made make.table alias to count.seqs command. added large parameter to count.seqs...

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index 1cf9fc325b0ecdc5d222ded20346f79134f3b6b7..b6cb71de5fdbb888f4a7c1614987f74cd0bf8b1a 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -11,22 +11,29 @@
 
 /***********************************************************************/
 
-ReadCluster::ReadCluster(string distfile, float c){
-               globaldata = GlobalData::getInstance();
+ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
                m = MothurOut::getInstance();
         distFile = distfile;
                cutoff = c;
+               outputDir = o;
+               sortWanted = s;
+               list = NULL;
 }
 
 /***********************************************************************/
 
-void ReadCluster::read(NameAssignment* nameMap){
+int ReadCluster::read(NameAssignment*& nameMap){
        try {
         
                if (format == "phylip") { convertPhylip2Column(nameMap); }
                else { list = new ListVector(nameMap->getListVector());  }
                
-               OutPutFile = sortFile(distFile);
+               if (m->control_pressed) { return 0; }
+               
+               if (sortWanted) {  OutPutFile = m->sortFile(distFile, outputDir);  }
+               else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
+               
+               return 0;
                        
        }
        catch(exception& e) {
@@ -36,7 +43,7 @@ void ReadCluster::read(NameAssignment* nameMap){
 }
 /***********************************************************************/
 
-void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
+int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
        try {   
                //convert phylip file to column file
                map<int, string> rowToName;
@@ -46,15 +53,20 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                ofstream out;
                string tempFile = distFile + ".column.temp";
                
-               openInputFile(distFile, in);
-               openOutputFile(tempFile, out);
+               m->openInputFile(distFile, in);  m->gobble(in);
+               m->openOutputFile(tempFile, out);
                
                float distance;
                int square, nseqs;
                string name;
                vector<string> matrixNames;
-        
-               in >> nseqs >> name;
+               
+               string numTest;
+               in >> numTest >> name;
+               
+               if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+               else { convert(numTest, nseqs); }
+               
                rowToName[0] = name;
                matrixNames.push_back(name);
                
@@ -96,6 +108,9 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                                        list->set(i, name);
                                        
                                        for(int j=0;j<i;j++){
+                                       
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+                                               
                                                in >> distance;
                                                
                                                if (distance == -1) { distance = 1000000; }
@@ -110,6 +125,9 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                                        if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                        
                                        for(int j=0;j<i;j++){
+                                               
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+                                               
                                                in >> distance;
                                                
                                                if (distance == -1) { distance = 1000000; }
@@ -130,6 +148,8 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                                if(nameMap == NULL){
                                        list->set(i, name);
                                        for(int j=0;j<nseqs;j++){
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+                                               
                                                in >> distance;
                                        
                                                if (distance == -1) { distance = 1000000; }
@@ -143,6 +163,8 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                                        if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                        
                                        for(int j=0;j<nseqs;j++){
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
+                                               
                                                in >> distance;
                         
                                                if (distance == -1) { distance = 1000000; }
@@ -159,36 +181,41 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                list->setLabel("0");
                in.close();
                out.close();
-               
+       
                if(nameMap == NULL){
                        nameMap = new NameAssignment();
                        for(int i=0;i<matrixNames.size();i++){
                                nameMap->push_back(matrixNames[i]);
                        }
-                       globaldata->nameMap = nameMap;
                }
                
        
                ifstream in2;
                ofstream out2;
                
-               string outputFile = getRootName(distFile) + "column.dist";
-               openInputFile(tempFile, in2);
-               openOutputFile(outputFile, out2);
+               string outputFile = m->getRootName(distFile) + "column.dist";
+               m->openInputFile(tempFile, in2);
+               m->openOutputFile(outputFile, out2);
                
                int first, second;
                float dist;
                
                while (in2) {
+                       if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(tempFile); m->mothurRemove(outputFile); return 0; }
+                       
                        in2 >> first >> second >> dist;
                        out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
-                       gobble(in2);
+                       m->gobble(in2);
                }
                in2.close();
                out2.close();
                
-               remove(tempFile.c_str());
+               m->mothurRemove(tempFile);
                distFile = outputFile;
+       
+               if (m->control_pressed) {  m->mothurRemove(outputFile);  }
+
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "ReadCluster", "convertPhylip2Column");