added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / clusterclassic.cpp

diff --git a/clusterclassic.cpp b/clusterclassic.cpp
index 287332ad628e33a6a460aee903ba8f7955027c85..0048dc6053d0bab06130eeaa6ab5d10b576aeb48 100644 (file)
--- a/clusterclassic.cpp
+++ b/clusterclassic.cpp
@@ -11,7 +11,7 @@
 #include "progress.hpp"
 
 /***********************************************************************/
-ClusterClassic::ClusterClassic(float c, string f) : method(f), smallDist(1e6), nseqs(0) {
+ClusterClassic::ClusterClassic(float c, string f, bool s) : method(f), smallDist(1e6), nseqs(0), sim(s) {
        try {
                mapWanted = false;  //set to true by mgcluster to speed up overlap merge
        
@@ -19,7 +19,6 @@ ClusterClassic::ClusterClassic(float c, string f) : method(f), smallDist(1e6), n
                cutoff = c;
                aboveCutoff = cutoff + 10000.0;
                m = MothurOut::getInstance();
-               globaldata = GlobalData::getInstance();
        }
        catch(exception& e) {
                m->errorOut(e, "ClusterClassic", "ClusterClassic");
@@ -102,7 +101,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
                                                                                fileHandle >> distance;
                                                        
                                                                                if (distance == -1) { distance = 1000000; }
-                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                                
                                                                                //if(distance < cutoff){
                                                                                        dMatrix[i][j] = distance;
@@ -124,7 +123,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
                                                                                if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
                                
                                                                                if (distance == -1) { distance = 1000000; }
-                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                                                
                                                                                //if(distance < cutoff){
                                                                                        if (distance < smallDist) { smallDist = distance; }
@@ -162,7 +161,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
                                                                                if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
                                                                                
                                                                                if (distance == -1) { distance = 1000000; }
-                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
+                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
                                                                                
                                                                                if(j < i){
                                                                                        if (distance < smallDist) { smallDist = distance; }
@@ -185,7 +184,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
                                                                                if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
                                                                                
                                                                           if (distance == -1) { distance = 1000000; }
-                                                                               else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.                                                        
+                                                                               else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.                                                        
                                                                                
                                                                                if(j < i){
                                                                                        if (distance < smallDist) { smallDist = distance; }
@@ -215,6 +214,8 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
                rabund = new RAbundVector(list->getRAbundVector());
                
                fileHandle.close();
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "ClusterClassic", "readPhylipFile");