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1623 lines
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<a class="el" href = "https://www.ncbi.nlm.nih.gov/toolkitbookgh/?term=CSeqportUtil">Search Toolkit Book for <i>CSeqportUtil</i></a>
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<p><code>#include <<a class="el" href="seqport__util_8hpp_source.html">objects/seq/seqport_util.hpp</a>></code></p>
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Classes</h2></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structCSeqportUtil_1_1CBadIndex.html">CBadIndex</a></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structCSeqportUtil_1_1CBadSymbol.html">CBadSymbol</a></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structCSeqportUtil_1_1CBadType.html">CBadType</a></td></tr>
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<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
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Public Types</h2></td></tr>
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<tr class="memitem:a6201a44edb80355c0f816e6df97a8ff6"><td class="memItemLeft" align="right" valign="top">typedef unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a></td></tr>
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<tr class="memitem:af1e9b1329793952929dbdaa9121ee611"><td class="memItemLeft" align="right" valign="top">typedef pair< <a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a>, <a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#af1e9b1329793952929dbdaa9121ee611">TPair</a></td></tr>
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<tr class="separator:af1e9b1329793952929dbdaa9121ee611"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
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Static Public Member Functions</h2></td></tr>
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<tr class="memitem:a685577e3a92659ae069cef11d4841574"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a685577e3a92659ae069cef11d4841574">Convert</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, <a class="el" href="classCSeq__data.html">CSeq_data</a> *out_seq, <a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> to_code, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0, <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> bAmbig=<a class="el" href="ftds14_2freetds_2freetds_2bool_8h.html#a65e9886d74aaee76545e83dd09011727">false</a>, <a class="el" href="group__Portability.html#ga7b0b4ab610750dd0972e12d57827a00f">Uint4</a> <a class="el" href="test__table_8cpp.html#a1447ad288a0a73454510f5777bdc3ed1">seed</a>=17734276)</td></tr>
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<tr class="memitem:a84a5411ae824a487119df032225bd879"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a84a5411ae824a487119df032225bd879">ConvertWithBlastAmbig</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, <a class="el" href="classCSeq__data.html">CSeq_data</a> *out_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> total_length, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> *out_seq_length, vector< <a class="el" href="group__Portability.html#ga7b0b4ab610750dd0972e12d57827a00f">Uint4</a> > *blast_ambig)</td></tr>
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<tr class="memitem:afeeecdf4a6ee2f467307293249badc5d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#afeeecdf4a6ee2f467307293249badc5d">Pack</a> (<a class="el" href="classCSeq__data.html">CSeq_data</a> *in_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=<a class="el" href="group__Portability.html#ga6c53672ed1d292925bf0f0635a083067">ncbi::numeric_limits</a>< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> >::<a class="el" href="njn__function_8hpp.html#a3eb1823953b6efad16c3a4b72939ff81">max</a>())</td></tr>
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<tr class="memitem:a5e8dec4c8278444279e61a8e676540db"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a5e8dec4c8278444279e61a8e676540db">FastValidate</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:af6204270735c7fb50c918e2ac8fa10ac"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#af6204270735c7fb50c918e2ac8fa10ac">Validate</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, vector< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > *badIdx, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:a96eb4a7b9a87f74389e91b9c4c717bf1"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a96eb4a7b9a87f74389e91b9c4c717bf1">GetAmbigs</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, <a class="el" href="classCSeq__data.html">CSeq_data</a> *out_seq, vector< <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> > *out_indices, <a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> to_code=<a class="el" href="group__dataspec__NCBI__Sequence.html#gga4ebe9e4dab723da143541cd84b40fbd3a8d199937a1e3b0a738e6adfa4a5ec926">CSeq_data::e_Ncbi2na</a>, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:aaaab5b3e1e4fd6529dde2cd646bc14a4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#aaaab5b3e1e4fd6529dde2cd646bc14a4">GetCopy</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, <a class="el" href="classCSeq__data.html">CSeq_data</a> *out_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:ac603b71a50ff9fed8b4ffeb1e551b1b2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#ac603b71a50ff9fed8b4ffeb1e551b1b2">Keep</a> (<a class="el" href="classCSeq__data.html">CSeq_data</a> *in_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:aff67916866d941ac731cb23744286dc8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#aff67916866d941ac731cb23744286dc8">Append</a> (<a class="el" href="classCSeq__data.html">CSeq_data</a> *out_seq, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq1, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx1, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength1, <a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq2, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx2, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength2)</td></tr>
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<tr class="memitem:ac39b6c7bd97377a1dff17c4dd6055ec4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#ac39b6c7bd97377a1dff17c4dd6055ec4">Complement</a> (<a class="el" href="classCSeq__data.html">CSeq_data</a> *in_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:a80283ac0370ab44788299ac647f5e9d5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a80283ac0370ab44788299ac647f5e9d5">Complement</a> (<a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> &in_seq, <a class="el" href="classCSeq__data.html">CSeq_data</a> *out_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:a2f3a604e1ae1346d36a4566482f861ba"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a2f3a604e1ae1346d36a4566482f861ba">Reverse</a> (<a class="el" href="classCSeq__data.html">CSeq_data</a> *in_seq, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uBeginIdx=0, <a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> uLength=0)</td></tr>
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<tr class="memitem:a4990db795f93ee4a134247b93c2ff154"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a4990db795f93ee4a134247b93c2ff154">IsCodeAvailable</a> (<a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> code_type)</td></tr>
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<tr class="memitem:a272e9d67c5dede98eb01f1c777b9421a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCSeqportUtil.html#af1e9b1329793952929dbdaa9121ee611">TPair</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a272e9d67c5dede98eb01f1c777b9421a">GetCodeIndexFromTo</a> (<a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> code_type)</td></tr>
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<tr class="memitem:aa8c63d143fc3ae0a99132178c8ebb26d"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#aa8c63d143fc3ae0a99132178c8ebb26d">GetMapToIndex</a> (<a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> from_type, <a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> to_type, <a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a> from_idx)</td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-static-methods"></a>
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Static Private Member Functions</h2></td></tr>
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<tr class="memitem:a25d43486f12618e8fb0c3ece979057f5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="Genetic__code__table_8cpp.html#aa261b98e7b0037f2a9f13cbb4b8539d7">static</a> <a class="el" href="classCSeqportUtil__implementation.html">CSeqportUtil_implementation</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classCSeqportUtil.html#a25d43486f12618e8fb0c3ece979057f5">x_GetImplementation</a> (void)</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8hpp_source.html#l00051">51</a> of file <a class="el" href="seqport__util_8hpp_source.html">seqport_util.hpp</a>.</p>
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<a id="a6201a44edb80355c0f816e6df97a8ff6"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a6201a44edb80355c0f816e6df97a8ff6">◆ </a></span>TIndex</h2>
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<td class="memname">typedef unsigned <a class="el" href="group__mdb__copy.html#ga10cfb7d4996b006d5675b53b9c7f0fb5">int</a> <a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">CSeqportUtil::TIndex</a></td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8hpp_source.html#l00056">56</a> of file <a class="el" href="seqport__util_8hpp_source.html">seqport_util.hpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af1e9b1329793952929dbdaa9121ee611">◆ </a></span>TPair</h2>
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<td class="memname">typedef pair<<a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a>, <a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">TIndex</a>> <a class="el" href="classCSeqportUtil.html#af1e9b1329793952929dbdaa9121ee611">CSeqportUtil::TPair</a></td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8hpp_source.html#l00057">57</a> of file <a class="el" href="seqport__util_8hpp_source.html">seqport_util.hpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aff67916866d941ac731cb23744286dc8">◆ </a></span>Append()</h2>
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<td class="paramtype"><a class="el" href="classCSeq__data.html">CSeq_data</a> * </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01010">1010</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02304">CSeqportUtil_implementation::Append()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="variation__util_8cpp_source.html#l00811">variation_ref::CVariationUtil::s_CatLiterals()</a>, and <a class="el" href="variation__util2_8cpp_source.html#l01695">variation::CVariationUtil::s_CatLiterals()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a80283ac0370ab44788299ac647f5e9d5">◆ </a></span>Complement() <span class="overload">[1/2]</span></h2>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01035">1035</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02353">CSeqportUtil_implementation::Complement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01025">1025</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02353">CSeqportUtil_implementation::Complement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l00917">917</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">Referenced by <a class="el" href="unit__test__validator_8cpp_source.html#l15520">BOOST_AUTO_TEST_CASE()</a>, <a class="el" href="blastfmtutil_8cpp_source.html#l00392">CBlastFormattingMatrix::CBlastFormattingMatrix()</a>, <a class="el" href="validerror__bioseq_8cpp_source.html#l03100">CountNs()</a>, <a class="el" href="discrepancy__context_8cpp_source.html#l00237">CountNucleotides()</a>, <a class="el" href="blast__aux_8cpp_source.html#l00588">FindGeneticCode()</a>, <a class="el" href="Pssm_8cpp_source.html#l00077">CPssm::GetQuerySequenceData()</a>, <a class="el" href="algo_2winmask_2demo_2win__mask__app_8cpp_source.html#l00237">CWinMaskDemoApplication::Run()</a>, <a class="el" href="nmer__repeats_8cpp_source.html#l00117">CNmer_repeatsApplication::Run()</a>, <a class="el" href="msa__pssm__input_8cpp_source.html#l00151">s_GetQuerySequenceData()</a>, <a class="el" href="feature_8cpp_source.html#l00274">s_GetRnaRefLabel()</a>, <a class="el" href="feature__item_8cpp_source.html#l03331">CFeatureItem::x_AddQualsVariation()</a>, <a class="el" href="validerror__bioseq_8cpp_source.html#l10531">CValidError_bioseq::x_CountAdjacentNs()</a>, <a class="el" href="variation__util2_8cpp_source.html#l01410">variation::CVariationUtil::x_InferNAfromAA()</a>, <a class="el" href="variation__util_8cpp_source.html#l00676">variation_ref::CVariationUtil::x_ProtToPrecursor()</a>, <a class="el" href="misc_2hgvs_2hgvs__parser_8cpp_source.html#l01946">variation_ref::CHgvsParser::x_SeqLiteralToStr()</a>, <a class="el" href="hgvs__writer2_8cpp_source.html#l00427">variation::CHgvsParser::x_SeqLiteralToStr()</a>, <a class="el" href="querydata__unit__test_8cpp_source.html#l00449">CSequenceDataTester::x_TestSingleNucleotide_Remote()</a>, and <a class="el" href="querydata__unit__test_8cpp_source.html#l00428">CSequenceDataTester::x_TestSingleProtein_Remote()</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02010">CSeqportUtil_implementation::Convert()</a>, <a class="el" href="Seq__data___8hpp_source.html#l00106">CSeq_data_Base::e_Ncbi2na</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<td class="paramtype"><a class="el" href="zconf__cf_8h.html#a2c212835823e3c54a8ab6d95c652660e">const</a> <a class="el" href="classCSeq__data.html">CSeq_data</a> & </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l00954">954</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02144">CSeqportUtil_implementation::FastValidate()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l00975">975</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">Referenced by <a class="el" href="single__aln__tests_8cpp_source.html#l00173">CTestSingleAln_All::RunTest()</a>, and <a class="el" href="xcript__tests_8cpp_source.html#l00980">s_CountAmbiguities()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01115">1115</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">Referenced by <a class="el" href="asci__blk_8cpp_source.html#l01786">GetDNAConv()</a>, <a class="el" href="asci__blk_8cpp_source.html#l01814">GetProteinConv()</a>, <a class="el" href="feature_8cpp_source.html#l00274">s_GetRnaRefLabel()</a>, and <a class="el" href="hgvs__parser2_8cpp_source.html#l01201">variation::CHgvsParser::s_hgvsaa2ncbieaa()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01122">1122</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01143">1143</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05874">CSeqportUtil_implementation::GetIndex()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="pssmcreate__unit__test_8cpp_source.html#l00388">CPssmInputTestData::SetupQueryAlignedWithInternalGaps()</a>, and <a class="el" href="alnmulti__renderer_8cpp_source.html#l00370">CAlnMultiRenderer::x_GetRowTooltip()</a>.</p>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__SeqCode.html#gaa32c42f88e10a3037ae9e17b271b44f2">ESeq_code_type</a> </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01150">1150</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05874">CSeqportUtil_implementation::GetIndex()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<td class="memname"><a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">CSeqportUtil::TIndex</a> CSeqportUtil::GetIndexComplement </td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01157">1157</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05903">CSeqportUtil_implementation::GetIndexComplement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<td class="memname"><a class="el" href="classCSeqportUtil.html#a6201a44edb80355c0f816e6df97a8ff6">CSeqportUtil::TIndex</a> CSeqportUtil::GetIndexComplement </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01164">1164</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05903">CSeqportUtil_implementation::GetIndexComplement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01088">1088</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">Referenced by <a class="el" href="feature_8cpp_source.html#l00274">s_GetRnaRefLabel()</a>, and <a class="el" href="hgvs__parser2_8cpp_source.html#l01201">variation::CHgvsParser::s_hgvsaa2ncbieaa()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01171">1171</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__SeqCode.html#gaa32c42f88e10a3037ae9e17b271b44f2">ESeq_code_type</a> </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01136">1136</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05847">CSeqportUtil_implementation::GetCodeOrName()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeqportUtil::IsCodeAvailable </td>
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<td class="paramtype"><a class="el" href="group__dataspec__NCBI__Sequence.html#ga4ebe9e4dab723da143541cd84b40fbd3">CSeq_data::E_Choice</a> </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01093">1093</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05794">CSeqportUtil_implementation::IsCodeAvailable()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<td class="memname"><a class="el" href="static__set_8hpp.html#af6a258d8f3ee5206d682d799316314b1">bool</a> CSeqportUtil::IsCodeAvailable </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01098">1098</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l05794">CSeqportUtil_implementation::IsCodeAvailable()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeqportUtil::Keep </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01000">1000</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02276">CSeqportUtil_implementation::Keep()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l00945">945</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">Referenced by <a class="el" href="Delta__ext_8cpp_source.html#l00089">CDelta_ext::AddLiteral()</a>, <a class="el" href="gene__model_8cpp_source.html#l01170">AddLiteral()</a>, <a class="el" href="fasta_8cpp_source.html#l01351">CFastaReader::AssembleSeq()</a>, <a class="el" href="asci__blk_8cpp_source.html#l03490">DeltaBioseqPack()</a>, <a class="el" href="seq__edit_8cpp_source.html#l00045">g_ConvertDeltaToRawSeq()</a>, <a class="el" href="asci__blk_8cpp_source.html#l03478">RawBioseqPack()</a>, <a class="el" href="update__seq__input_8cpp_source.html#l00511">CUpdateSeq_Input::s_ConvertDeltaToRawBioseq()</a>, <a class="el" href="update__seq_8cpp_source.html#l00988">CSequenceUpdater::s_UpdateSeqInst()</a>, <a class="el" href="algo_2sequence_2util_8cpp_source.html#l00045">SeqLocToBioseq()</a>, <a class="el" href="gui_2objutils_2utils_8cpp_source.html#l00601">CSeqUtils::SeqLocToBioseq()</a>, <a class="el" href="seq__entry__edit_8cpp_source.html#l02449">UpdateSeqLength()</a>, <a class="el" href="gene__model_8cpp_source.html#l01215">CFeatureGenerator::SImplementation::x_CollectMrnaSequence()</a>, <a class="el" href="phrap_8cpp_source.html#l00333">CPhrap_Seq::x_FillSeqData()</a>, <a class="el" href="aln__reader_8cpp_source.html#l00703">CAlnReader::x_GetSeqInst()</a>, <a class="el" href="update__seq__input_8cpp_source.html#l00601">CUpdateSeq_Input::x_ReadAccession()</a>, <a class="el" href="update__seq_8cpp_source.html#l00775">CSequenceUpdater::x_ReplaceSequence()</a>, and <a class="el" href="vectortrimpanel_8cpp_source.html#l00552">CVectorTrimPanel::x_SetSeqData()</a>.</p>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01077">1077</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02465">CSeqportUtil_implementation::ReverseComplement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#ad5fc35e63ec91157fcaf67a8b2f31756">◆ </a></span>ReverseComplement() <span class="overload">[2/2]</span></h2>
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<td class="memname"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> CSeqportUtil::ReverseComplement </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="classCSeq__data.html">CSeq_data</a> * </td>
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<td class="paramname"><em>in_seq</em>, </td>
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<td class="paramtype"><a class="el" href="group__AppFramework.html#ga7576cbabf7b457b1a66d0a1d985fe176">TSeqPos</a> </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l01067">1067</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02465">CSeqportUtil_implementation::ReverseComplement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="variation__util2_8cpp_source.html#l02074">variation::CVariationUtil::FlipStrand()</a>, <a class="el" href="sequence_8cpp_source.html#l05142">ReverseComplement()</a>, <a class="el" href="hgvs__writer2_8cpp_source.html#l00224">variation::CHgvsParser::x_AsHgvsExpression()</a>, <a class="el" href="phrap_8cpp_source.html#l00333">CPhrap_Seq::x_FillSeqData()</a>, and <a class="el" href="misc_2hgvs_2hgvs__parser_8cpp_source.html#l01946">variation_ref::CHgvsParser::x_SeqLiteralToStr()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#af6204270735c7fb50c918e2ac8fa10ac">◆ </a></span>Validate()</h2>
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<td class="memname">void CSeqportUtil::Validate </td>
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<td class="paramname"><em>badIdx</em>, </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l00964">964</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">References <a class="el" href="seqport__util_8cpp_source.html#l02172">CSeqportUtil_implementation::Validate()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00904">x_GetImplementation()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="fasta_8cpp_source.html#l01351">CFastaReader::AssembleSeq()</a>, <a class="el" href="validerror__bioseq_8cpp_source.html#l04392">CValidError_bioseq::ValidateDelta()</a>, <a class="el" href="misc_2hgvs_2hgvs__parser_8cpp_source.html#l00891">variation_ref::CHgvsParser::x_raw_seq()</a>, and <a class="el" href="hgvs__parser2_8cpp_source.html#l01234">variation::CHgvsParser::x_raw_seq()</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a25d43486f12618e8fb0c3ece979057f5">◆ </a></span>x_GetImplementation()</h2>
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<td class="memname"><a class="el" href="classCSeqportUtil__implementation.html">CSeqportUtil_implementation</a> & CSeqportUtil::x_GetImplementation </td>
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<p class="definition">Definition at line <a class="el" href="seqport__util_8cpp_source.html#l00904">904</a> of file <a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a>.</p>
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<p class="reference">Referenced by <a class="el" href="seqport__util_8cpp_source.html#l01011">Append()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01026">Complement()</a>, <a class="el" href="seqport__util_8cpp_source.html#l00918">Convert()</a>, <a class="el" href="seqport__util_8cpp_source.html#l00932">ConvertWithBlastAmbig()</a>, <a class="el" href="seqport__util_8cpp_source.html#l00955">FastValidate()</a>, <a class="el" href="seqport__util_8cpp_source.html#l00976">GetAmbigs()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01116">GetCode()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01104">GetCodeIndexFromTo()</a>, <a class="el" href="seqport__util_8cpp_source.html#l00989">GetCopy()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01144">GetIndex()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01158">GetIndexComplement()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01088">GetIupacaa3()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01172">GetMapToIndex()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01130">GetName()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01093">IsCodeAvailable()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01001">Keep()</a>, <a class="el" href="seqport__util_8cpp_source.html#l00946">Pack()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01047">Reverse()</a>, <a class="el" href="seqport__util_8cpp_source.html#l01068">ReverseComplement()</a>, and <a class="el" href="seqport__util_8cpp_source.html#l00965">Validate()</a>.</p>
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<hr/>The documentation for this class was generated from the following files:<ul>
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<li>include/objects/seq/<a class="el" href="seqport__util_8hpp_source.html">seqport_util.hpp</a></li>
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<li>src/objects/seq/<a class="el" href="seqport__util_8cpp_source.html">seqport_util.cpp</a></li>
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Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.0
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<address style="align: right;"><small>Modified on Fri Sep 20 14:58:25 2024 by modify_doxy.py rev. 669887</small></address>
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