+int ReadColumnMatrix::read(CountTable* countTable){
+ try {
+
+ string firstName, secondName;
+ float distance;
+ int nseqs = countTable->size();
+
+ DMatrix->resize(nseqs);
+ list = new ListVector(countTable->getListVector());
+
+ Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int lt = 1;
+ int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+ int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
+
+ //need to see if this is a square or a triangular matrix...
+
+ while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
+
+
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; // get the row and column names and distance
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ int itA = countTable->get(firstName);
+ int itB = countTable->get(secondName);
+
+ if (m->control_pressed) { exit(1); }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && itA != itB){
+ if(itA > itB){
+ PDistCell value(itA, distance);
+
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+ DMatrix->addCell(itB, value);
+ }
+ else if(refRow == itA && refCol == itB){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itB, value);
+ }
+ }
+ else if(itA < itB){
+ PDistCell value(itB, distance);
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+ DMatrix->addCell(itA, value);
+ }
+ else if(refRow == itB && refCol == itA){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itA, value);
+ }
+ }
+ reading->update(itA * nseqs);
+ }
+ m->gobble(fileHandle);
+ }
+
+ if(lt == 0){ // oops, it was square
+
+ fileHandle.close(); //let's start over
+ DMatrix->clear(); //let's start over
+
+ m->openInputFile(distFile, fileHandle); //let's start over
+
+ while(fileHandle){
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; // get the row and column names and distance
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ int itA = countTable->get(firstName);
+ int itB = countTable->get(secondName);
+
+
+ if (m->control_pressed) { exit(1); }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && itA > itB){
+ PDistCell value(itA, distance);
+ DMatrix->addCell(itB, value);
+ reading->update(itA * nseqs);
+ }
+
+ m->gobble(fileHandle);
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ fileHandle.close();
+
+ list->setLabel("0");
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadColumnMatrix", "read");
+ exit(1);
+ }