sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index a359607a3ea11fa118efed129407ee608d4903e5..d1cf7299a46c522255eb725dccb058673f6b1c78 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -20,6 +20,10 @@ Sequence::Sequence(string newName, string sequence) {
                m = MothurOut::getInstance();
                initialize();   
                name = newName;
+        
+        for (int i = 0; i < name.length(); i++) {
+            if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
+        }
                
                //setUnaligned removes any gap characters for us
                setUnaligned(sequence);
@@ -36,6 +40,10 @@ Sequence::Sequence(string newName, string sequence, string justUnAligned) {
                m = MothurOut::getInstance();
                initialize();   
                name = newName;
+        
+        for (int i = 0; i < name.length(); i++) {
+            if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
+        }
                
                //setUnaligned removes any gap characters for us
                setUnaligned(sequence);
@@ -53,11 +61,9 @@ Sequence::Sequence(istringstream& fastaString){
                m = MothurOut::getInstance();
        
                initialize();
-               fastaString >> name;
-               
-               if (name.length() != 0) { 
+        name = getSequenceName(fastaString);
                
-                       name = name.substr(1);
+               if (!m->control_pressed) { 
                        string sequence;
                
                        //read comments
@@ -84,8 +90,7 @@ Sequence::Sequence(istringstream& fastaString){
                        setUnaligned(sequence); 
                        
                        if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
-               
-               }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               }
                
        }
        catch(exception& e) {
@@ -100,11 +105,9 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
                m = MothurOut::getInstance();
        
                initialize();
-               fastaString >> name;
-               
-               if (name.length() != 0) { 
+               name = getSequenceName(fastaString);
                
-                       name = name.substr(1);
+               if (!m->control_pressed) { 
                        string sequence;
                
                        //read comments
@@ -131,7 +134,7 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
                        
                        if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
                        
-               }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               }
                
        }
        catch(exception& e) {
@@ -147,11 +150,9 @@ Sequence::Sequence(ifstream& fastaFile){
        try {
                m = MothurOut::getInstance();
                initialize();
-               fastaFile >> name;
-               
-               if (name.length() != 0) { 
+               name = getSequenceName(fastaFile);
                
-                       name = name.substr(1); 
+               if (!m->control_pressed) { 
                        
                        string sequence;
                
@@ -181,7 +182,7 @@ Sequence::Sequence(ifstream& fastaFile){
                        
                        if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
                        
-               }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               }
 
        }
        catch(exception& e) {
@@ -195,13 +196,11 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
        try {
                m = MothurOut::getInstance();
                initialize();
-               fastaFile >> name;
         extraInfo = "";
                
-               if (name.length() != 0) { 
-            
-                       name = name.substr(1); 
-                       
+               name = getSequenceName(fastaFile);
+               
+               if (!m->control_pressed) {                      
                        string sequence;
             
                        //read comments
@@ -221,7 +220,7 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
                        //read info after sequence name
                        while (!fastaFile.eof())        {       
                 char c = fastaFile.get(); 
-                if (c == 10 || c == 13){  break;       }       
+                if (c == 10 || c == 13 || c == -1){  break;    }
                 extraInfo += c;
             } 
                        
@@ -233,8 +232,7 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
                        setUnaligned(sequence); 
                        
                        if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
-                       
-               }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               }
         
        }
        catch(exception& e) {
@@ -248,10 +246,9 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
        try {
                m = MothurOut::getInstance();
                initialize();
-               fastaFile >> name;
+               name = getSequenceName(fastaFile);
                
-               if (name.length() != 0) { 
-                       name = name.substr(1);
+               if (!m->control_pressed) { 
                        string sequence;
                        
                        //read comments
@@ -279,7 +276,7 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
                        
                        if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
                        
-               }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+               }
                
        }
        catch(exception& e) {
@@ -287,7 +284,54 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
                exit(1);
        }                                                       
 }
-
+//********************************************************************************************************************
+string Sequence::getSequenceName(ifstream& fastaFile) {
+       try {
+               string name = "";
+               
+        fastaFile >> name;
+               
+               if (name.length() != 0) { 
+            
+                       name = name.substr(1); 
+            
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
+            }
+            
+        }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
+        
+               return name;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "getSequenceName");
+               exit(1);
+       }
+}
+//********************************************************************************************************************
+string Sequence::getSequenceName(istringstream& fastaFile) {
+       try {
+               string name = "";
+               
+        fastaFile >> name;
+               
+               if (name.length() != 0) { 
+            
+                       name = name.substr(1); 
+            
+            for (int i = 0; i < name.length(); i++) {
+                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
+            }
+            
+        }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
+        
+               return name;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Sequence", "getSequenceName");
+               exit(1);
+       }
+}
 //********************************************************************************************************************
 string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
        try {
@@ -300,7 +344,7 @@ string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
                        if(letter == '>'){
                                fastaFile.putback(letter);
                                break;
-                       }
+                       }else if (letter == ' ') {;}
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
@@ -354,7 +398,7 @@ string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
                        if(letter == '>'){
                                fastaFile.putback(letter);
                                break;
-                       }
+                       }else if (letter == ' ') {;}
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
@@ -531,6 +575,15 @@ string Sequence::getUnaligned(){
 int Sequence::getNumBases(){
        return numBases;
 }
+//********************************************************************************************************************
+
+int Sequence::getNumNs(){
+    int numNs = 0;
+       for (int i = 0; i < unaligned.length(); i++) {
+        if(toupper(unaligned[i]) == 'N') { numNs++; }
+    }
+    return numNs;
+}
 
 //********************************************************************************************************************
 
@@ -719,6 +772,8 @@ void Sequence::trim(int length){
        if(numBases > length){
                unaligned = unaligned.substr(0,length);
                numBases = length;
+        aligned = "";
+        isAligned = 0;
        }
        
 }