Run astyle on all cc/hh files in lib

Moved suppressions to inline comments, update Makefile accordingly and remove unused suppressions.txt Fix assign_partition_id to use .empty() instead of .size() Move cppcheck suppressions to same line as variables Fix suppressions comment format, properly wrap nbfilled in ifdef
dib-lab · Sep 19, 2014 · 5dcc6a7 · 5dcc6a7
1 parent 8890e22
commit 5dcc6a7
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Showing 18 changed files with 194 additions and 112 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,14 @@
+2014-09-19  Ben Taylor  <taylo886@msu.edu>
+
+    * Makefile: add --inline-suppr to cppcheck, cppcheck-result.xml targets
+    * khmer/_khmermodule.cc: Add comments to address cppcheck false positives
+    * lib/hashtable.cc, lib/hashtable.hh: take args to filter_if_present by
+    reference, address scope in destructor
+    * lib/read_parsers.cc: Add comments to address cppcheck false positives
+    * lib/subset.cc, lib/subset.hh: Adjust output_partitioned_file,
+    find_unpart to take args by reference, fix assign_partition_id to use
+    .empty() instead of .size()
+
 2014-09-10  Titus Brown  <titus@idyll.org>
 
     * sandbox/calc-median-distribution.py: catch exceptions generated by reads

diff --git a/Makefile b/Makefile
@@ -69,12 +69,12 @@ cppcheck-result.xml: $(CPPSOURCES)
 	ls lib/*.cc khmer/_khmermodule.cc | grep -v test | cppcheck -DNDEBUG \
 		-DVERSION=0.0.cppcheck -UNO_UNIQUE_RC --enable=all \
 		--file-list=- -j8 --platform=unix64 --std=posix --xml \
-		--xml-version=2 2> cppcheck-result.xml
+		--inline-suppr --xml-version=2 2> cppcheck-result.xml
 
 cppcheck: $(CPPSOURCES)
 	ls lib/*.cc khmer/_khmermodule.cc | grep -v test | cppcheck -DNDEBUG \
 		-DVERSION=0.0.cppcheck -UNO_UNIQUE_RC --enable=all \
-		--file-list=- -j8 --platform=unix64 --std=posix --quiet
+		--file-list=- -j8 --platform=unix64 --std=posix --inline-suppr --quiet
 
 pep8: $(PYSOURCES) $(wildcard tests/*.py)
 	pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ || true

diff --git a/khmer/_khmermodule.cc b/khmer/_khmermodule.cc
@@ -745,9 +745,9 @@ _ReadPairIterator_iternext( PyObject * self )
     uint8_t         pair_mode = myself->pair_mode;
 
     ReadPair    the_read_pair;
-
-    bool    stop_iteration      = false;
-    bool    invalid_file_format     = false;
+		// cppcheck-suppress unreadVariable
+    bool    stop_iteration      = false;  
+		bool    invalid_file_format     = false;
     char    exc_message[ CHAR_MAX ];
     bool    unknown_pair_reading_mode   = false;
     bool    invalid_read_pair       = false;
@@ -1991,8 +1991,9 @@ static PyObject * hash_abundance_distribution_with_reads_parser(
 
     read_parsers:: IParser * rparser = rparser_obj->parser;
     Hashbits * hashbits = tracking_obj->hashbits;
-
-    HashIntoType * dist = NULL;
+
+		// cppcheck-suppress unreadVariable
+    HashIntoType * dist = NULL;  
 
     Py_BEGIN_ALLOW_THREADS
     dist = counting->abundance_distribution(rparser, hashbits);

diff --git a/lib/counting.hh b/lib/counting.hh
@@ -40,7 +40,8 @@ protected:
 
     Byte ** _counts;
 
-    virtual void _allocate_counters() {
+    virtual void _allocate_counters()
+    {
         _n_tables = _tablesizes.size();
 
         _counts = new Byte*[_n_tables];
@@ -58,7 +59,8 @@ public:
             get_active_config( ).get_number_of_threads( )
     ) :
         khmer::Hashtable(ksize, number_of_threads),
-        _use_bigcount(false), _bigcount_spin_lock(false) {
+        _use_bigcount(false), _bigcount_spin_lock(false)
+    {
         _tablesizes.push_back(single_tablesize);
 
         _allocate_counters();
@@ -71,12 +73,14 @@ public:
     ) :
         khmer::Hashtable(ksize, number_of_threads),
         _use_bigcount(false), _bigcount_spin_lock(false),
-        _tablesizes(tablesizes) {
+        _tablesizes(tablesizes)
+    {
 
         _allocate_counters();
     }
 
-    virtual ~CountingHash() {
+    virtual ~CountingHash()
+    {
         if (_counts) {
             for (size_t i = 0; i < _n_tables; i++) {
                 if (_counts[i]) {
@@ -92,40 +96,47 @@ public:
         }
     }
 
-    virtual BoundedCounterType test_and_set_bits(const char * kmer) {
+    virtual BoundedCounterType test_and_set_bits(const char * kmer)
+    {
         BoundedCounterType x = get_count(kmer); // @CTB just hash it, yo.
         count(kmer);
         return !x;
     }
 
-    virtual BoundedCounterType test_and_set_bits(HashIntoType khash) {
+    virtual BoundedCounterType test_and_set_bits(HashIntoType khash)
+    {
         BoundedCounterType x = get_count(khash);
         count(khash);
         return !x;
     }
 
-    std::vector<HashIntoType> get_tablesizes() const {
+    std::vector<HashIntoType> get_tablesizes() const
+    {
         return _tablesizes;
     }
 
-    void set_use_bigcount(bool b) {
+    void set_use_bigcount(bool b)
+    {
         _use_bigcount = b;
     }
-    bool get_use_bigcount() {
+    bool get_use_bigcount()
+    {
         return _use_bigcount;
     }
 
     virtual void save(std::string);
     virtual void load(std::string);
 
     // accessors to get table info
-    const HashIntoType n_entries() const {
+    const HashIntoType n_entries() const
+    {
         return _tablesizes[0];
     }
 
     // count number of occupied bins
     virtual const HashIntoType n_occupied(HashIntoType start=0,
-                                          HashIntoType stop=0) const {
+                                          HashIntoType stop=0) const
+    {
         HashIntoType n = 0;
         if (stop == 0) {
             stop = _tablesizes[0];
@@ -138,12 +149,14 @@ public:
         return n;
     }
 
-    virtual void count(const char * kmer) {
+    virtual void count(const char * kmer)
+    {
         HashIntoType hash = _hash(kmer, _ksize);
         count(hash);
     }
 
-    virtual void count(HashIntoType khash) {
+    virtual void count(HashIntoType khash)
+    {
 
         unsigned int  n_full	  = 0;
 
@@ -177,13 +190,15 @@ public:
     } // count
 
     // get the count for the given k-mer.
-    virtual const BoundedCounterType get_count(const char * kmer) const {
+    virtual const BoundedCounterType get_count(const char * kmer) const
+    {
         HashIntoType hash = _hash(kmer, _ksize);
         return get_count(hash);
     }
 
     // get the count for the given k-mer hash.
-    virtual const BoundedCounterType get_count(HashIntoType khash) const {
+    virtual const BoundedCounterType get_count(HashIntoType khash) const
+    {
         unsigned int	  max_count	= _max_count;
         BoundedCounterType  min_count	= max_count;
         for (unsigned int i = 0; i < _n_tables; i++) {
@@ -269,7 +284,8 @@ public:
 class CountingHashGzFileWriter : public CountingHashFile
 {
 public:
-    CountingHashGzFileWriter(const std::string &outfilename, const CountingHash &ht);
+    CountingHashGzFileWriter(const std::string &outfilename,
+                             const CountingHash &ht);
 };
 };
 

diff --git a/lib/hashbits.hh b/lib/hashbits.hh
@@ -26,7 +26,8 @@ protected:
     HashIntoType _n_overlap_kmers;
     Byte ** _counts;
 
-    virtual void _allocate_counters() {
+    virtual void _allocate_counters()
+    {
         _n_tables = _tablesizes.size();
 
         _counts = new Byte*[_n_tables];
@@ -43,15 +44,17 @@ protected:
 public:
     Hashbits(WordLength ksize, std::vector<HashIntoType>& tablesizes)
         : khmer::Hashtable(ksize),
-          _tablesizes(tablesizes) {
+          _tablesizes(tablesizes)
+    {
         _occupied_bins = 0;
         _n_unique_kmers = 0;
         _n_overlap_kmers = 0;
 
         _allocate_counters();
     }
 
-    ~Hashbits() {
+    ~Hashbits()
+    {
         if (_counts) {
             for (size_t i = 0; i < _n_tables; i++) {
                 delete[] _counts[i];
@@ -65,15 +68,17 @@ public:
 
     }
 
-    std::vector<HashIntoType> get_tablesizes() const {
+    std::vector<HashIntoType> get_tablesizes() const
+    {
         return _tablesizes;
     }
 
     virtual void save(std::string);
     virtual void load(std::string);
 
     // for overlap k-mer counting
-    void consume_fasta_overlap(const std::string &filename,HashIntoType curve[2][100],
+    void consume_fasta_overlap(const std::string &filename,
+                               HashIntoType curve[2][100],
                                khmer::Hashbits &ht2,
                                unsigned int &total_reads,
                                unsigned long long &n_consumed,
@@ -92,21 +97,24 @@ public:
 
     // count number of occupied bins
     virtual const HashIntoType n_occupied(HashIntoType start=0,
-                                          HashIntoType stop=0) const {
+                                          HashIntoType stop=0) const
+    {
         // @@ CTB need to be able to *save* this...
         return _occupied_bins/_n_tables;
     }
 
     virtual const HashIntoType n_kmers(HashIntoType start=0,
-                                       HashIntoType stop=0) const {
+                                       HashIntoType stop=0) const
+    {
         return _n_unique_kmers;	// @@ CTB need to be able to *save* this...
     }
 
     // Get and set the hashbits for the given kmer.
     inline
     virtual
     BoundedCounterType
-    test_and_set_bits(const char * kmer) {
+    test_and_set_bits(const char * kmer)
+    {
         HashIntoType hash = _hash(kmer, _ksize);
         return test_and_set_bits(hash);
     }
@@ -119,7 +127,8 @@ public:
     inline
     virtual
     BoundedCounterType
-    test_and_set_bits( HashIntoType khash ) {
+    test_and_set_bits( HashIntoType khash )
+    {
         bool is_new_kmer = false;
 
         for (size_t i = 0; i < _n_tables; i++) {
@@ -143,16 +152,19 @@ public:
     } // test_and_set_bits
 
     virtual const HashIntoType n_overlap_kmers(HashIntoType start=0,
-            HashIntoType stop=0) const {
+            HashIntoType stop=0) const
+    {
         return _n_overlap_kmers;	// @@ CTB need to be able to *save* this...
     }
 
-    virtual void count(const char * kmer) {
+    virtual void count(const char * kmer)
+    {
         HashIntoType hash = _hash(kmer, _ksize);
         count(hash);
     }
 
-    virtual void count(HashIntoType khash) {
+    virtual void count(HashIntoType khash)
+    {
         bool is_new_kmer = false;
 
         for (size_t i = 0; i < _n_tables; i++) {
@@ -170,7 +182,8 @@ public:
         }
     }
 
-    virtual bool check_overlap(HashIntoType khash, Hashbits &ht2) {
+    virtual bool check_overlap(HashIntoType khash, Hashbits &ht2)
+    {
 
         for (size_t i = 0; i < ht2._n_tables; i++) {
             HashIntoType bin = khash % ht2._tablesizes[i];
@@ -183,12 +196,14 @@ public:
         return true;
     }
 
-    virtual void count_overlap(const char * kmer, Hashbits &ht2) {
+    virtual void count_overlap(const char * kmer, Hashbits &ht2)
+    {
         HashIntoType hash = _hash(kmer, _ksize);
         count_overlap(hash,ht2);
     }
 
-    virtual void count_overlap(HashIntoType khash, Hashbits &ht2) {
+    virtual void count_overlap(HashIntoType khash, Hashbits &ht2)
+    {
         bool is_new_kmer = false;
 
         for (size_t i = 0; i < _n_tables; i++) {
@@ -210,13 +225,15 @@ public:
     }
 
     // get the count for the given k-mer.
-    virtual const BoundedCounterType get_count(const char * kmer) const {
+    virtual const BoundedCounterType get_count(const char * kmer) const
+    {
         HashIntoType hash = _hash(kmer, _ksize);
         return get_count(hash);
     }
 
     // get the count for the given k-mer hash.
-    virtual const BoundedCounterType get_count(HashIntoType khash) const {
+    virtual const BoundedCounterType get_count(HashIntoType khash) const
+    {
         for (size_t i = 0; i < _n_tables; i++) {
             HashIntoType bin = khash % _tablesizes[i];
             HashIntoType byte = bin / 8;

diff --git a/lib/khmer.hh b/lib/khmer.hh
@@ -92,7 +92,8 @@ typedef std::queue<HashIntoType> NodeQueue;
 typedef std::map<PartitionID, PartitionID*> PartitionToPartitionPMap;
 typedef std::map<HashIntoType, unsigned int> TagCountMap;
 typedef std::map<PartitionID, unsigned int> PartitionCountMap;
-typedef std::map<unsigned long long, unsigned long long> PartitionCountDistribution;
+typedef std::map<unsigned long long, unsigned long long>
+PartitionCountDistribution;
 
 // types used in @camillescott's sparse labeling extension
 typedef unsigned long long int Label;

diff --git a/lib/khmer_exception.hh b/lib/khmer_exception.hh
@@ -14,7 +14,7 @@
 namespace khmer
 {
 
-/// 
+///
 // A base class for all exceptions.
 //
 // All exceptions should be derived from this base class.
@@ -27,7 +27,10 @@ public:
         : _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;

diff --git a/lib/labelhash.cc b/lib/labelhash.cc
@@ -129,11 +129,12 @@ LabelHash::consume_fasta_and_tag_with_labels(
 
 }
 
-void LabelHash::consume_partitioned_fasta_and_tag_with_labels(const std::string &filename,
-        unsigned int &total_reads,
-        unsigned long long &n_consumed,
-        CallbackFn callback,
-        void * callback_data)
+void LabelHash::consume_partitioned_fasta_and_tag_with_labels(
+    const std::string &filename,
+    unsigned int &total_reads,
+    unsigned long long &n_consumed,
+    CallbackFn callback,
+    void * callback_data)
 {
     total_reads = 0;
     n_consumed = 0;