# -*- coding: iso-8859-1 -*-# $Id: pajek.py,v 1.7 2005/08/22 13:34:10 mrsva Exp $"""Functions to work with Pajek files@author: Marcio Rosa da Silva@organization: Systems Biology Group / GBF@contact: mrs@gbf.de@license: GPL"""import sysfrom network import *def importPajek(obj, filename = '-'):    """Imports network from Pajek's .net file    @param obj: network    @param filename: .net file    """    #obj.reset()    def processEdge():        node1 = obj.nodes[int(l[0])-1]        node2 = obj.nodes[int(l[1])-1]        e = Edge(node1, node2, nedges)        obj.edges.append(e)        obj.nedges += 1        # update nodes from/to list        node1.outEdges.append(node2)        node2.inEdges.append(node1)        if len(l) == 3:            e.setWeight(int(l[2]))        else:            e.setWeight(1)        return e    if filename == '-':        arq = sys.stdin    else:        arq = open(filename, 'r')    l = arq.readline()    obj.nnodes = int(l.split()[1]) #@@    for i in range(0, obj.nnodes):        l = arq.readline().split()        # take " out of the name        if l[1][0] == '"' and l[1][-1] == '"':            l[1] = l[1][1:-1]        n = Node(l[1], i)        obj.nodes.append(n)        n.setAttribute('id', len(obj.nodes)-1)        if len(l) > 4:            n.setX(float(l[2]))            n.setY(float(l[3]))        if len(l) == 5:            n.setZ(float(l[4]))    nedges = 0    # Read "*Arcs"    l = arq.readline()    # Read first arc    l = arq.readline().split()    if l[0] != '*Edges':        # do *Arcs        while (len(l) > 1):            e = processEdge()            e.directed(1)            l = arq.readline().split()            if len(l) < 1: break            if l[0] == '*Edges':                break    # do *Edges now    l = arq.readline().split()    while (len(l) > 1):        e = processEdge()        e.directed(0)        l = arq.readline().split()    if filename != '-':        arq.close()def exportPajek(obj, filename = '-'):    """Exports network to Pajek's .net file    @param obj: network    @param filename: .net file    """    if filename == '-':        arq = sys.stdout    else:        arq = open(filename, 'w')    arq.write("*Vertices    %s\n" % obj.nnodes)    for i in range(0, obj.nnodes):        arq.write('%8d "%s"' % (i+1, obj.nodes[i].getName()))        pos = obj.nodes[i].getXYZ()        for i in range(0,len(pos)):            arq.write(" %16.8f" % float(pos[i]))        arq.write("\n")    arq.write("*Arcs\n")    for e in obj.edges:        if e.directed():            arq.write("%4d %4d %4d\n"%(int(e.getNode1().getAttribute('id'))+1,                                       int(e.getNode2().getAttribute('id'))+1,                                       int(e.getWeight())))    arq.write("*Edges\n")    for e in obj.edges:        if not e.directed():            arq.write("%4d %4d %4d\n"%(int(e.getNode1().getAttribute('id'))+1,                                       int(e.getNode2().getAttribute('id'))+1,                                       int(e.getWeight())))    if filename != '-':        arq.close()def importPajekClu(obj, filename = '-'):    """Import cluster information from Pajek's .clu file    @param obj: network    @param filename: .clu file    """    if filename == '-':        arq = sys.stdin    else:        arq = open(filename, 'r')    clusters = {}    # ignore header    arq.readline()    node = 0    for i in arq:        if len(i.split()) < 1: continue        obj.nodes[node].setCluster(int(i)-1)        node += 1        clusters[i] = 1    if filename != '-':        arq.close    obj.clusterType = 'clu'    obj.coordsModel = 'pajek'    obj.nclusters = len(clusters)def exportPajekClu(obj, filename = '-'):    """Exports cluster information to Pajek's .clu file    @param obj: network    @param filename: .clu file    """    if filename == '-':        arq = sys.stdout    else:        arq = open(filename, 'w')    arq.write("*Vertices %d\n" % obj.nnodes)    for i in range(0, obj.nnodes):        if obj.clusterType == 'clu':            arq.write("%s\n" % (int(obj.nodes[i].getCluster())+1))        if obj.clusterType == 'attr':            arq.write("%s\n" % (obj.nodes[i].getCluster()+1))    if filename != '-':        arq.close()