readtree.cpp

   1 /*
   2  *  readtree.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/22/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readtree.h"
  11
  12 /***********************************************************************/
  13 ReadTree::ReadTree() {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 m = MothurOut::getInstance();
  17                 globaldata->gTree.clear();
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "ReadTree", "ReadTree");
  21                 exit(1);
  22         }
  23 }
  24 /***********************************************************************/
  25 int ReadTree::readSpecialChar(istream& f, char c, string name) {
  26     try {
  27
  28                 m->gobble(f);
  29                 char d = f.get();
  30
  31                 if(d == EOF){
  32                         m->mothurOut("Error: Input file ends prematurely, expecting a " + name + "\n");
  33                         exit(1);
  34                 }
  35                 if(d != c){
  36                         m->mothurOut("Error: Expected " + name + " in input file.  Found " + toString(d) + ".\n");
  37                         exit(1);
  38                 }
  39                 if(d == ')' && f.peek() == '\n'){
  40                         m->gobble(f);
  41                 }
  42                 return d;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "ReadTree", "readSpecialChar");
  46                 exit(1);
  47         }
  48 }
  49 /**************************************************************************************************/
  50
  51 int ReadTree::readNodeChar(istream& f) {
  52         try {
  53 //              while(isspace(d=f.get()))               {;}
  54                 m->gobble(f);
  55                 char d = f.get();
  56
  57                 if(d == EOF){
  58                         m->mothurOut("Error: Input file ends prematurely, expecting a left parenthesis\n");
  59                         exit(1);
  60                 }
  61                 return d;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "ReadTree", "readNodeChar");
  65                 exit(1);
  66         }
  67 }
  68
  69 /**************************************************************************************************/
  70
  71 float ReadTree::readBranchLength(istream& f) {
  72     try {
  73                 float b;
  74
  75                 if(!(f >> b)){
  76                         m->mothurOut("Error: Missing branch length in input tree.\n");
  77                         exit(1);
  78                 }
  79                 m->gobble(f);
  80                 return b;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "ReadTree", "readBranchLength");
  84                 exit(1);
  85         }
  86 }
  87
  88 /***********************************************************************/
  89 /***********************************************************************/
  90
  91 //Child Classes Below
  92
  93 /***********************************************************************/
  94 /***********************************************************************/
  95 //This class reads a file in Newick form and stores it in a tree.
  96
  97 int ReadNewickTree::read() {
  98         try {
  99                 holder = "";
 100                 int c, error;
 101                 int comment = 0;
 102
 103                 //if you are not a nexus file
 104                 if ((c = filehandle.peek()) != '#') {
 105                         while((c = filehandle.peek()) != EOF) {
 106                                 while ((c = filehandle.peek()) != EOF) {
 107                                         // get past comments
 108                                         if(c == '[') {
 109                                                 comment = 1;
 110                                         }
 111                                         if(c == ']'){
 112                                                 comment = 0;
 113                                         }
 114                                         if((c == '(') && (comment != 1)){ break; }
 115                                         filehandle.get();
 116                                 }
 117
 118                                 //make new tree
 119                                 T = new Tree();
 120
 121                                 numNodes = T->getNumNodes();
 122                                 numLeaves = T->getNumLeaves();
 123
 124                                 error = readTreeString();
 125
 126                                 //save trees for later commands
 127                                 globaldata->gTree.push_back(T);
 128                                 m->gobble(filehandle);
 129                         }
 130                 //if you are a nexus file
 131                 }else if ((c = filehandle.peek()) == '#') {
 132                         holder = nexusTranslation();  //reads file through the translation and updates treemap
 133                         while((c = filehandle.peek()) != EOF) {
 134                                 // get past comments
 135                                 while ((c = filehandle.peek()) != EOF) {
 136                                         if(holder == "[" || holder == "[!"){
 137                                                 comment = 1;
 138                                         }
 139                                         if(holder == "]"){
 140                                                 comment = 0;
 141                                         }
 142                                         if((holder == "tree" || holder == "end;") && comment != 1){ holder = ""; comment = 0; break;}
 143                                         filehandle >> holder;
 144                                 }
 145
 146                                 //pass over the "tree rep.6878900 = "
 147                                 while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 148
 149                                 if (c == EOF ) { break; }
 150                                 filehandle.putback(c);  //put back first ( of tree.
 151
 152                                 //make new tree
 153                                 T = new Tree();
 154                                 numNodes = T->getNumNodes();
 155                                 numLeaves = T->getNumLeaves();
 156
 157                                 //read tree info
 158                                 error = readTreeString();
 159
 160                                 //save trees for later commands
 161                                 globaldata->gTree.push_back(T);
 162                         }
 163                 }
 164
 165                 if (error != 0) { readOk = error; }
 166
 167                 filehandle.close();
 168
 169                 return readOk;
 170         }
 171         catch(exception& e) {
 172                 m->errorOut(e, "ReadNewickTree", "read");
 173                 exit(1);
 174         }
 175 }
 176 /**************************************************************************************************/
 177 //This function read the file through the translation of the sequences names and updates treemap.
 178 string ReadNewickTree::nexusTranslation() {
 179         try {
 180
 181                 holder = "";
 182                 //int numSeqs = globaldata->gTreemap->getNumSeqs(); //must save this some when we clear old names we can still know how many sequences there were
 183                 int comment = 0;
 184
 185                 // get past comments
 186                 while(holder != "translate" && holder != "Translate"){
 187                         if(holder == "[" || holder == "[!"){
 188                                 comment = 1;
 189                         }
 190                         if(holder == "]"){
 191                                 comment = 0;
 192                         }
 193                         filehandle >> holder;
 194                         if(holder == "tree" && comment != 1){return holder;}
 195                 }
 196
 197                 //update treemap
 198                 globaldata->gTreemap->namesOfSeqs.clear();
 199
 200                 char c;
 201                 string number, name;
 202                 while ((c = filehandle.peek()) != EOF) {
 203
 204                         filehandle >> number;
 205
 206                         if ((number == "tree") || (number == ";") ) {  name = number; break;  }
 207
 208                         filehandle >> name;
 209
 210                         char lastChar;
 211                         if (name.length() != 0) { lastChar = name[name.length()-1]; }
 212
 213                         if ((name == "tree") || (name == ";") ) {  break;  }
 214
 215                         if (lastChar == ',') {  name.erase(name.end()-1); } //erase the comma
 216
 217                         //insert new one with new name
 218                         string group = globaldata->gTreemap->getGroup(name);
 219                         globaldata->gTreemap->treemap[toString(number)].groupname = group;
 220                         globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->getIndex(name);
 221                         //erase old one.  so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
 222                         globaldata->gTreemap->treemap.erase(name);
 223                         globaldata->gTreemap->namesOfSeqs.push_back(number);
 224                 }
 225
 226                 return name;
 227         }
 228         catch(exception& e) {
 229                 m->errorOut(e, "ReadNewickTree", "nexusTranslation");
 230                 exit(1);
 231         }
 232 }
 233
 234 /**************************************************************************************************/
 235 int ReadNewickTree::readTreeString() {
 236         try {
 237
 238                 int n = 0;
 239                 int lc, rc;
 240
 241                 int rooted = 0;
 242
 243                 int ch = filehandle.peek();
 244
 245                 if(ch == '('){
 246                         n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 247
 248                         lc = readNewickInt(filehandle, n, T);
 249                         if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
 250
 251                         if(filehandle.peek()==','){
 252                                 readSpecialChar(filehandle,',',"comma");
 253                         }
 254                         // ';' means end of tree.
 255                         else if((ch=filehandle.peek())==';' || ch=='['){
 256                                 rooted = 1;
 257                         }
 258
 259                         if(rooted != 1){
 260                                 rc = readNewickInt(filehandle, n, T);
 261                                 if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
 262                                 if(filehandle.peek() == ')'){
 263                                         readSpecialChar(filehandle,')',"right parenthesis");
 264                                 }
 265                         }
 266                 }
 267                 //note: treeclimber had the code below added - not sure why?
 268                 else{
 269                         filehandle.putback(ch);
 270                         char name[MAX_LINE];
 271                         filehandle.get(name, MAX_LINE,'\n');
 272                         SKIPLINE(filehandle, ch);
 273
 274                         n = T->getIndex(name);
 275
 276                         if(n!=0){
 277                                 m->mothurOut("Internal error: The only taxon is not taxon 0.\n");
 278                                 //exit(1);
 279                                 readOk = -1; return -1;
 280                         }
 281                         lc = rc = -1;
 282                 }
 283
 284                 while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}
 285
 286                 if(rooted != 1){
 287                         T->tree[n].setChildren(lc,rc);
 288                         T->tree[n].setBranchLength(0);
 289                         T->tree[n].setParent(-1);
 290                         if(lc!=-1){             T->tree[lc].setParent(n);               }
 291                         if(rc!=-1){             T->tree[rc].setParent(n);               }
 292                 }
 293
 294                 //T->printTree(); cout << endl;
 295                 return 0;
 296
 297         }
 298         catch(exception& e) {
 299                 m->errorOut(e, "ReadNewickTree", "readTreeString");
 300                 exit(1);
 301         }
 302 }
 303 /**************************************************************************************************/
 304
 305 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 306         try {
 307
 308                 if (m->control_pressed) { return -1; }
 309
 310                 int c = readNodeChar(f);
 311
 312                 if(c == '('){
 313
 314                         //to account for multifurcating trees generated by fasttree, we are forcing them to be bifurcating
 315                         //read all children
 316                         vector<int> childrenNodes;
 317                         while(f.peek() != ')'){
 318                                 int child = readNewickInt(f, n, T);
 319                                 if (child == -1) { return -1; } //reports an error in reading
 320                 //cout << "child = " << child << endl;
 321                                 childrenNodes.push_back(child);
 322
 323                                 //after a child you either have , or ), check for both
 324                                 if(f.peek()==')'){  break;  }
 325                                 else if (f.peek()==',') {   readSpecialChar(f,',',"comma");  }
 326                                 else {;}
 327                         }
 328         //cout << childrenNodes.size() << endl;
 329                         if (childrenNodes.size() < 2) {  m->mothurOut("Error in tree, please correct."); m->mothurOutEndLine(); return -1; }
 330
 331                         //then force into 2 node structure
 332                         for (int i = 1; i < childrenNodes.size(); i++) {
 333
 334                                 int lc, rc;
 335                                 if (i == 1) { lc = childrenNodes[i-1]; rc = childrenNodes[i]; }
 336                                 else { lc = n-1; rc = childrenNodes[i]; }
 337                         //cout << i << '\t' << lc << '\t' << rc << endl;
 338                                 T->tree[n].setChildren(lc,rc);
 339                                 T->tree[lc].setParent(n);
 340                                 T->tree[rc].setParent(n);
 341
 342                                 //T->printTree(); cout << endl;
 343                                 n++;
 344                         }
 345
 346                         //to account for extra ++ in looping
 347                         n--;
 348
 349                         if(f.peek()==')'){
 350                                 readSpecialChar(f,')',"right parenthesis");
 351                                 //to pass over labels in trees
 352                                 c=filehandle.get();
 353                                 while((c!=',') && (c != -1) && (c!= ':') && (c!=';')&& (c!=')')){ c=filehandle.get(); }
 354                                 filehandle.putback(c);
 355                         }
 356
 357                         if(f.peek() == ':'){
 358                                 readSpecialChar(f,':',"colon");
 359
 360                                 if(n >= numNodes){ m->mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
 361
 362                                 T->tree[n].setBranchLength(readBranchLength(f));
 363                         }else{
 364                                 T->tree[n].setBranchLength(0.0);
 365                         }
 366
 367                         //T->tree[n].setChildren(lc,rc);
 368                         //T->tree[lc].setParent(n);
 369                         //T->tree[rc].setParent(n);
 370                         //T->printTree();  cout << endl;
 371
 372                         return n++;
 373
 374                 }else{
 375                         f.putback(c);
 376                         string name = "";
 377                         char d=f.get();
 378                         while(d != ':' && d != ',' && d!=')' && d!='\n'){
 379                                 name += d;
 380                                 d=f.get();
 381                         }
 382 //cout << name << endl;
 383                         int blen = 0;
 384                         if(d == ':')    {               blen = 1;       }
 385
 386                         f.putback(d);
 387
 388                         //set group info
 389                         string group = globaldata->gTreemap->getGroup(name);
 390
 391                         //find index in tree of name
 392                         int n1 = T->getIndex(name);
 393
 394                         //adds sequence names that are not in group file to the "xxx" group
 395                         if(group == "not found") {
 396                                 m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
 397
 398                                 globaldata->gTreemap->namesOfSeqs.push_back(name);
 399                                 globaldata->gTreemap->treemap[name].groupname = "xxx";
 400
 401                                 map<string, int>::iterator it;
 402                                 it = globaldata->gTreemap->seqsPerGroup.find("xxx");
 403                                 if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
 404                                         globaldata->gTreemap->namesOfGroups.push_back("xxx");
 405                                         globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
 406                                 }else {
 407                                         globaldata->gTreemap->seqsPerGroup["xxx"]++;
 408                                 }
 409
 410                                 group = "xxx";
 411                         }
 412
 413                         vector<string> tempGroup; tempGroup.push_back(group);
 414
 415                         T->tree[n1].setGroup(tempGroup);
 416                         T->tree[n1].setChildren(-1,-1);
 417
 418                         if(blen == 1){
 419                                 f.get();
 420                                 T->tree[n1].setBranchLength(readBranchLength(f));
 421                         }else{
 422                                 T->tree[n1].setBranchLength(0.0);
 423                         }
 424
 425                         while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )              {;}
 426
 427                         f.putback(c);
 428
 429                         return n1;
 430                 }
 431         }
 432         catch(exception& e) {
 433                 m->errorOut(e, "ReadNewickTree", "readNewickInt");
 434                 exit(1);
 435         }
 436 }
 437 /**************************************************************************************************/
 438 /**************************************************************************************************/
 439