X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readtree.cpp;h=b9c38e973f2cea531c03c17071ed65a155bf65a3;hp=be7dc79509abbc78aeeb0a66ab45ca57b0d1324a;hb=615301e57c25e241356a9c2380648d117709458d;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6 diff --git a/readtree.cpp b/readtree.cpp index be7dc79..b9c38e9 100644 --- a/readtree.cpp +++ b/readtree.cpp @@ -107,7 +107,7 @@ float ReadTree::readBranchLength(istream& f) { /***********************************************************************/ //This class reads a file in Newick form and stores it in a tree. -int ReadNewickTree::read(TreeMap* tmap) { +int ReadNewickTree::read(CountTable* ct) { try { holder = ""; int c, error; @@ -115,8 +115,10 @@ int ReadNewickTree::read(TreeMap* tmap) { //if you are not a nexus file if ((c = filehandle.peek()) != '#') { - while((c = filehandle.peek()) != EOF) { + while((c = filehandle.peek()) != EOF) { + if (m->control_pressed) { filehandle.close(); return 0; } while ((c = filehandle.peek()) != EOF) { + if (m->control_pressed) { filehandle.close(); return 0; } // get past comments if(c == '[') { comment = 1; @@ -129,12 +131,12 @@ int ReadNewickTree::read(TreeMap* tmap) { } //make new tree - T = new Tree(tmap); + T = new Tree(ct); numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); - error = readTreeString(tmap); + error = readTreeString(ct); //save trees for later commands Trees.push_back(T); @@ -143,12 +145,14 @@ int ReadNewickTree::read(TreeMap* tmap) { //if you are a nexus file }else if ((c = filehandle.peek()) == '#') { //get right number of seqs from nexus file. - Tree* temp = new Tree(tmap); delete temp; + Tree* temp = new Tree(ct); delete temp; - nexusTranslation(tmap); //reads file through the translation and updates treemap - while((c = filehandle.peek()) != EOF) { + nexusTranslation(ct); //reads file through the translation and updates treemap + while((c = filehandle.peek()) != EOF) { + if (m->control_pressed) { filehandle.close(); return 0; } // get past comments - while ((c = filehandle.peek()) != EOF) { + while ((c = filehandle.peek()) != EOF) { + if (m->control_pressed) { filehandle.close(); return 0; } if(holder == "[" || holder == "[!"){ comment = 1; } @@ -166,12 +170,12 @@ int ReadNewickTree::read(TreeMap* tmap) { filehandle.putback(c); //put back first ( of tree. //make new tree - T = new Tree(tmap); + T = new Tree(ct); numNodes = T->getNumNodes(); numLeaves = T->getNumLeaves(); //read tree info - error = readTreeString(tmap); + error = readTreeString(ct); //save trees for later commands Trees.push_back(T); @@ -191,7 +195,7 @@ int ReadNewickTree::read(TreeMap* tmap) { } /**************************************************************************************************/ //This function read the file through the translation of the sequences names and updates treemap. -string ReadNewickTree::nexusTranslation(TreeMap* tmap) { +string ReadNewickTree::nexusTranslation(CountTable* ct) { try { holder = ""; @@ -209,42 +213,14 @@ string ReadNewickTree::nexusTranslation(TreeMap* tmap) { filehandle >> holder; if(holder == "tree" && comment != 1){return holder;} } - - //update treemap - tmap->namesOfSeqs.clear(); - - /*char c; - string number, name; - while ((c = filehandle.peek()) != EOF) { - - filehandle >> number; - - if ((number == "tree") || (number == ";") ) { name = number; break; } - - filehandle >> name; - - char lastChar; - if (name.length() != 0) { lastChar = name[name.length()-1]; } - - if ((name == "tree") || (name == ";") ) { break; } - - if (lastChar == ',') { name.erase(name.end()-1); } //erase the comma - */ - + string number, name; for(int i=0;i> number; filehandle >> name; name.erase(name.end()-1); //erase the comma - - //insert new one with new name - string group = tmap->getGroup(name); - tmap->treemap[toString(number)].groupname = group; - tmap->treemap[toString(number)].vectorIndex = tmap->getIndex(name); - //erase old one. so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah. - tmap->treemap.erase(name); - tmap->namesOfSeqs.push_back(number); + ct->renameSeq(name, toString(number)); } return name; @@ -256,7 +232,7 @@ string ReadNewickTree::nexusTranslation(TreeMap* tmap) { } /**************************************************************************************************/ -int ReadNewickTree::readTreeString(TreeMap* tmap) { +int ReadNewickTree::readTreeString(CountTable* ct) { try { int n = 0; @@ -269,8 +245,8 @@ int ReadNewickTree::readTreeString(TreeMap* tmap) { if(ch == '('){ n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off - lc = readNewickInt(filehandle, n, T, tmap); - if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading + lc = readNewickInt(filehandle, n, T, ct); + if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); m->control_pressed = true; return -1; } //reports an error in reading if(filehandle.peek()==','){ readSpecialChar(filehandle,',',"comma"); @@ -281,8 +257,8 @@ int ReadNewickTree::readTreeString(TreeMap* tmap) { } if(rooted != 1){ - rc = readNewickInt(filehandle, n, T, tmap); - if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading + rc = readNewickInt(filehandle, n, T, ct); + if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); m->control_pressed = true; return -1; } //reports an error in reading if(filehandle.peek() == ')'){ readSpecialChar(filehandle,')',"right parenthesis"); } @@ -326,7 +302,7 @@ int ReadNewickTree::readTreeString(TreeMap* tmap) { } /**************************************************************************************************/ -int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) { +int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, CountTable* ct) { try { if (m->control_pressed) { return -1; } @@ -339,7 +315,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) { //read all children vector childrenNodes; while(f.peek() != ')'){ - int child = readNewickInt(f, n, T, tmap); + int child = readNewickInt(f, n, T, ct); if (child == -1) { return -1; } //reports an error in reading //cout << "child = " << child << endl; childrenNodes.push_back(child); @@ -387,12 +363,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) { }else{ T->tree[n].setBranchLength(0.0); } - - //T->tree[n].setChildren(lc,rc); - //T->tree[lc].setParent(n); - //T->tree[rc].setParent(n); - //T->printTree(); cout << endl; - + return n++; }else{ @@ -410,33 +381,27 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) { f.putback(d); //set group info - string group = tmap->getGroup(name); - + vector group = ct->getGroups(name); + //cout << name << endl; //find index in tree of name int n1 = T->getIndex(name); //adds sequence names that are not in group file to the "xxx" group - if(group == "not found") { + if(group.size() == 0) { m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1; - tmap->namesOfSeqs.push_back(name); - tmap->treemap[name].groupname = "xxx"; - - map::iterator it; - it = tmap->seqsPerGroup.find("xxx"); - if (it == tmap->seqsPerGroup.end()) { //its a new group - tmap->namesOfGroups.push_back("xxx"); - tmap->seqsPerGroup["xxx"] = 1; - }else { - tmap->seqsPerGroup["xxx"]++; - } - - group = "xxx"; - } - - vector tempGroup; tempGroup.push_back(group); - - T->tree[n1].setGroup(tempGroup); + vector currentGroups = ct->getNamesOfGroups(); + if (!m->inUsersGroups("xxx", currentGroups)) { ct->addGroup("xxx"); } + currentGroups = ct->getNamesOfGroups(); + vector thisCounts; thisCounts.resize(currentGroups.size(), 0); + for (int h = 0; h < currentGroups.size(); h++) { + if (currentGroups[h] == "xxx") { thisCounts[h] = 1; break; } + } + ct->push_back(name, thisCounts); + + group.push_back("xxx"); + } + T->tree[n1].setGroup(group); T->tree[n1].setChildren(-1,-1); if(blen == 1){