new documentation, renamed functions to be more self explainable

src/pappsomspp/spectrum/spectrum.cpp

@@ -299,7 +299,7 @@ Spectrum Spectrum::xtandemRemoveC13() const {
     return new_spectrum;
 }
 
-Spectrum Spectrum::applyCutOff(pappso_double mz_min) const {
+Spectrum Spectrum::removeMzUnder(pappso_double mz_min) const {
     Spectrum new_spectrum;
     for (auto && peak : _v_peaks) {
         if (mz_min < peak.mz) {
@@ -309,10 +309,10 @@ Spectrum Spectrum::applyCutOff(pappso_double mz_min) const {
     return new_spectrum;
 }
 
-Spectrum Spectrum::cleanPeakIntensity(float percentIntMIn) const {
+Spectrum Spectrum::removeIntensityPercentUnder(float percentIntMIn) const {
     pappso_double max = this->getMaxIntensity().intensity;
     pappso_double intCutOff = max * (pappso_double) percentIntMIn;
-    return this->applyCutOff(intCutOff);
+    return this->removeMzUnder(intCutOff);
 }
 
 

src/pappsomspp/spectrum/spectrum.h

@@ -110,16 +110,17 @@ public:
      * */
     Spectrum takeNmostIntense(unsigned int n) const;
     
-    /** \brief filter spectrum to remove peaks less intense than absolute threshold
+    /** \brief filter spectrum to remove peaks with mz < mz_min
      * */
-    Spectrum applyCutOff(pappso_double mz_min)const;
+    Spectrum removeMzUnder(pappso_double mz_min)const;
     Spectrum applyDynamicRange(pappso_double dynamic_range)const;
     Spectrum round() const;
     Spectrum floor() const;
     
     /** \brief filter spectrum to remove peaks less intense than percent threshold
      * */
-    Spectrum cleanPeakIntensity(float percentIntMIn) const;
+    Spectrum removeIntensityPercentUnder(float percentIntMIn) const;
+    
     //Spectrum removeParent(const PeptideSp & peptideSp, unsigned int parent_ion_charge, pappso_double lower_dalton, pappso_double upper_dalton) const;
     /** \brief remove a mass range from the spectrum
      */
@@ -149,3 +150,4 @@ private:
 
 }
 #endif /*SPECTRUM_H_*/
+