Fixed doxygen warnings

build-tools/doxygen_pp

@@ -135,11 +135,11 @@ sub handleLinkto
   if ($linkstr =~ m|<linkto\s+class\s*=\s*([^:#]*?)\s*>|i) {
     # A link to a class.
     $linkstr =~ s|<linkto\s+class\s*=\s*['"]?(.*?)['"]?\s*>| \\link casacore::$1 |i;
-    $endlink = " \\endlink";
+    $endlink = "\\endlink";
   } elsif ($linkstr =~ m%<linkto\s+module\s*=\s*([^:#]*?)\s*>%i) {
     # A link to a module.
     $linkstr =~ s%<linkto\s+module\s*=\s*['"]?(.*?)['"]?\s*>% \\ref $1_module_anchor "%i;
-    $endlink = "\"";
+    $endlink = '"';
   } else {
     # A link to an anchor in a group or file.
     if ($linkstr =~ m%<linkto\s+(group|file)\s*=\s*(.*?)[:#](.*?)\s*>%i) {
@@ -159,7 +159,7 @@ sub handleLinkto
       my $classnm = $1;
       my $funcnm = $2;
       $linkstr =~ s%<linkto(.*?)>% \\link ${classnm}::$funcnm() %i;
-      $endlink = ' \\endlink';
+      $endlink = '\\endlink';
     } elsif ($linkstr =~ m%<linkto\s+(class|module)\s*=\s*(.*?)[:#](.*?)\s*>%) {
       # A link to a class or module anchor.
       my $grpnm = $2;
@@ -233,6 +233,7 @@ sub change_comment_style
   $extraline = "";
   $grouplevel = 0;
   $namedgrouplevel = 0;
+  $nexamples = 0;
   $code = 0;           # no <src> block found
   $link = 0;           # no <linkto> block found
   $linkfr = 0;         # no <linkfrom> found
@@ -365,13 +366,14 @@ sub change_comment_style
 	# Replace it by a doxygen \anchor tag and an <a name=> tag.
 	# Prepend the doxygen name with the header name.
 	# The latter one is used for internal <a href=> references.
-	if ( $comment =~ m|<anchor\s+name\s*=\s*(.*)\s*>|i ) {
+	if ( $comment =~ m|<anchor\s+name\s*=\s*(.*?)\s*>|i ) {
 	  my $nm = $1;
+          my $rem = $2;
 	  my $dnm = $nm;
 	  $dnm =~ s|\s*['".]\s*||g;
 	  $dnm =~ s|\s+|_|g;
 	  $dnm =~ s|:|_|g;
-	  $comment =~ s|<anchor\s+name\s*=\s*(.*)\s*>| \\anchor $dnm <a name=$nm>|i;
+	  $comment =~ s|<anchor\s+name\s*=\s*(.*?)\s*>| \\anchor $dnm <a name=$nm>|i;
 	}
 	$comment =~ s|</anchor>||ig;
 
@@ -428,7 +430,10 @@ sub change_comment_style
 	$comment =~ s|</motivation>||ig;
 	$comment =~ s|<synopsis>|<h3>Synopsis</h3>|ig;
 	$comment =~ s|</synopsis>||ig;
-	$comment =~ s|<example>|<h3>Example</h3> \\anchor ${hdrnm}_example|ig;
+	if ( $comment =~ m|<example>|i ) {
+          $nexamples += 1;
+          $comment =~ s|<example>|<h3>Example</h3> \\anchor ${hdrnm}_example${nexamples}|ig;
+        }
 	$comment =~ s|</example>||ig;
 	$comment =~ s|<etymology>|<h3>Etymology</h3>|ig;
 	$comment =~ s|</etymology>||ig;
@@ -641,9 +646,8 @@ sub change_comment_style
         $line = "//$comment\n";
         $newstate = $NON_COMMENT_BLOCK;
       }
-    }
-    # A blank line does not change anything.
-    elsif ($line =~ /^\s*$/) {
+    } elsif ($line =~ /^\s*$/) {
+      # A blank line does not change anything.
       $newstate = $state;
       if ($nadded > 0) {
 	$nadded -= 1;
@@ -653,6 +657,11 @@ sub change_comment_style
     } else {
       $keephash = 0;
     }
+    # Remove stray spaces left before ) or after ( . and ,.
+    $comment =~ s/\(\s+/(/g;
+    $comment =~ s/\s+\)/)/g;
+    $comment =~ s/\s+\././g;
+    $comment =~ s/\s+,/,/g;
 
     # Act depending on new and old state.
     if ($skip == 0) {

casa/Arrays/Array.h

@@ -220,7 +220,7 @@ template<class T> class Array : public ArrayBase
     // Otherwise, <src>allocator</src> is ignored.
     // It is strongly recommended to allocate and initialize <src>storage</src> with <src>DefaultAllocator<T></src>
     // rather than new[] or <src>NewDelAllocator<T></src> because new[] can't decouple allocation and initialization.
-    // <src>DefaultAllocator<T>::type</src> is a subclass of std::allocator. You can allocate <src>storage</src> via
+    // <src>DefaultAllocator<T></src> is a subclass of std::allocator. You can allocate <src>storage</src> via
     // the allocator as below.
     // <srcblock>
     //   FILE *fp = ...;
@@ -779,7 +779,7 @@ template<class T> class Array : public ArrayBase
   class ConstIteratorSTL: public BaseIteratorSTL
     {
     public:
-      // <group name=STL-iterator-typedefs>
+      // <group name=STL-const-iterator-typedefs>
       typedef T                 value_type;
       typedef const value_type* pointer;
       typedef const value_type& reference;
@@ -842,7 +842,7 @@ template<class T> class Array : public ArrayBase
     // If the array is contiguous, it is possible to use the
     // <src>cbegin</src> and <src>cend</src> functions which are
     // about 10% faster.
-    // <group name=STL-iterator>
+    // <group name=iterator-typedefs>
     // STL-style typedefs.
     // <group>
     typedef T                value_type;

casa/Containers/RecordDesc.h

@@ -85,7 +85,7 @@ class AipsIO;
 //
 // <example>
 // See the example in the description of the 
-// <linkto class="Record:example">Record</linkto> class.
+// <linkto class="Record:example1">Record</linkto> class.
 // </example>
 //
 // <motivation>

casa/Containers/RecordDescRep.h

@@ -73,7 +73,7 @@ class AipsIO;
 
 // <example>
 // See the example in the description of the 
-// <linkto class="Record:example">Record</linkto> class.
+// <linkto class="Record:example1">Record</linkto> class.
 // </example>
 
 // <motivation>

doxygen.cfg

@@ -382,7 +382,8 @@ TYPEDEF_HIDES_STRUCT   = NO
 # the optimal cache size from a speed point of view.
 # Minimum value: 0, maximum value: 9, default value: 0.
 
-LOOKUP_CACHE_SIZE      = 0
+# Set to 1 based on feedback from a doxygen run
+LOOKUP_CACHE_SIZE      = 1
 
 #---------------------------------------------------------------------------
 # Build related configuration options
@@ -804,7 +805,8 @@ EXCLUDE_PATTERNS       = */build_* \
                          */test/* \
                          */include/* \
                          */fortran/* \
-                         */.git/*
+                         */.git/* \
+                         */*sav*/* 
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -1799,18 +1801,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify a XML schema, which can be used by a
-# validating XML parser to check the syntax of the XML files.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_SCHEMA             =
-
-# The XML_DTD tag can be used to specify a XML DTD, which can be used by a
-# validating XML parser to check the syntax of the XML files.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_DTD                =
-
 # If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
 # listings (including syntax highlighting and cross-referencing information) to
 # the XML output. Note that enabling this will significantly increase the size

ms/MSOper/MSConcat.h

@@ -57,9 +57,6 @@ template <class T> class Block;
 // </reviewed>
 
 // <prerequisite>
-//   <li> SomeClass
-//   <li> SomeOtherClass
-//   <li> some concept
 // </prerequisite>
 //
 // <etymology>
@@ -74,20 +71,7 @@ template <class T> class Block;
 // <motivation>
 // </motivation>
 //
-// <templating arg=T>
-//    <li>
-//    <li>
-// </templating>
-//
-// <thrown>
-//    <li>
-//    <li>
-// </thrown>
-//
 // <todo asof="yyyy/mm/dd">
-//   <li> add this feature
-//   <li> fix this bug
-//   <li> start discussion of this possible extension
 // </todo>
 
 class MSConcat: public MSColumns
@@ -100,16 +84,16 @@ class MSConcat: public MSColumns
 		     const String& obsidAndScanTableName="");
 
   void concatenate(const MeasurementSet& otherMS,
-		   const uInt handling=0,   // 0 (default): complete concat of all tables
-                                            // 1 : don't concatenate the MAIN table
-                                            // 2 : don't concatenate the POINTING table
-                                            // 3 : neither concat MAIN nor POINTING table
-                   const String& destMSName=""); // support for virtual concat
+		   const uInt handling=0,   //# 0 (default): complete concat of all tables
+                                            //# 1 : don't concatenate the MAIN table
+                                            //# 2 : don't concatenate the POINTING table
+                                            //# 3 : neither concat MAIN nor POINTING table
+                   const String& destMSName=""); //# support for virtual concat
 
   void setTolerance(Quantum<Double>& freqTol, Quantum<Double>& dirTol); 
   void setWeightScale(const Float weightScale); 
-  void setRespectForFieldName(const Bool respectFieldName); // If True, fields of same direction are not merged
-                                                            // if their name is different
+  void setRespectForFieldName(const Bool respectFieldName); //# If True, fields of same direction are not merged
+                                                            //# if their name is different
 
 private:
   MSConcat();
@@ -126,7 +110,7 @@ class MSConcat: public MSColumns
   Bool copySysCal(const MSSysCal& otherSysCal, const Block<uInt>& newAndIndices);
   Bool copyWeather(const MSWeather& otherWeather, const Block<uInt>& newAndIndices);
   Int copyObservation(const MSObservation& otherObs, const Bool remRedunObsId=True);
-                             // by default remove redundant observation table rows
+                             //# by default remove redundant observation table rows
   Block<uInt> copyAntennaAndFeed(const MSAntenna& otherAnt,
 				 const MSFeed& otherFeed);
   Block<uInt> copyState(const MSState& otherState);

msfits/MSFits/MSFitsOutput.h

@@ -58,10 +58,10 @@ class MSFitsOutput {
         const String& column
     );
 
-    //  @param startchan     1st channel
+    //  @param startChan     1st channel
     //  @param nchan         # of channels
-    //  @param stepchan      # of channels to stride by
-    //  @param avgchan       average every N channels
+    //  @param stepChan      # of channels to stride by
+    //  @param avgChan       average every N channels
     void setChannelInfo(
         Int startChan, Int nchan, Int stepChan, Int avgChan
     );
@@ -114,6 +114,7 @@ class MSFitsOutput {
     //                       as needed to fit the IF structure.  Does not yet
     //                       support spws with different shapes.
     //  @param avgchan       average every N channels
+    //  @param fieldNumber   field number
     //  @param overwrite     overwrite existing file?
     static Bool writeFitsFile(
         const String& fitsfile, const MeasurementSet& ms,
@@ -141,21 +142,12 @@ class MSFitsOutput {
     //    @param refFreq
     //    @param chanbw
     //    @param outFITSFile
-    //    @param rawms
-    //    @param column         data column to write
     //    @param spwidMap       spwidMap[inp_spw] = output_spw, if inp_spw is selected
     //                                              -1 otherwise.
     //    @param nrspw          # of selected spws.
-    //    @param startchan      First channel
-    //    @param nchan          # of channels
-    //    @param stepchan       channel stride
     //    @param fieldidMap     fieldidMap[inp_fld] = output_fld, if inp_fld is selected
     //                                                -1 otherwise.
     //    @param asMultiSource  If true, write a multisource UVFITS file.
-    //    @param combineSpw     If true, export the spectral window(s) as IF(s).
-    //    @param padWithFlags   If true && combineSpw==true, pad the spws with
-    //                          flags as necessary to fit the IF structure.
-    //    @param avgchan        average every N channels
     FitsOutput* _writeMain(
         Int& refPixelFreq, Double& refFreq,
         Double& chanbw, const String& outFITSFile,

scimath/Mathematics/AutoDiff.h

@@ -165,9 +165,7 @@ namespace casacore { //# NAMESPACE CASACORE - BEGIN
 //
 // All operators and functions are declared in <linkto file=AutoDiffMath.h> 
 // AutoDiffMath</linkto>. The output operator in 
-// <linkto file=AutoDiffIO.h>AutoDiffIO</linkto>. The actual structure of the
-// data block used by <src>AutoDiff</src> is described in 
-// <linkto class=AutoDiffRep>AutoDiffRep</linkto>.
+// <linkto file=AutoDiffIO.h>AutoDiffIO</linkto>.
 // </synopsis>
 //
 // <example>

tables/LogTables/LoggerHolder.h

@@ -317,7 +317,7 @@ class LoggerHolderRep
   //    cout << iter.message() << endl;
   //  }
   // </srcblock>
-  // <group name=STL-iterator>
+  // <group name=STL-iterator-rep>
   // STL-style typedefs.
   typedef LoggerHolderIterator const_iterator;
   // Get the begin and end iterator object.