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                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  20                 exit(1);
  21         }
  22         catch(...) {
  23                 cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26 }
  27 /***********************************************************************/
  28 int ReadTree::readSpecialChar(istream& f, char c, string name) {
  29     try {
  30                 char d;
  31
  32                 while(isspace(d=f.get()))               {;}
  33                 if(d == EOF){
  34                         cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
  35                         exit(1);
  36                 }
  37                 if(d != c){
  38                         cerr << "Error: Expected " << name << " in input file.  Found " << d << ".\n";
  39                         exit(1);
  40                 }
  41                 if(d == ')' && f.peek() == '\n'){
  42                         while(isspace(d=f.get()))               {;}
  43                         f.putback(d);
  44                 }
  45
  46                 return d;
  47         }
  48         catch(exception& e) {
  49                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readSpecialChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  50                 exit(1);
  51         }
  52         catch(...) {
  53                 cout << "An unknown error has occurred in the ReadTree class function readSpecialChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56 }
  57 /**************************************************************************************************/
  58
  59 int ReadTree::readNodeChar(istream& f) {
  60         try {
  61                 char d;
  62                 while(isspace(d=f.get()))               {;}
  63                 if(d == EOF){
  64                         cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
  65                         exit(1);
  66                 }
  67                 return d;
  68         }
  69         catch(exception& e) {
  70                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readNodeChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  71                 exit(1);
  72         }
  73         catch(...) {
  74                 cout << "An unknown error has occurred in the ReadTree class function readNodeChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  75                 exit(1);
  76         }
  77 }
  78
  79 /**************************************************************************************************/
  80
  81 float ReadTree::readBranchLength(istream& f) {
  82     try {
  83                 float b;
  84
  85                 if(!(f >> b)){
  86                         cerr << "Error: Missing branch length in input tree.\n";
  87                         exit(1);
  88                 }
  89
  90                 return b;
  91         }
  92         catch(exception& e) {
  93                 cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readBranchLength. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  94                 exit(1);
  95         }
  96         catch(...) {
  97                 cout << "An unknown error has occurred in the ReadTree class function readBranchLength. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  98                 exit(1);
  99         }
 100 }
 101
 102
 103 /***********************************************************************/
 104 /***********************************************************************/
 105
 106
 107 //Child Classes Below
 108
 109 /***********************************************************************/
 110 /***********************************************************************/
 111 //This class reads a file in Newick form and stores it in a tree.
 112
 113 void ReadNewickTree::read() {
 114         try {
 115                 int c;
 116                 int comment = 0;
 117
 118                 //if you are not a nexus file
 119                 if ((c = filehandle.peek()) != '#') {
 120                         while((c = filehandle.peek()) != EOF) {
 121                                 //make new tree
 122                                 T = new Tree();
 123                                 numNodes = T->getNumNodes();
 124                                 numLeaves = T->getNumLeaves();
 125
 126                                 readTreeString();
 127                                 //save trees for later commands
 128                                 globaldata->gTree.push_back(T);
 129                         }
 130                 //if you are a nexus file
 131                 }else if ((c = filehandle.peek()) == '#') {
 132                         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                                 readTreeString();
 159                                 //save trees for later commands
 160                                 globaldata->gTree.push_back(T);
 161                         }
 162                 }
 163
 164         }
 165         catch(exception& e) {
 166                 cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 167                 exit(1);
 168         }
 169         catch(...) {
 170                 cout << "An unknown error has occurred in the ReadNewickTree class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 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                 cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function nexus. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 212                 exit(1);
 213         }
 214         catch(...) {
 215                 cout << "An unknown error has occurred in the ReadNewickTree class function nexus. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 216                 exit(1);
 217         }
 218 }
 219
 220 /**************************************************************************************************/
 221 void ReadNewickTree::readTreeString() {
 222         try {
 223
 224                 int n = 0;
 225                 int lc, rc;
 226
 227                 int rooted = 0;
 228
 229                 int ch = filehandle.peek();
 230
 231                 if(ch == '('){
 232                         n = numLeaves;  //number of leaves / sequences, we want node 1 to start where the leaves left off
 233                         lc = readNewickInt(filehandle, n, T);
 234
 235                         if(filehandle.peek()==','){
 236                                 readSpecialChar(filehandle,',',"comma");
 237                         }
 238                         // ';' means end of tree.
 239                         else if((ch=filehandle.peek())==';' || ch=='['){
 240                                 rooted = 1;
 241                         }
 242                         if(rooted != 1){
 243                                 rc = readNewickInt(filehandle, n, T);
 244                                 if(filehandle.peek() == ')'){
 245                                         readSpecialChar(filehandle,')',"right parenthesis");
 246                                 }
 247                         }
 248                 }
 249                 //note: treeclimber had the code below added - not sure why?
 250                 else{
 251                         filehandle.putback(ch);
 252                         char name[MAX_LINE];
 253                         filehandle.get(name, MAX_LINE,'\n');
 254                         SKIPLINE(filehandle, ch);
 255
 256
 257                         n = T->getIndex(name);
 258                         if(n!=0){
 259                                 cerr << "Internal error: The only taxon is not taxon 0.\n";
 260                                 exit(1);
 261                         }
 262                         lc = rc = -1;
 263                 }
 264
 265                 while((ch=filehandle.get())!=';'){;}
 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
 274         }
 275         catch(exception& e) {
 276                 cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 277                 exit(1);
 278         }
 279         catch(...) {
 280                 cout << "An unknown error has occurred in the ReadNewickTree class function readTreeString. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 281                 exit(1);
 282         }
 283
 284 }
 285 /**************************************************************************************************/
 286
 287 int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
 288         try {
 289                 int c = readNodeChar(f);
 290
 291                 if(c == '('){
 292                         int lc = readNewickInt(f, n, T);
 293                         readSpecialChar(f,',',"comma");
 294
 295                         int rc = readNewickInt(f, n, T);
 296                         if(f.peek()==')'){
 297                                 readSpecialChar(f,')',"right parenthesis");
 298                         }
 299
 300                         if(f.peek() == ':'){
 301                                 readSpecialChar(f,':',"colon");
 302                                 if(n >= numNodes){      cerr << "Error: Too many nodes in input tree\n";  exit(1); }
 303                                 T->tree[n].setBranchLength(readBranchLength(f));
 304                         }else{T->tree[n].setBranchLength(0.0); }
 305
 306                         T->tree[n].setChildren(lc,rc);
 307                         T->tree[lc].setParent(n);
 308                         T->tree[rc].setParent(n);
 309
 310                         return n++;
 311                 }else{
 312                         f.putback(c);
 313                         string name = "";
 314                         char d=f.get();
 315                         while(d != ':' && d != ',' && d!=')' && d!='\n'){
 316                                 name += d;
 317                                 d=f.get();
 318                         }
 319
 320                         int blen = 0;
 321                         if(d == ':')    {               blen = 1;                       }
 322
 323                         f.putback(d);
 324
 325                         //set group info
 326                         string group = globaldata->gTreemap->getGroup(name);
 327
 328                         //find index in tree of name
 329                         int n1 = T->getIndex(name);
 330
 331                         if(n1 == -1){cerr << "Name: " << name << " not found\n"; exit(1);}
 332
 333                         else T->tree[n1].setGroup(group);
 334
 335                         T->tree[n1].setChildren(-1,-1);
 336
 337                         if(blen == 1){
 338                                 f.get();
 339                                 T->tree[n1].setBranchLength(readBranchLength(f));
 340                         }else{
 341                                 T->tree[n1].setBranchLength(0.0);
 342                         }
 343
 344                         while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') )              {;}
 345                         f.putback(c);
 346
 347                         return n1;
 348                 }
 349         }
 350         catch(exception& e) {
 351                 cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 352                 exit(1);
 353         }
 354         catch(...) {
 355                 cout << "An unknown error has occurred in the ReadNewickTree class function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 356                 exit(1);
 357         }
 358 }
 359 /**************************************************************************************************/
 360 /**************************************************************************************************/
 361