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ADAPTION.char+array.html
ADAPTION.std_3a_3a_F_I_L_E+_2a.html
ADAPTION.std_3a_3abasic__string.html
ADAPTION.std_3a_3aiostream.html
ADAPTION.std_3a_3alist.html
ADAPTION.std_3a_3avector.html
CLASS_Align.html
CLASS_Align_Cols.html
CLASS_Align_Config.html
CLASS_Align_Quality_Store_Element.html
CLASS_Aligned_Read_Layout.html
CLASS_Aligned_Read_Store_Element.html
CLASS_Allocator.html
CLASS_Async_Request.html
CLASS_Auto_Seq_Format.html
CLASS_Blast_Hit.html
CLASS_Blast_Hsp.html
CLASS_Blast_Report.html
CLASS_Bundle2.html
CLASS_Bundle3.html
CLASS_Bundle5.html
CLASS_Command_Line_Option.html
CLASS_Command_Line_Parser.html
CLASS_Concatenator_Many_To_One.html
CLASS_Contig_File.html
CLASS_Contig_Store_Element.html
CLASS_Dequeue.html
CLASS_Edge_Stump.html
CLASS_External+_Property+_Map.html
CLASS_File.html
CLASS_File_Format.html
CLASS_Finder.html
CLASS_Fragment.html
CLASS_Fragment_Store.html
CLASS_Frequency_Distribution.html
CLASS_Functor_Complement.html
CLASS_Functor_Convert.html
CLASS_Functor_Lowcase.html
CLASS_Functor_Upcase.html
CLASS_Gap_Anchor.html
CLASS_Gaps.html
CLASS_Graph.html
CLASS_Hardwired_Shape.html
CLASS_Holder.html
CLASS_Id_Manager.html
CLASS_Index.html
CLASS_Internal_Map.html
CLASS_Internal_Pointer_Map.html
CLASS_Internal_Raw_Map.html
CLASS_Interval_And_Cargo.html
CLASS_Interval_Tree.html
CLASS_Interval_Tree_Node.html
CLASS_Iter.html
CLASS_Lexical.html
CLASS_Library_Store_Element.html
CLASS_Local_Alignment_Finder.html
CLASS_Map.html
CLASS_Markov_Model.html
CLASS_Mate_Pair_Store_Element.html
CLASS_Matrix.html
CLASS_Memory_Manager.html
CLASS_Modified_Alphabet.html
CLASS_Modified_Iterator.html
CLASS_Modified_String.html
CLASS_Motif_Finder.html
CLASS_Name_Store_Cache.html
CLASS_Pair.html
CLASS_Pattern.html
CLASS_Pdf.html
CLASS_Pipe.html
CLASS_Point_And_Cargo.html
CLASS_Pool.html
CLASS_Priority_Type.html
CLASS_Property_Map.html
CLASS_Proxy.html
CLASS_Pseudocount.html
CLASS_Read_Store_Element.html
CLASS_Rng.html
CLASS_Score.html
CLASS_Seed.html
CLASS_Seed_Set.html
CLASS_Segment.html
CLASS_Shape.html
CLASS_Simple_Type.html
CLASS_String.html
CLASS_String_Set.html
CLASS_Tag_Selector.html
CLASS_To_Std_Allocator.html
CLASS_Triple.html
CLASS_Tuple.html
CONCEPT_Allocator.html
CONCEPT_Container.html
CONCEPT_Finder.html
CONCEPT_Iterator.html
CONCEPT_Pattern.html
CONCEPT_Rooted+_Iterator.html
CONCEPT_Simple+_Type.html
DEMO_All+_Pairs+_Shortest+_Path.html
DEMO_Allocators.html
DEMO_Alphabets.html
DEMO_Approximate+_Searching.html
DEMO_Bellman-_Ford+_Algorithm.html
DEMO_Blast+_Reports.html
DEMO_Breadth-_First+_Search.html
DEMO_Constraint+_Iterator.html
DEMO_Depth-_First+_Search.html
DEMO_Dijkstras+_Algorithm.html
DEMO_Exact+_Searching.html
DEMO_File+_Format+_I_2f_O.html
DEMO_Floyd-_Warshall+_Algorithm.html
DEMO_Global+_Alignments.html
DEMO_H_M_M+_Silent+_States.html
DEMO_H_M_M.html
DEMO_Heaviest+_Increasing+_Subsequence.html
DEMO_Index+_Finder+_String_Set.html
DEMO_Index+_Finder.html
DEMO_Iterator+_Basics.html
DEMO_Kruskals+_Algorithm.html
DEMO_Local+_Alignments.html
DEMO_Longest+_Common+_Subsequence.html
DEMO_Longest+_Increasing+_Subsequence.html
DEMO_Maximal+_Repeats.html
DEMO_Maximal+_Unique+_Matches.html
DEMO_Maximum+_Flow.html
DEMO_Mod_Reverse.html
DEMO_Mod_View.html
DEMO_Motif+_Finder.html
DEMO_Mummy.html
DEMO_Nested+_Modifiers.html
DEMO_Pizza+_26+_Chili+_Index.html
DEMO_Prims+_Algorithm.html
DEMO_Rooted+_Iterators.html
DEMO_Shortest+_Path+in+_D_A_Gs.html
DEMO_String+_Basics.html
DEMO_Strongly+_Connected+_Components.html
DEMO_Suffix+_Array.html
DEMO_Supermaximal+_Repeats.html
DEMO_Topological+_Sort.html
DEMO_Transitive+_Closure.html
DEMO_Wildcard+_Searching.html
FUNCTION.abs_Freq_Of_Letters_In_Seq.html
FUNCTION.abs_Freq_Of_Letters_In_Set_Of_Seqs.html
FUNCTION.add_Argument_Text.html
FUNCTION.add_Child.html
FUNCTION.add_Edge.html
FUNCTION.add_Edges.html
FUNCTION.add_Help_Line.html
FUNCTION.add_Interval.html
FUNCTION.add_Line.html
FUNCTION.add_Option.html
FUNCTION.add_Section.html
FUNCTION.add_Seed.html
FUNCTION.add_Seeds.html
FUNCTION.add_Title_Line.html
FUNCTION.add_Usage_Line.html
FUNCTION.add_Value.html
FUNCTION.add_Version_Line.html
FUNCTION.add_Vertex.html
FUNCTION.adjust_Top.html
FUNCTION.alignment.html
FUNCTION.alignment_Evaluation.html
FUNCTION.all_Pairs_Shortest_Path.html
FUNCTION.allocate.html
FUNCTION.append.html
FUNCTION.append_Aligned_Read.html
FUNCTION.append_Diag.html
FUNCTION.append_Mate_Pair.html
FUNCTION.append_Name.html
FUNCTION.append_Read.html
FUNCTION.append_Seqs.html
FUNCTION.append_Value.html
FUNCTION.argument_Count.html
FUNCTION.argument_Text.html
FUNCTION.array_Clear_Space.html
FUNCTION.array_Construct.html
FUNCTION.array_Construct_Copy.html
FUNCTION.array_Construct_Move.html
FUNCTION.array_Copy.html
FUNCTION.array_Copy_Backward.html
FUNCTION.array_Copy_Forward.html
FUNCTION.array_Destruct.html
FUNCTION.array_Fill.html
FUNCTION.array_Move.html
FUNCTION.array_Move_Backward.html
FUNCTION.array_Move_Forward.html
FUNCTION.assign.html
FUNCTION.assign_Begin_State.html
FUNCTION.assign_Cargo.html
FUNCTION.assign_Cropped_Seq_Id.html
FUNCTION.assign_Emission_Probability.html
FUNCTION.assign_End_State.html
FUNCTION.assign_Next_S.html
FUNCTION.assign_Next_T.html
FUNCTION.assign_Property.html
FUNCTION.assign_Qual.html
FUNCTION.assign_Qual_Id.html
FUNCTION.assign_Qualities.html
FUNCTION.assign_Quality_Value.html
FUNCTION.assign_Root.html
FUNCTION.assign_Seq.html
FUNCTION.assign_Seq_Id.html
FUNCTION.assign_Silent_Status.html
FUNCTION.assign_Source.html
FUNCTION.assign_String_Set.html
FUNCTION.assign_Target.html
FUNCTION.assign_Transition_Probability.html
FUNCTION.assign_Value.html
FUNCTION.assign_Value_By_Id.html
FUNCTION.async_Read_At.html
FUNCTION.async_Write_At.html
FUNCTION.at_Begin.html
FUNCTION.at_End.html
FUNCTION.at_End_Of_Sequence.html
FUNCTION.at_Nil.html
FUNCTION.atomic_Add.html
FUNCTION.atomic_Cas.html
FUNCTION.atomic_Dec.html
FUNCTION.atomic_Inc.html
FUNCTION.atomic_Max.html
FUNCTION.atomic_Min.html
FUNCTION.atomic_Or.html
FUNCTION.atomic_Xor.html
FUNCTION.back.html
FUNCTION.background_Frequency.html
FUNCTION.backward_Algorithm.html
FUNCTION.banded_Alignment.html
FUNCTION.banded_Chain_Alignment.html
FUNCTION.begin.html
FUNCTION.begin_Position.html
FUNCTION.begin_Read.html
FUNCTION.begin_State.html
FUNCTION.begin_Write.html
FUNCTION.bellman_Ford_Algorithm.html
FUNCTION.binomial_Coefficient.html
FUNCTION.blast_23get_Alignment.html
FUNCTION.breadth_First_Search.html
FUNCTION.bundle2.html
FUNCTION.bundle3.html
FUNCTION.bundle5.html
FUNCTION.bwt_At.html
FUNCTION.calculate_Insert_Sizes.html
FUNCTION.calculate_Mate_Indices.html
FUNCTION.can_Parse_String.html
FUNCTION.cancel.html
FUNCTION.capacity.html
FUNCTION.cargo.html
FUNCTION.child_At.html
FUNCTION.child_Vertex.html
FUNCTION.children_Are_Leaves.html
FUNCTION.clear.html
FUNCTION.clear_Edges.html
FUNCTION.clear_Gaps.html
FUNCTION.clear_Reads.html
FUNCTION.clear_Vertices.html
FUNCTION.clipped_Begin_Position.html
FUNCTION.clipped_End_Position.html
FUNCTION.close.html
FUNCTION.col.html
FUNCTION.collect_Leaves.html
FUNCTION.cols.html
FUNCTION.compact_Aligned_Reads.html
FUNCTION.compact_Pair_Match_Ids.html
FUNCTION.compare.html
FUNCTION.complement.html
FUNCTION.complete_Profile.html
FUNCTION.compute_Generous_Capacity.html
FUNCTION.concat.html
FUNCTION.connected_Components.html
FUNCTION.container.html
FUNCTION.convert.html
FUNCTION.convert_Alignment.html
FUNCTION.convert_Impl.html
FUNCTION.convert_Matches_To_Global_Alignment.html
FUNCTION.convert_Pair_Wise_To_Global_Alignment.html
FUNCTION.convert_Pattern_To_Profile.html
FUNCTION.convert_Residue_To_Frequency_Dist.html
FUNCTION.convert_Set_Of_Patterns_To_Profile.html
FUNCTION.count_Characters.html
FUNCTION.count_Children.html
FUNCTION.count_Gaps.html
FUNCTION.count_Occurrences.html
FUNCTION.count_Occurrences_Multiple.html
FUNCTION.cpu_Time.html
FUNCTION.create.html
FUNCTION.create_B_W_Table.html
FUNCTION.create_Childtab.html
FUNCTION.create_Count_Array.html
FUNCTION.create_Interval_Tree.html
FUNCTION.create_Lcp_Table.html
FUNCTION.create_Oracle.html
FUNCTION.create_Oracle_On_Reverse.html
FUNCTION.create_Q_Gram_Index.html
FUNCTION.create_Q_Gram_Index_Dir_Only.html
FUNCTION.create_Q_Gram_Index_S_A_Only.html
FUNCTION.create_Root.html
FUNCTION.create_Source.html
FUNCTION.create_Suffix_Array.html
FUNCTION.create_Suffix_Trie.html
FUNCTION.create_Trie.html
FUNCTION.create_Trie_On_Reverse.html
FUNCTION.create_Wotd_Index.html
FUNCTION.dag_Shortest_Path.html
FUNCTION.database_Name.html
FUNCTION.database_Orientation_Plus.html
FUNCTION.deallocate.html
FUNCTION.degree.html
FUNCTION.dependent.html
FUNCTION.dependent_Source.html
FUNCTION.depth_First_Search.html
FUNCTION.detach.html
FUNCTION.determine_Consensus_Seq.html
FUNCTION.difference.html
FUNCTION.dijkstra.html
FUNCTION.dimension.html
FUNCTION.dir_At.html
FUNCTION.display.html
FUNCTION.display_Result.html
FUNCTION.em.html
FUNCTION.emission_Probability.html
FUNCTION.empty.html
FUNCTION.empty_Parent_Edge.html
FUNCTION.empty_Source.html
FUNCTION.end.html
FUNCTION.end_Diagonal.html
FUNCTION.end_Position.html
FUNCTION.end_Read.html
FUNCTION.end_State.html
FUNCTION.end_Write.html
FUNCTION.erase.html
FUNCTION.erase_Back.html
FUNCTION.expectation.html
FUNCTION.extend_Seed.html
FUNCTION.extend_Seed_Score.html
FUNCTION.extend_Seeds.html
FUNCTION.extend_Seeds_Score.html
FUNCTION.factorial.html
FUNCTION.find.html
FUNCTION.find_Begin.html
FUNCTION.find_Edge.html
FUNCTION.find_Intervals.html
FUNCTION.find_Intervals_Exclude_Touching.html
FUNCTION.find_Motif.html
FUNCTION.find_Vertex.html
FUNCTION.flatten.html
FUNCTION.floyd_Warshall_Algorithm.html
FUNCTION.flush.html
FUNCTION.ford_Fulkerson_Algorithm.html
FUNCTION.forward_Algorithm.html
FUNCTION.fragment_Begin.html
FUNCTION.fragment_Length.html
FUNCTION.front.html
FUNCTION.gap_Value.html
FUNCTION.gap_Value_Impl.html
FUNCTION.generate_Sequence.html
FUNCTION.get_Adjacency_Matrix.html
FUNCTION.get_Alignment.html
FUNCTION.get_Argument_Value.html
FUNCTION.get_Argument_Values.html
FUNCTION.get_Begin_Score.html
FUNCTION.get_Begin_State.html
FUNCTION.get_Bit_Score.html
FUNCTION.get_Cargo.html
FUNCTION.get_Database_Begin.html
FUNCTION.get_Database_End.html
FUNCTION.get_Database_Name.html
FUNCTION.get_Distance_Matrix.html
FUNCTION.get_E_Value.html
FUNCTION.get_E_Value_Cutoff.html
FUNCTION.get_Emission_Probability.html
FUNCTION.get_End_State.html
FUNCTION.get_Fibre.html
FUNCTION.get_First_Covered_Position.html
FUNCTION.get_Frequency.html
FUNCTION.get_Gapped_Kappa.html
FUNCTION.get_Gapped_Lambda.html
FUNCTION.get_Get_Extension.html
FUNCTION.get_Get_Open.html
FUNCTION.get_Id_By_Name.html
FUNCTION.get_Id_Lower_Bound.html
FUNCTION.get_Id_Upper_Bound.html
FUNCTION.get_Kappa.html
FUNCTION.get_Kmer_Similarity_Matrix.html
FUNCTION.get_Lambda.html
FUNCTION.get_Last_Covered_Position.html
FUNCTION.get_Left_Boundary.html
FUNCTION.get_Mate_No.html
FUNCTION.get_Motif.html
FUNCTION.get_Next.html
FUNCTION.get_Next_S.html
FUNCTION.get_Next_T.html
FUNCTION.get_Nil.html
FUNCTION.get_Num_Gaps.html
FUNCTION.get_Occurrence.html
FUNCTION.get_Occurrences.html
FUNCTION.get_Occurrences_Bwt.html
FUNCTION.get_Option_Value_Long.html
FUNCTION.get_Option_Value_Short.html
FUNCTION.get_Option_Values_Long.html
FUNCTION.get_Option_Values_Short.html
FUNCTION.get_Projected_Position.html
FUNCTION.get_Property.html
FUNCTION.get_Query_Begin.html
FUNCTION.get_Query_End.html
FUNCTION.get_Query_Name.html
FUNCTION.get_Read.html
FUNCTION.get_Right_Boundary.html
FUNCTION.get_Root.html
FUNCTION.get_Score.html
FUNCTION.get_Seq_No.html
FUNCTION.get_Seq_Offset.html
FUNCTION.get_Source.html
FUNCTION.get_Step_Size.html
FUNCTION.get_String_Set.html
FUNCTION.get_Successor.html
FUNCTION.get_Swift_Hits.html
FUNCTION.get_Target.html
FUNCTION.get_Transition_Probability.html
FUNCTION.get_Value.html
FUNCTION.get_Value_By_Id.html
FUNCTION.global_Alignment.html
FUNCTION.global_Chaining.html
FUNCTION.global_Msa_Alignment.html
FUNCTION.go_Begin.html
FUNCTION.go_Down.html
FUNCTION.go_End.html
FUNCTION.go_Further.html
FUNCTION.go_Next.html
FUNCTION.go_Nil.html
FUNCTION.go_Previous.html
FUNCTION.go_Right.html
FUNCTION.go_Root.html
FUNCTION.go_Up.html
FUNCTION.guess_File_Format.html
FUNCTION.guess_Format.html
FUNCTION.guess_Format_From_Filename.html
FUNCTION.hamming_Distance.html
FUNCTION.has_Option_Long.html
FUNCTION.has_Option_Short.html
FUNCTION.has_Prefix.html
FUNCTION.hash.html
FUNCTION.hash2.html
FUNCTION.hash2_Next.html
FUNCTION.hash2_Upper.html
FUNCTION.hash_Next.html
FUNCTION.hash_Upper.html
FUNCTION.haystack.html
FUNCTION.heaviest_Increasing_Subsequence.html
FUNCTION.help.html
FUNCTION.help_Text.html
FUNCTION.host.html
FUNCTION.host_Graph.html
FUNCTION.host_Hit.html
FUNCTION.host_Report.html
FUNCTION.id.html
FUNCTION.id_Count.html
FUNCTION.id_In_Use.html
FUNCTION.id_To_Position.html
FUNCTION.in_Degree.html
FUNCTION.index_Bucket_Map.html
FUNCTION.index_Bwt.html
FUNCTION.index_Childtab.html
FUNCTION.index_Counts.html
FUNCTION.index_Counts_Dir.html
FUNCTION.index_Create.html
FUNCTION.index_Dir.html
FUNCTION.index_Lcp.html
FUNCTION.index_Lcpe.html
FUNCTION.index_Raw_S_A.html
FUNCTION.index_Raw_Text.html
FUNCTION.index_Require.html
FUNCTION.index_S_A.html
FUNCTION.index_Shape.html
FUNCTION.index_Supplied.html
FUNCTION.index_Text.html
FUNCTION.infimum_Value_Impl.html
FUNCTION.infix.html
FUNCTION.infix_With_Length.html
FUNCTION.insert.html
FUNCTION.insert_Gap.html
FUNCTION.insert_Gaps.html
FUNCTION.insert_Value.html
FUNCTION.integrate_Align.html
FUNCTION.inverse_Hash.html
FUNCTION.is_Boolean_Option.html
FUNCTION.is_Double_Option.html
FUNCTION.is_Equal.html
FUNCTION.is_Gap.html
FUNCTION.is_Greater.html
FUNCTION.is_Greater_Or_Equal.html
FUNCTION.is_Hidden_Option.html
FUNCTION.is_Int_Option.html
FUNCTION.is_Label_Option.html
FUNCTION.is_Left_Maximal.html
FUNCTION.is_Less.html
FUNCTION.is_Less_Or_Equal.html
FUNCTION.is_Not_Equal.html
FUNCTION.is_Option_List.html
FUNCTION.is_Option_Mandatory.html
FUNCTION.is_Partially_Left_Extensible.html
FUNCTION.is_Prefix.html
FUNCTION.is_Reversed.html
FUNCTION.is_Right_Terminal.html
FUNCTION.is_Root.html
FUNCTION.is_Set_Long.html
FUNCTION.is_Set_Short.html
FUNCTION.is_Silent.html
FUNCTION.is_String_Option.html
FUNCTION.is_Unique.html
FUNCTION.iter.html
FUNCTION.key.html
FUNCTION.kruskals_Algorithm.html
FUNCTION.label.html
FUNCTION.layout_Alignment.html
FUNCTION.lca.html
FUNCTION.lcp.html
FUNCTION.lcp_At.html
FUNCTION.lcp_Length.html
FUNCTION.lcpe_At.html
FUNCTION.left_Boundary.html
FUNCTION.left_Diagonal.html
FUNCTION.left_Dim0.html
FUNCTION.left_Dim1.html
FUNCTION.left_Position.html
FUNCTION.length.html
FUNCTION.load_Contig.html
FUNCTION.load_Contigs.html
FUNCTION.load_Reads.html
FUNCTION.load_Score_Matrix.html
FUNCTION.local_Alignment.html
FUNCTION.lock_Contig.html
FUNCTION.lock_Contigs.html
FUNCTION.log2.html
FUNCTION.logarithmize.html
FUNCTION.long_Name.html
FUNCTION.longest_Common_Subsequence.html
FUNCTION.longest_Increasing_Subsequence.html
FUNCTION.lower_Bound_Aligned_Reads.html
FUNCTION.map_23add.html
FUNCTION.map_23cargo.html
FUNCTION.map_23erase.html
FUNCTION.map_23erase_All.html
FUNCTION.map_23find.html
FUNCTION.map_23has_Key.html
FUNCTION.map_23insert.html
FUNCTION.map_23value.html
FUNCTION.map_Value.html
FUNCTION.match_Refinement.html
FUNCTION.max_Value.html
FUNCTION.maximum_Distance.html
FUNCTION.min_Value.html
FUNCTION.motif_Count.html
FUNCTION.move.html
FUNCTION.move_Source.html
FUNCTION.move_Value.html
FUNCTION.mt_Rand.html
FUNCTION.mt_Rand_Double.html
FUNCTION.mt_Rand_Init.html
FUNCTION.multi_Local_Alignment.html
FUNCTION.needle.html
FUNCTION.next_S.html
FUNCTION.next_T.html
FUNCTION.node_Depth.html
FUNCTION.node_Hull_Predicate.html
FUNCTION.node_Predicate.html
FUNCTION.node_Up.html
FUNCTION.normalize.html
FUNCTION.num_Children.html
FUNCTION.num_Edges.html
FUNCTION.num_Hits.html
FUNCTION.num_Hsps.html
FUNCTION.num_Tree_Edges.html
FUNCTION.num_Vertices.html
FUNCTION.obtain_I_D.html
FUNCTION.obtain_Id.html
FUNCTION.open.html
FUNCTION.open_Temp.html
FUNCTION.ord_Value.html
FUNCTION.order_Occurrences.html
FUNCTION.out_Degree.html
FUNCTION.parent_Edge_First_Char.html
FUNCTION.parent_Edge_Label.html
FUNCTION.parent_Edge_Length.html
FUNCTION.parent_Rep_Length.html
FUNCTION.parent_Vertex.html
FUNCTION.parse.html
FUNCTION.parse_String.html
FUNCTION.pick_Random_Number.html
FUNCTION.pop.html
FUNCTION.pos_Globalize.html
FUNCTION.pos_Local_To_X.html
FUNCTION.pos_Localize.html
FUNCTION.pos_Of_Max.html
FUNCTION.position.html
FUNCTION.position_Range.html
FUNCTION.position_Range_No_Clip.html
FUNCTION.position_To_Id.html
FUNCTION.prefix.html
FUNCTION.prepend_Value.html
FUNCTION.prims_Algorithm.html
FUNCTION.print_Alignment.html
FUNCTION.print_Debug_Level.html
FUNCTION.progressive_Alignment.html
FUNCTION.property.html
FUNCTION.push.html
FUNCTION.quality_Value.html
FUNCTION.query_Name.html
FUNCTION.query_Orientation_Plus.html
FUNCTION.range.html
FUNCTION.rawsa_At.html
FUNCTION.rawtext_At.html
FUNCTION.re_Align.html
FUNCTION.read.html
FUNCTION.read_At.html
FUNCTION.read_Feature.html
FUNCTION.read_Line_Type.html
FUNCTION.read_Meta.html
FUNCTION.refresh.html
FUNCTION.release_All.html
FUNCTION.release_I_D.html
FUNCTION.release_Id.html
FUNCTION.remove_All_Children.html
FUNCTION.remove_Child.html
FUNCTION.remove_Edge.html
FUNCTION.remove_Gap.html
FUNCTION.remove_Gaps.html
FUNCTION.remove_In_Edges.html
FUNCTION.remove_Out_Edges.html
FUNCTION.remove_Value_By_Id.html
FUNCTION.remove_Vertex.html
FUNCTION.rep_Length.html
FUNCTION.replace.html
FUNCTION.representative.html
FUNCTION.required_Arguments.html
FUNCTION.reserve.html
FUNCTION.resize.html
FUNCTION.resize_Edge_Map.html
FUNCTION.resize_Space.html
FUNCTION.resize_Vertex_Map.html
FUNCTION.reverse.html
FUNCTION.reverse_Complement.html
FUNCTION.rewind.html
FUNCTION.right_Boundary.html
FUNCTION.right_Diagonal.html
FUNCTION.right_Dim0.html
FUNCTION.right_Dim1.html
FUNCTION.right_Position.html
FUNCTION.root.html
FUNCTION.row.html
FUNCTION.rows.html
FUNCTION.sa_At.html
FUNCTION.score.html
FUNCTION.score_Gap.html
FUNCTION.score_Gap_Extend.html
FUNCTION.score_Gap_Extend_Horizontal.html
FUNCTION.score_Gap_Extend_Vertical.html
FUNCTION.score_Gap_Horizontal.html
FUNCTION.score_Gap_Open.html
FUNCTION.score_Gap_Open_Horizontal.html
FUNCTION.score_Gap_Open_Vertical.html
FUNCTION.score_Gap_Vertical.html
FUNCTION.score_Limit.html
FUNCTION.score_Match.html
FUNCTION.score_Mismatch.html
FUNCTION.score_Seed.html
FUNCTION.scoring_Scheme.html
FUNCTION.seed_Score.html
FUNCTION.seek.html
FUNCTION.sequence_Id.html
FUNCTION.set.html
FUNCTION.set_Begin.html
FUNCTION.set_Begin_Position.html
FUNCTION.set_Default_Score_Matrix.html
FUNCTION.set_End.html
FUNCTION.set_End_Position.html
FUNCTION.set_Eof.html
FUNCTION.set_Haystack.html
FUNCTION.set_Help_Text.html
FUNCTION.set_Host.html
FUNCTION.set_Left_Diagonal.html
FUNCTION.set_Left_Dim0.html
FUNCTION.set_Left_Dim1.html
FUNCTION.set_Left_Position.html
FUNCTION.set_Long_Name.html
FUNCTION.set_Maximum_Distance.html
FUNCTION.set_Needle.html
FUNCTION.set_Option_Type.html
FUNCTION.set_Position.html
FUNCTION.set_Quality_Value.html
FUNCTION.set_Right_Diagonal.html
FUNCTION.set_Right_Dim0.html
FUNCTION.set_Right_Dim1.html
FUNCTION.set_Right_Position.html
FUNCTION.set_Score.html
FUNCTION.set_Score_Gap.html
FUNCTION.set_Score_Gap_Extend.html
FUNCTION.set_Score_Gap_Open.html
FUNCTION.set_Score_Limit.html
FUNCTION.set_Score_Match.html
FUNCTION.set_Score_Mismatch.html
FUNCTION.set_Scoring_Scheme.html
FUNCTION.set_Short_Name.html
FUNCTION.set_Source.html
FUNCTION.set_Step_Size.html
FUNCTION.set_Strings.html
FUNCTION.set_Value.html
FUNCTION.shape_To_String.html
FUNCTION.share_Resources.html
FUNCTION.short_Help.html
FUNCTION.short_Name.html
FUNCTION.shrink_To_Fit.html
FUNCTION.shuffle.html
FUNCTION.silent_Status.html
FUNCTION.size.html
FUNCTION.slow_Nj_Tree.html
FUNCTION.sort_Aligned_Reads.html
FUNCTION.source.html
FUNCTION.source_Begin.html
FUNCTION.source_End.html
FUNCTION.source_Length.html
FUNCTION.source_Segment.html
FUNCTION.source_Vertex.html
FUNCTION.split.html
FUNCTION.start_Diagonal.html
FUNCTION.string_Set.html
FUNCTION.string_Set_Limits.html
FUNCTION.string_To_Shape.html
FUNCTION.strongly_Connected_Components.html
FUNCTION.suffix.html
FUNCTION.sum.html
FUNCTION.sum_Of_Pairs_Score.html
FUNCTION.supremum_Value_Impl.html
FUNCTION.swap.html
FUNCTION.sys_Time.html
FUNCTION.target.html
FUNCTION.target_Vertex.html
FUNCTION.tell.html
FUNCTION.text_At.html
FUNCTION.to_C_String.html
FUNCTION.to_Lower.html
FUNCTION.to_Source_Position.html
FUNCTION.to_Upper.html
FUNCTION.to_View_Position.html
FUNCTION.topological_Sort.html
FUNCTION.transition_Probability.html
FUNCTION.transitive_Closure.html
FUNCTION.transpose.html
FUNCTION.triplet_Library_Extension.html
FUNCTION.unlock_And_Free_Contig.html
FUNCTION.unlock_And_Free_Contigs.html
FUNCTION.unlock_Contig.html
FUNCTION.unlock_Contigs.html
FUNCTION.upgma_Tree.html
FUNCTION.upper_Bound_Aligned_Reads.html
FUNCTION.value.html
FUNCTION.value_By_Id.html
FUNCTION.value_Construct.html
FUNCTION.value_Construct_Move.html
FUNCTION.value_Destruct.html
FUNCTION.variance.html
FUNCTION.version.html
FUNCTION.viterbi_Algorithm.html
FUNCTION.wait_For.html
FUNCTION.weight.html
FUNCTION.window_Find_Begin.html
FUNCTION.window_Find_End.html
FUNCTION.window_Find_Next.html
FUNCTION.write.html
FUNCTION.write_At.html
FUNCTION.write_Contigs.html
FUNCTION.zscore.html
FUNCTION_Allocator_23clear.html
FUNCTION_Automaton_23label.html
FUNCTION_Blast_23get_Blast_Match_Score.html
FUNCTION_Fileformat_23read.html
FUNCTION_Fileformat_23write.html
FUNCTION_Graph_23assign_Source.html
FUNCTION_Graph_23is_Leaf.html
FUNCTION_Graph_23is_Root.html
FUNCTION_Index_23is_Leaf.html
FUNCTION_Pipelining_23front.html
FUNCTION_Priority_Type_23pop.html
FUNCTION_Priority_Type_23push.html
FUNCTION_Priority_Type_23top.html
INDEXPAGE_Adaption.html
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TYPEDEF_Fragment_Store_23_T_Mate_Pair_Name_Store.html
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TYPEDEF_Fragment_Store_23_T_Read_Seq_Store.html
TYPEDEF_Fragment_Store_23_T_Read_Store.html
alignment.cpp
alignmentGraph.png
alignment_local.cpp
allocator.cpp
alphabet.cpp
automatonGraph.png
blast_report.cpp
dddoc.js
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dddoc_html.css
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directedGraph.png
file_format.cpp
find_approx.cpp
find_exact.cpp
find_motif.cpp
find_wild.cpp
graph_algo_bfs.cpp
graph_algo_dfs.cpp
graph_algo_flow_fordfulkerson.cpp
graph_algo_his.cpp
graph_algo_lcs.cpp
graph_algo_lis.cpp
graph_algo_path_allpairs.cpp
graph_algo_path_bellmanford.cpp
graph_algo_path_dag.cpp
graph_algo_path_dijkstra.cpp
graph_algo_path_floydwarshall.cpp
graph_algo_path_transitive.cpp
graph_algo_scc.cpp
graph_algo_topsort.cpp
graph_algo_tree_kruskal.cpp
graph_algo_tree_prim.cpp
graph_hmm.cpp
graph_hmm_silent.cpp
index.html
index_find.cpp
index_find_stringset.cpp
index_maxrepeats.cpp
index_mummy.cpp
index_mums.cpp
index_node_predicate.cpp
index_sufarray.cpp
index_supermaxrepeats.cpp
iterator.cpp
modifier_modreverse.cpp
modifier_modview.cpp
modifier_nested.cpp
pizzachili.cpp
rooted_iterator.cpp
searchfile.js
seqan_logo.gif
seqan_logo_large.png
shape_predefined.h
treeGraph.png
trieGraph.png
undirectedGraph.png
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