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