Algo: Use unsigned loop variables when needed

That solves signed/unsigned compilation warnings.
This had no effect in practice but that makes the compiler happy.

algo/core/cluster-junctions.cpp

@@ -74,9 +74,9 @@ void comp_matrix::load(string file){
 
   char* tampon=(char*)malloc(windows.size()*sizeof(char));
   ifstream in_comp(file.c_str());
-  for(int i=0; i<windows.size();i++){
+  for(unsigned int i=0; i<windows.size();i++){
     in_comp.read(tampon, windows.size()*sizeof(char));
-    for(int j=0;j<windows.size(); j++){
+    for(unsigned int j=0;j<windows.size(); j++){
 	m[i][j]=tampon[j];
       }
   }
@@ -90,7 +90,7 @@ void comp_matrix::save(string file){
   
   ofstream out_comp(file.c_str());
   
-  for(int i=0; i<windows.size();i++){
+  for(unsigned int i=0; i<windows.size();i++){
     out_comp.write((char *)m[i],windows.size()*sizeof(char));
   }
   
@@ -99,7 +99,7 @@ void comp_matrix::save(string file){
  
 
 void comp_matrix::del(){
-  for (int i=0;i<windows.size();i++){
+  for (unsigned int i=0;i<windows.size();i++){
 	free(m[i]);
   }
   free(m);

algo/core/dynprog.cpp

@@ -343,11 +343,11 @@ void DynProg::backtrack()
   linkgap = new int[x.size()+1];
   gap2 = new int[y.size()+1];
       
-  for (int i = 0; i <=x.size(); i++) {
+  for (unsigned int i = 0; i <=x.size(); i++) {
     gap1[i] = 0;
     linkgap[i] = 0;
   }
-  for (int i = 0; i <= y.size(); i++) {
+  for (unsigned int i = 0; i <= y.size(); i++) {
     gap2[i] = 0;
   }
   

algo/core/fasta.cpp

@@ -197,7 +197,7 @@ void OnlineFasta::next() {
 
     // Compute seq
     current.seq = new int[current.sequence.length()];
-    for (int i=0; i< current.sequence.length(); i++)
+    for (unsigned int i=0; i< current.sequence.length(); i++)
       {
 	current.seq[i] = nuc_to_int(current.sequence[i]) ;
       }

algo/core/lazy_msa.cpp

@@ -52,7 +52,7 @@ void LazyMsa::alignOne(string *align, int one){
   
   ostringstream stream;
     
-    for (int i=0; i<ref.size(); i++){
+    for (unsigned int i=0; i<ref.size(); i++){
       for (int j=0; j<gapRef[one][i] ; j++){
 	stream <<"-";
       }
@@ -66,7 +66,7 @@ void LazyMsa::alignOne(string *align, int one){
 
   ostringstream stream2;
     
-    for (int i=0; i<sequences[one].size(); i++){
+    for (unsigned int i=0; i<sequences[one].size(); i++){
       for (int j=0; j<gapSeq[one][i] ; j++){
 	stream2 <<"-";
       }
@@ -84,19 +84,19 @@ void LazyMsa::align(string *align){
   
   int *maxGap= new int [ref.size()+1];
   
-  for (int i = 0; i< ref.size()+1; i++){
+  for (unsigned int i = 0; i< ref.size()+1; i++){
     maxGap[i]=0;
   }
   
   for (int i=0; i<sizeUsed+1; i++){
-   for (int j=0; j<ref.size()+1; j++){
+   for (unsigned int j=0; j<ref.size()+1; j++){
      if ( gapRef[i][j] > maxGap[j] ) maxGap[j]=gapRef[i][j];
    }
   }
   
   ostringstream stream;
     
-    for (int i=0; i<ref.size(); i++){
+    for (unsigned int i=0; i<ref.size(); i++){
       for (int j=0; j<maxGap[i] ; j++){
 	stream <<"-";
       }
@@ -111,11 +111,11 @@ void LazyMsa::align(string *align){
   for (int i=0; i<sizeUsed+1; i++){
     ostringstream stream2;
   
-    for (int j = 0; j< ref.size()+1; j++){
+    for (unsigned int j = 0; j< ref.size()+1; j++){
       gapSeq[i][link[i][j]]+=maxGap[j]-gapRef[i][j];
     }
     
-    for (int j=0; j<sequences[i].size(); j++){
+    for (unsigned int j=0; j<sequences[i].size(); j++){
       for (int k=0; k<gapSeq[i][j] ; k++){
 	stream2 <<"-";
       }

algo/core/windows.cpp

@@ -29,7 +29,7 @@ vector<int> WindowsStorage::getStatus(junction window) {
 JsonList WindowsStorage::statusToJson(junction window) {
     JsonList result;
     
-    for (int i=0; i<status_by_window[window].size(); i++){
+    for (unsigned int i=0; i<status_by_window[window].size(); i++){
         if (status_by_window[window][i] !=0){
             ostringstream oss; 
             oss << i;