added trim overlap parameter to make.contigs

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
index 1420f84b992a54ed6dfb6d3a28d8452a083691de..f4605b6dbe1613fdb3e1a6beb1929a3585ff5fe7 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -42,14 +42,15 @@ FlowData::FlowData(int numFlows, float signal, float noise, int maxHomoP, string
 bool FlowData::getNext(ifstream& flowFile){
        
        try {
-               flowFile >> seqName >> endFlow; 
-               //cout << "in Flowdata " + seqName << endl;
-               for(int i=0;i<numFlows;i++)     {       flowFile >> flowData[i];        }
-               //cout << "in Flowdata read " << seqName + " done" << endl;
-               updateEndFlow(); 
-               translateFlow();
-               
-               m->gobble(flowFile);
+        seqName = getSequenceName(flowFile);
+               flowFile >> endFlow;    
+        if (!m->control_pressed) {
+            for(int i=0;i<numFlows;i++)        {       flowFile >> flowData[i];        }
+            updateEndFlow(); 
+            translateFlow();
+            m->gobble(flowFile);
+               }
+           
                if(flowFile){   return 1;       }
                else            {       return 0;       }
        }
@@ -59,22 +60,44 @@ bool FlowData::getNext(ifstream& flowFile){
        }
        
 }
+//********************************************************************************************************************
+string FlowData::getSequenceName(ifstream& flowFile) {
+       try {
+               string name = "";
+               
+        flowFile >> name;
+               
+               if (name.length() != 0) { 
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
+            }
+        }else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
+        
+               return name;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "getSequenceName");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 
 void FlowData::updateEndFlow(){
        try{
                
+        if (baseFlow.length() > 4) { return; }
+        
                //int currLength = 0;
                float maxIntensity = (float) maxHomoP + 0.49;
                
                int deadSpot = 0;
-                               
+                       
                while(deadSpot < endFlow){
                        int signal = 0;
                        int noise = 0;
                        
-                       for(int i=0;i<4;i++){
+                       for(int i=0;i<baseFlow.length();i++){
                                float intensity = flowData[i + deadSpot];
                                if(intensity > signalIntensity){
                                        signal++;
@@ -89,7 +112,7 @@ void FlowData::updateEndFlow(){
                                break;
                        }
                
-                       deadSpot += 4;
+                       deadSpot += baseFlow.length();
                }
                endFlow = deadSpot;
 
@@ -108,13 +131,13 @@ void FlowData::translateFlow(){
                sequence = "";
                for(int i=0;i<endFlow;i++){
                        int intensity = (int)(flowData[i] + 0.5);
-                       char base = baseFlow[i % 4];
+                       char base = baseFlow[i % baseFlow.length()];
                        
                        for(int j=0;j<intensity;j++){
                                sequence += base;
                        }
                }
-
+        
                if(sequence.size() > 4){
                        sequence = sequence.substr(4);
                }