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                                 numNodes = T->getNumNodes();
 120                                 numLeaves = T->getNumLeaves();
 121
 122                                 error = readTreeString();
 123
 124                                 //save trees for later commands
 125                                 globaldata->gTree.push_back(T);
 126                                 gobble(filehandle);
 127                         }
 128                 //if you are a nexus file
 129                 }else if ((c = filehandle.peek()) == '#') {
 130                         nexusTranslation();  //reads file through the translation and updates treemap
 131                         while((c = filehandle.peek()) != EOF) {
 132                                 // get past comments
 133                                 while ((c = filehandle.peek()) != EOF) {
 134                                         if(holder == "[" || holder == "[!"){
 135                                                 comment = 1;
 136                                         }
 137                                         if(holder == "]"){
 138                                                 comment = 0;
 139                                         }
 140                                         if((holder == "tree" || holder == "end;") && comment != 1){ holder = ""; comment = 0; break;}
 141                                         filehandle >> holder;
 142                                 }
 143
 144                                 //pass over the "tree rep.6878900 = "
 145                                 while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
 146
 147                                 if (c == EOF ) { break; }
 148                                 filehandle.putback(c);  //put back first ( of tree.
 149
 150                                 //make new tree
 151                                 T = new Tree();
 152                                 numNodes = T->getNumNodes();
 153                                 numLeaves = T->getNumLeaves();
 154
 155                                 //read tree info
 156                                 error = readTreeString();
 157
 158                                 //save trees for later commands
 159                                 globaldata->gTree.push_back(T);
 160                         }
 161                 }
 162
 163                 if (error != 0) { readOk = error; }
 164
 165                 filehandle.close();
 166                 return readOk;
 167         }
 168         catch(exception& e) {
 169                 errorOut(e, "ReadNewickTree", "read");
 170                 exit(1);
 171         }
 172 }
 173 /**************************************************************************************************/
 174 //This function read the file through the translation of the sequences names and updates treemap.
 175 void ReadNewickTree::nexusTranslation() {
 176         try {
 177
 178                 holder = "";
 179                 int numSeqs = globaldata->gTreemap->getNumSeqs(); //must save this some when we clear old names we can still know how many sequences there were
 180                 int comment = 0;
 181
 182                 // get past comments
 183                 while(holder != "translate" && holder != "Translate"){
 184                         if(holder == "[" || holder == "[!"){
 185                                 comment = 1;
 186                         }
 187                         if(holder == "]"){
 188                                 comment = 0;
 189                         }
 190                         filehandle >> holder;
 191                         if(holder == "tree" && comment != 1){return;}
 192                 }
 193
 194                 //update treemap
 195                 globaldata->gTreemap->namesOfSeqs.clear();
 196                 for(int i=0;i<numSeqs;i++){
 197                         string number, name;
 198                         filehandle >> number;
 199                         filehandle >> name;
 200                         name.erase(name.end()-1);  //erase the comma
 201                         //insert new one with new name
 202                         globaldata->gTreemap->treemap[toString(number)].groupname = globaldata->gTreemap->treemap[name].groupname;
 203                         globaldata->gTreemap->treemap[toString(number)].vectorIndex = globaldata->gTreemap->treemap[name].vectorIndex;
 204                         //erase old one.  so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
 205                         globaldata->gTreemap->treemap.erase(name);
 206                         globaldata->gTreemap->namesOfSeqs.push_back(number);
 207                 }
 208         }
 209         catch(exception& e) {
 210                 errorOut(e, "ReadNewickTree", "nexusTranslation");
 211                 exit(1);
 212         }
 213 }
 214
 215 /**************************************************************************************************/
 216 int ReadNewickTree::readTreeString() {
 217         try {
 218
 219                 int n = 0;
 220                 int lc, rc;
 221
 222                 int rooted = 0;
 223
 224                 int ch = filehandle.peek();
 225
 226                 if(ch == '('){
 227                         n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 228
 229                         lc = readNewickInt(filehandle, n, T);
 230                         if (lc == -1) { mothurOut("error with lc"); mothurOutEndLine(); return -1; } //reports an error in reading
 231
 232                         if(filehandle.peek()==','){
 233                                 readSpecialChar(filehandle,',',"comma");
 234                         }
 235                         // ';' means end of tree.
 236                         else if((ch=filehandle.peek())==';' || ch=='['){
 237                                 rooted = 1;
 238                         }
 239                         if(rooted != 1){
 240                                 rc = readNewickInt(filehandle, n, T);
 241                                 if (rc == -1) { mothurOut("error with rc"); mothurOutEndLine(); return -1; } //reports an error in reading
 242                                 if(filehandle.peek() == ')'){
 243                                         readSpecialChar(filehandle,')',"right parenthesis");
 244                                 }
 245                         }
 246                 }
 247                 //note: treeclimber had the code below added - not sure why?
 248                 else{
 249                         filehandle.putback(ch);
 250                         char name[MAX_LINE];
 251                         filehandle.get(name, MAX_LINE,'\n');
 252                         SKIPLINE(filehandle, ch);
 253
 254                         n = T->getIndex(name);
 255
 256                         if(n!=0){
 257                                 mothurOut("Internal error: The only taxon is not taxon 0.\n");
 258                                 //exit(1);
 259                                 readOk = -1; return -1;
 260                         }
 261                         lc = rc = -1;
 262                 }
 263
 264                 while(((ch=filehandle.get())!=';') && (filehandle.eof() != true)){;}
 265                 if(rooted != 1){
 266                         T->tree[n].setChildren(lc,rc);
 267                         T->tree[n].setBranchLength(0);
 268                         T->tree[n].setParent(-1);
 269                         if(lc!=-1){             T->tree[lc].setParent(n);               }
 270                         if(rc!=-1){             T->tree[rc].setParent(n);               }
 271                 }
 272                 return 0;
 273
 274         }
 275         catch(exception& e) {
 276                 errorOut(e, "ReadNewickTree", "readTreeString");
 277                 exit(1);
 278         }
 279 }
 280 /**************************************************************************************************/
 281
 282 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 283         try {
 284                 int c = readNodeChar(f);
 285
 286                 if(c == '('){
 287                         int lc = readNewickInt(f, n, T);
 288                         if (lc == -1) { return -1; } //reports an error in reading
 289                         readSpecialChar(f,',',"comma");
 290
 291                         int rc = readNewickInt(f, n, T);
 292                         if (rc == -1) { return -1; }  //reports an error in reading
 293                         if(f.peek()==')'){
 294                                 readSpecialChar(f,')',"right parenthesis");
 295                                 //to pass over labels in trees
 296                                 c=filehandle.get();
 297                                 while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
 298                                 filehandle.putback(c);
 299
 300                         }
 301
 302                         if(f.peek() == ':'){
 303                                 readSpecialChar(f,':',"colon");
 304
 305                                 if(n >= numNodes){      mothurOut("Error: Too many nodes in input tree\n");  readOk = -1; return -1; }
 306
 307                                 T->tree[n].setBranchLength(readBranchLength(f));
 308                         }else{
 309                                 T->tree[n].setBranchLength(0.0);
 310                         }
 311
 312                         T->tree[n].setChildren(lc,rc);
 313                         T->tree[lc].setParent(n);
 314                         T->tree[rc].setParent(n);
 315
 316                         return n++;
 317                 }else{
 318                         f.putback(c);
 319                         string name = "";
 320                         char d=f.get();
 321                         while(d != ':' && d != ',' && d!=')' && d!='\n'){
 322                                 name += d;
 323                                 d=f.get();
 324                         }
 325
 326                         int blen = 0;
 327                         if(d == ':')    {               blen = 1;       }
 328
 329                         f.putback(d);
 330
 331                         //set group info
 332                         string group = globaldata->gTreemap->getGroup(name);
 333
 334                         //find index in tree of name
 335                         int n1 = T->getIndex(name);
 336
 337                         //adds sequence names that are not in group file to the "xxx" group
 338                         if(group == "not found") {
 339                                 mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n");  //readOk = -1; return n1;
 340
 341                                 globaldata->gTreemap->namesOfSeqs.push_back(name);
 342                                 globaldata->gTreemap->treemap[name].groupname = "xxx";
 343
 344                                 map<string, int>::iterator it;
 345                                 it = globaldata->gTreemap->seqsPerGroup.find("xxx");
 346                                 if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
 347                                         globaldata->gTreemap->namesOfGroups.push_back("xxx");
 348                                         globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
 349                                 }else {
 350                                         globaldata->gTreemap->seqsPerGroup["xxx"]++;
 351                                 }
 352
 353                                 group = "xxx";
 354                         }
 355
 356                         T->tree[n1].setGroup(group);
 357                         T->tree[n1].setChildren(-1,-1);
 358
 359                         if(blen == 1){
 360                                 f.get();
 361                                 T->tree[n1].setBranchLength(readBranchLength(f));
 362                         }else{
 363                                 T->tree[n1].setBranchLength(0.0);
 364                         }
 365
 366                         while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )              {;}
 367                         f.putback(c);
 368
 369                         return n1;
 370                 }
 371         }
 372         catch(exception& e) {
 373                 errorOut(e, "ReadNewickTree", "readNewickInt");
 374                 exit(1);
 375         }
 376 }
 377 /**************************************************************************************************/
 378 /**************************************************************************************************/
 379