From 5af8b13c0f60d0929ab9af8c4208ab3e1fb4fdd2 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Tue, 14 Mar 2006 22:12:16 +0000
Subject: [PATCH] make doxygen output more focused make all of our exceptions
 derive from one base class so doxygen will group them.

Also stop generating docs for mussa_fltk.

And in the process I found that I hadn't updated the main cxx for mussa
fltk to the new cpp standard
---
 Doxyfile                    |  2 +-
 module.mk                   |  6 +++---
 mussa_exceptions.hpp        | 23 +++++++++++++++--------
 mussa.cpp => mussa_fltk.cpp |  0
 4 files changed, 19 insertions(+), 12 deletions(-)
 rename mussa.cpp => mussa_fltk.cpp (100%)

diff --git a/Doxyfile b/Doxyfile
index dcb2701..3f2a47d 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -450,7 +450,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = gui alg qui .
+INPUT                  = alg qui .
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
diff --git a/module.mk b/module.mk
index 0a9517b..b24137d 100644
--- a/module.mk
+++ b/module.mk
@@ -1,10 +1,10 @@
 CURDIR := $(BASEDIR)
 
-SOURCES.cxx := mussa.cxx \
+SOURCES.cpp := mussa_fltk.cpp \
 							 #seqcomp.cxx \ #(old seqcomp)
 							 #mussa_nway_refine.cxx \ (broken code)
 
-MUSSASRC := $(addprefix $(CURDIR), $(SOURCES.cxx))
+MUSSASRC := $(addprefix $(CURDIR), $(SOURCES.cpp))
 
 SRC += $(MUSSASRC)
 CXXFLAGS += -I$(CURDIR)
@@ -12,5 +12,5 @@ CXXFLAGS += -I$(CURDIR)
 MUSSA := $(CURDIR)/mussa$(BINEXT) 
 TARGETBINS += $(MUSSA)
 
-$(MUSSA): $(MUSSASRC:.cxx=$(OBJEXT)) $(MUSSA_FLTK_OBJ) $(MUSSA_ALG_OBJ)
+$(MUSSA): $(MUSSASRC:.cpp=$(OBJEXT)) $(MUSSA_FLTK_OBJ) $(MUSSA_ALG_OBJ)
 	g++ $(CXXFLAGS) -lfltk -o $@ $^
diff --git a/mussa_exceptions.hpp b/mussa_exceptions.hpp
index 53c167c..bf76e3b 100644
--- a/mussa_exceptions.hpp
+++ b/mussa_exceptions.hpp
@@ -2,33 +2,40 @@
 #define _MUSSA_EXCEPTIONS_H_
 #include <stdexcept>
 
+//! base mussa exception
+class mussa_error : public std::runtime_error
+{
+public:
+  explicit mussa_error(const std::string& msg): std::runtime_error(msg) {};
+};
+
 //! Error processing commandline arguments
-class cmdline_error : public std::runtime_error
+class cmdline_error : public mussa_error
 {
 public:
-  explicit cmdline_error(const std::string& msg): std::runtime_error(msg) {};
+  explicit cmdline_error(const std::string& msg): mussa_error(msg) {};
 };
 
 //! Error loading information
-class mussa_load_error : public std::runtime_error
+class mussa_load_error : public mussa_error
 {
 public:
   explicit mussa_load_error(const std::string& msg) : 
-    std::runtime_error(msg) {};
+    mussa_error(msg) {};
 };
 
 //! failure running analysis
-class mussa_analysis_error : public std::runtime_error
+class mussa_analysis_error : public mussa_error
 {
 public:
   explicit mussa_analysis_error(const std::string& msg) : 
-    std::runtime_error(msg) {};
+    mussa_error(msg) {};
 };
 
-class motif_normalize_error : public std::runtime_error
+class motif_normalize_error : public mussa_error
 {
 public:
   explicit motif_normalize_error(const std::string& msg) : 
-    std::runtime_error(msg) {};
+    mussa_error(msg) {};
 };
 #endif
diff --git a/mussa.cpp b/mussa_fltk.cpp
similarity index 100%
rename from mussa.cpp
rename to mussa_fltk.cpp
-- 
2.30.2