Resolve some FIXME comments

drroe · drroe · commit 2e0ecb490d3e · 2021-02-11T13:40:18.000-05:00
diff --git a/src/Action_MakeStructure.h b/src/Action_MakeStructure.h
@@ -20,7 +20,7 @@ class Action_MakeStructure : public Action {
         SS_TYPE(double ph,double ps,double ph2,double ps2,int t,std::string const& n) :
           phi(ph), psi(ps), phi2(ph2), psi2(ps2), isTurn(t), type_arg(n) {}
         bool empty() { return (isTurn == -1); }
-        double phi, psi, phi2, psi2; // Angle(s) FIXME: Should this be an array?
+        double phi, psi, phi2, psi2; // Angle(s) TODO: Should this be an array?
         int isTurn; // 0=phi/psi, 1=Turn (phi/psi/phi2/psi2), 2=Single Dihedral(phi)
         std::string type_arg;
     };
diff --git a/src/Action_OrderParameter.h b/src/Action_OrderParameter.h
@@ -41,7 +41,6 @@ class Action_OrderParameter : public Action {
   AtomMask tailend_mask_;
   AtomMask unsat_mask_;
 
-  // FIXME:
   // std::vector<std::pair<AtomMask, bool> > masks_;
   std::vector<AtomMask> masks_;
   std::vector<std::vector<int> > dbonds_;
diff --git a/src/Analysis_Spline.cpp b/src/Analysis_Spline.cpp
@@ -3,7 +3,6 @@
 #include "Constants.h" // SMALL
 
 Analysis_Spline::Analysis_Spline() :
-  outfile_(0),
   meshsize_(0),
   meshmin_(0.0),
   meshmax_(0.0),
@@ -21,7 +20,7 @@ void Analysis_Spline::Help() const {
 Analysis::RetType Analysis_Spline::Setup(ArgList& analyzeArgs, AnalysisSetup& setup, int debugIn)
 {
   std::string setname = analyzeArgs.GetStringKey("name");
-  outfile_ = setup.DFL().AddDataFile(analyzeArgs.GetStringKey("out"), analyzeArgs);
+  DataFile* outfile = setup.DFL().AddDataFile(analyzeArgs.GetStringKey("out"), analyzeArgs);
   meshsize_ = analyzeArgs.getKeyInt("meshsize", 0);
   meshfactor_ = -1.0;
   if (meshsize_ < 3) {
@@ -66,7 +65,7 @@ Analysis::RetType Analysis_Spline::Setup(ArgList& analyzeArgs, AnalysisSetup& se
     ds->SetLegend( "Spline(" + (*dsIn)->Meta().Legend() + ")" );
     // TODO: Set individually based on input_dsets_
     ds->SetDim(Dimension::X, Xdim);
-    if (outfile_ != 0) outfile_->AddDataSet( ds );
+    if (outfile != 0) outfile->AddDataSet( ds );
     output_dsets_.push_back( (DataSet_Mesh*)ds );
   }
 
@@ -83,10 +82,10 @@ Analysis::RetType Analysis_Spline::Setup(ArgList& analyzeArgs, AnalysisSetup& se
     mprintf(" Mesh max= %f\n", meshmax_);
   else
     mprintf(" Mesh max will be input set max.\n");
-  if (outfile_ != 0) {
+  if (outfile != 0) {
     if (!setname.empty())
       mprintf("\tOutput set name: %s\n", setname.c_str());
-    mprintf("\tOutfile name: %s\n", outfile_->DataFilename().base());
+    mprintf("\tOutfile name: %s\n", outfile->DataFilename().base());
   }
   //for (Array1D::const_iterator set = input_dsets_.begin(); set != input_dsets_.end(); ++set)
   //  mprintf("\t%s\n", (*set)->legend());
diff --git a/src/Analysis_Spline.h b/src/Analysis_Spline.h
@@ -12,7 +12,6 @@ class Analysis_Spline : public Analysis {
     Analysis::RetType Setup(ArgList&, AnalysisSetup&, int);
     Analysis::RetType Analyze();
   private:
-    DataFile* outfile_; // FIXME: May not need to be class var
     Array1D input_dsets_;
     std::vector<DataSet_Mesh*> output_dsets_;
     int meshsize_;       ///< Mesh size will be DataSet.Size * meshfactor
diff --git a/src/AtomMap.h b/src/AtomMap.h
@@ -8,7 +8,7 @@ class AtomMap {
     AtomMap();
 
     MapAtom& operator[](int);
-    const MapAtom& operator[](int i) const { return mapatoms_[i]; } // FIXME: bounds
+    const MapAtom& operator[](int i) const { return mapatoms_[i]; }
     /// \return the number of atoms in the AtomMap.
     int Natom() const { return (int)mapatoms_.size(); }
     /// Set the debug level of the AtomMap.
diff --git a/src/ClusterNode.h b/src/ClusterNode.h
@@ -24,7 +24,6 @@ class ClusterNode {
     void CalcEccentricity(DataSet_Cmatrix const&);
     /// Calculate centroid of members of this cluster.
     void CalculateCentroid(ClusterDist* Cdist) {
-      // FIXME: Could potentially get rid of this branch.
       if (centroid_ == 0)
         centroid_ = Cdist->NewCentroid( frameList_ );
       else
diff --git a/src/DataIO_RemLog.h b/src/DataIO_RemLog.h
@@ -20,7 +20,7 @@ class DataIO_RemLog : public DataIO {
     enum LogType { UNKNOWN = 0, TREMD, HREMD, MREMD, RXSGLD, PHREMD };
     static const char* LogDescription[];
     typedef std::vector<std::string> Sarray; // TODO FileName array?
-    typedef std::map<double,int> TmapType; // FIXME: Use ReplicaMap
+    typedef std::map<double,int> TmapType; // TODO: Use ReplicaMap
     typedef DataSet_RemLog::IdxArray IdxArray;
 
     /// Read remlog header
diff --git a/src/DataSet.h b/src/DataSet.h
@@ -49,7 +49,7 @@ class DataSet {
     virtual SizeArray DimSizes() const { return SizeArray(); }
     /// Print DataSet information //TODO return string instead?
     virtual void Info() const = 0;
-    /// Write data to file given start indices. FIXME Buffer? Should this function take number of elements as well?
+    /// Write data to file given start indices.
     virtual void WriteBuffer(CpptrajFile&, SizeArray const&) const = 0;
     /// \return value of coordinate for specified dimension d and position p.
     /** NOTE: It is assumed this can ALWAYS be represented as double precision. */
diff --git a/src/DataSetList.h b/src/DataSetList.h
@@ -30,7 +30,7 @@ class DataSetList {
 
     DataSetList& operator+=(DataSetList const&);
     /// \return DataSet at didx.
-    DataSet* operator[](int didx) const { return DataList_[didx]; } // FIXME: No bounds check
+    DataSet* operator[](int didx) const { return DataList_[didx]; }
     /// DataSetList default iterator
     typedef DataListType::const_iterator const_iterator;
     /// Iterator to beginning of dataset list
diff --git a/src/DataSet_2D.h b/src/DataSet_2D.h
@@ -12,7 +12,7 @@ class DataSet_2D : public DataSet {
       DataSet(tIn, MATRIX_2D, fIn, 2) {}
     // TODO enable Append?
     int Append(DataSet*) { return 1; }
-    int Allocate(SizeArray const& s) { return Allocate2D(s[0], s[1]); } // FIXME bounds check
+    int Allocate(SizeArray const& s) { return Allocate2D(s[0], s[1]); }
     // TODO: 1 allocate using MatrixKind?
     /// Set up matrix for given # columns and rows. // TODO replace with Allocate
     virtual int Allocate2D(size_t, size_t) = 0;
diff --git a/src/DataSet_3D.h b/src/DataSet_3D.h
@@ -4,7 +4,7 @@
 #include "GridBin.h"
 class Box;
 /// Interface for 3D DataSets.
-// FIXME: Use DataSet Dims?
+// TODO: Use DataSet Dims?
 class DataSet_3D : public DataSet {
   public:
     DataSet_3D() : gridBin_(0) {}
diff --git a/src/DataSet_Coords_TRJ.h b/src/DataSet_Coords_TRJ.h
@@ -22,7 +22,7 @@ class DataSet_Coords_TRJ : public DataSet_Coords {
     void Info() const;
     void Add( size_t, const void* )              { return;            }
     int Allocate(SizeArray const&)               { return 0;          }
-    size_t MemUsageInBytes() const { return IDX_.DataSize() + readFrame_.DataSize(); } // FIXME
+    size_t MemUsageInBytes() const { return IDX_.DataSize() + readFrame_.DataSize(); }
     // ----- DataSet_Coords functions ------------
     /// DISABLED: Add a frame.
     void AddFrame(Frame const& fIn) { }
diff --git a/src/DataSet_GridDbl.h b/src/DataSet_GridDbl.h
@@ -26,7 +26,7 @@ class DataSet_GridDbl : public DataSet_3D {
     // ----- DataSet functions -------------------
     size_t Size()                        const { return grid_.size();        }
 #   ifdef MPI
-    // FIXME: Currently just sums up. Should this be a separate Sync function?
+    // TODO: Currently just sums up. Should this be a separate Sync function?
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&);
 #   endif
     void Info()                          const { return; }
diff --git a/src/DataSet_GridFlt.h b/src/DataSet_GridFlt.h
@@ -26,7 +26,7 @@ class DataSet_GridFlt : public DataSet_3D {
     // ----- DataSet functions -------------------
     size_t Size()                        const { return grid_.size();        }
 #   ifdef MPI
-    // FIXME: Currently just sums up. Should this be a separate Sync function?
+    // TODO: Currently just sums up. Should this be a separate Sync function?
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&);
 #   endif
     void Info()                          const { return; }
diff --git a/src/DataSet_MatrixDbl.h b/src/DataSet_MatrixDbl.h
@@ -14,7 +14,7 @@ class DataSet_MatrixDbl : public DataSet_2D {
     // ----- DataSet functions -------------------
     size_t Size()                        const { return mat_.size();        }
 #   ifdef MPI
-    // FIXME: Currently just sums up. Should this be a separate Sync function?
+    // TODO: Currently just sums up. Should this be a separate Sync function?
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&);
 #   endif
     void Info()                          const { return;                    }
diff --git a/src/DataSet_MatrixFlt.h b/src/DataSet_MatrixFlt.h
@@ -11,7 +11,7 @@ class DataSet_MatrixFlt : public DataSet_2D {
     // ----- DataSet functions -------------------
     size_t Size()                        const { return mat_.size();        }
 #   ifdef MPI
-    // FIXME: Currently just sums up. Should this be a separate Sync function?
+    // TODO: Currently just sums up. Should this be a separate Sync function?
     int Sync(size_t, std::vector<int> const&, Parallel::Comm const&);
     int SendSet(int, Parallel::Comm const&);
     int RecvSet(int, Parallel::Comm const&);
diff --git a/src/Ewald_Regular.h b/src/Ewald_Regular.h
@@ -39,7 +39,7 @@ class Ewald_Regular : public Ewald {
     Iarray mlim2_;        ///< Hold m2 reciprocal indices
     int multCut_;         ///< Hold index after which multiplier should be 2.0.
 #   endif
-    double maxexp_;       ///< Determines how far out recip vectors go? FIXME check!
+    double maxexp_;       ///< Determines how far out recip vectors go? TODO check!
     double rsumTol_;      ///< Reciprocal space sum tolerance.
     int mlimit_[3];       ///< Number of units in each direction to calc recip. sum. / nfft
     int maxmlim_;         ///< The max of the three mlimit_ values. / pme spline order
diff --git a/src/Frame.h b/src/Frame.h
@@ -286,7 +286,7 @@ class Frame {
     double T_;      ///< Temperature
     double pH_;     ///< pH
     double redox_;  ///< RedOx potential
-    double time_;   ///< Time FIXME Should this be float?
+    double time_;   ///< Time
     double* X_;     ///< Coord array, X0 Y0 Z0 X1 Y1 Z1 ...
     double* V_;     ///< Velocities (same arrangement as Coords).
     double* F_;     ///< Frame (same arrangement as Coords).
diff --git a/src/MetaData.h b/src/MetaData.h
@@ -25,7 +25,7 @@ class MetaData {
       CHI2,    CHI3, CHI4,  CHI5,
       PUCKER,
       NOE,
-      DIST,    COVAR,     MWCOVAR, //FIXME: May need more descriptive names 
+      DIST,    COVAR,     MWCOVAR,
       CORREL,  DISTCOVAR, IDEA,
       IREDMAT, DIHCOVAR,
       IREDVEC,
diff --git a/src/OutputTrajCommon.h b/src/OutputTrajCommon.h
@@ -44,8 +44,8 @@ class OutputTrajCommon {
     /// \return 'true' if output frame range has been set up
     inline bool HasRange() const { return hasRange_ || !frameCount_.DefaultSettings(); }
   private:
-    FileName trajName_; // FIXME: Save this here?
-    Topology* trajParm_;// FIXME: Save this here?
+    FileName trajName_;                ///< Output file name
+    Topology* trajParm_;               ///< Pointer to associated Topology
     CoordinateInfo cInfo_;             ///< Coordinate info for trajectory
     int NframesToWrite_;               ///< Expected number of frames to be written.
     // Track frame numbers
diff --git a/src/Parallel.h b/src/Parallel.h
@@ -8,7 +8,7 @@
 # undef MPI
 # define CPPTRAJ_MPI
 # include <mpi.h>
-# include <sys/types.h> // off_t FIXME necessary?
+# include <sys/types.h> // off_t 
 # ifdef PARALLEL_DEBUG_VERBOSE
 #   include <cstdio> // for FILE
 # endif
diff --git a/src/ParameterTypes.h b/src/ParameterTypes.h
@@ -399,7 +399,7 @@ class NonbondParmType {
     void SetNHBterms(int n)   { hbarray_.assign( n, HB_ParmType() ); }
     /// Set specified HB term
     HB_ParmType& SetHB(int i) { return hbarray_[i];                  }
-    /// Set specified nbindex location to given value. FIXME no bounds check
+    /// Set specified nbindex location to given value.
     void SetNbIdx(int idx, int nbidx) { nbindex_[idx] = nbidx; }
     /// Add given LJ term to nonbond array and update nonbond index array.
     /** Certain routines in sander (like the 1-4 calcs) do NOT use the 
diff --git a/src/TrajoutList.h b/src/TrajoutList.h
@@ -19,7 +19,7 @@ class TrajoutList {
     ~TrajoutList();
     void SetDebug(int);
     void Clear();
-    /// FIXME legacy function to maintain pytraj compatibility
+    /// NOTE: legacy function to maintain pytraj compatibility
     int AddTrajout(std::string const&, ArgList const&, Topology*);
     /// Add output trajectory to the list and associate with given topology.
     int AddTrajout(std::string const&, ArgList const&, DataSetList const&, Topology*);
diff --git a/src/Trajout_Single.h b/src/Trajout_Single.h
@@ -12,10 +12,10 @@ class DataSetList;
   * however in case we do want to inherit in the future in a manner
   * similar to Trajin.
   */
-// FIXME: Should open state be tracked and error given if setup called
+// TODO: Should open state be tracked and error given if setup called
 //        twice for already open traj? Should append be default if
 //        traj is opened twice?
-// FIXME: Should take ArgList&, not const, so we can determine if there are unknown args later.
+// TODO: Should take ArgList&, not const, so we can determine if there are unknown args later.
 class Trajout_Single {
   public:
     Trajout_Single() : trajio_(0), debug_(0) {}
