	/**
46			* Constructs Graph object by passing ArrayList with contacts and TreeMap with nodes (res serials and types)
47	duarte	206	* Must also pass contact type, cutoff, pdbCode and chainCode
48	duarte	134	* @param contacts
49			* @param nodes
50			* @param sequence
51			* @param cutoff
52			* @param ct
53	duarte	206	* @param pdbCode
54			* @param chainCode
55	duarte	134	*/
56	duarte	252	public Graph (EdgeSet contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String pdbCode, String chainCode, String pdbChainCode) {
57	duarte	123	this.contacts=contacts;
58			this.cutoff=cutoff;
59	duarte	129	this.nodes=nodes;
60			this.sequence=sequence;
61	duarte	206	this.pdbCode=pdbCode;
62			this.chainCode=chainCode;
63			this.pdbChainCode=pdbChainCode;
64	duarte	123	this.ct=ct;
65	duarte	159	this.fullLength=sequence.length();
66			this.obsLength=nodes.size();
67			this.numContacts=contacts.size();
68	duarte	175	this.modified=false;
69	duarte	208	this.directed=false;
70	duarte	129	if (ct.contains("/")){
71			directed=true;
72			}
73	stehr	217
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	duarte	123	}
77	duarte	135
78	duarte	129
79	duarte	135	//TODO implement (from python) write_graph_to_db, do we really need it here??
80
81	duarte	144	public void write_graph_to_file (String outfile) throws IOException {
82			PrintStream Out = new PrintStream(new FileOutputStream(outfile));
83	duarte	208	Out.println("#AGLAPPE GRAPH FILE ver: "+GRAPHFILEFORMATVERSION);
84	duarte	144	Out.println("#SEQUENCE: "+sequence);
85	duarte	206	Out.println("#PDB: "+pdbCode);
86			Out.println("#PDB CHAIN CODE: "+pdbChainCode);
87			Out.println("#CHAIN: "+chainCode);
88	duarte	144	Out.println("#CT: "+ct);
89			Out.println("#CUTOFF: "+cutoff);
90	duarte	234	for (Edge pair:contacts){
91	duarte	144	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	duarte	175
98	duarte	159	/**
99	duarte	234	* Gets list of contacts as a new EdgeSet (deep copied)
100	duarte	175	*
101			*/
102	duarte	234	public EdgeSet getContacts(){
103			EdgeSet newContacts = new EdgeSet();
104			for (Edge cont:contacts){
105			newContacts.add(new Edge(cont.i,cont.j));
106	duarte	175	}
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	duarte	206	return new Graph(getContacts(),getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
128	duarte	175	}
129
130			/**
131	duarte	232	* 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	duarte	159	* 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	duarte	234	for (Edge cont:contacts){
149	duarte	159	int i_resser = cont.i;
150			int j_resser = cont.j;
151			cm[i_resser-1][j_resser-1]=1;
152	duarte	129	}
153			return cm;
154			}
155	duarte	159
156	duarte	165	/**
157	duarte	179	* 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	duarte	165	* Gets node neighbourhood given a residue serial
167			* @param resser
168			* @return
169			*/
170	duarte	179	public NodeNbh getNodeNbh(int resser){
171			NodeNbh nbh = new NodeNbh(resser, getResType(resser));
172	duarte	165	//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	duarte	179	//however we would then have the overhead of creating the matrix
175	duarte	234	for (Edge cont:contacts){
176	duarte	165	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	duarte	179	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	duarte	175	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	duarte	165	}
201			return nbh;
202			}
203	duarte	232
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	duarte	234	public void addEdge(Edge cont){
225	duarte	240	if (!directed && cont.i>cont.j){
226	duarte	239	// we invert in case of undirected and i>j because in undirected we have only the half of the matrix j>i
227			// if we added an edge i>j it could happen that the edge was already there but inverted and wouldn't be detected as a duplicate
228	duarte	240	cont = new Edge(cont.j,cont.i);
229	duarte	239	}
230	duarte	234	contacts.add(cont); // contacts is a TreeSet and thus takes care of duplicates
231			int oldNumContacts = numContacts;
232			numContacts=getNumContacts();
233			// if number of contacts changed that means we actually added a new contact and thus we modified the graph
234			if (numContacts!=oldNumContacts) modified=true;
235
236	duarte	175	}
237
238	duarte	234	public void delEdge(Edge cont){
239	duarte	240	if (!directed && cont.i>cont.j){
240			// we invert in case of undirected and i>j because in undirected we have only the half of the matrix j>i
241			// if we try to delete an edge i>j it won't be there, we have to invert it and then try to delete
242			cont = new Edge(cont.j,cont.i);
243			}
244	duarte	175	contacts.remove(cont);
245	duarte	240	int oldNumContacts = numContacts;
246			numContacts=getNumContacts();
247			// if number of contacts changed that means we actually added a new contact and thus we modified the graph
248			if (numContacts!=oldNumContacts) modified=true;
249	duarte	175	}
250
251			public void restrictContactsToMaxRange(int range){
252	duarte	234	EdgeSet edgesToDelete = new EdgeSet();
253			for (Edge cont:contacts){
254	duarte	179	if (cont.getRange()>range) edgesToDelete.add(cont);
255	duarte	175	}
256	duarte	234	for (Edge cont:edgesToDelete){
257	duarte	179	delEdge(cont);
258			}
259	duarte	175	}
260
261			public void restrictContactsToMinRange(int range){
262	duarte	234	EdgeSet edgesToDelete = new EdgeSet();
263			for (Edge cont:contacts){
264	duarte	179	if (cont.getRange()<range) edgesToDelete.add(cont);
265	duarte	175	}
266	duarte	234	for (Edge cont:edgesToDelete){
267	duarte	179	delEdge(cont);
268			}
269	duarte	175	}
270	duarte	189
271	duarte	191	/**
272			* Returns a HashMap with all edge neighbourhood sizes (if they are >0) for each cell in the contact map
273			* @return
274			*/
275	duarte	234	public HashMap<Edge,Integer> getAllEdgeNbhSizes() {
276			HashMap<Edge,Integer> sizes = new HashMap<Edge, Integer>();
277	duarte	191	if (!directed) {
278			for (int i=1; i<fullLength;i++){
279			for (int j=i+1; j<fullLength;j++){
280			int size = getEdgeNbh(i, j).size();
281	duarte	234	if (size>0) sizes.put(new Edge(i,j), size);
282	duarte	191	}
283			}
284			} else {
285			for (int i=1; i<fullLength;i++){
286			for (int j=1; j<fullLength;j++){
287			if (i!=j){
288			int size = getEdgeNbh(i, j).size();
289	duarte	234	if (size>0) sizes.put(new Edge(i,j), size);
290	duarte	191	}
291			}
292			}
293			}
294			return sizes;
295			}
296
297	duarte	189	//TODO not sure what kind of return we want, for now is a HashMap with three graph objects
298			public HashMap<String,Graph> compare(Graph other) throws Exception{
299			//first check that other has same sequence than this, otherwise throw exception
300			if (!this.sequence.equals(other.sequence)){
301			//TODO throw specific exception
302			throw new Exception("Sequence of 2 graphs to compare differ, can't compare them.");
303			}
304	duarte	234	EdgeSet common = new EdgeSet();
305			EdgeSet onlythis = new EdgeSet();
306			EdgeSet onlyother = new EdgeSet();
307			for (Edge cont:this.contacts){
308	duarte	189	if (other.contacts.contains(cont)) {
309			common.add(cont);
310			} else{
311			onlythis.add(cont);
312			}
313			}
314	duarte	234	for (Edge cont:other.contacts){
315	duarte	189	if (!this.contacts.contains(cont)){
316			onlyother.add(cont);
317			}
318			}
319	duarte	206	Graph commongraph = new Graph (common,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
320			Graph onlythisgraph = new Graph (onlythis,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode);
321			Graph onlyothergraph = new Graph (onlyother,getNodes(),sequence,cutoff,ct,other.pdbCode,other.chainCode,other.pdbChainCode);
322	duarte	189	HashMap<String,Graph> result = new HashMap<String,Graph>();
323			result.put("common", commongraph);
324			result.put("onlythis", onlythisgraph);
325			result.put("onlyother",onlyothergraph);
326			return result;
327			}
328	duarte	206
329			public boolean isModified(){
330			return modified;
331			}
332
333			public boolean isDirected(){
334			return directed;
335			}
336
337			public String getPdbCode() {
338			return pdbCode;
339			}
340
341			public String getPdbChainCode(){
342			return pdbChainCode;
343			}
344
345			public String getChainCode(){
346			return chainCode;
347			}
348
349			public String getSequence(){
350			return sequence;
351			}
352
353			public int getFullLength(){
354			return fullLength;
355			}
356
357			public int getObsLength(){
358			return obsLength;
359			}
360
361			public int getNumContacts(){
362			// in theory we could return just numContacts, because we have taken care of updating it every time contacts changed
363			// however we call directly contacts.size() as I feel is safer
364			return contacts.size();
365			}
366
367			public String getContactType() {
368			return ct;
369			}
370
371			public double getCutoff(){
372			return cutoff;
373			}
374	duarte	249
375			public boolean containsContact(Edge cont){
376			// be careful with order, this checks strictly whether the cont.i, cont.j is given, strictly in that order!
377			// in undirected case contacts are stored only in 1 direction (j>i) and thus if wrong order given it won't be found
378			return contacts.contains(cont);
379			}
380
381			public void resetContacts(){
382			this.contacts = new EdgeSet();
383			}
384	duarte	123	}