<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Std</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <h1 class="toc">Module Std</h1> <hr /> <h2 class="toc">Classes</h2> <a target="mainFrame" href="Bio.Std.StdTerm-class.html" >StdTerm</a><br /> <h2 class="toc">Functions</h2> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_check_attrs" >_check_attrs</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_check_gapchar" >_check_gapchar</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_check_name" >_check_name</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_complain_if_given" >_complain_if_given</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_must_have" >_must_have</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_must_have_set" >_must_have_set</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_must_not_have" >_must_not_have</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_set_if_given" >_set_if_given</a><br /> </div> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_settag" >_settag</a><br /> </div> <a target="mainFrame" href="Bio.Std-module.html#alphabet" >alphabet</a><br /> <a target="mainFrame" href="Bio.Std-module.html#application_name" >application_name</a><br /> <a target="mainFrame" href="Bio.Std-module.html#application_version" >application_version</a><br /> <a target="mainFrame" href="Bio.Std-module.html#database_name" >database_name</a><br /> <a target="mainFrame" href="Bio.Std-module.html#database_num_letters" >database_num_letters</a><br /> <a target="mainFrame" href="Bio.Std-module.html#database_num_sequences" >database_num_sequences</a><br /> <a target="mainFrame" href="Bio.Std-module.html#dbid" >dbid</a><br /> <a target="mainFrame" href="Bio.Std-module.html#dbxref" >dbxref</a><br /> <a target="mainFrame" href="Bio.Std-module.html#dbxref_dbid" >dbxref_dbid</a><br /> <a target="mainFrame" href="Bio.Std-module.html#dbxref_dbname" >dbxref_dbname</a><br /> <a target="mainFrame" href="Bio.Std-module.html#dbxref_negate" >dbxref_negate</a><br /> <a target="mainFrame" href="Bio.Std-module.html#description" >description</a><br /> <a target="mainFrame" href="Bio.Std-module.html#description_block" >description_block</a><br /> <a target="mainFrame" href="Bio.Std-module.html#description_line" >description_line</a><br /> <a target="mainFrame" href="Bio.Std-module.html#fast_dbxref" >fast_dbxref</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature" >feature</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_block" >feature_block</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_description" >feature_description</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_location" >feature_location</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_location_end" >feature_location_end</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_location_start" >feature_location_start</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_name" >feature_name</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_qualifier" >feature_qualifier</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_qualifier_description" >feature_qualifier_description</a><br /> <a target="mainFrame" href="Bio.Std-module.html#feature_qualifier_name" >feature_qualifier_name</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hit" >hit</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hit_description" >hit_description</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hit_length" >hit_length</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp" >hsp</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_frame" >hsp_frame</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign" >hsp_seqalign</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_homology_seq" >hsp_seqalign_homology_seq</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_query_end" >hsp_seqalign_query_end</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_query_leader" >hsp_seqalign_query_leader</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_query_name" >hsp_seqalign_query_name</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_query_seq" >hsp_seqalign_query_seq</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_query_start" >hsp_seqalign_query_start</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_subject_end" >hsp_seqalign_subject_end</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_subject_name" >hsp_seqalign_subject_name</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_subject_seq" >hsp_seqalign_subject_seq</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_seqalign_subject_start" >hsp_seqalign_subject_start</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_strand" >hsp_strand</a><br /> <a target="mainFrame" href="Bio.Std-module.html#hsp_value" >hsp_value</a><br /> <a target="mainFrame" href="Bio.Std-module.html#query_description" >query_description</a><br /> <a target="mainFrame" href="Bio.Std-module.html#query_description_block" >query_description_block</a><br /> <a target="mainFrame" href="Bio.Std-module.html#query_size" >query_size</a><br /> <a target="mainFrame" href="Bio.Std-module.html#record" >record</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_header" >search_header</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_parameter" >search_parameter</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_statistic" >search_statistic</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_table" >search_table</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_table_description" >search_table_description</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_table_entry" >search_table_entry</a><br /> <a target="mainFrame" href="Bio.Std-module.html#search_table_value" >search_table_value</a><br /> <a target="mainFrame" href="Bio.Std-module.html#sequence" >sequence</a><br /> <a target="mainFrame" href="Bio.Std-module.html#sequence_block" >sequence_block</a><br /> <h2 class="toc">Variables</h2> <a target="mainFrame" href="Bio.Std-module.html#NS" >NS</a><br /> <a target="mainFrame" href="Bio.Std-module.html#XMLNS" >XMLNS</a><br /> <div class="private"> <a target="mainFrame" href="Bio.Std-module.html#_use_hack" >_use_hack</a><br /> </div> <a target="mainFrame" href="Bio.Std-module.html#namespace" >namespace</a><br /><hr /> <span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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