#include "common.h"#include "maf.h"Include dependency graph for mafScore.c:
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Data Structures | |
| struct | gap_scores |
Defines | |
| #define | CLEN(s) (sizeof((s))-1) |
| #define | NACHARS 128 |
| #define | SS(c, d) ss[(uchar)c][(uchar)d] |
| #define | GAP(w, x, y, z) gop[(gtype[w]<<6)+(gtype[x]<<4)+(gtype[y]<<2)+gtype[z]] |
| #define | DASH '-' |
Typedefs | |
| typedef gap_scores | gap_scores_t |
| typedef int | ss_t [NACHARS][NACHARS] |
| typedef unsigned char | uchar |
Functions | |
| static void | DNA_scores (ss_t ss) |
| static void | gap_costs (int *gop, int *gtype, int gap_open) |
| double | mafScoreRangeMultiz (struct mafAli *maf, int start, int size) |
| double | mafScoreMultiz (struct mafAli *maf) |
| double | mafScoreMultizMaxCol (int species) |
| void | mafColMinMaxScore (struct mafAli *maf, double *retMin, double *retMax) |
Variables | |
| static char const | rcsid [] = "$Id: mafScore.c,v 1.9 2005/11/23 17:20:50 braney Exp $" |
| static ss_t | ss |
| static gap_scores_t | ds |
| static int | gop [256] |
| static int | gtype [128] |
| static const uchar | nchars [] = "ACGT" |
| static const int | HOXD70_sym [4][4] |
| #define CLEN | ( | s | ) | (sizeof((s))-1) |
| #define DASH '-' |
| #define NACHARS 128 |
| typedef struct gap_scores gap_scores_t |
| typedef int ss_t[NACHARS][NACHARS] |
Definition at line 22 of file mafScore.c.
| typedef unsigned char uchar |
Definition at line 23 of file mafScore.c.
| static void DNA_scores | ( | ss_t | ss | ) | [static] |
Definition at line 38 of file mafScore.c.
References CLEN, HOXD70_sym, NACHARS, and nchars.
Referenced by mafScoreRangeMultiz().
00039 { 00040 int i, j, bad, a, b, A, B; 00041 00042 for (i = 0; i < NACHARS; ++i) 00043 for (j = 0; j < NACHARS; ++j) 00044 ss[i][j] = -100; 00045 for (i = 0; i < (signed)CLEN(nchars); ++i) { 00046 A = nchars[i]; 00047 a = tolower(A); 00048 for (j = 0; j < (signed)CLEN(nchars); ++j) { 00049 B = nchars[j]; 00050 b = tolower(B); 00051 ss[A][B] = ss[a][B] = ss[A][b] = ss[a][b] = 00052 HOXD70_sym[i][j]; 00053 } 00054 } 00055 bad = -1000; 00056 for (i = 0; i < NACHARS; ++i) 00057 ss['X'][i] = ss[i]['X'] = ss['x'][i] = ss[i]['x'] = bad; 00058 }
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| static void gap_costs | ( | int * | gop, | |
| int * | gtype, | |||
| int | gap_open | |||
| ) | [static] |
Definition at line 61 of file mafScore.c.
Referenced by mafScoreRangeMultiz().
00062 { 00063 int i, X, D; 00064 00065 for (i = 0; i < 128; ++i) 00066 gtype[i] = 0; 00067 D = DASH; 00068 gtype[D] = 1; 00069 00070 for (i = 0; i < 256; ++i) 00071 gop[i] = 0; 00072 X = (uchar)'A'; 00073 GAP(X,X,X,D) = gap_open; 00074 GAP(X,X,D,X) = gap_open; 00075 GAP(X,D,D,X) = gap_open; 00076 GAP(D,X,X,D) = gap_open; 00077 GAP(D,D,X,D) = gap_open; 00078 GAP(D,D,D,X) = gap_open; 00079 }
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| void mafColMinMaxScore | ( | struct mafAli * | maf, | |
| double * | retMin, | |||
| double * | retMax | |||
| ) |
Definition at line 146 of file mafScore.c.
References mafAli::components, mafScoreMultizMaxCol(), and slCount().
00149 { 00150 *retMax = mafScoreMultizMaxCol(slCount(maf->components)); 00151 *retMin = -*retMax; 00152 }
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| double mafScoreMultiz | ( | struct mafAli * | maf | ) |
Definition at line 130 of file mafScore.c.
References mafScoreRangeMultiz(), and mafAli::textSize.
00133 { 00134 return mafScoreRangeMultiz(maf, 0, maf->textSize); 00135 }
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| double mafScoreMultizMaxCol | ( | int | species | ) |
Definition at line 137 of file mafScore.c.
Referenced by mafColMinMaxScore().
00139 { 00140 int i, count = 0; 00141 for (i=1; i<species; ++i) 00142 count += i; 00143 return 100.0*count; 00144 }
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| double mafScoreRangeMultiz | ( | struct mafAli * | maf, | |
| int | start, | |||
| int | size | |||
| ) |
Definition at line 81 of file mafScore.c.
References mafAli::components, DASH, DNA_scores(), ds, gap_scores::E, errAbort(), GAP, gap_costs(), gop, gtype, HOXD70_sym, mafComp::next, gap_scores::O, mafComp::size, SS, ss, mafComp::text, and mafAli::textSize.
Referenced by mafScoreMultiz().
00082 : 00083 * maf - the alignment 00084 * start - the (zero based) offset to start calculating score 00085 * size - the size of the subset 00086 * The following relationship should hold: 00087 * scoreRange(maf,start,size) = 00088 * scoreRange(maf,0,start+size) - scoreRange(maf,0,start) 00089 */ 00090 { 00091 uchar ai, ar, bi, br; 00092 int i; 00093 double score; 00094 struct mafComp *c1, *c2; 00095 00096 if (start < 0 || size <= 0 || 00097 start+size > maf->textSize) { 00098 errAbort( "mafScoreRange: start = %d, size = %d, textSize = %d\n", 00099 start, size, maf->textSize); 00100 } 00101 if (ss['A']['A'] != HOXD70_sym[0][0]) { 00102 DNA_scores(ss); 00103 ds.E = 30; 00104 ds.O = 400; 00105 for (i = 0; i < 128; ++i) 00106 ss[i][DASH] = ss[DASH][i] = -ds.E; 00107 ss[DASH][DASH] = 0; 00108 gap_costs(gop, gtype, ds.O); /* quasi-natural gap costs */ 00109 } 00110 score = 0.0; 00111 for (i = start; i < start+size; ++i) { 00112 for (c1 = maf->components; c1 != NULL; c1 = c1->next) { 00113 if (c1->size == 0) continue; 00114 br = c1->text[i]; 00115 for (c2 = c1->next; c2 != NULL; c2 = c2->next) { 00116 if (c2->size == 0) continue; 00117 bi = c2->text[i]; 00118 score += SS(br, bi); 00119 if (i > 0) { 00120 ar = c1->text[i-1]; 00121 ai = c2->text[i-1]; 00122 score -= GAP(ar,ai,br,bi); 00123 } 00124 } 00125 } 00126 } 00127 return score; 00128 }
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gap_scores_t ds [static] |
Definition at line 26 of file mafScore.c.
Referenced by dyStringAppend(), dyStringAppendC(), dyStringAppendMultiC(), dyStringAppendN(), dyStringBumpBufSize(), dyStringCannibalize(), dyStringExpandBuf(), dyStringPrintf(), dyStringResize(), dyStringVaPrintf(), freeDyString(), freeDyStringList(), interpolate(), mafScoreRangeMultiz(), newDyString(), nodeNames(), oligoTm(), phyloFindPath(), and phyloNodeNames().
int gop[256] [static] |
int gtype[128] [static] |
const int HOXD70_sym[4][4] [static] |
Initial value:
{
{ 91, -114, -31, -123 },
{-114, 100, -125, -31 },
{ -31, -125, 100, -114 },
{-123, -31, -114, 91 },
}
Definition at line 30 of file mafScore.c.
Referenced by DNA_scores(), and mafScoreRangeMultiz().
char const rcsid[] = "$Id: mafScore.c,v 1.9 2005/11/23 17:20:50 braney Exp $" [static] |
Definition at line 8 of file mafScore.c.
Definition at line 25 of file mafScore.c.
Referenced by affineAlign(), axtAffine(), axtAffine2Level(), axtPrintTraditional(), axtScore(), axtScoreDnaDefault(), axtScoreFilterRepeats(), axtScoreProteinDefault(), axtScoreSchemeDefault(), axtScoreSchemeDnaWrite(), axtScoreSchemeFromBlastzMatrix(), axtScoreSchemeFromProteinText(), axtScoreSchemeProteinDefault(), axtScoreSchemeProteinRead(), axtScoreSchemeRead(), axtScoreSchemeReadLf(), axtScoreSchemeRnaDefault(), axtScoreSchemeRnaFill(), axtScoreSchemeSimpleDna(), axtScoreSym(), axtScoreSymFilterRepeats(), axtScoreUngapped(), axtSubsetOnT(), bafWriteLine(), bandedExtend(), bandExt(), bandExtAfter(), bandExtBefore(), bandExtFf(), bCmpSeqSource(), blastiodAxtOutput(), calcSpliceScore(), chainCalcScore(), chainCalcScoreSubChain(), countPositives(), dnaQuery(), findFromSmallerSeeds(), findSource(), gfAlignTrans(), gfAlignTransTrans(), gfClumpDump(), gfIndexNibsAndTwoBits(), gfLargeIndexSeq(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), gfSmallIndexSeq(), gfText(), hardRefineSplice(), interpolate(), kForwardAffine(), mafScoreRangeMultiz(), pcrQuery(), propagateCase(), searchOneIndex(), smoothOneGap(), spaceSaverAdd(), spaceSaverAddOverflow(), spaceSaverFinish(), spaceSaverFree(), spaceSaverMaxCellsNew(), targetClump(), transIndexBothStrands(), transQuery(), and transTransQuery().
1.5.2