From 92135e8032e499167dec6098c663f7ebb0b0b499 Mon Sep 17 00:00:00 2001
From: Ivan Gonzalez <iglpdc@gmail.com>
Date: Tue, 22 Jul 2014 21:40:17 +0200
Subject: [PATCH] All exceptions defined in khmer are derived class from
 khmer::khmer_exception, including khmer::khmer_file_exception.

---
 lib/khmer.hh           |  4 ++--
 lib/khmer_exception.hh | 18 +++++++++++++-----
 lib/perf_metrics.hh    |  4 +---
 lib/read_parsers.hh    | 12 ++++++------
 lib/thread_id_map.hh   |  5 ++---
 5 files changed, 24 insertions(+), 19 deletions(-)

diff --git a/lib/khmer.hh b/lib/khmer.hh
index 612b93240e..93f856cda9 100644
--- a/lib/khmer.hh
+++ b/lib/khmer.hh
@@ -58,7 +58,7 @@ __attribute__((cpychecker_type_object_for_typedef(typename)))
 #   define MIN( a, b )	(((a) > (b)) ? (b) : (a))
 #   define MAX( a, b )	(((a) < (b)) ? (b) : (a))
 
-#include <khmer_exception.hh>
+#include "khmer_exception.hh"
 namespace khmer
 {
 // largest number we can count up to, exactly. (8 bytes)
@@ -79,7 +79,7 @@ typedef void (*CallbackFn)(const char * info, void * callback_data,
                            unsigned long long n_reads,
                            unsigned long long other);
 
-struct InvalidStreamBuffer : public std:: exception {
+struct InvalidStreamBuffer : public khmer_exception {
 };
 
 
diff --git a/lib/khmer_exception.hh b/lib/khmer_exception.hh
index 7ecedc9838..741e3babc5 100644
--- a/lib/khmer_exception.hh
+++ b/lib/khmer_exception.hh
@@ -9,6 +9,7 @@
 #define KHMER_EXCEPTION_HH
 
 #include <exception>
+#include <string>
 
 namespace khmer
 {
@@ -21,19 +22,26 @@ namespace khmer
 class khmer_exception : public std::exception
 {
 public:
-    khmer_exception(const char * msg) : _msg(msg) { };
+    explicit khmer_exception(const char * msg) : _msg(msg) { }
+    explicit khmer_exception(const std::string& msg = "Generic khmer exception")
+        : _msg(msg.c_str()) { }
+
+    virtual ~khmer_exception() throw() { }
+    virtual const char* what() const throw () { return _msg; }
 
-    virtual const char* what() const throw() {
-        return _msg;
-    }
 protected:
     const char * _msg;
 };
 
+///
+// A base class for file exceptions.
+//
 class khmer_file_exception : public khmer_exception
 {
 public:
-    khmer_file_exception(const char * msg) : khmer_exception(msg) { };
+    explicit khmer_file_exception(const char * msg) : khmer_exception(msg) { }
+    explicit khmer_file_exception(const std::string& msg)
+        : khmer_exception(msg) { }
 };
 
 }
diff --git a/lib/perf_metrics.hh b/lib/perf_metrics.hh
index c4a377b9a1..aecd21d879 100644
--- a/lib/perf_metrics.hh
+++ b/lib/perf_metrics.hh
@@ -12,16 +12,14 @@
 #include <cstring>
 #include <ctime>
 
-#include <exception>
 
 #include "khmer.hh"
 
-
 namespace khmer
 {
 
 #ifdef WITH_INTERNAL_METRICS
-struct InvalidPerformanceMetricsKey : public std:: exception {
+struct InvalidPerformanceMetricsKey : public khmer_exception {
 };
 
 
diff --git a/lib/read_parsers.hh b/lib/read_parsers.hh
index cba6bef8da..6668c87e7f 100644
--- a/lib/read_parsers.hh
+++ b/lib/read_parsers.hh
@@ -84,22 +84,22 @@ public:
 
 };
 
-struct CacheSegmentUnavailable : public std:: exception {
+struct CacheSegmentUnavailable : public  khmer_exception {
 };
 
-struct CacheSegmentBoundaryViolation : public std:: exception {
+struct CacheSegmentBoundaryViolation : public  khmer_exception {
 };
 
-struct InvalidCacheSizeRequested : public std:: exception {
+struct InvalidCacheSizeRequested : public  khmer_exception {
 };
 
-struct NoMoreReadsAvailable : public std:: exception {
+struct NoMoreReadsAvailable : public  khmer_exception {
 };
 
-struct UnknownPairReadingMode : public std:: exception {
+struct UnknownPairReadingMode : public  khmer_exception {
 };
 
-struct InvalidReadPair : public std:: exception {
+struct InvalidReadPair : public  khmer_exception {
 };
 
 #ifdef WITH_INTERNAL_METRICS
diff --git a/lib/thread_id_map.hh b/lib/thread_id_map.hh
index b1e718d95a..4d3d7f3124 100644
--- a/lib/thread_id_map.hh
+++ b/lib/thread_id_map.hh
@@ -8,7 +8,6 @@
 #ifndef THREAD_ID_MAP_HH
 #   define THREAD_ID_MAP_HH
 
-#include <exception>
 #include <map>
 
 // TODO? Just use 'pthread_t' everywhere.
@@ -31,10 +30,10 @@ namespace khmer
 {
 
 
-struct InvalidNumberOfThreadsRequested : public std:: exception {
+struct InvalidNumberOfThreadsRequested : public khmer_exception {
 };
 
-struct TooManyThreads : public std:: exception {
+struct TooManyThreads : public khmer_exception {
 };