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+<body class="indexpage">
+
+
+ <h1>RDoc Documentation</h1>
+
+
+ <p>This is the API documentation for 'RDoc Documentation'.</p>
+
+
+
+
+
+ <h2 id="classes">Classes/Modules</h2>
+ <ul>
+
+ <li class="class"><a href="Biopieces.html">Biopieces</a></li>
+
+ <li class="class"><a href="CastError.html">CastError</a></li>
+
+ <li class="class"><a href="Casts.html">Casts</a></li>
+
+ <li class="class"><a href="Digest.html">Digest</a></li>
+
+ <li class="class"><a href="DigestError.html">DigestError</a></li>
+
+ <li class="class"><a href="Fasta.html">Fasta</a></li>
+
+ <li class="class"><a href="FastaError.html">FastaError</a></li>
+
+ <li class="class"><a href="OptionHandler.html">OptionHandler</a></li>
+
+ <li class="class"><a href="Seq.html">Seq</a></li>
+
+ <li class="class"><a href="SeqError.html">SeqError</a></li>
+
+ <li class="class"><a href="Status.html">Status</a></li>
+
+ <li class="class"><a href="Stream.html">Stream</a></li>
+
+ </ul>
+
+ <h2 id="methods">Methods</h2>
+ <ul>
+
+ <li><a href="Biopieces.html#method-c-new">::new — Biopieces</a></li>
+
+ <li><a href="Digest.html#method-c-new">::new — Digest</a></li>
+
+ <li><a href="OptionHandler.html#method-c-new">::new — OptionHandler</a></li>
+
+ <li><a href="Seq.html#method-c-new">::new — Seq</a></li>
+
+ <li><a href="Casts.html#method-c-new">::new — Casts</a></li>
+
+ <li><a href="Fasta.html#method-c-new">::new — Fasta</a></li>
+
+ <li><a href="Stream.html#method-c-nread">::nread — Stream</a></li>
+
+ <li><a href="Stream.html#method-c-nwrite">::nwrite — Stream</a></li>
+
+ <li><a href="Fasta.html#method-c-open">::open — Fasta</a></li>
+
+ <li><a href="Stream.html#method-c-open">::open — Stream</a></li>
+
+ <li><a href="Stream.html#method-c-read">::read — Stream</a></li>
+
+ <li><a href="Stream.html#method-c-write">::write — Stream</a></li>
+
+ <li><a href="Stream.html#method-c-zipped%3F">::zipped? — Stream</a></li>
+
+ <li><a href="Fasta.html#method-c-zopen">::zopen — Fasta</a></li>
+
+ <li><a href="Stream.html#method-c-zread">::zread — Stream</a></li>
+
+ <li><a href="Stream.html#method-c-zwrite">::zwrite — Stream</a></li>
+
+ <li><a href="Casts.html#method-i-check">#check — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_duplicates">#check_duplicates — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_keys">#check_keys — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_allowed">#check_val_allowed — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_default">#check_val_default — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_disallowed">#check_val_disallowed — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_long">#check_val_long — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_mandatory">#check_val_mandatory — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_short">#check_val_short — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_val_type">#check_val_type — Casts</a></li>
+
+ <li><a href="Casts.html#method-i-check_values">#check_values — Casts</a></li>
+
+ <li><a href="Fasta.html#method-i-close">#close — Fasta</a></li>
+
+ <li><a href="Seq.html#method-i-complement">#complement — Seq</a></li>
+
+ <li><a href="Status.html#method-i-delete">#delete — Status</a></li>
+
+ <li><a href="Digest.html#method-i-disambiguate">#disambiguate — Digest</a></li>
+
+ <li><a href="Biopieces.html#method-i-each">#each — Biopieces</a></li>
+
+ <li><a href="Fasta.html#method-i-each">#each — Fasta</a></li>
+
+ <li><a href="Digest.html#method-i-each">#each — Digest</a></li>
+
+ <li><a href="Biopieces.html#method-i-each_record">#each_record — Biopieces</a></li>
+
+ <li><a href="Seq.html#method-i-generate">#generate — Seq</a></li>
+
+ <li><a href="Fasta.html#method-i-get_entry">#get_entry — Fasta</a></li>
+
+ <li><a href="Status.html#method-i-get_tmpdir">#get_tmpdir — Status</a></li>
+
+ <li><a href="Seq.html#method-i-is_dna%3F">#is_dna? — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-is_protein%3F">#is_protein? — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-is_rna%3F">#is_rna? — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-len">#len — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-length">#length — Seq</a></li>
+
+ <li><a href="Status.html#method-i-log">#log — Status</a></li>
+
+ <li><a href="Casts.html#method-i-long_to_sym">#long_to_sym — Casts</a></li>
+
+ <li><a href="Biopieces.html#method-i-mktmpdir">#mktmpdir — Biopieces</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check">#options_check — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_allowed">#options_check_allowed — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_dir">#options_check_dir — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_disallowed">#options_check_disallowed — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_file">#options_check_file — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_files">#options_check_files — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_int">#options_check_int — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_mandatory">#options_check_mandatory — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_check_uint">#options_check_uint — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_default">#options_default — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_glob">#options_glob — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-options_parse">#options_parse — OptionHandler</a></li>
+
+ <li><a href="Biopieces.html#method-i-parse">#parse — Biopieces</a></li>
+
+ <li><a href="Status.html#method-i-path">#path — Status</a></li>
+
+ <li><a href="OptionHandler.html#method-i-print_usage_and_exit">#print_usage_and_exit — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-print_usage_full%3F">#print_usage_full? — OptionHandler</a></li>
+
+ <li><a href="OptionHandler.html#method-i-print_usage_short%3F">#print_usage_short? — OptionHandler</a></li>
+
+ <li><a href="Biopieces.html#method-i-puts">#puts — Biopieces</a></li>
+
+ <li><a href="Fasta.html#method-i-puts">#puts — Fasta</a></li>
+
+ <li><a href="Seq.html#method-i-revcomp">#revcomp — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-reverse">#reverse — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-reverse_complement">#reverse_complement — Seq</a></li>
+
+ <li><a href="Status.html#method-i-set">#set — Status</a></li>
+
+ <li><a href="Status.html#method-i-set_tmpdir">#set_tmpdir — Status</a></li>
+
+ <li><a href="Status.html#method-i-time_diff">#time_diff — Status</a></li>
+
+ <li><a href="Seq.html#method-i-to_bp">#to_bp — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-to_dna">#to_dna — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-to_fasta">#to_fasta — Seq</a></li>
+
+ <li><a href="Seq.html#method-i-to_rna">#to_rna — Seq</a></li>
+
+ <li><a href="Casts.html#method-i-ubiquitous">#ubiquitous — Casts</a></li>
+
+ <li><a href="OptionHandler.html#method-i-wiki_path">#wiki_path — OptionHandler</a></li>
+
+ </ul>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ Rdoc Generator</a> 1.1.6</small>.</p>
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