1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195
|
/* Helper functions in the module
*
* Wise2_Align_strings_ProteinSmithWaterman
* Wise2_Align_Sequences_ProteinSmithWaterman
* Wise2_Align_Proteins_SmithWaterman
* Wise2_Align_Proteins_ABC
* Wise2_Align_Sequences_ProteinABC
* Wise2_Hscore_from_ProteinSW
* Wise2_Hscore_from_ProteinABC
* Wise2_Hscore_from_ProteinBA
*
/* These functions are not associated with an object */
/* Function: Wise2_Align_strings_ProteinSmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
*
* Descrip: This is the most *stupidly* abstracted view of two sequences
* getting aligned, being two strings.
*
* It would be much better if you used Sequence objects or Protein
* objects to carry the proteins.
*
*
* Arg: one string of the first sequence [char *]
* Arg: two string of the second sequence [char *]
* Arg: comp Comparison Matrix [Wise2_CompMat *]
* Arg: gap gap penalty [int]
* Arg: ext extension penalty [int]
* Arg: dpenv Undocumented argument [Wise2_DPEnvelope *]
* Arg: dpri Undocumented argument [Wise2_DPRunImpl *]
*
* Returns Undocumented return value [Wise2_AlnBlock *]
*
*/
Wise2_AlnBlock * Wise2_Align_strings_ProteinSmithWaterman( char * one,char * two,Wise2_CompMat * comp,int gap,int ext,Wise2_DPEnvelope * dpenv,Wise2_DPRunImpl * dpri);
/* Function: Wise2_Align_Sequences_ProteinSmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
*
* Descrip: This function is a mid-level abstraction of
* comparing two sequences, which could be
* generic types (eg DNA!). This is tested
* for and warnings are given but the alignment
* is still calculated. To prevent this test
* warning either make sure the Sequence types
* are set to PROTEIN or, better still, use the
* high level abstraction Align_Proteins_SmithWaterman
*
* Otherwise this performs a standard smith waterman
* protein alignment...
*
* To display the alignment use write_pretty_seq_align
*
*
* Arg: one First sequence to compare [Wise2_Sequence *]
* Arg: two Second sequecne to compare [Wise2_Sequence *]
* Arg: comp Comparison matrix to use [Wise2_CompMat *]
* Arg: gap gap penalty. Must be negative or 0 [int]
* Arg: ext ext penalty. Must be negative or 0 [int]
* Arg: dpenv Undocumented argument [Wise2_DPEnvelope *]
* Arg: dpri Undocumented argument [Wise2_DPRunImpl *]
*
* Returns new AlnBlock structure representing the alignment [Wise2_AlnBlock *]
*
*/
Wise2_AlnBlock * Wise2_Align_Sequences_ProteinSmithWaterman( Wise2_Sequence * one,Wise2_Sequence * two,Wise2_CompMat * comp,int gap,int ext,Wise2_DPEnvelope * dpenv,Wise2_DPRunImpl * dpri);
/* Function: Wise2_Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpenv,dpri)
*
* Descrip: This is the most correct way of aligning two Proteins,
* using Protein objects, which can be assummed to be
* proteins with no objections
*
* To display the alignment use write_pretty_Protein_align
*
*
*
* Arg: one Protein to align [Wise2_Protein *]
* Arg: two Protein to align [Wise2_Protein *]
* Arg: comp Comparison Matrix [Wise2_CompMat *]
* Arg: gap gap penalty [int]
* Arg: ext extension penalty [int]
* Arg: dpenv Undocumented argument [Wise2_DPEnvelope *]
* Arg: dpri Undocumented argument [Wise2_DPRunImpl *]
*
* Returns Undocumented return value [Wise2_AlnBlock *]
*
*/
Wise2_AlnBlock * Wise2_Align_Proteins_SmithWaterman( Wise2_Protein * one,Wise2_Protein * two,Wise2_CompMat * comp,int gap,int ext,Wise2_DPEnvelope * dpenv,Wise2_DPRunImpl * dpri);
/* Function: Wise2_Align_Proteins_ABC(one,two,comp,a,b,c,dpenv,dpri)
*
* Descrip: Analogous to Align_Proteins_SmithWaterman for ABC model
*
*
* Arg: one protein to align [Wise2_Protein *]
* Arg: two protein to align [Wise2_Protein *]
* Arg: comp comparison matrix [Wise2_CompMat *]
* Arg: a generalized affine gap cost a [int]
* Arg: b generalized affine gap cost b [int]
* Arg: c generalized affine gap cost c [int]
* Arg: dpenv Undocumented argument [Wise2_DPEnvelope *]
* Arg: dpri Undocumented argument [Wise2_DPRunImpl *]
*
* Returns Undocumented return value [Wise2_AlnBlock *]
*
*/
Wise2_AlnBlock * Wise2_Align_Proteins_ABC( Wise2_Protein * one,Wise2_Protein * two,Wise2_CompMat * comp,int a,int b,int c,Wise2_DPEnvelope * dpenv,Wise2_DPRunImpl * dpri);
/* Function: Wise2_Align_Sequences_ProteinABC(one,two,comp,a,b,c,dpenv,dpri)
*
* Descrip: Align_Sequences_ProteinABC
* this function is analogous to Align_Sequences_ProteinSmithWaterman
* but using the abc model
*
*
* Arg: one Sequence to align [Wise2_Sequence *]
* Arg: two Sequence to align [Wise2_Sequence *]
* Arg: comp Comparison Matrix [Wise2_CompMat *]
* Arg: a genearlized affine gap cost [int]
* Arg: b genearlized affine gap cost [int]
* Arg: c genearlized affine gap cost [int]
* Arg: dpenv Undocumented argument [Wise2_DPEnvelope *]
* Arg: dpri Undocumented argument [Wise2_DPRunImpl *]
*
* Returns Undocumented return value [Wise2_AlnBlock *]
*
*/
Wise2_AlnBlock * Wise2_Align_Sequences_ProteinABC( Wise2_Sequence * one,Wise2_Sequence * two,Wise2_CompMat * comp,int a,int b,int c,Wise2_DPEnvelope * dpenv,Wise2_DPRunImpl * dpri);
/* Function: Wise2_Hscore_from_ProteinSW(querydb,targetdb,comp,gap,ext,bits_cutoff,report_level,die_on_error,dbsi)
*
* Descrip: Runs a database psw search
*
*
* Arg: querydb query database [Wise2_ProteinDB*]
* Arg: targetdb target database [Wise2_ProteinDB*]
* Arg: comp comparison matrix [Wise2_CompMat*]
* Arg: gap gap penalty [int]
* Arg: ext extension penalty [int]
* Arg: bits_cutoff [double]
* Arg: report_level [int]
* Arg: die_on_error [boolean]
* Arg: dbsi [Wise2_DBSearchImpl*]
*
* Returns Undocumented return value [Wise2_Hscore *]
*
*/
Wise2_Hscore * Wise2_Hscore_from_ProteinSW( Wise2_ProteinDB* querydb,Wise2_ProteinDB* targetdb,Wise2_CompMat* comp,int gap,int ext,double bits_cutoff,int report_level,boolean die_on_error,Wise2_DBSearchImpl* dbsi);
/* Function: Wise2_Hscore_from_ProteinABC(querydb,targetdb,comp,a,b,c,bits_cutoff,report_level,die_on_error,dbsi)
*
* Descrip: Runs a database abc search
*
*
* Arg: querydb query database [Wise2_ProteinDB*]
* Arg: targetdb target database [Wise2_ProteinDB*]
* Arg: comp comparison matrix [Wise2_CompMat*]
* Arg: a generalized affine gap cost a [int]
* Arg: b generalized affine gap cost b [int]
* Arg: c generalized affine gap cost c [int]
* Arg: bits_cutoff [double]
* Arg: report_level [int]
* Arg: die_on_error [boolean]
* Arg: dbsi [Wise2_DBSearchImpl*]
*
* Returns Undocumented return value [Wise2_Hscore *]
*
*/
Wise2_Hscore * Wise2_Hscore_from_ProteinABC( Wise2_ProteinDB* querydb,Wise2_ProteinDB* targetdb,Wise2_CompMat* comp,int a,int b,int c,double bits_cutoff,int report_level,boolean die_on_error,Wise2_DBSearchImpl* dbsi);
/* Function: Wise2_Hscore_from_ProteinBA(querydb,targetdb,comp,bentry,bexit,bfor_trans,b_self_trans,b3exit,bits_cutoff,report_level,dbsi)
*
* Descrip: Runs a database pba search
*
*
* Arg: querydb query database [Wise2_ProteinDB*]
* Arg: targetdb target database [Wise2_ProteinDB*]
* Arg: comp comparison matrix [Wise2_CompMat*]
* Arg: bentry [Score]
* Arg: bexit [Score]
* Arg: bfor_trans [Score]
* Arg: b_self_trans [Score]
* Arg: b3exit [Score]
* Arg: bits_cutoff [double]
* Arg: report_level [int]
* Arg: dbsi [Wise2_DBSearchImpl*]
*
* Returns Undocumented return value [Wise2_Hscore *]
*
*/
Wise2_Hscore * Wise2_Hscore_from_ProteinBA( Wise2_ProteinDB* querydb,Wise2_ProteinDB* targetdb,Wise2_CompMat* comp,Score bentry,Score bexit,Score bfor_trans,Score b_self_trans,Score b3exit,double bits_cutoff,int report_level,Wise2_DBSearchImpl* dbsi);
|