Thallinger changes to cluster command.

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 088f711e0d6dd6f191493bbaf802db3a7bae1fbb..579f848bdb75b10b1350d1eb61b589de8f543ee0 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -70,7 +70,7 @@ ReadDistCommand::ReadDistCommand(string option){
                        else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a read.dist command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
                
                        if (columnfile != "") {
-                               if (namefile == "") {  mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
+                               if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
                        }
                
                        //check for optional parameter and set defaults
@@ -129,7 +129,7 @@ void ReadDistCommand::help(){
                mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
                mothurOut("The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command.\n");
                mothurOut("For this use the read.dist command should be in the following format: \n");
-               mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use. \n");
+               mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use.  \n");
                mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile).\n\n");
        }
        catch(exception& e) {
@@ -141,6 +141,9 @@ void ReadDistCommand::help(){
 //**********************************************************************************************************************
 
 ReadDistCommand::~ReadDistCommand(){
+       if (abort == false) {
+               if (format != "matrix") { delete read; delete nameMap; }
+       }
 }
 
 //**********************************************************************************************************************
@@ -148,6 +151,9 @@ int ReadDistCommand::execute(){
        try {
                
                if (abort == true) {    return 0;       }
+
+               time_t start = time(NULL);
+               size_t numDists = 0;
                
                if (format == "matrix") {
                        ifstream in;
@@ -157,7 +163,8 @@ int ReadDistCommand::execute(){
                        //memory leak prevention
                        if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
                        globaldata->gMatrix = matrix; //save matrix for coverage commands
-               }else {
+                       numDists = matrix->getSizes()[1];
+               } else {
                        read->read(nameMap);
                        //to prevent memory leak
 
@@ -166,10 +173,36 @@ int ReadDistCommand::execute(){
 
                        if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix;  }
                        globaldata->gSparseMatrix = read->getMatrix();
-                       delete read; delete nameMap;
+                       numDists = globaldata->gSparseMatrix->getNNodes();
+ 
+      int lines = cutoff / (1.0/precision);
+      vector<float> dist_cutoff(lines+1,0);
+                       for (int i = 0; i <= lines;i++) {       
+       dist_cutoff[i] = (i + 0.5) / precision; 
+      } 
+      vector<int> dist_count(lines+1,0);
+      list<PCell>::iterator currentCell;
+      SparseMatrix* smatrix = globaldata->gSparseMatrix;
+               for (currentCell = smatrix->begin(); currentCell != smatrix->end(); currentCell++) {
+                               for (int i = 0; i <= lines;i++) {       
+                                       if (currentCell->dist < dist_cutoff[i]) {
+                                               dist_count[i]++;
+            break;
+          }
+        }
+                       }
 
+      string dist_string = "Dist:";
+      string count_string = "Count: ";
+                       for (int i = 0; i <= lines;i++) {       
+       dist_string = dist_string.append("\t").append(toString(dist_cutoff[i]));
+       count_string = count_string.append("\t").append(toString(dist_count[i]));
+                       }
+      mothurOut(dist_string); mothurOutEndLine(); mothurOut(count_string); mothurOutEndLine();
                }
+               mothurOut("It took " + toString(time(NULL) - start) + " secs to read " + toString(numDists) + " distances (cutoff: " + toString(cutoff) + ")"); mothurOutEndLine();
                return 0;
+               
        }
        catch(exception& e) {
                errorOut(e, "ReadDistCommand", "execute");