added summary output to catchall command

[mothur.git] / readcolumn.cpp

diff --git a/readcolumn.cpp b/readcolumn.cpp
index f61a40c483b69f7418ca4d2702ca995f4180f3e2..2782bd08a84efd8a596364f14c56015e04407241 100644 (file)
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -14,7 +14,7 @@
 
 ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
        
-       successOpen = openInputFile(distFile, fileHandle);
+       successOpen = m->openInputFile(distFile, fileHandle);
        
 }
 
@@ -53,6 +53,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                        if(itB == nameMap->end()){
                                cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
                        }
+//if (((itA->second == 8) && (itB->second == 1588)) || ((itA->second == 1588) && (itB->second == 8))) { cout << "found it" << endl; }
 
                        if (distance == -1) { distance = 1000000; }
                        else if (globaldata->sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
@@ -90,7 +91,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                                }
                                reading->update(itA->second * nseqs);
                        }
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
 
                if(lt == 0){  // oops, it was square
@@ -98,7 +99,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                        fileHandle.close();  //let's start over
                        D->clear();  //let's start over
                   
-                       openInputFile(distFile, fileHandle);  //let's start over
+                       m->openInputFile(distFile, fileHandle);  //let's start over
 
                        while(fileHandle){
                                fileHandle >> firstName >> secondName >> distance;
@@ -124,7 +125,7 @@ int ReadColumnMatrix::read(NameAssignment* nameMap){
                                        reading->update(itA->second * nseqs);
                                }
                
-                               gobble(fileHandle);
+                               m->gobble(fileHandle);
                        }
                }