Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D().

Adds esl_free(), which allows ptr to be NULL. This is actually
unnecessary. C99 free() accepts NULL as a no-op.

Adds esl_msa_Sizeof(), which I intend to use to pull some alirecsize
capability into esl-alistat. Also, utest_Sizeof() unit test for it.

[SRE:H4/146]

Makefile.in

@@ -96,7 +96,8 @@ endif
 HDRS = 	easel.h\
 	esl_alloc.h\
 	esl_alphabet.h\
-	esl_vmx.h\
+	esl_arr2.h\
+	esl_arr3.h\
 	esl_avx.h\
 	esl_avx512.h\
 	esl_buffer.h\
@@ -162,13 +163,16 @@ HDRS = 	easel.h\
 	esl_threads.h\
 	esl_tree.h\
 	esl_vectorops.h\
+	esl_vmx.h\
 	esl_weibull.h\
 	esl_workqueue.h\
 	esl_wuss.h
 
 OBJS =	easel.o\
 	esl_alloc.o\
 	esl_alphabet.o\
+	esl_arr2.o\
+	esl_arr3.o\
 	esl_buffer.o\
 	esl_cluster.o\
 	esl_composition.o\

easel.c

@@ -327,6 +327,22 @@ esl_fatal(const char *format, ...)
  * 2. Memory allocation/deallocation conventions.
  *****************************************************************/
 
+/* Function:  esl_free()
+ * Synopsis:  free(), while allowing ptr to be NULL.
+ * Incept:    SRE, Fri Nov  3 17:12:01 2017
+ *
+ * Purpose:   Easel uses a convention of initializing ptrs to be NULL
+ *            before allocating them. When cleaning up after errors, a
+ *            routine can check for non-NULL ptrs to know what to
+ *            free(). Easel code is slightly cleaner if we have a
+ *            free() that no-ops on NULL ptrs.
+ */
+void
+esl_free(void *p)
+{
+  if (p) free(p);
+}
+
 /* Function:  esl_Free2D()
  *
  * Purpose:   Free a 2D pointer array <p>, where first dimension is
@@ -335,6 +351,8 @@ esl_fatal(const char *format, ...)
  *            sparse arrays.
  *
  * Returns:   void.
+ *
+ * DEPRECATED. Replace with esl_arr2_Destroy()
  */
 void
 esl_Free2D(void **p, int dim1)
@@ -356,6 +374,8 @@ esl_Free2D(void **p, int dim1)
  *            pointers being NULL, to allow sparse arrays.
  *
  * Returns:   void.
+ *
+ * DEPRECATED. Replace with esl_arr3_Destroy()
  */
 void
 esl_Free3D(void ***p, int dim1, int dim2)

easel.h

@@ -438,6 +438,7 @@ extern void esl_nonfatal_handler(int errcode, int use_errno, char *sourcefile, i
 extern void esl_fatal(const char *format, ...) ESL_ATTRIBUTE_NORETURN;
 
 /* 2. Memory allocation/deallocation conventions. */
+extern void esl_free(void *p);
 extern void esl_Free2D(void  **p, int dim1);
 extern void esl_Free3D(void ***p, int dim1, int dim2);
 

esl_arr2.c

@@ -0,0 +1,57 @@
+#include "esl_config.h"
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "easel.h"
+
+
+
+/* Function:  esl_arr2_SSizeof()
+ * Synopsis:  Returns size of a 2D array of \0-terminated strings, in bytes
+ * Incept:    SRE, Fri Nov  3 15:15:56 2017
+ */
+size_t
+esl_arr2_SSizeof(char **s, int dim1)
+{
+  size_t n = 0;
+  int    i;
+
+  if (s)
+    {
+      n += sizeof(char *) * dim1;
+      for (i = 0; i < dim1; i++)
+        if (s[i]) 
+          n += sizeof(char) * (1 + strlen(s[i]));
+    }
+  return n;
+}
+
+/* Function:  esl_arr2_Destroy()
+ * Synopsis:  Free a 2D array.
+ * Incept:    SRE, Fri Nov  3 15:32:21 2017
+ *
+ * Purpose:   Free a 2D pointer array <p>, where first dimension is
+ *            <dim1>. (That is, the array is <p[0..dim1-1][]>.)
+ *            Tolerates any of the pointers being NULL, to allow
+ *            sparse arrays.
+ *
+ * Returns:   (void)
+ *
+ * Throws:    (no abnormal error conditions)
+ *
+ * Xref:      Was <esl_Free2D()>.
+ */
+void
+esl_arr2_Destroy(void **p, int dim1)
+{
+  int i;
+
+  if (p) 
+    {
+      for (i = 0; i < dim1; i++)
+        if (p[i]) 
+          free(p[i]);
+      free(p);
+    }
+}

esl_arr2.h

@@ -0,0 +1,9 @@
+#ifndef eslARR2_INCLUDED
+#define eslARR2_INCLUDED
+
+#include <stdlib.h>
+
+extern size_t esl_arr2_SSizeof(char **s, int dim1);
+extern void   esl_arr2_Destroy(void **p, int dim1);
+
+#endif // eslARR2_INCLUDED

esl_arr3.c

@@ -0,0 +1,69 @@
+#include "esl_config.h"
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "easel.h"
+
+/* Function:  esl_arr3_SSizeof()
+ * Synopsis:  Returns size of 3D array of \0-terminated strings, in bytes
+ * Incept:    SRE, Fri Nov  3 15:19:53 2017
+ */
+size_t
+esl_arr3_SSizeof(char ***s, int dim1, int dim2)
+{
+  size_t n = 0;
+  int    i,j;
+
+  if (s)
+    {
+      n += sizeof(char **) * dim1;
+      for (i = 0; i < dim1; i++)
+        if (s[i])
+          {
+            n += sizeof(char *) * dim2;
+            for (j = 0; j < dim2; j++)
+              {
+                if (s[i][j]) 
+                  n += sizeof(char) * (1 + strlen(s[i][j]));
+              }
+          }
+    }
+  return n;
+}
+
+
+
+/* Function:  esl_arr3_Destroy()
+ * Synopsis:  Free a 3D array.
+ * Incept:    SRE, Fri Nov  3 15:38:39 2017
+ *
+ * Purpose:   Free a 3D pointer array <p>, where first and second
+ *            dimensions are <dim1>,<dim2>. (That is, the array is
+ *            <p[0..dim1-1][0..dim2-1][]>.) Tolerates any of the
+ *            pointers being NULL, to allow sparse arrays.
+ *
+ * Returns:   (void)
+ *
+ * Throws:    (no abnormal error conditions)
+ *
+ * Xref:      Was <esl_Free3D()>.
+ */
+void
+esl_arr3_Destroy(void ***p, int dim1, int dim2)
+{
+  int i, j;
+
+  if (p)
+    {
+      for (i = 0; i < dim1; i++)
+        if (p[i]) 
+          {
+            for (j = 0; j < dim2; j++)
+              if (p[i][j])
+                free(p[i][j]);
+            free(p[i]);
+          }
+      free(p);
+    }
+}

esl_arr3.h

@@ -0,0 +1,9 @@
+#ifndef eslARR3_INCLUDED
+#define eslARR3_INCLUDED
+
+#include <stdlib.h>
+
+extern size_t esl_arr3_SSizeof(char ***s, int dim1, int dim2);
+extern void   esl_arr3_Destroy(void ***p, int dim1, int dim2);
+
+#endif // eslARR3_INCLUDED

esl_distance.c

@@ -1414,6 +1414,7 @@ utest_XJukesCantorMx(ESL_ALPHABET *abc, char **as, ESL_DSQ **ax, int N)
 #ifdef eslDISTANCE_TESTDRIVE
 #include "easel.h"
 #include "esl_alphabet.h"
+#include "esl_arr2.h"
 #include "esl_dmatrix.h"
 #include "esl_getopts.h"
 #include "esl_random.h"
@@ -1505,9 +1506,9 @@ main(int argc, char **argv)
 
 
   esl_randomness_Destroy(r);
-  esl_Free2D((void **) as, N);
   esl_alphabet_Destroy(abc);
-  esl_Free2D((void **) ax, N);
+  esl_arr2_Destroy((void **) as, N);
+  esl_arr2_Destroy((void **) ax, N);
   return eslOK;
 
  ERROR:

esl_keyhash.c

@@ -145,10 +145,13 @@ esl_keyhash_Sizeof(const ESL_KEYHASH *kh)
 {
   size_t n = 0;
 
-  n += sizeof(ESL_KEYHASH);
-  n += sizeof(int)  * kh->hashsize;
-  n += sizeof(int)  * kh->kalloc * 2;
-  n += sizeof(char) * kh->salloc;
+  if (kh)
+    {
+      n += sizeof(ESL_KEYHASH);
+      n += sizeof(int)  * kh->hashsize;
+      n += sizeof(int)  * kh->kalloc * 2;
+      n += sizeof(char) * kh->salloc;
+    }
   return n;
 }