search_biomodel 1.0.0 → 1.0.1

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_document.h

@@ -1,23 +0,0 @@
-#ifndef NOKOGIRI_XML_DOCUMENT
-#define NOKOGIRI_XML_DOCUMENT
-
-#include <nokogiri.h>
-
-struct _nokogiriTuple {
-  xmlDocPtr     doc;
-  st_table     *unlinkedNodes;
-  VALUE         node_cache;
-};
-typedef struct _nokogiriTuple nokogiriTuple;
-typedef nokogiriTuple * nokogiriTuplePtr;
-
-void init_xml_document();
-VALUE Nokogiri_wrap_xml_document(VALUE klass, xmlDocPtr doc);
-
-#define DOC_RUBY_OBJECT_TEST(x) ((nokogiriTuplePtr)(x->_private))
-#define DOC_RUBY_OBJECT(x) ((VALUE)((nokogiriTuplePtr)(x->_private))->doc)
-#define DOC_UNLINKED_NODE_HASH(x) (((nokogiriTuplePtr)(x->_private))->unlinkedNodes)
-#define DOC_NODE_CACHE(x) ((VALUE)((nokogiriTuplePtr)(x->_private))->node_cache)
-
-extern VALUE cNokogiriXmlDocument ;
-#endif

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_document_fragment.c

@@ -1,48 +0,0 @@
-#include <xml_document_fragment.h>
-
-/*
- * call-seq:
- *  new(document)
- *
- * Create a new DocumentFragment element on the +document+
- */
-static VALUE new(int argc, VALUE *argv, VALUE klass)
-{
-  xmlDocPtr xml_doc;
-  xmlNodePtr node;
-  VALUE document;
-  VALUE rest;
-  VALUE rb_node;
-
-  rb_scan_args(argc, argv, "1*", &document, &rest);
-
-  Data_Get_Struct(document, xmlDoc, xml_doc);
-
-  node = xmlNewDocFragment(xml_doc->doc);
-
-  NOKOGIRI_ROOT_NODE(node);
-
-  rb_node = Nokogiri_wrap_xml_node(klass, node);
-  rb_obj_call_init(rb_node, argc, argv);
-
-  if(rb_block_given_p()) rb_yield(rb_node);
-
-  return rb_node;
-}
-
-VALUE cNokogiriXmlDocumentFragment;
-void init_xml_document_fragment()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-  VALUE node = rb_define_class_under(xml, "Node", rb_cObject);
-
-  /*
-   * DocumentFragment represents a DocumentFragment node in an xml document.
-   */
-  VALUE klass = rb_define_class_under(xml, "DocumentFragment", node);
-
-  cNokogiriXmlDocumentFragment = klass;
-
-  rb_define_singleton_method(klass, "new", new, -1);
-}

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_document_fragment.h

@@ -1,10 +0,0 @@
-#ifndef NOKOGIRI_XML_DOCUMENT_FRAGMENT
-#define NOKOGIRI_XML_DOCUMENT_FRAGMENT
-
-#include <nokogiri.h>
-
-void init_xml_document_fragment();
-
-extern VALUE cNokogiriXmlDocumentFragment;
-#endif
-

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_dtd.c

@@ -1,202 +0,0 @@
-#include <xml_dtd.h>
-
-static void notation_copier(void *payload, void *data, xmlChar *name)
-{
-  VALUE hash = (VALUE)data;
-  VALUE klass = rb_const_get(mNokogiriXml, rb_intern("Notation"));
-
-  xmlNotationPtr c_notation = (xmlNotationPtr)payload;
-  VALUE notation;
-  VALUE argv[3];
-  argv[0] = (c_notation->name ? NOKOGIRI_STR_NEW2(c_notation->name) : Qnil);
-  argv[1] = (c_notation->PublicID ? NOKOGIRI_STR_NEW2(c_notation->PublicID) : Qnil);
-  argv[2] = (c_notation->SystemID ? NOKOGIRI_STR_NEW2(c_notation->SystemID) : Qnil);
-
-  notation = rb_class_new_instance(3, argv, klass);
-
-  rb_hash_aset(hash, NOKOGIRI_STR_NEW2(name),notation);
-}
-
-static void element_copier(void *_payload, void *data, xmlChar *name)
-{
-  VALUE hash = (VALUE)data;
-  xmlNodePtr payload = (xmlNodePtr)_payload;
-
-  VALUE element = Nokogiri_wrap_xml_node(Qnil, payload);
-
-  rb_hash_aset(hash, NOKOGIRI_STR_NEW2(name), element);
-}
-
-/*
- * call-seq:
- *   entities
- *
- * Get a hash of the elements for this DTD.
- */
-static VALUE entities(VALUE self)
-{
-  xmlDtdPtr dtd;
-  VALUE hash;
-
-  Data_Get_Struct(self, xmlDtd, dtd);
-
-  if(!dtd->entities) return Qnil;
-
-  hash = rb_hash_new();
-
-  xmlHashScan((xmlHashTablePtr)dtd->entities, element_copier, (void *)hash);
-
-  return hash;
-}
-
-/*
- * call-seq:
- *   notations
- *
- * Get a hash of the notations for this DTD.
- */
-static VALUE notations(VALUE self)
-{
-  xmlDtdPtr dtd;
-  VALUE hash;
-
-  Data_Get_Struct(self, xmlDtd, dtd);
-
-  if(!dtd->notations) return Qnil;
-
-  hash = rb_hash_new();
-
-  xmlHashScan((xmlHashTablePtr)dtd->notations, notation_copier, (void *)hash);
-
-  return hash;
-}
-
-/*
- * call-seq:
- *   attributes
- *
- * Get a hash of the attributes for this DTD.
- */
-static VALUE attributes(VALUE self)
-{
-  xmlDtdPtr dtd;
-  VALUE hash;
-
-  Data_Get_Struct(self, xmlDtd, dtd);
-
-  hash = rb_hash_new();
-
-  if(!dtd->attributes) return hash;
-
-  xmlHashScan((xmlHashTablePtr)dtd->attributes, element_copier, (void *)hash);
-
-  return hash;
-}
-
-/*
- * call-seq:
- *   elements
- *
- * Get a hash of the elements for this DTD.
- */
-static VALUE elements(VALUE self)
-{
-  xmlDtdPtr dtd;
-  VALUE hash;
-
-  Data_Get_Struct(self, xmlDtd, dtd);
-
-  if(!dtd->elements) return Qnil;
-
-  hash = rb_hash_new();
-
-  xmlHashScan((xmlHashTablePtr)dtd->elements, element_copier, (void *)hash);
-
-  return hash;
-}
-
-/*
- * call-seq:
- *   validate(document)
- *
- * Validate +document+ returning a list of errors
- */
-static VALUE validate(VALUE self, VALUE document)
-{
-  xmlDocPtr doc;
-  xmlDtdPtr dtd;
-  xmlValidCtxtPtr ctxt;
-  VALUE error_list;
-
-  Data_Get_Struct(self, xmlDtd, dtd);
-  Data_Get_Struct(document, xmlDoc, doc);
-  error_list = rb_ary_new();
-
-  ctxt = xmlNewValidCtxt();
-
-  xmlSetStructuredErrorFunc((void *)error_list, Nokogiri_error_array_pusher);
-
-  xmlValidateDtd(ctxt, doc, dtd);
-
-  xmlSetStructuredErrorFunc(NULL, NULL);
-
-  xmlFreeValidCtxt(ctxt);
-
-  return error_list;
-}
-
-/*
- * call-seq:
- *   system_id
- *
- * Get the System ID for this DTD
- */
-static VALUE system_id(VALUE self)
-{
-  xmlDtdPtr dtd;
-  Data_Get_Struct(self, xmlDtd, dtd);
-
-  if(!dtd->SystemID) return Qnil;
-
-  return NOKOGIRI_STR_NEW2(dtd->SystemID);
-}
-
-/*
- * call-seq:
- *   external_id
- *
- * Get the External ID for this DTD
- */
-static VALUE external_id(VALUE self)
-{
-  xmlDtdPtr dtd;
-  Data_Get_Struct(self, xmlDtd, dtd);
-
-  if(!dtd->ExternalID) return Qnil;
-
-  return NOKOGIRI_STR_NEW2(dtd->ExternalID);
-}
-
-VALUE cNokogiriXmlDtd;
-
-void init_xml_dtd()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-  VALUE node = rb_define_class_under(xml, "Node", rb_cObject);
-
-  /*
-   * Nokogiri::XML::DTD wraps DTD nodes in an XML document
-   */
-  VALUE klass = rb_define_class_under(xml, "DTD", node);
-
-  cNokogiriXmlDtd = klass;
-
-  rb_define_method(klass, "notations", notations, 0);
-  rb_define_method(klass, "elements", elements, 0);
-  rb_define_method(klass, "entities", entities, 0);
-  rb_define_method(klass, "validate", validate, 1);
-  rb_define_method(klass, "attributes", attributes, 0);
-  rb_define_method(klass, "system_id", system_id, 0);
-  rb_define_method(klass, "external_id", external_id, 0);
-}

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_dtd.h

@@ -1,10 +0,0 @@
-#ifndef NOKOGIRI_XML_DTD
-#define NOKOGIRI_XML_DTD
-
-#include <nokogiri.h>
-
-extern VALUE cNokogiriXmlDtd;
-
-void init_xml_dtd();
-
-#endif

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_element_content.c

@@ -1,123 +0,0 @@
-#include <xml_element_content.h>
-
-VALUE cNokogiriXmlElementContent;
-
-/*
- * call-seq:
- *  name
- *
- * Get the require element +name+
- */
-static VALUE get_name(VALUE self)
-{
-  xmlElementContentPtr elem;
-  Data_Get_Struct(self, xmlElementContent, elem);
-
-  if(!elem->name) return Qnil;
-  return NOKOGIRI_STR_NEW2(elem->name);
-}
-
-/*
- * call-seq:
- *  type
- *
- * Get the element content +type+.  Possible values are PCDATA, ELEMENT, SEQ,
- * or OR.
- */
-static VALUE get_type(VALUE self)
-{
-  xmlElementContentPtr elem;
-  Data_Get_Struct(self, xmlElementContent, elem);
-
-  return INT2NUM((long)elem->type);
-}
-
-/*
- * call-seq:
- *  c1
- *
- * Get the first child.
- */
-static VALUE get_c1(VALUE self)
-{
-  xmlElementContentPtr elem;
-  Data_Get_Struct(self, xmlElementContent, elem);
-
-  if(!elem->c1) return Qnil;
-  return Nokogiri_wrap_element_content(rb_iv_get(self, "@document"), elem->c1);
-}
-
-/*
- * call-seq:
- *  c2
- *
- * Get the first child.
- */
-static VALUE get_c2(VALUE self)
-{
-  xmlElementContentPtr elem;
-  Data_Get_Struct(self, xmlElementContent, elem);
-
-  if(!elem->c2) return Qnil;
-  return Nokogiri_wrap_element_content(rb_iv_get(self, "@document"), elem->c2);
-}
-
-/*
- * call-seq:
- *  occur
- *
- * Get the element content +occur+ flag.  Possible values are ONCE, OPT, MULT
- * or PLUS.
- */
-static VALUE get_occur(VALUE self)
-{
-  xmlElementContentPtr elem;
-  Data_Get_Struct(self, xmlElementContent, elem);
-
-  return INT2NUM((long)elem->ocur);
-}
-
-/*
- * call-seq:
- *  prefix
- *
- * Get the element content namespace +prefix+.
- */
-static VALUE get_prefix(VALUE self)
-{
-  xmlElementContentPtr elem;
-  Data_Get_Struct(self, xmlElementContent, elem);
-
-  if(!elem->prefix) return Qnil;
-
-  return NOKOGIRI_STR_NEW2(elem->prefix);
-}
-
-VALUE Nokogiri_wrap_element_content(VALUE doc, xmlElementContentPtr element)
-{
-  VALUE elem = Data_Wrap_Struct(cNokogiriXmlElementContent, 0, 0, element);
-
-  /* Setting the document is necessary so that this does not get GC'd until */
-  /* the document is GC'd */
-  rb_iv_set(elem, "@document", doc);
-
-  return elem;
-}
-
-void init_xml_element_content()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-
-  VALUE klass = rb_define_class_under(xml, "ElementContent", rb_cObject);
-
-  cNokogiriXmlElementContent = klass;
-
-  rb_define_method(klass, "name", get_name, 0);
-  rb_define_method(klass, "type", get_type, 0);
-  rb_define_method(klass, "occur", get_occur, 0);
-  rb_define_method(klass, "prefix", get_prefix, 0);
-
-  rb_define_private_method(klass, "c1", get_c1, 0);
-  rb_define_private_method(klass, "c2", get_c2, 0);
-}

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_element_content.h

@@ -1,10 +0,0 @@
-#ifndef NOKOGIRI_XML_ELEMENT_CONTENT
-#define NOKOGIRI_XML_ELEMENT_CONTENT
-
-#include <nokogiri.h>
-
-
-VALUE Nokogiri_wrap_element_content(VALUE doc, xmlElementContentPtr element);
-void init_xml_element_content();
-
-#endif

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_element_decl.c

@@ -1,69 +0,0 @@
-#include <xml_element_decl.h>
-
-static ID id_document;
-
-/*
- * call-seq:
- *  element_type
- *
- * The element_type
- */
-static VALUE element_type(VALUE self)
-{
-  xmlElementPtr node;
-  Data_Get_Struct(self, xmlElement, node);
-  return INT2NUM((long)node->etype);
-}
-
-/*
- * call-seq:
- *  content
- *
- * The allowed content for this ElementDecl
- */
-static VALUE content(VALUE self)
-{
-  xmlElementPtr node;
-  Data_Get_Struct(self, xmlElement, node);
-
-  if(!node->content) return Qnil;
-
-  return Nokogiri_wrap_element_content(
-      rb_funcall(self, id_document, 0),
-      node->content
-  );
-}
-
-/*
- * call-seq:
- *  prefix
- *
- * The namespace prefix for this ElementDecl
- */
-static VALUE prefix(VALUE self)
-{
-  xmlElementPtr node;
-  Data_Get_Struct(self, xmlElement, node);
-
-  if(!node->prefix) return Qnil;
-
-  return NOKOGIRI_STR_NEW2(node->prefix);
-}
-
-VALUE cNokogiriXmlElementDecl;
-
-void init_xml_element_decl()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE xml = rb_define_module_under(nokogiri, "XML");
-  VALUE node = rb_define_class_under(xml, "Node", rb_cObject);
-  VALUE klass = rb_define_class_under(xml, "ElementDecl", node);
-
-  cNokogiriXmlElementDecl = klass;
-
-  rb_define_method(klass, "element_type", element_type, 0);
-  rb_define_method(klass, "content", content, 0);
-  rb_define_method(klass, "prefix", prefix, 0);
-
-  id_document = rb_intern("document");
-}

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_element_decl.h

@@ -1,9 +0,0 @@
-#ifndef NOKOGIRI_XML_ELEMENT_DECL
-#define NOKOGIRI_XML_ELEMENT_DECL
-
-#include <nokogiri.h>
-
-void init_xml_element_decl();
-
-extern VALUE cNokogiriXmlElementDecl;
-#endif

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_encoding_handler.c

@@ -1,79 +0,0 @@
-#include <xml_encoding_handler.h>
-
-/*
- * call-seq: Nokogiri::EncodingHandler.[](name)
- *
- * Get the encoding handler for +name+
- */
-static VALUE get(VALUE klass, VALUE key)
-{
-  xmlCharEncodingHandlerPtr handler;
-
-  handler = xmlFindCharEncodingHandler(StringValuePtr(key));
-  if(handler)
-    return Data_Wrap_Struct(klass, NULL, NULL, handler);
-
-  return Qnil;
-}
-
-/*
- * call-seq: Nokogiri::EncodingHandler.delete(name)
- *
- * Delete the encoding alias named +name+
- */
-static VALUE delete(VALUE klass, VALUE name)
-{
-  if(xmlDelEncodingAlias(StringValuePtr(name))) return Qnil;
-
-  return Qtrue;
-}
-
-/*
- * call-seq: Nokogiri::EncodingHandler.alias(from, to)
- *
- * Alias encoding handler with name +from+ to name +to+
- */
-static VALUE alias(VALUE klass, VALUE from, VALUE to)
-{
-  xmlAddEncodingAlias(StringValuePtr(from), StringValuePtr(to));
-
-  return to;
-}
-
-/*
- * call-seq: Nokogiri::EncodingHandler.clear_aliases!
- *
- * Remove all encoding aliases.
- */
-static VALUE clear_aliases(VALUE klass)
-{
-  xmlCleanupEncodingAliases();
-
-  return klass;
-}
-
-/*
- * call-seq: name
- *
- * Get the name of this EncodingHandler
- */
-static VALUE name(VALUE self)
-{
-  xmlCharEncodingHandlerPtr handler;
-
-  Data_Get_Struct(self, xmlCharEncodingHandler, handler);
-
-  return NOKOGIRI_STR_NEW2(handler->name);
-}
-
-void init_xml_encoding_handler()
-{
-  VALUE nokogiri = rb_define_module("Nokogiri");
-  VALUE klass = rb_define_class_under(nokogiri, "EncodingHandler", rb_cObject);
-
-  rb_define_singleton_method(klass, "[]", get, 1);
-  rb_define_singleton_method(klass, "delete", delete, 1);
-  rb_define_singleton_method(klass, "alias", alias, 2);
-  rb_define_singleton_method(klass, "clear_aliases!", clear_aliases, 0);
-  rb_define_method(klass, "name", name, 0);
-}

data/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/ext/nokogiri/xml_encoding_handler.h

@@ -1,8 +0,0 @@
-#ifndef NOKOGIRI_XML_ENCODING_HANDLER
-#define NOKOGIRI_XML_ENCODING_HANDLER
-
-#include <nokogiri.h>
-
-void init_xml_encoding_handler();
-
-#endif