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      <arglist>(pos_type al, pos_type ar, pos_type bl, pos_type br, ScoringView sv)</arglist>
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      <arglist>(ScoringView sv)</arglist>
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      <arglist>(Arc arcA, pos_type bl, pos_type max_br)</arglist>
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      <arglist>(index_t al, matidx_t i_index, matidx_t j_index, seq_pos_t i_seq_pos, seq_pos_t i_prev_seq_pos, ScoringView sv)</arglist>
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      <arglist>(index_t bl, matidx_t i_index, matidx_t j_index, seq_pos_t i_seq_pos, seq_pos_t i_prev_seq_pos, ScoringView sv)</arglist>
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      <arglist>(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool top_level, ScoringView sv)</arglist>
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      <arglist>(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool top_level, ScoringView sv)</arglist>
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      <arglist>(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool tl, ScoringView sv)</arglist>
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      <arglist>(pos_type al, pos_type i, pos_type bl, pos_type j, bool top_level, ScoringView sv)</arglist>
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      <arglist>(const Arc &amp;arcA, const Arc &amp;arcB, ScoringView sv)</arglist>
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      <arglist>(const Arc &amp;arcA, const Arc &amp;arcB, ScoringView sv)</arglist>
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      <arglist>(pos_type xl, pos_type i, const Arc &amp;arcY, ScoringView sv)</arglist>
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      <arglist>()</arglist>
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      <arglist>(pos_type al, pos_type bl)</arglist>
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      <type>infty_score_t &amp;</type>
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      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
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      <arglist>(const ArcMatch &amp;am)</arglist>
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      <type>infty_score_t &amp;</type>
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      <arglist>(const Arc &amp;arcX, const Arc &amp;arcY)</arglist>
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      <type>infty_score_t &amp;</type>
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      <arglist>(const Arc &amp;arcA, const Arc &amp;arcB)</arglist>
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      <type>infty_score_t &amp;</type>
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      <arglist>(const pos_type i, const Arc &amp;arc)</arglist>
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      <type>infty_score_t &amp;</type>
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      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
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      <arglist>(const Arc &amp;arc1, const Arc &amp;arc2)</arglist>
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      <arglist>(const pos_type i, const Arc &amp;b)</arglist>
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      <type>infty_score_t &amp;</type>
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      <arglist>(const Arc &amp;a, const pos_type k)</arglist>
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    <member kind="function" protection="protected">
      <type>void</type>
      <name>trace</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a55d8772374207808fbe6b537cea4dc77</anchor>
      <arglist>(ScoringView sv)</arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const AlignerNParams *</type>
      <name>params</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>afd8c8ec8d5ec27f6854b94a573d8e84c</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const Scoring *</type>
      <name>scoring</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a647823e4fe010752ec2325fb62e1bf73</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>Scoring *</type>
      <name>mod_scoring</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>af62f97427f05aa11763cf67a74dc90b1</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const Sequence &amp;</type>
      <name>seqA</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a41c6579e8c46b6b1620181dde9161717</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const Sequence &amp;</type>
      <name>seqB</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a8f250dc8ada8c9edcf374b2b6462f22b</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const SparsificationMapper &amp;</type>
      <name>mapperA</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a16d961d43feb3e408c07f2a46735155c</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const SparsificationMapper &amp;</type>
      <name>mapperB</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a570da535cf8920d44fe21a53ef622f98</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const ArcMatches &amp;</type>
      <name>arc_matches</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a0bb65484b9aafa17b29440c8e7fe088b</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const BasePairs &amp;</type>
      <name>bpsA</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a85aec24bd920c1c6591d217ffee7eeeb</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const BasePairs &amp;</type>
      <name>bpsB</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a96cce8fa87b07acb044a27f152918a98</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>AlignerRestriction</type>
      <name>r</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>acf5827bab0b7055e5db75f8f0ffa7be7</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>Dmat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a89f0a2d54c79c75cfa17d34f49336636</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>IAmat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a97586c6734b8b2683f0065969e1dcf52</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>IBmat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>abf41bae03b329d51404ebb21ca7e5af2</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>IADmat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a6c379a3205a2729c70b5ebd42aea70fa</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>IBDmat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a1ec6dfd2303f308fd92180ff7fc46136</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>Emat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a6cc451f1b96c32f355d2bd8dd9a06b48</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>Fmat</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a705b601f794bfa670a5d817cb764c059</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>M_matrix_t</type>
      <name>M</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>ae46b1f15731f4ab0a1701f44c3402bc8</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>gapCostMatA</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>aab91c085c105c25a97507a8691c05396</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ScoreMatrix</type>
      <name>gapCostMatB</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>af7256d0a058dd356fba16f5f53164511</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>int</type>
      <name>min_i</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>af8dcaee22d832a5e8b8e4d4cc51a6b96</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>int</type>
      <name>min_j</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>ab3217801764448fd5f74bf71f3ad2569</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>int</type>
      <name>max_i</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a676ad75e94615bd3822ab1d8906cde76</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>int</type>
      <name>max_j</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a75e170e65557f20d6d895af8ac03b446</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>bool</type>
      <name>D_created</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>ade1a4d893b368a0e7fe300ab37de65bf</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>Alignment</type>
      <name>alignment</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a30b248141a175e74e69071f4842e0a43</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const UnmodifiedScoringViewN</type>
      <name>def_scoring_view</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>ad2bb8d7ee3c1b5b895145ccb1f72098e</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>ModifiedScoringViewN</type>
      <name>mod_scoring_view</name>
      <anchorfile>classLocARNA_1_1AlignerN.html</anchorfile>
      <anchor>a97605d94ec33d3f84c2f2bc2322cdce0</anchor>
      <arglist></arglist>
    </member>
  </compound>
  <compound kind="class">
    <name>LocARNA::AlignerN::ModifiedScoringViewN</name>
    <filename>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</filename>
    <member kind="function">
      <type></type>
      <name>ModifiedScoringViewN</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>ab2baec1aa337738fc2cde477d24a26cb</anchor>
      <arglist>(const AlignerN *alignerN)</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>set_lambda</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>a1447dc87d2423d9f41064264f68829fb</anchor>
      <arglist>(score_t lambda)</arglist>
    </member>
    <member kind="function">
      <type>const Scoring *</type>
      <name>scoring</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>a3cb5e002f18f992f5fb264062553f132</anchor>
      <arglist>() const </arglist>
    </member>
    <member kind="function">
      <type>infty_score_t</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>a049cbff85d5b92fe0000895fbde461ef</anchor>
      <arglist>(const Arc &amp;a, const Arc &amp;b) const </arglist>
    </member>
    <member kind="function">
      <type>infty_score_t</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>af19058e782d740fd169bdb002386309b</anchor>
      <arglist>(const ArcMatch &amp;am) const </arglist>
    </member>
    <member kind="function" protection="protected">
      <type>size_t</type>
      <name>arc_length</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>ac0f08b884c8a8456b25e2c579d000e93</anchor>
      <arglist>(const Arc &amp;a) const </arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const AlignerN *</type>
      <name>alignerN_</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>abd94164f7163e194e879c5ca3a955442</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>score_t</type>
      <name>lambda_</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1ModifiedScoringViewN.html</anchorfile>
      <anchor>a1a3a1d3eafb83e6aedc1d1afc1d6765c</anchor>
      <arglist></arglist>
    </member>
  </compound>
  <compound kind="class">
    <name>LocARNA::AlignerN::UnmodifiedScoringViewN</name>
    <filename>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</filename>
    <member kind="function">
      <type></type>
      <name>UnmodifiedScoringViewN</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</anchorfile>
      <anchor>ac178d4cb3a65e0cae75c0dcb2e43645a</anchor>
      <arglist>(const AlignerN *alignerN)</arglist>
    </member>
    <member kind="function">
      <type>const Scoring *</type>
      <name>scoring</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</anchorfile>
      <anchor>a2e4fad9e53b1b63001352d96e141b930</anchor>
      <arglist>() const </arglist>
    </member>
    <member kind="function">
      <type>infty_score_t</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</anchorfile>
      <anchor>ad00b65e84697d9d26446d71167bc4027</anchor>
      <arglist>(const Arc &amp;a, const Arc &amp;b) const </arglist>
    </member>
    <member kind="function">
      <type>infty_score_t</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</anchorfile>
      <anchor>add9a2cbd7056a09165fd18059d68b170</anchor>
      <arglist>(bool isA, const Arc &amp;arcX, const Arc &amp;arcY)</arglist>
    </member>
    <member kind="function">
      <type>infty_score_t</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</anchorfile>
      <anchor>aa2402dab3eb937ad4c2d255680707ca8</anchor>
      <arglist>(const ArcMatch &amp;am) const </arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const AlignerN *</type>
      <name>alignerN_</name>
      <anchorfile>classLocARNA_1_1AlignerN_1_1UnmodifiedScoringViewN.html</anchorfile>
      <anchor>ac0f6ad1397a646b7ef0783fcaea4c5c5</anchor>
      <arglist></arglist>
    </member>
  </compound>
  <compound kind="class">
    <name>LocARNA::AlignerP</name>
    <filename>classLocARNA_1_1AlignerP.html</filename>
    <member kind="typedef">
      <type>size_t</type>
      <name>size_type</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a8c6488fac2344d885ec42e70eb551b02</anchor>
      <arglist></arglist>
    </member>
    <member kind="typedef">
      <type>std::pair&lt; size_type, size_type &gt;</type>
      <name>size_pair</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ab26d0e70d4bf3d2d7c709799a593a248</anchor>
      <arglist></arglist>
    </member>
    <member kind="typedef">
      <type>BasePairs__Arc</type>
      <name>Arc</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>af20ce35f2c8f88abe43bd37350a5ed63</anchor>
      <arglist></arglist>
    </member>
    <member kind="function">
      <type></type>
      <name>AlignerP</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a12974ee4f851903bf9e11973d0c146db</anchor>
      <arglist>(const AlignerParams &amp;ap)</arglist>
    </member>
    <member kind="function">
      <type></type>
      <name>AlignerP</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a13ed2ee85b4ae8d83502eba4021c35a1</anchor>
      <arglist>(const AlignerP &amp;p)</arglist>
    </member>
    <member kind="function">
      <type></type>
      <name>~AlignerP</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a0efce50b055c2e2c80d9a48b691496a3</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function">
      <type>pf_score_t</type>
      <name>align_inside</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ad14178c3adda951743868eabb0d07bfd</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>align_outside</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a9453e09d4bf3322975ede0b78b605133</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>compute_basematch_probabilities</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>af7b216b9da49293ccc2f9868917d1c38</anchor>
      <arglist>(bool basematch_probs_include_arcmatch)</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>compute_arcmatch_probabilities</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a6bc3173d92c0a8d7f67881e05bc22abf</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>write_arcmatch_probabilities</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a36b0f0e9e2fe7acd10912d2b0eadfc13</anchor>
      <arglist>(std::ostream &amp;out)</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>write_basematch_probabilities</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ae4999b093cb856aaed25f1c5ca9b3604</anchor>
      <arglist>(std::ostream &amp;out)</arglist>
    </member>
    <member kind="function">
      <type>pf_score_t</type>
      <name>virtual_Mprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>acd50dd0dcc4d830a22a801e5c2afa7de</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j, size_type max_ar, size_type max_br) const </arglist>
    </member>
    <member kind="function">
      <type>double</type>
      <name>compute_fragment_match_prob</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>acdf481c16e9eab249bbe9c08526ca2eb</anchor>
      <arglist>(size_type i, size_type j, size_type k, size_type l)</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>freeD</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aa94482070e5756a57645bf457f3ebe3e</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function">
      <type>void</type>
      <name>freeMprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>afe4ce798e21d4c2c458e2acb320103c3</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function" static="yes">
      <type>static AlignerPParams</type>
      <name>create</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a93c50b5ac639f093da9fdf318ba57163</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>init_M</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a9648f3aedf9b07ac8b877570a67ee2a5</anchor>
      <arglist>(size_type al, size_type ar, size_type bl, size_type br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>init_E</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a10331c51bb8d474a25035f1bd5683657</anchor>
      <arglist>(size_type al, size_type ar, size_type bl, size_type br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>init_Mrev</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a048096d6065075f027592e244940c323</anchor>
      <arglist>(size_type al, size_type ar, size_type bl, size_type br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>init_Erev</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a2860e7f9c1eabc7f896aacd1d8902ce2</anchor>
      <arglist>(size_type al, size_type ar, size_type bl, size_type br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_E_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>af567c40854108b4495c9de79cd5310bd</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_F_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a32e3bf46a27d39df8305971c664b7827</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_M_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a4aa6e31ecdda644a495b7a5191121855</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_Mprime_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a18274b246f725a6bb3d00f3ca7e1b6f8</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j, size_type max_ar, size_type max_br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_Eprime_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a2e05620979e54037b88d61ec2c96405b</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_Fprime_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a41732b3f63daa7d0ddd06db8065635ce</anchor>
      <arglist>(size_type al, size_type bl, size_type i, size_type j)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_Erev_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ad8a1e2b3eb8626f79281139cab8ff84e</anchor>
      <arglist>(size_type i, size_type j)</arglist>
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    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_Frev_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a0117ad6744f8e0da7a30bf764e2853ea</anchor>
      <arglist>(size_type i, size_type j)</arglist>
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    <member kind="function" protection="protected">
      <type>pf_score_t</type>
      <name>comp_Mrev_entry</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a4c302f9054f45b273d0744e785850b68</anchor>
      <arglist>(size_type i, size_type j, size_type ar, size_type br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>align_inside_arcmatch</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a20dd37f624493328d9e3a40b13c0ad6c</anchor>
      <arglist>(size_type al, size_type ar, size_type bl, size_type br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>align_outside_arcmatch</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a3ccec64a931dab3777269e11f278f53d</anchor>
      <arglist>(size_type al, size_type ar, size_type max_ar, size_type bl, size_type br, size_type max_br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>align_reverse</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>abbede00258d36de97e6212caed412172</anchor>
      <arglist>(size_type al, size_type ar, size_type bl, size_type br, bool copy=false)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>align_D</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a8103e9acf1e0dbac6b6dc528f6e585ff</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>align_Dprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aee621e019448210fa8aec92e0890c997</anchor>
      <arglist>()</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>fill_D</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ac97a4c332942e89554cce19f17eff147</anchor>
      <arglist>(size_type al, size_type bl, size_type max_ar, size_type max_br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>void</type>
      <name>fill_Dprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a8ac2c4bdfcfaf4631d1509b6bff7ec7b</anchor>
      <arglist>(size_type al, size_type bl, size_type min_ar, size_type min_br, size_type max_ar, size_type max_br)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t &amp;</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a0a90fec814517740e24cf193e82a05f7</anchor>
      <arglist>(const ArcMatch &amp;am)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t &amp;</type>
      <name>D</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a54128ac60d3d3d8d10ae99d1400a7434</anchor>
      <arglist>(const Arc &amp;arcA, const Arc &amp;arcB)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t &amp;</type>
      <name>Dprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a6a2416a53ec3390a8ddecdd27ae5c9c7</anchor>
      <arglist>(const ArcMatch &amp;am)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>pf_score_t &amp;</type>
      <name>Dprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a56e80816b832b7e26f02eb6d15ffb138</anchor>
      <arglist>(const Arc &amp;arcA, const Arc &amp;arcB)</arglist>
    </member>
    <member kind="function" protection="protected">
      <type>size_type</type>
      <name>leftmost_covering_arc</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a795d5d84fcf563d075982972155a8909</anchor>
      <arglist>(size_type s, const BasePairs &amp;bps, size_type l, size_type r) const </arglist>
    </member>
    <member kind="function" protection="protected">
      <type>std::pair&lt; size_type, size_type &gt;</type>
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      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a5ec3e139bf6b14a37f89726009b1192c</anchor>
      <arglist>(size_type al, size_type bl, size_type ar, size_type br) const </arglist>
    </member>
    <member kind="function" protection="protected">
      <type>size_type</type>
      <name>rightmost_covering_arc</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a003c291f085c6b6854d434a4a4be2735</anchor>
      <arglist>(const BasePairs &amp;bps, size_type l, size_type r, size_type s) const </arglist>
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    <member kind="function" protection="protected">
      <type>std::pair&lt; size_type, size_type &gt;</type>
      <name>rightmost_covering_arcmatch</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a192b36201f135857db71d6ecc097746d</anchor>
      <arglist>(size_type al, size_type bl, size_type ar, size_type br) const </arglist>
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    <member kind="function" protection="protected">
      <type>void</type>
      <name>alloc_inside_matrices</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a8e15c1a6b5c45071a154362e1d49a92c</anchor>
      <arglist>()</arglist>
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    <member kind="function" protection="protected">
      <type>void</type>
      <name>alloc_outside_matrices</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a3195e61202d3b0d29fec444c0465916b</anchor>
      <arglist>()</arglist>
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    <member kind="variable" protection="protected">
      <type>const AlignerPParams *</type>
      <name>params</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aea7a6d0d7eac4cb4da3f8a6df933b503</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const Scoring *</type>
      <name>scoring</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a8c52ea7529d26d1a54c94741f4f25f51</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const Sequence &amp;</type>
      <name>seqA</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a983ebb790682b00bbe5cef34c7462f70</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const BasePairs &amp;</type>
      <name>bpsA</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aebecd8c99053b506d39e0fe007686591</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const Sequence &amp;</type>
      <name>seqB</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ae8a919ab9e4de562c31bbd1d2f8fbcac</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const BasePairs &amp;</type>
      <name>bpsB</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a031edd86ba3ee500c65f7cec5205c465</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>const ArcMatches &amp;</type>
      <name>arc_matches</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a524173c1b3f697ae0fad5d675676ba2d</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>AlignerPRestriction</type>
      <name>r</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a77659d2611644be84455a75e6e7307a5</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>pf_score_t</type>
      <name>pf_scale</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a961d4c999c1c106f5417edcb5c4be94f</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>pf_score_t</type>
      <name>partFunc</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a7cff76a08a2342270e576cd77c41257e</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>Dmat</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a14cadf644b23562383c6b8c2c7fd8def</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>PFScoreVector</type>
      <name>E</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a7e5a83342b7ef9ba38df1dbc02b96cf8</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>pf_score_t</type>
      <name>F</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>af921fbf04ad200a06aa8576ce582797f</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>M</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a6ff79820570f57cf58ed5009f2a7cc98</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>Mrev</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a929f14cb0008a3b08ee10b20e12d96d5</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>PFScoreVector</type>
      <name>Erev</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aac26d357bc89616032d77cfc6ecbe9c1</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>pf_score_t</type>
      <name>Frev</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>af0c5e069258134e8c469a889e86dade1</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>Erev_mat</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a840119ec5054808a1acfe4d4fd4d5e85</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>Frev_mat</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a9127a4fbdce7c506d9d5bacd13c4d716</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>Dmatprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>acd1b14f7fce404ebebda4d3bdb79dd75</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>PFScoreVector</type>
      <name>Eprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a40981e7a7a8f71e771aec27f5fbe7550</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>pf_score_t</type>
      <name>Fprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ae060b56647ab3609c0988ba5f5f77c9d</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>PFScoreMatrix</type>
      <name>Mprime</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aa718ba788a078b2aaef5735fc4e0b40e</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>SparseProbMatrix</type>
      <name>am_prob</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>aa79099c234c26b6a86a96e5fa9ccbddf</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>SparsePFScoreMatrix</type>
      <name>bm_prob</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>adbee5ac15d0aafc9220eff367d0c1f01</anchor>
      <arglist></arglist>
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    <member kind="variable" protection="protected">
      <type>bool</type>
      <name>D_created</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>a6f2d85a280f15ec68b54848991a09ba1</anchor>
      <arglist></arglist>
    </member>
    <member kind="variable" protection="protected">
      <type>bool</type>
      <name>Dprime_created</name>
      <anchorfile>classLocARNA_1_1AlignerP.html</anchorfile>
      <anchor>ae163b297cdcec855ae8978d787ab4a55</anchor>
      <arglist></arglist>
    </member>
  </compound>
  <compound kind="class">
    <name>LocARNA::AlignerRestriction</name>
    <filename>classLocARNA_1_1AlignerRestriction.html</filename>
    <member kind="function">
      <type></type>
      <name>AlignerRestriction</name>
      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>ac531674e470d24ae99caa4853d532b70</anchor>
      <arglist>(int startA, int startB, int endA, int endB)</arglist>
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    <member kind="function">
      <type>size_t</type>
      <name>startA</name>
      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>abaedbb692940963eac0855e70ee1fa99</anchor>
      <arglist>() const </arglist>
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      <type>size_t</type>
      <name>endA</name>
      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a8057904d28cb394c5b6d6c2d9228107a</anchor>
      <arglist>() const </arglist>
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      <type>size_t</type>
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      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a0f50b7938a26ef7cb0787289e7de8cc4</anchor>
      <arglist>() const </arglist>
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      <type>size_t</type>
      <name>endB</name>
      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a85ac10395ea9cd20ae157f90744ca267</anchor>
      <arglist>() const </arglist>
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      <type>void</type>
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      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a1f6dff979266ca98fca6f9917a5c7adf</anchor>
      <arglist>(size_t p)</arglist>
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    <member kind="function">
      <type>void</type>
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      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a73b3941c4ba600914676dcf1822f61d4</anchor>
      <arglist>(size_t p)</arglist>
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    <member kind="function">
      <type>void</type>
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      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a8be24a1a053cdf80c05ef9603c50a4b8</anchor>
      <arglist>(size_t p)</arglist>
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    <member kind="function">
      <type>void</type>
      <name>set_endB</name>
      <anchorfile>classLocARNA_1_1AlignerRestriction.html</anchorfile>
      <anchor>a5baf81836ae82e743567e2792ce1dced</anchor>
      <arglist>(size_t p)</arglist>
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  <compound kind="class">
    <name>LocARNA::EdgeEnd</name>
    <filename>classLocARNA_1_1EdgeEnd.html</filename>
    <member kind="function">
      <type></type>
      <name>EdgeEnd</name>
      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a6dcbd4897c0216aa495c591d2c29eaf3</anchor>
      <arglist>()</arglist>
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    <member kind="function">
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      <name>EdgeEnd</name>
      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a7b170a9599a91288d429fefe5654ea9e</anchor>
      <arglist>(pos_type end)</arglist>
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      <type></type>
      <name>EdgeEnd</name>
      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a1cd155f707729a2143d3b43e25d49b0b</anchor>
      <arglist>(Gap end)</arglist>
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      <type>bool</type>
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      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a3c72a993d681fc87b9921ce43c31e767</anchor>
      <arglist>() const </arglist>
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      <type>bool</type>
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      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a0ddd7b32d0ed2fa4df833623d85b3491</anchor>
      <arglist>() const </arglist>
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      <type>Gap</type>
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      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a2edd961490c6331234a2efd323005a38</anchor>
      <arglist>() const </arglist>
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      <type></type>
      <name>operator pos_type</name>
      <anchorfile>classLocARNA_1_1EdgeEnd.html</anchorfile>
      <anchor>a2ccaa1c9ba68a3fafa9ce57cf0e3b82f</anchor>
      <arglist>() const </arglist>
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    <filename>classLocARNA_1_1AlignmentEdges.html</filename>
    <member kind="function">
      <type></type>
      <name>AlignmentEdges</name>
      <anchorfile>classLocARNA_1_1AlignmentEdges.html</anchorfile>
      <anchor>adfd9fa0ce3f9277202caa8e98d42511b</anchor>
      <arglist>(const edge_ends_t &amp;x, const edge_ends_t &amp;y)</arglist>
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    <member kind="function">
      <type>size_t</type>
      <name>size</name>
      <anchorfile>classLocARNA_1_1AlignmentEdges.html</anchorfile>
      <anchor>a27e8d0897e5523a4b42be68c00355c7b</anchor>
      <arglist>() const </arglist>
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  <compound kind="class">
    <name>LocARNA::Alignment</name>
    <filename>classLocARNA_1_1Alignment.html</filename>
    <member kind="typedef">
      <type>EdgeEnd</type>
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      <anchorfile>classLocARNA_1_1Alignment.html</anchorfile>
      <anchor>ab81bbb18f0400395fb7a59f4a0e79831</anchor>
      <arglist></arglist>
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    <member kind="typedef">
      <type>Alignment__edge_ends_t</type>
      <name>edge_ends_t</name>
      <anchorfile>classLocARNA_1_1Alignment.html</anchorfile>
      <anchor>a34883169ddd697e22223ebeaea7b713c</anchor>
      <arglist></arglist>
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    <member kind="typedef">
      <type>AlignmentEdges</type>
      <name>edges_t</name>
      <anchorfile>classLocARNA_1_1Alignment.html</anchorfile>
      <anchor>ad23971780771de3de6ae98942132a7bc</anchor>
      <arglist></arglist>
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      <name>Alignment</name>
      <anchorfile>classLocARNA_1_1Alignment.html</anchorfile>
      <anchor>a1060eb44ae603a4cfc20b88b8ba55c5a</anchor>
      <arglist>(const Sequence &amp;seqA, const Sequence &amp;seqB)</arglist>
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    <member kind="function">
      <type></type>
      <name>~Alignment</name>
      <anchorfile>classLocARNA_1_1Alignment.html</anchorfile>
      <anchor>ae7615717fe1d55deaeb61ade051bd749</anchor>
      <arglist>()</arglist>
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      <type></type>
      <name>Alignment</name>
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      <arglist>(const Sequence &amp;seqA_, const Sequence &amp;seqB_, const std::string &amp;arcmatch_scores_file, int probability_scale, size_type max_length_diff, size_type max_diff_at_am, const MatchController &amp;trace_controller, const AnchorConstraints &amp;constraints)</arglist>
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      <arglist>(const RnaData &amp;rnadataA, const RnaData &amp;rnadataB, double min_prob, size_type max_length_diff, size_type max_diff_at_am, const MatchController &amp;trace_controller, const AnchorConstraints &amp;constraints)</arglist>
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      <arglist>(const Scoring &amp;scoring)</arglist>
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      <arglist>(const ArcMatch &amp;am) const </arglist>
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      <arglist>() const </arglist>
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      <arglist>(size_type al, size_type bl, size_type *max_ar, size_type *max_br, bool no_lonely_pairs) const </arglist>
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      <arglist>(const ArcMatch &amp;am) const </arglist>
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      <arglist>(const ArcMatch &amp;am) const </arglist>
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      <arglist>(const Sequence &amp;seqA_, const Sequence &amp;seqB_, const RnaData &amp;rna_dataA_, const RnaData &amp;rna_dataB_, const ArcMatches &amp;arc_matches_, const SparseTraceController &amp;sparse_trace_controller_, PatternPairMap &amp;foundEPMs_, int alpha_1_, int alpha_2_, int alpha_3_, score_t difference_to_opt_score_, score_t min_score_, long int max_number_of_EPMs_, bool inexact_struct_match_, score_t struct_mismatch_score_, bool apply_filter_, bool verbose_)</arglist>
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      <arglist>()</arglist>
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      <arglist>(bool suboptimal)</arglist>
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      <arglist>(const RnaEnsemble &amp;rna_ensemble, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &amp;pfoldparams)</arglist>
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      <arglist>(const std::string &amp;filename, double p_bpcut, double p_bpilcut, double p_uilcut, double max_bps_length_ratio, double max_uil_length_ratio, double max_bpil_length_ratio, const PFoldParams &amp;pfoldparams)</arglist>
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      <arglist>()</arglist>
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      <arglist>(pos_type i, pos_type j, pos_type p, pos_type q) const </arglist>
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      <arglist>(pos_type i, pos_type j) const </arglist>
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      <arglist>(pos_type k, pos_type p, pos_type q) const </arglist>
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      <arglist>(const RnaEnsemble &amp;rna_ensemble, const PFoldParams &amp;pfoldparams)</arglist>
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      <arglist></arglist>
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      <arglist>(size_t keep)</arglist>
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      <arglist>(double ratio)</arglist>
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      <arglist></arglist>
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      <arglist>(double p_bpcut, size_t max_bp_span)</arglist>
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      <arglist></arglist>
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