void pbStampFreeList(struct pbStamp **pList)
/* Free a list of dynamically allocated pbStamp's */
{
struct pbStamp *el, *next;
for (el = *pList; el != NULL; el = next)
{
next = el->next;
pbStampFree(&el);
}
*pList = NULL;
}
void doStamps(char *proteinID, char *mrnaID, char *aa, struct vGfx *vg, int *yOffp)
/* draw proteome browser stamps */
{
int i,j,l;
char cond_str[200];
char *valStr;
char valStr2[50];
char *answer;
double pI=0.0;
double exonCount;
char *chp;
int len;
int cCnt;
int xPosition;
int yPosition;
int stampWidth, stampHeight;
int aaResCnt[30];
double aaResFreqDouble[30];
int aaResFound;
int totalResCnt;
double molWeight=0.0;
double hydroSum;
struct pbStamp *stampDataPtr;
for (j=0; j<23; j++)
{
aaResCnt[j] = 0;
}
l=len = strlen(aa);
chp = aa;
for (i=0; i<l; i++)
{
aaResFound = 0;
for (j=0; j<23; j++)
{
if (*chp == aaAlphabet[j])
{
aaResFound = 1;
aaResCnt[j] ++;
}
}
chp++;
}
totalResCnt = 0;
for (i=0; i<23; i++)
{
totalResCnt = totalResCnt + aaResCnt[i];
}
for (i=0; i<20; i++)
{
aaResFreqDouble[i] = ((double)aaResCnt[i])/((double)totalResCnt);
}
AllocVar(stampPictPtr);
stampWidth = 75*(1+pbScale/3);
stampHeight = 60*(1+pbScale/3);
xPosition = 15;
yPosition = *yOffp + 135;
if (pbScale >= 6) yPosition = yPosition + 20;
boundaryColor = vgFindColorIx(g_vg, 170, 170, 170);
/* draw pI stamp */
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
answer = sqlGetField(database, "pepPi", "count(*)", cond_str);
/* either 0 or multiple rows are not valid */
if (strcmp(answer, "1") == 0)
{
answer = sqlGetField(database, "pepPi", "pI", cond_str);
pI = (double)atof(answer);
stampDataPtr = getStampData("pepPi");
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScaleNonInt(stampDataPtr, stampPictPtr, 2);
safef(valStr2, sizeof(valStr2), "%.1f", pI);
markStamp(stampDataPtr, stampPictPtr, pI, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
}
else
{
stampDataPtr = getStampData("pepPi");
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScale(stampDataPtr, stampPictPtr, 2);
safef(valStr2, sizeof(valStr2), "N/A");
markStamp0(stampDataPtr, stampPictPtr, pI, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
}
/* skip Mol Wt, if it is GSID */
if (!hIsGsidServer())
{
/* draw Mol Wt stamp */
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
answer = sqlGetField(database, "pepMwAa", "MolWeight", cond_str);
if (answer != NULL)
{
safef(valStr2, sizeof(valStr2), "%s Da", answer);
molWeight = (double)atof(answer);
stampDataPtr = getStampData("pepMolWt");
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScaleMW(stampDataPtr, stampPictPtr, 50000);
markStamp(stampDataPtr, stampPictPtr, molWeight, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
}
else
{
safef(valStr2, sizeof(valStr2), "N/A");
stampDataPtr = getStampData("pepMolWt");
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScaleMW(stampDataPtr, stampPictPtr, 50000);
markStamp0(stampDataPtr, stampPictPtr, molWeight, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
}
}
if (!proteinInSupportedGenome)
{
if (!hIsGsidServer())
xPosition = xPosition + stampWidth + stampWidth/8;
goto skip_exon;
}
/* draw exon count stamp */
if (kgVersion == KG_III)
{
safef(cond_str, sizeof(cond_str), "qName='%s'", mrnaID);
}
else
{
safef(cond_str, sizeof(cond_str), "qName='%s'", proteinID);
}
answer = sqlGetField(database, kgProtMapTableName, "blockCount", cond_str);
if (answer != NULL)
{
valStr = cloneString(answer);
exonCount = (double)atoi(answer);
stampDataPtr = getStampData("exonCnt");
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScale(stampDataPtr, stampPictPtr, 5);
markStamp(stampDataPtr, stampPictPtr, exonCount, valStr, tx, ty);
pbStampFree(&stampDataPtr);
}
skip_exon:
if (!hIsGsidServer())
{
/* draw AA residual anomolies stamp */
if (answer != NULL)
{
stampDataPtr = getStampData("pepRes");
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition,
3*stampWidth/2, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
for (i=0; i<20; i++)
{
markResStamp(aaAlphabet[i], stampDataPtr, stampPictPtr, i, aaResFreqDouble[i],
tx, ty, avg, stddev);
}
pbStampFree(&stampDataPtr);
}
xPosition = 15;
yPosition = yPosition + 170;
}
/* skip swInterPro if it is GSID */
if (!hIsGsidServer())
{
/* draw family size stamp */
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
answer = sqlGetField(protDbName, "swInterPro", "count(*)", cond_str);
if (answer != NULL)
{
valStr = cloneString(answer);
stampDataPtr = getStampData("intPCnt");
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScale(stampDataPtr, stampPictPtr, 1);
markStamp(stampDataPtr, stampPictPtr, (double)(atoi(answer)), valStr, tx, ty);
pbStampFree(&stampDataPtr);
}
else
{
valStr = cloneString("N/A");
stampDataPtr = getStampData("intPCnt");
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScale(stampDataPtr, stampPictPtr, 1);
markStamp0(stampDataPtr, stampPictPtr, (double)(atoi(answer)), valStr, tx, ty);
pbStampFree(&stampDataPtr);
}
}
/* draw hydrophobicity stamp */
chp = protSeq;
hydroSum = 0;
for (i=0; i<protSeqLen; i++)
{
hydroSum = hydroSum + aa_hydro[(int)(*chp)];
chp++;
}
stampDataPtr = getStampData("hydro");
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScaleHydro(stampDataPtr, stampPictPtr, 1.0);
safef(valStr2, sizeof(valStr2), "%.1f", hydroSum/(double)len);
markStamp(stampDataPtr, stampPictPtr, hydroSum/(double)len, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
/* draw Cystein Count stamp */
chp = protSeq;
cCnt = 0;
for (i=0; i<len; i++)
{
if (*chp == 'C') cCnt ++;
chp++;
}
stampDataPtr = getStampData("cCnt");
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScale(stampDataPtr, stampPictPtr, 10);
safef(valStr2, sizeof(valStr2), "%d", cCnt);
markStamp(stampDataPtr, stampPictPtr, (double)cCnt, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
/* if it is GSID, draw AA residual anomolies here */
if (hIsGsidServer())
{
xPosition = 15;
yPosition = yPosition + 170;
/* draw AA residual anomolies stamp */
if (answer != NULL)
{
stampDataPtr = getStampData("pepRes");
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition,
3*stampWidth/2, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
for (i=0; i<20; i++)
{
markResStamp(aaAlphabet[i], stampDataPtr, stampPictPtr, i, aaResFreqDouble[i],
tx, ty, avg, stddev);
}
pbStampFree(&stampDataPtr);
}
}
/* draw AA residual anomolies stddev stamp */
if (answer != NULL)
{
exonCount = (double)atof(answer);
stampDataPtr = getStampData("pepRes");
if (hIsGsidServer())
{
xPosition = xPosition + stampWidth*1.62 + stampWidth/8;
}
else
{
xPosition = xPosition + stampWidth + stampWidth/8;
}
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, 3*stampWidth/2, stampHeight);
stampDataPtr->ymin = -4.0;
stampDataPtr->ymax = 4.0;
for (i=0; i<20; i++)
{
markResStdvStamp(stampDataPtr, stampPictPtr, i, aaResFreqDouble[i], tx, ty, avg, stddev);
}
/* draw background after bars drawn so that "... stddev" labels do not get covered by bars */
stampDataPtr = getStampData("pepRes");
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, 3*stampWidth/2, stampHeight);
drawPbStampB(stampDataPtr, stampPictPtr);
pbStampFree(&stampDataPtr);
}
/* The follwing section was used to plot freq distribution for each AA so that we can view than to decide on
whether +/- 2 stddev is applicable and what cutoff thresholds to use. Keep it here for possible
future reuse. */
/*
vertLabel = cloneString("Frequency");
for (i=strlen(vertLabel)-1; i>=0; i--)
{
vertLabel[i+1] = '\0';
vgTextCentered(g_vg, 3, 45+i*10, 10, 10, MG_BLACK, g_font, vertLabel+i);
vgTextCentered(g_vg, 3, 215+i*10, 10, 10, MG_BLACK, g_font, vertLabel+i);
}
xPosition = xPosition + 80;
for (j=0; j<20; j++)
{
safef(tempStr, sizeof(tempStr), "%c", aaAlphabet[j]);
stampDataPtr = getStampData(tempStr);
xPosition = xPosition + stampWidth + stampWidth/8;
setPbStampPict(stampPictPtr, stampDataPtr, xPosition, yPosition, stampWidth, stampHeight);
drawPbStamp(stampDataPtr, stampPictPtr);
drawXScale(stampDataPtr, stampPictPtr, 10);
safef(valStr2, sizeof(valStr2), "%c", aaAlphabet[j]);
markStamp(stampDataPtr, stampPictPtr, 0.0, valStr2, tx, ty);
pbStampFree(&stampDataPtr);
}
*/
}
