Fix/508 for code review

ChangeLog

@@ -1,3 +1,12 @@
+2014-07-24  Ivan Gonzalez  <iglpdc@gmail.com>
+
+    * lib/khmer.hh, lib/khmer_exception.hh: All exceptions are now derived from
+	a new base class exception, khmer::khmer_exception. Issue #508.
+    * lib/counting.cc, lib/hashbits.cc, lib/hashtable.{cc,hh},lib/kmer_hash.cc,
+	lib/labelhash.cc, lib/perf_metrics.hh, lib/read_parsers.{cc,hh},
+	lib/subset.cc, lib/thread_id_map.hh: All exceptions thrown are now
+	instances (or derived from) khmer::khmer_exception.
+
 2014-07-22  Jeramia Ory <jeramia.ory@gmail.com>
 
     * khmer/_khmermodule.cc: removed unused KhmerError, issue #503

lib/counting.cc

@@ -107,7 +107,7 @@ CountingHash::abundance_distribution(
     // if not, could lead to overflow.
     if (sizeof(BoundedCounterType) != 2) {
         delete[] dist;
-        throw std::exception();
+        throw khmer_exception();
     }
 
     while(!parser->is_complete()) {
@@ -282,7 +282,7 @@ void CountingHash::get_kadian_count(
     }
 
     if (!counts.size()) {
-        throw std::exception();
+        throw khmer_exception();
     }
     unsigned int kpos = nk * _ksize;
 
@@ -658,7 +658,7 @@ CountingHashFileWriter::CountingHashFileWriter(
     const CountingHash  &ht)
 {
     if (!ht._counts[0]) {
-        throw std::exception();
+        throw khmer_exception();
     }
 
     unsigned int save_ksize = ht._ksize;
@@ -711,7 +711,7 @@ CountingHashGzFileWriter::CountingHashGzFileWriter(
     const CountingHash  &ht)
 {
     if (!ht._counts[0]) {
-        throw std::exception();
+        throw khmer_exception();
     }
 
     unsigned int save_ksize = ht._ksize;

lib/hashbits.cc

@@ -19,7 +19,7 @@ using namespace khmer:: read_parsers;
 void Hashbits::save(std::string outfilename)
 {
     if (!_counts[0]) {
-        throw std::exception();
+        throw khmer_exception();
     }
 
     unsigned int save_ksize = _ksize;

lib/hashtable.cc

@@ -316,7 +316,7 @@ void Hashtable::get_median_count(const std::string &s,
     }
 
     if (!counts.size()) {
-        throw std::exception();
+        throw khmer_exception();
     }
 
     if (!counts.size()) {
@@ -1159,7 +1159,7 @@ const
         }
 
         if (!(breadth >= cur_breadth)) { // keep track of watermark, for debugging.
-            throw std::exception();
+            throw khmer_exception();
         }
         if (breadth > cur_breadth) {
             cur_breadth = breadth;
@@ -1524,7 +1524,7 @@ const
         }
 
         if (!(breadth >= cur_breadth)) { // keep track of watermark, for debugging.
-            throw std::exception();
+            throw khmer_exception();
         }
         if (breadth > cur_breadth) {
             cur_breadth = breadth;
@@ -1729,7 +1729,7 @@ const
         }
 
         if (!(breadth >= cur_breadth)) { // keep track of watermark, for debugging.
-            throw std::exception();
+            throw khmer_exception();
         }
         if (breadth > cur_breadth) {
             cur_breadth = breadth;
@@ -2036,7 +2036,7 @@ void Hashtable::extract_unique_paths(std::string seq,
         // then extract.
 
         if (!(j == min_length)) {
-            throw std::exception();
+            throw khmer_exception();
         }
         if ( ((float)seen_counter / (float) j) <= max_seen) {
             unsigned int start = i;

lib/hashtable.hh

@@ -10,7 +10,6 @@
 
 #include <vector>
 #include <iostream>
-#include <exception>
 #include <list>
 #include <queue>
 
@@ -21,6 +20,7 @@
 #include <queue>
 
 #include "khmer.hh"
+#include "khmer_exception.hh"
 #include "read_parsers.hh"
 #include "subset.hh"
 #include "kmer_hash.hh"
@@ -109,7 +109,7 @@ public:
 
     HashIntoType next(HashIntoType& f, HashIntoType& r) {
         if (done()) {
-            throw std::exception();
+            throw khmer_exception();
         }
 
         if (!initialized) {
@@ -120,7 +120,7 @@ public:
         unsigned char ch = _seq[index];
         index++;
         if (!(index <= length)) {
-            throw std::exception();
+            throw khmer_exception();
         }
 
         // left-shift the previous hash over
@@ -211,7 +211,7 @@ protected:
             _ksize( ksize ) {
         _tag_density = DEFAULT_TAG_DENSITY;
         if (!(_tag_density % 2 == 0)) {
-            throw std::exception();
+            throw khmer_exception();
         }
         partition = new SubsetPartition(this);
         _init_bitstuff();
@@ -398,7 +398,7 @@ public:
     // for debugging/testing purposes only!
     void _set_tag_density(unsigned int d) {
         if (!(d % 2 == 0) || !all_tags.empty()) { // must be even and tags must exist
-            throw std::exception();
+            throw khmer_exception();
         }
         _tag_density = d;
     }

lib/khmer.hh

@@ -34,12 +34,12 @@ __attribute__((cpychecker_type_object_for_typedef(typename)))
 #define CPYCHECKER_TYPE_OBJECT_FOR_TYPEDEF(typename)
 #endif
 
-// C++ standard exceptions are subclassed almost ubiquitously.
-#include <exception>
 #include <set>
 #include <map>
 #include <queue>
 
+#include "khmer_exception.hh"
+
 #   define MAX_COUNT 255
 #   define MAX_BIGCOUNT 65535
 #   define DEFAULT_TAG_DENSITY 40   // must be even
@@ -80,10 +80,6 @@ typedef void (*CallbackFn)(const char * info, void * callback_data,
                            unsigned long long n_reads,
                            unsigned long long other);
 
-struct InvalidStreamBuffer : public std:: exception {
-};
-
-
 typedef unsigned int PartitionID;
 typedef std::set<HashIntoType> SeenSet;
 typedef std::set<PartitionID> PartitionSet;
@@ -116,34 +112,6 @@ void deallocate_ptr_set(T& s)
     }
 }
 
-class khmer_file_exception : public std::exception
-{
-public:
-    khmer_file_exception(const char * msg) : _msg(msg) { };
-
-    virtual const char* what() const throw() {
-        return _msg;
-    }
-protected:
-    const char * _msg;
-};
-
-class InvalidStreamHandle : public khmer_file_exception
-{
-public:
-    InvalidStreamHandle()
-        : khmer_file_exception("Generic InvalidStreamHandle error") {}
-    InvalidStreamHandle(const char * msg) : khmer_file_exception(msg) {}
-};
-
-class StreamReadError : public khmer_file_exception
-{
-public:
-    StreamReadError()
-        : khmer_file_exception("Generic StreamReadError error") {}
-    StreamReadError(const char * msg) : khmer_file_exception(msg) {}
-};
-
 }
 
 #endif // KHMER_HH

lib/khmer_exception.hh

@@ -0,0 +1,70 @@
+//
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2009-2013. It is licensed under
+// the three-clause BSD license; see doc/LICENSE.txt.
+// Contact: khmer-project@idyll.org
+//
+
+#ifndef KHMER_EXCEPTION_HH
+#define KHMER_EXCEPTION_HH
+
+#include <exception>
+#include <string>
+
+namespace khmer
+{
+
+/// 
+// A base class for all exceptions.
+//
+// All exceptions should be derived from this base class.
+//
+class khmer_exception : public std::exception
+{
+public:
+    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; }
+
+protected:
+    const char * _msg;
+};
+
+///
+// A base class for file exceptions.
+//
+class khmer_file_exception : public khmer_exception
+{
+public:
+    explicit khmer_file_exception(const char * msg) : khmer_exception(msg) { }
+    explicit khmer_file_exception(const std::string& msg)
+        : khmer_exception(msg) { }
+};
+
+struct InvalidStreamBuffer : public khmer_exception {
+};
+
+class InvalidStreamHandle : public khmer_file_exception
+{
+public:
+    InvalidStreamHandle()
+        : khmer_file_exception("Generic InvalidStreamHandle error") {}
+    InvalidStreamHandle(const char * msg) : khmer_file_exception(msg) {}
+};
+
+class StreamReadError : public khmer_file_exception
+{
+public:
+    StreamReadError()
+        : khmer_file_exception("Generic StreamReadError error") {}
+    StreamReadError(const char * msg) : khmer_file_exception(msg) {}
+};
+
+}
+
+#endif // KHMER_EXCEPTION_HH
+
+// vim: set sts=2 sw=2:

lib/kmer_hash.cc

@@ -28,7 +28,7 @@ HashIntoType _hash(const char * kmer, const WordLength k,
 {
     // sizeof(HashIntoType) * 8 bits / 2 bits/base
     if (!(k <= sizeof(HashIntoType)*4) || !(strlen(kmer) >= k)) {
-        throw std::exception();
+        throw khmer_exception();
     }
 
     HashIntoType h = 0, r = 0;

lib/labelhash.cc

@@ -320,7 +320,7 @@ unsigned int LabelHash::sweep_label_neighborhood(const std::string& seq,
     //printf("range=%u ", range);
     if (range == 0) {
         if (!(num_traversed == seq.length()-ksize()+1)) {
-            throw std::exception();
+            throw khmer_exception();
         }
     }
     tagged_kmers.clear();

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 {
 };
 
 

lib/read_parsers.cc

@@ -1411,23 +1411,23 @@ IParser(
             REG_EXTENDED | REG_NOSUB
         );
     if (regex_rc) {
-        throw std::exception();
+        throw khmer_exception();
     }
     regex_rc =
         regcomp(
             &_re_read_1,
             "^.+(/1| 1:[YN]:[[:digit:]]+:[[:alpha:]]+).{0}", REG_EXTENDED
         );
     if (regex_rc) {
-        throw std::exception();
+        throw khmer_exception();
     }
     regex_rc =
         regcomp(
             &_re_read_2,
             "^.+(/2| 2:[YN]:[[:digit:]]+:[[:alpha:]]+).{0}", REG_EXTENDED
         );
     if (regex_rc) {
-        throw std::exception();
+        throw khmer_exception();
     }
 }
 

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