Cleaned up the namespaces.

CAveragine.h

@@ -21,12 +21,10 @@ limitations under the License.
 #include "CHardklorVariant.h"
 #include "CPeriodicTable.h"
 
-#include <cstdlib>
+//#include <cstdlib>
 #include <fstream>
 #include <vector>
-#include <cstring>
-
-using namespace std;
+#include <string>
 
 /*
 const double AVE_MASS = 111.1254;
@@ -47,22 +45,19 @@ const double AVE_S = 0.0390;
 typedef struct atomInfo {
   char symbol[3];
   int numIsotopes;
-  vector<double> *mass;
-  vector<double> *abundance;
+  std::vector<double> *mass;
+  std::vector<double> *abundance;
   atomInfo(){
     strcpy(symbol,"X");
     numIsotopes=0;
-    mass = new vector<double>;
-    abundance = new vector<double>;
+    mass = new std::vector<double>;
+    abundance = new std::vector<double>;
   }
   atomInfo(const atomInfo& a){
     strcpy(symbol,a.symbol);
     numIsotopes=a.numIsotopes;
-    mass = new vector<double>;
-    abundance = new vector<double>;
-    unsigned int i;
-    for(i=0;i<a.mass->size();i++) mass->push_back(a.mass->at(i));
-    for(i=0;i<a.abundance->size();i++) abundance->push_back(a.abundance->at(i));
+    mass = new std::vector<double>(*a.mass);
+    abundance = new std::vector<double>(*a.abundance);
   }
   ~atomInfo(){
     delete mass;
@@ -74,11 +69,8 @@ typedef struct atomInfo {
       numIsotopes=a.numIsotopes;
       delete mass;
       delete abundance;
-      mass = new vector<double>;
-      abundance = new vector<double>;
-      unsigned int i;
-      for(i=0;i<a.mass->size();i++) mass->push_back(a.mass->at(i));
-      for(i=0;i<a.abundance->size();i++) abundance->push_back(a.abundance->at(i));
+      mass = new std::vector<double>(*a.mass);
+      abundance = new std::vector<double>(*a.abundance);
     }
     return *this;
   }
@@ -110,7 +102,7 @@ class CAveragine {
   //Data Members:
   int *atoms;
   CPeriodicTable *PT;
-  vector<atomInfo> *enrich;
+  std::vector<atomInfo> *enrich;
 
 };
 

CHardklor.cpp

@@ -46,8 +46,9 @@ limitations under the License.
 #include "CSpecAnalyze.h"
 #include "Smooth.h"
 #include <iomanip>
-using namespace std;
 
+using namespace std;
+using namespace MSToolkit;
 
 SSObject::SSObject(){
 	pepVar = new vector<sInt>;

CHardklor.h

@@ -39,14 +39,12 @@ limitations under the License.
 #include <sys/time.h>
 #endif
 
-using namespace std;
-
 #define PminusE 1.00672791
 
 class SSObject {
 public:
 	//Data members
-  vector<sInt> *pepVar;
+  std::vector<sInt> *pepVar;
   double corr;
 
 	//Constructors & Destructors
@@ -76,7 +74,7 @@ class CHardklor{
 
   //Methods:
 	void Echo(bool b);
-  int GoHardklor(CHardklorSetting sett, Spectrum* s=NULL);
+  int GoHardklor(CHardklorSetting sett, MSToolkit::Spectrum* s=NULL);
 	void SetAveragine(CAveragine *a);
 	void SetMercury(CMercury8 *m);
   void SetResultsToMemory(bool b);
@@ -86,14 +84,14 @@ class CHardklor{
 
  private:
   //Methods:
-  void Analyze(Spectrum* s=NULL);
+  void Analyze(MSToolkit::Spectrum* s=NULL);
   bool AnalyzePeaks(CSpecAnalyze& sa);
   int compareData(const void*, const void*);
   double LinReg(float *match, float *mismatch);
   void ResultToMem(SSObject& obj, CPeriodicTable* PT);
-  void WriteParams(fstream& fptr, int format=1); 
-  void WritePepLine(SSObject& obj, CPeriodicTable* PT, fstream& fptr, int format=0); 
-  void WriteScanLine(Spectrum& s, fstream& fptr, int format=0); 
+  void WriteParams(std::fstream& fptr, int format = 1);
+  void WritePepLine(SSObject& obj, CPeriodicTable* PT, std::fstream& fptr, int format = 0);
+  void WriteScanLine(MSToolkit::Spectrum& s, std::fstream& fptr, int format = 0);
 
 	//Finished analysis algorithms
 	void BasicMethod(float *match, float *mismatch,SSObject* combo, int depth, int maxDepth, int start);
@@ -120,13 +118,13 @@ class CHardklor{
 	bool bEcho;
   bool bMem;
   int currentScanNumber;
-	fstream fptr; //TODO: Get rid of this and use FILE* instead.
+  std::fstream fptr; //TODO: Get rid of this and use FILE* instead.
 
 	//Vector for holding peptide list of distribution
-  vector<CHardklorVariant> pepVariants;
+  std::vector<CHardklorVariant> pepVariants;
 
   //Vector for holding results in memory should that be needed
-  vector<hkMem> vResults;
+  std::vector<hkMem> vResults;
 
   //Temporary Data Members:
   char bestCh[200];

CHardklor2.cpp

@@ -14,8 +14,12 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
 */
+
 #include "CHardklor2.h"
 
+using namespace std;
+using namespace MSToolkit;
+
 CHardklor2::CHardklor2(CAveragine *a, CMercury8 *m, CModelLibrary *lib){
   averagine=a;
   mercury=m;

CHardklor2.h

@@ -38,8 +38,6 @@ limitations under the License.
 #include <sys/time.h>
 #endif
 
-using namespace std;
-
 class CHardklor2{
 
  public:
@@ -52,46 +50,46 @@ class CHardklor2{
 
   //Methods:
   void  Echo(bool b);
-  int   GoHardklor(CHardklorSetting sett, Spectrum* s=NULL);
-  void    QuickCharge(Spectrum& s, int index, vector<int>& v);
+  int   GoHardklor(CHardklorSetting sett, MSToolkit::Spectrum* s=NULL);
+  void  QuickCharge(MSToolkit::Spectrum& s, int index, std::vector<int>& v);
   void  SetResultsToMemory(bool b);
   int   Size();
 
  protected:
 
  private:
   //Methods:
-  int     BinarySearch(Spectrum& s, double mz, bool floor);
+  int     BinarySearch(MSToolkit::Spectrum& s, double mz, bool floor);
   double  CalcFWHM(double mz,double res,int iType);
-  void    Centroid(Spectrum& s, Spectrum& out);
-  bool    CheckForPeak(vector<Result>& vMR, Spectrum& s, int index);
+  void    Centroid(MSToolkit::Spectrum& s, MSToolkit::Spectrum& out);
+  bool    CheckForPeak(std::vector<Result>& vMR, MSToolkit::Spectrum& s, int index);
   int     CompareData(const void*, const void*);
-  double  LinReg(vector<float>& mer, vector<float>& obs);
-  bool    MatchSubSpectrum(Spectrum& s, int peakIndex, pepHit& pep);
-  double  PeakMatcher(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, int& indexOverlap, vector<int>& vMatchIndex, vector<float>& vMatchIntensity);
-  double  PeakMatcherB(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, vector<int>& vMatchIndex, vector<float>& vMatchIntensity);
-  void    QuickHardklor(Spectrum& s, vector<pepHit>& vPeps);
-  void    RefineHits(vector<pepHit>& vPeps, Spectrum& s);
-  void    ResultToMem(pepHit& ph, Spectrum& s);
-  void    WritePepLine(pepHit& ph, Spectrum& s, FILE* fptr, int format=0); 
-  void    WriteScanLine(Spectrum& s, FILE* fptr, int format=0); 
+  double  LinReg(std::vector<float>& mer, std::vector<float>& obs);
+  bool    MatchSubSpectrum(MSToolkit::Spectrum& s, int peakIndex, pepHit& pep);
+  double  PeakMatcher(std::vector<Result>& vMR, MSToolkit::Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, int& indexOverlap, std::vector<int>& vMatchIndex, std::vector<float>& vMatchIntensity);
+  double  PeakMatcherB(std::vector<Result>& vMR, MSToolkit::Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, std::vector<int>& vMatchIndex, std::vector<float>& vMatchIntensity);
+  void    QuickHardklor(MSToolkit::Spectrum& s, std::vector<pepHit>& vPeps);
+  void    RefineHits(std::vector<pepHit>& vPeps, MSToolkit::Spectrum& s);
+  void    ResultToMem(pepHit& ph, MSToolkit::Spectrum& s);
+  void    WritePepLine(pepHit& ph, MSToolkit::Spectrum& s, FILE* fptr, int format=0); 
+  void    WriteScanLine(MSToolkit::Spectrum& s, FILE* fptr, int format=0); 
 
   static int CompareBPI(const void *p1, const void *p2);
 
   //Data Members:
-  CHardklorSetting  cs;
-  CAveragine*       averagine;
-  CMercury8*        mercury;
-  CModelLibrary*    models;
-  CPeriodicTable*   PT;
-  Spectrum          mask;
-  hkMem             hkm;
-  bool              bEcho;
-  bool              bMem;
-  int               currentScanNumber;
+  CHardklorSetting    cs;
+  CAveragine*         averagine;
+  CMercury8*          mercury;
+  CModelLibrary*      models;
+  CPeriodicTable*     PT;
+  MSToolkit::Spectrum mask;
+  hkMem               hkm;
+  bool                bEcho;
+  bool                bMem;
+  int                 currentScanNumber;
 
   //Vector for holding results in memory should that be needed
-  vector<hkMem> vResults;
+  std::vector<hkMem> vResults;
 
   //Temporary Data Members:
   char bestCh[200];

CHardklorFileReader.h

@@ -48,12 +48,12 @@ class CHardklorFileReader {
   int posNR;
   CHardklorSetting cs;
   CNoiseReduction nr;
-  MSReader r;
-  deque<Spectrum> sNative;
-  deque<Spectrum> sNR;
+  MSToolkit::MSReader r;
+  std::deque<MSToolkit::Spectrum> sNative;
+  std::deque<MSToolkit::Spectrum> sNR;
 
-  deque<cpar> dc;
+  std::deque<cpar> dc;
 
-  vector<int> vScans;
+  std::vector<int> vScans;
 
 };

CHardklorOutput.cpp

@@ -16,6 +16,8 @@ limitations under the License.
 */
 #include "CHardklorOutput.h"
 
+using namespace std;
+
 bool CHardklorOutput::openFile(char* fileName, hkOutputFormat format){
 
 	if(outFile!=NULL) closeFile();

CHardklorOutput.h

@@ -20,8 +20,6 @@ limitations under the License.
 #include "HardklorTypes.h"
 #include <iostream>
 
-using namespace std;
-
 class CHardklorOutput {
 public:
 

CHardklorParser.cpp

@@ -17,6 +17,7 @@ limitations under the License.
 #include "CHardklorParser.h"
 
 using namespace std;
+using namespace MSToolkit;
 
 CHardklorParser::CHardklorParser(){
   vQueue = new vector<CHardklorSetting>;

CHardklorParser.h

@@ -25,8 +25,6 @@ limitations under the License.
 #include "CPeriodicTable.h"
 #include "MSToolkitTypes.h"
 
-using namespace std;
-
 class CHardklorParser {
 
  public:
@@ -38,7 +36,7 @@ class CHardklorParser {
   void parse(char*);
   bool parseCMD(int argc, char* argv[]);
   bool parseConfig(char*);
-  MSFileFormat getFileFormat(char* c);
+  MSToolkit::MSFileFormat getFileFormat(char* c);
   CHardklorSetting& queue(int);
   int size();
 
@@ -51,7 +49,7 @@ class CHardklorParser {
 
    //Data Members
    CHardklorSetting global;
-   vector<CHardklorSetting> *vQueue;
+   std::vector<CHardklorSetting> *vQueue;
 };
 
 

CHardklorProtein.h

@@ -21,8 +21,6 @@ limitations under the License.
 
 #include "HardklorTypes.h"
 
-using namespace std;
-
 class CHardklorProtein {
  public:
   //Constructors & Destructors:
@@ -51,7 +49,7 @@ class CHardklorProtein {
  protected:
  private:
   //Data Members:
-  vector<sEnrichMercury> *enrich;
+  std::vector<sEnrichMercury> *enrich;
 
 };
 

CHardklorSetting.cpp

@@ -17,6 +17,7 @@ limitations under the License.
 #include "CHardklorSetting.h"
 
 using namespace std;
+using namespace MSToolkit;
 
 CHardklorSetting::CHardklorSetting(){
   noBase=false;

CHardklorSetting.h

@@ -18,15 +18,12 @@ limitations under the License.
 #define _CHARDKLORSETTING_H
 
 #include <cstdio>
-#include <cstring>
 #include <string>
 #include <vector>
 
 #include "HardklorTypes.h"
 #include "CHardklorVariant.h"
 
-using namespace std;
-
 /* 
    Defined as a class instead of a struct so
    that default parameters are used. Data access
@@ -94,9 +91,9 @@ class CHardklorSetting {
 
   specType msType;                    //Type of mass spectrometer used to acquire data
   hkAlgorithm algorithm;              //Deconvolving algorithm to use
-  vector<CHardklorVariant> *variant;  //Variants to make to averagine
-  MSFileFormat fileFormat;            //File format
-  MSSpectrumType mzXMLFilter;         //Filter for mzXML files
+  std::vector<CHardklorVariant> *variant;  //Variants to make to averagine
+  MSToolkit::MSFileFormat fileFormat;            //File format
+  MSToolkit::MSSpectrumType mzXMLFilter;         //Filter for mzXML files
 
  protected:
  private:

CHardklorVariant.h

@@ -21,8 +21,6 @@ limitations under the License.
 
 #include "HardklorTypes.h"
 
-using namespace std;
-
 class CHardklorVariant {
  public:
   //Constructors & Destructors:
@@ -50,9 +48,9 @@ class CHardklorVariant {
  protected:
 
  private:
-  //Data Members:
-  vector<sInt> *atoms;
-  vector<sEnrichMercury> *enrich;
+   //Data Members:
+   std::vector<sInt> *atoms;
+   std::vector<sEnrichMercury> *enrich;
 
 };