trunk/proteinstructure/Graph.java

package proteinstructure;

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

import java.sql.SQLException;
import java.sql.Statement;

import java.sql.ResultSet;

import tools.MySQLConnection;

/**
 * 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";
        
        private final static String SINGLEMODELS_DB = "ioannis";        //TODO: Is this being used??
        
        public EdgeSet contacts; // we keep it public to be able to re-reference the object directly (getContacts() copies it)
        
        protected TreeMap<Edge,Double> weights;
        
        protected TreeMap<Integer,String> nodes; // nodes is a TreeMap of residue serials to residue types (3 letter code)
        protected SecondaryStructure secondaryStructure; // secondary structure annotation for this protein graph

        protected String sequence;                              // the full sequence (with unobserved residues and non-standard aas ='X')
        protected String pdbCode;
        protected String chainCode;
        protected String pdbChainCode;
        protected int model;
        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
         * @param pdbChainCode
         * @param model
         * @param ssElems
         * @param rs2ss
         */
        public Graph (EdgeSet contacts, TreeMap<Integer,String> nodes, String sequence, double cutoff,String ct, String pdbCode, String chainCode, String pdbChainCode, int model, SecondaryStructure secStruct, TreeMap<Edge,Double> weights) {
                this.contacts=contacts;
                this.weights=weights;
                this.cutoff=cutoff;
                this.nodes=nodes;
                this.sequence=sequence;
                this.pdbCode=pdbCode;
                this.chainCode=chainCode;
                this.pdbChainCode=pdbChainCode;
                this.model=model;
                this.ct=ct;
                // in case of pdb was read from file and there was no SEQRES field then fullLength here shouldn't be sequence length but maximum observed residue (see Pdb class)
                this.fullLength=Math.max(sequence.length(),Collections.max(nodes.keySet()));
                this.obsLength=nodes.size();
                this.numContacts=contacts.size();
                this.modified=false;
                this.directed=false;
                if (ct.contains("/")){
                        directed=true;
                }
                if(secStruct == null) {
                        // we allow null to be passed to simplify graph construction
                        this.secondaryStructure = new SecondaryStructure();
                } else {
                        this.secondaryStructure = secStruct;
                }
                
                // do some verification checks
                assert(secondaryStructure != null);
                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
        }
        
        /**
         * Write graph to given db, using our db graph aglappe format, 
         * i.e. tables: chain_graph, single_model_graph, single_model_node, single_model_edge
         * @param conn
         * @param db
         * @throws SQLException
         */
        public void write_graph_to_db(MySQLConnection conn, String db) throws SQLException{
                // we are fixing these 3 values to what corresponds to our graphs 
                String CW = "1";
                String CR = "(true)";
                String EXPBB = "0";
                
                int pgraphid=0;
                int graphid=0;
                String sql = "SELECT graph_id FROM "+db+".chain_graph " +
                                        " WHERE accession_code='"+pdbCode+"' AND pchain_code='"+chainCode+"' LIMIT 1";
                Statement stmt = conn.createStatement();
                ResultSet rsst = stmt.executeQuery(sql);
                if (rsst.next()){       // if the pdbCode + chainCode were already in chain_graph then we take the graph_id as the pgraphid
                        pgraphid = rsst.getInt(1);
                } else {                        // no pdbCode + chainCode found, we insert them in chain_graph, thus assigning a new graph_id (pgraphid)
                        // we are inserting same number for num_obs_res and num_nodes (the difference would be the non-standard aas, but we can't get that number from this object at the moment)
                        sql = "INSERT INTO "+db+".chain_graph (accession_code,pchain_code,model_serial,dist,expBB,method,num_res,num_obs_res,num_nodes,sses,date) " +
                                        "VALUES ('"+pdbCode+"', '"+chainCode+"', "+model+", "+cutoff+", "+EXPBB+", 'rc-cutoff', "+getFullLength()+", "+getObsLength()+", "+getObsLength()+", "+secondaryStructure.getNumElements()+", now())";
                        Statement stmt2 = conn.createStatement();
                        stmt2.executeUpdate(sql);
                        // now we take the newly assigned graph_id as pgraphid
                        sql = "SELECT LAST_INSERT_ID() FROM "+db+".chain_graph LIMIT 1";
                        ResultSet rsst2 = stmt2.executeQuery(sql);
                        if (rsst2.next()){
                                pgraphid = rsst2.getInt(1);
                        }
                        stmt2.close();
                        rsst2.close();
                }
                rsst.close();
                // now we insert the graph info into single_model_graph
                String ctStr = ct;
                if (ct.equals("ALL")){
                        ctStr = "BB+SC+BB/SC";
                }
                // 1st we grab the single_model_id
                int singlemodelid = 0;
                sql = "SELECT single_model_id  FROM "+SINGLEMODELS_DB+".single_model WHERE CR='"+CR+"' AND CW='"+CW+"' AND expBB="+EXPBB+" AND CT='"+ctStr+"' AND dist="+cutoff+";";
                rsst = stmt.executeQuery(sql);
                if (rsst.next()){
                        singlemodelid = rsst.getInt(1);
                }
                rsst.close();
                // and then insert to single_model_graph
                sql = "INSERT INTO "+db+".single_model_graph (pgraph_id,graph_type,accession_code,single_model_id,dist,expBB,CW,CT,CR,num_nodes,date) " +
                                " VALUES ("+pgraphid+", 'chain', '"+pdbCode+"', "+singlemodelid+", "+cutoff+", "+EXPBB+", '"+CW+"','"+ctStr+"', '"+CR+"', "+getObsLength()+", now())";
                stmt.executeUpdate(sql);
                // and we grab the graph_id just assigned in single_model_graph
                sql = "SELECT LAST_INSERT_ID() FROM "+db+".single_model_graph LIMIT 1";
                rsst = stmt.executeQuery(sql);
                if (rsst.next()){
                        graphid = rsst.getInt(1);
                }
                rsst.close();
                stmt.close();
                // inserting edges
                for (Edge cont:contacts){
                        String i_res = AA.threeletter2oneletter(getResType(cont.i));
                        String j_res = AA.threeletter2oneletter(getResType(cont.j));
                        char i_secStructType=SecStrucElement.OTHER;
                        if (secondaryStructure.getSecStrucElement(cont.i)!=null){
                                i_secStructType = secondaryStructure.getSecStrucElement(cont.i).getType();
                        }
                        char j_secStructType=SecStrucElement.OTHER;
                        if (secondaryStructure.getSecStrucElement(cont.j)!=null){
                                j_secStructType = secondaryStructure.getSecStrucElement(cont.j).getType();
                        }
                        sql = "INSERT INTO "+db+".single_model_edge (graph_id,i_num,i_cid,i_res,i_sstype,j_num,j_cid,j_res,j_sstype,weight) " +
                                        " VALUES ("+graphid+", "+cont.i+", '"+chainCode+"', '"+i_res+"', '"+i_secStructType+"',"+cont.j+", '"+chainCode+"', '"+j_res+"', '"+j_secStructType+"', "+Math.round(weights.get(cont))+")";
                        stmt = conn.createStatement();
                        stmt.executeUpdate(sql);
                }
                if (!directed){ // we want both side of the matrix in the table to follow Ioannis' convention
                        // so we insert the reverse contacts by doing the same but swapping i, j in insertion
                        for (Edge cont:contacts){
                                String i_res = AA.threeletter2oneletter(getResType(cont.i));
                                String j_res = AA.threeletter2oneletter(getResType(cont.j));
                                char i_secStructType=SecStrucElement.OTHER;
                                if (secondaryStructure.getSecStrucElement(cont.i)!=null){
                                        i_secStructType = secondaryStructure.getSecStrucElement(cont.i).getType();
                                }
                                char j_secStructType=SecStrucElement.OTHER;
                                if (secondaryStructure.getSecStrucElement(cont.j)!=null){
                                        j_secStructType = secondaryStructure.getSecStrucElement(cont.j).getType();
                                }
                                sql = "INSERT INTO "+db+".single_model_edge (graph_id,i_num,i_cid,i_res,i_sstype,j_num,j_cid,j_res,j_sstype,weight) " +
                                                " VALUES ("+graphid+", "+cont.j+", '"+chainCode+"', '"+j_res+"', '"+j_secStructType+"',"+cont.i+", '"+chainCode+"', '"+i_res+"', '"+i_secStructType+"', "+Math.round(weights.get(cont))+")";
                                stmt.executeUpdate(sql);
                        }
                }
                // inserting nodes
                for (int resser:nodes.keySet()) {
                        String res = AA.threeletter2oneletter(getResType(resser));
                        NodeNbh nbh = getNodeNbh(resser);
                        char secStructType=SecStrucElement.OTHER;
                        if (secondaryStructure.getSecStrucElement(resser)!=null){
                                secStructType = secondaryStructure.getSecStrucElement(resser).getType();
                        }
                        if (directed){  // we insert k_in and k_out
                                sql = "INSERT INTO "+db+".single_model_node (graph_id,num,cid,res,sstype,k,k_in,k_out,n,nwg,n_num) " +
                                        " VALUES ("+graphid+", "+resser+", '"+chainCode+"', '"+res+"', '"+secStructType+"', "+0+", "+getInDegree(resser)+", "+getOutDegree(resser)+", '"+nbh.getMotifNoGaps()+"', '"+nbh.getMotif()+"', '"+nbh.getCommaSeparatedResSerials()+"')";
                        } else {                // we insert k (and no k_in or k_out)
                                sql = "INSERT INTO "+db+".single_model_node (graph_id,num,cid,res,sstype,k,n,nwg,n_num) " +
                                " VALUES ("+graphid+", "+resser+", '"+chainCode+"', '"+res+"', '"+secStructType+"',"+getDegree(resser)+", '"+nbh.getMotifNoGaps()+"', '"+nbh.getMotif()+"', '"+nbh.getCommaSeparatedResSerials()+"')";
                        }
                        stmt.executeUpdate(sql);
                }
                stmt.close();
        }
                
        /**
         * Write graph to given outfile in aglappe format
         * @param outfile
         * @throws IOException
         */
        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;
                        double weight=weights.get(pair);
                        Out.printf(Locale.US,i_resser+"\t"+j_resser+"\t%6.3f\n",weight);
                }
                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;
        }
        
        /**
         * Gets TreeMap of weights, deep copyingg
         * @return
         */
        public TreeMap<Edge,Double> getWeights(){
                TreeMap<Edge,Double> newWeights = new TreeMap<Edge, Double>();
                for (Edge cont:weights.keySet()){
                        newWeights.put(new Edge(cont.i,cont.j), weights.get(cont));
                }
                return newWeights;
        }
        
        /**
         * Deep copies this Graph object returning new one
         * @return
         */
        public Graph copy(){
                return new Graph(getContacts(),getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode,model,secondaryStructure.copy(),getWeights());              
        }
        
        /**
         * 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,model,secondaryStructure.copy(),getWeights());           
        }       
        
        /**
         * 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,model,secondaryStructure.copy(),getWeights());
                Graph onlythisgraph = new Graph (onlythis,getNodes(),sequence,cutoff,ct,pdbCode,chainCode,pdbChainCode,model,secondaryStructure.copy(),getWeights());
                Graph onlyothergraph = new Graph (onlyother,getNodes(),sequence,cutoff,ct,other.pdbCode,other.chainCode,other.pdbChainCode,model,secondaryStructure.copy(),getWeights());
                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 double getWeight(Edge cont){
                return this.weights.get(cont);
        }
        
        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();
        }
        
        public int getDegree(int resser){
                if (directed) {
                        System.err.println("Can't get degree for a directed graph, only in or out degree");
                        return 0;
                }
                int k = 0;
                for (Edge cont:contacts){
                        if (cont.i==resser || cont.j==resser) {
                                k++;
                        }
                }
                return k;
        }
        
        public int getInDegree(int resser){
                if (!directed){
                        System.err.println("Can't get in degree for an undirected graph");
                        return 0;
                }
                int k = 0;
                for (Edge cont:contacts){
                        if (cont.j==resser) {
                                k++;
                        }
                }               
                return k;
        }
        
        public int getOutDegree(int resser){
                if (!directed){
                        System.err.println("Can't get out degree for an undirected graph");
                        return 0;
                }
                int k = 0;
                for (Edge cont:contacts){
                        if (cont.i==resser) {
                                k++;
                        }
                }               
                return k;
        }

        // secondary structure related methods
        
        /** 
         * Returns true if secondary structure information is available, false otherwise. 
         */
        public boolean hasSecondaryStructure() {
                return !this.secondaryStructure.isEmpty();
        }
        
        /**
         * Returns the secondary structure annotation object of this graph.
         */
        public SecondaryStructure getSecondaryStructure() {
                return this.secondaryStructure;
        }

}
Revision:	284
Committed:	Thu Aug 16 14:57:31 2007 UTC (17 years, 6 months ago) by duarte
File size:	21085 byte(s)
Log Message:	Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)