Added simple print routines as an exercise in navigating the NCBI object structure.

11 files changed, 193 insertions, 0 deletions

diff --git a/src/model/asn_print/README b/src/model/asn_print/README
new file mode 100644
index 0000000..44ceb1f
--- a/dev/null
+++ b/src/model/asn_print/README
@@ -0,0 +1,3 @@
+The routines in asn_print are convenience routines done as an exercise
+to gain familiarity with the ASN.1 native structures and their
+hierarchy.
diff --git a/src/model/asn_print/asn_print_authlist.c b/src/model/asn_print/asn_print_authlist.c
new file mode 100644
index 0000000..c14e7d6
--- a/dev/null
+++ b/src/model/asn_print/asn_print_authlist.c
@@ -0,0 +1,31 @@
+#include "asn_print_authlist.h"
+#include "asn_print_personid.h"
+
+void
+asn_print_authlist (AuthListPtr a)
+{
+  switch (a->choice)
+    {
+    case 1 :
+      {
+	ValNodePtr name = a->names;
+	while (name != NULL)
+	  {
+	    AuthorPtr ap = (AuthorPtr)name->data.ptrvalue;
+	    PersonIdPtr pid = ap->name;
+	    printf ("        AUTHOR\n");
+	    asn_print_personid (pid);
+
+	    name = name->next;
+	  }
+	break;
+      }
+      
+    default:
+      printf ("AUTHLIST-CHOICE UNHANDLED: %i\n", a->choice);
+      exit (-1);
+      break;
+    }
+
+  return;
+}
diff --git a/src/model/asn_print/asn_print_authlist.h b/src/model/asn_print/asn_print_authlist.h
new file mode 100644
index 0000000..9fbbb52
--- a/dev/null
+++ b/src/model/asn_print/asn_print_authlist.h
@@ -0,0 +1,8 @@
+#ifndef ASN_PRINT_AUTHLIST_H
+#define ASN_PRINT_AUTHLIST_H
+
+#include <objbibli.h>
+
+void asn_print_authlist (AuthListPtr a);
+
+#endif // ASN_PRINT_AUTHLIST_H
diff --git a/src/model/asn_print/asn_print_citgen.c b/src/model/asn_print/asn_print_citgen.c
new file mode 100644
index 0000000..4e4edb3
--- a/dev/null
+++ b/src/model/asn_print/asn_print_citgen.c
@@ -0,0 +1,24 @@
+#include "asn_print_citgen.h"
+#include "asn_print_authlist.h"
+
+void
+asn_print_citgen (CitGenPtr c)
+{
+  printf ("      TYPE: %s\n", c->cit);
+
+  printf ("      TITLE: %s\n", c->title);
+
+  if (c->pmid != -1)
+    printf ("      PubMed ID: %i\n", c->pmid);
+
+  if (c->muid != -1)
+    printf ("      MEDLINE UID: %i\n", c->muid);
+
+  if (c->authors != NULL)
+    {
+      printf ("      AUTHORS\n");
+      asn_print_authlist (c->authors);
+    }
+  
+  return;
+}
diff --git a/src/model/asn_print/asn_print_citgen.h b/src/model/asn_print/asn_print_citgen.h
new file mode 100644
index 0000000..858dff6
--- a/dev/null
+++ b/src/model/asn_print/asn_print_citgen.h
@@ -0,0 +1,8 @@
+#ifndef ASN_PRINT_CITGEN_H
+#define ASN_PRINT_CITGEN_H
+
+#include <objbibli.h>
+
+void asn_print_citgen (CitGenPtr c);
+
+#endif // ASN_PRINT_CITGEN_H
diff --git a/src/model/asn_print/asn_print_citsub.c b/src/model/asn_print/asn_print_citsub.c
new file mode 100644
index 0000000..50878fc
--- a/dev/null
+++ b/src/model/asn_print/asn_print_citsub.c
@@ -0,0 +1,13 @@
+#include "asn_print_citsub.h"
+#include "asn_print_authlist.h"
+
+void
+asn_print_citsub (CitSubPtr s)
+{
+  if(s->authors != NULL)
+    {
+      printf ("      AUTHORS\n");
+      asn_print_authlist (s->authors);
+    }
+  return;
+}
diff --git a/src/model/asn_print/asn_print_citsub.h b/src/model/asn_print/asn_print_citsub.h
new file mode 100644
index 0000000..bd7dbe4
--- a/dev/null
+++ b/src/model/asn_print/asn_print_citsub.h
@@ -0,0 +1,8 @@
+#ifndef ASN_PRINT_CITSUB_H
+#define ASN_PRINT_CITSUB_H
+
+#include <objbibli.h>
+
+void asn_print_citsub (CitSubPtr s);
+
+#endif // ASN_PRINT_CITSUB_H
diff --git a/src/model/asn_print/asn_print_personid.c b/src/model/asn_print/asn_print_personid.c
new file mode 100644
index 0000000..b4b0711
--- a/dev/null
+++ b/src/model/asn_print/asn_print_personid.c
@@ -0,0 +1,42 @@
+#include "asn_print_personid.h"
+
+void
+asn_print_personid (PersonIdPtr p)
+{
+  switch (p->choice)
+    {
+    case 2 :
+      {
+	/*
+	 * Name
+	 *
+	 * Code affected by GCC Bug 37231 since this block starts with
+	 * a declaration.
+	 * [http://gcc.gnu.org/bugzilla/show_bug.cgi?id=37231]
+	 */
+	NameStdPtr n = p->data;
+	if (n->names[0] != NULL)
+	  printf ("          LAST: %s\n", n->names[0]);
+	if (n->names[1] != NULL)
+	  printf ("          FIRST: %s\n", n->names[1]);
+	if (n->names[2] != NULL)
+	  printf ("          MIDDLE: %s\n", n->names[2]);
+	if (n->names[3] != NULL)
+	  printf ("          FULL: %s\n", n->names[3]);
+	if (n->names[4] != NULL)
+	  printf ("          INITIALS: %s\n", n->names[4]);
+	if (n->names[5] != NULL)
+	  printf ("          SUFFIX: %s\n", n->names[5]);
+	if (n->names[6] != NULL)
+	  printf ("          TITLE: %s\n", n->names[6]);
+	break;
+      }
+      
+    default:
+      printf ("PERSONID-CHOICE UNHANDLED: %i\n", p->choice);
+      exit (-1);
+      break;
+    }
+
+  return;
+}
diff --git a/src/model/asn_print/asn_print_personid.h b/src/model/asn_print/asn_print_personid.h
new file mode 100644
index 0000000..e231c1e
--- a/dev/null
+++ b/src/model/asn_print/asn_print_personid.h
@@ -0,0 +1,8 @@
+#ifndef ASN_PRINT_PERSONID_H
+#define ASN_PRINT_PERSONID_H
+
+#include <objgen.h>
+
+void asn_print_personid (PersonIdPtr p);
+
+#endif // ASN_PRINT_PERSONID_H
diff --git a/src/model/asn_print/asn_print_pub.c b/src/model/asn_print/asn_print_pub.c
new file mode 100644
index 0000000..7880d03
--- a/dev/null
+++ b/src/model/asn_print/asn_print_pub.c
@@ -0,0 +1,40 @@
+#include "asn_print_pub.h"
+#include "asn_print_citgen.h"
+#include "asn_print_citsub.h"
+
+void
+asn_print_pub (PubPtr pub)
+{
+  while (pub != NULL)
+    {
+      switch (pub->choice)
+	{		  
+	case PUB_Gen:
+	  /*
+	   * Cit-gen
+	   */
+	  printf ("    GENERAL\n");
+	  CitGenPtr citgen = pub->data.ptrvalue;
+	  asn_print_citgen (citgen);
+	  break;
+	  
+	case PUB_Sub:
+	  /*
+	   * Cit-sub
+	   */
+	  printf ("    SUBMISSION\n");
+	  CitSubPtr citsub = pub->data.ptrvalue;
+	  asn_print_citsub (citsub);
+	  break;
+
+	default:
+	  printf ("    PUB CHOICE UNHANDLED=%i\n", pub->choice);
+	  exit (-1);
+	  break;
+	}
+
+      pub = pub->next;
+    }
+
+  return;
+}
diff --git a/src/model/asn_print/asn_print_pub.h b/src/model/asn_print/asn_print_pub.h
new file mode 100644
index 0000000..7f3407a
--- a/dev/null
+++ b/src/model/asn_print/asn_print_pub.h
@@ -0,0 +1,8 @@
+#ifndef ASN_PRINT_PUB_H
+#define ASN_PRINT_PUB_H
+
+#include <subutil.h>
+
+void asn_print_pub (PubPtr pub);
+
+#endif // ASN_PRINT_PUB_H