src/hg/protein/pbTracks/pbTracks.c 1.58
1.58 2009/08/06 19:13:55 fanhsu
Changed errAbort() to hUserAbort().
Index: src/hg/protein/pbTracks/pbTracks.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/pbTracks/pbTracks.c,v
retrieving revision 1.57
retrieving revision 1.58
diff -b -B -U 1000000 -r1.57 -r1.58
--- src/hg/protein/pbTracks/pbTracks.c 10 Jul 2009 01:42:22 -0000 1.57
+++ src/hg/protein/pbTracks/pbTracks.c 6 Aug 2009 19:13:55 -0000 1.58
@@ -1,535 +1,535 @@
/* pbTracks.c - UCSC Proteome Browser main cgi script. */
#include "common.h"
#include "hCommon.h"
#include "portable.h"
#include "jksql.h"
#include "vGfx.h"
#include "cheapcgi.h"
#include "htmshell.h"
#include "cart.h"
#include "hdb.h"
#include "web.h"
#include "hgColors.h"
#include "hui.h"
#include "pbStamp.h"
#include "pbStampPict.h"
#include "pbTracks.h"
#include "trashDir.h"
#include "psGfx.h"
static char const rcsid[] = "$Id$";
boolean hgDebug = FALSE; /* Activate debugging code. Set to true by hgDebug=on in command line*/
boolean IAmPbTracks = TRUE;
int kgVersion = KG_UNKNOWN;
boolean proteinInSupportedGenome=TRUE; /* The protein is in supported genome DB */
/* This is a new variable necessary for PB V1.0
and PB V1.1 sharing the same PB library */
struct cart *cart; /* The cart where we keep persistent variables. */
struct hash *oldVars = NULL; /* The cart vars before new cgi stuff added. */
/* These variables persist from one incarnation of this program to the
* next - living mostly in the cart. */
char *database; /* Name of database we're using. */
char *organism; /* Name of organism we're working on. */
char *hgsid;
char hgsidStr[50];
int gfxBorder = 1; /* Width of graphics border. */
int insideWidth; /* Width of area to draw tracks in in pixels. */
char *protDbName; /* Name of proteome database for this genome. */
struct tempName gifTn, gifTn2; /* gifTn for tracks image and gifTn2 for stamps image */
boolean hideControls = FALSE; /* Hide all controls? */
boolean suppressHtml = FALSE; /* If doing PostScript output we'll suppress most
* of HTML output. */
char *proteinID;
char *protDisplayID;
char *mrnaID;
char *description;
char *positionStr;
char *prevGBChrom; /* chrom previously chosen by Genome Browser */
int prevGBStartPos; /* start position previously chosen by Genome Browser */
int prevGBEndPos; /* end position previously chosen by Genome Browser */
int prevExonStartPos; /* start position chosen by Genome Browser, converted to exon pos */
int prevExonEndPos; /* end position chosen by Genome Browser, converted to exon pos */
char *ensPepName; /* Ensembl peptide name, used for Superfamily track */
int sfCount; /* count of Superfamily domains */
struct sqlConnection *spConn; /* Connection to SwissProt database. */
char aaAlphabet[30] = {"WCMHYNFIDQKRTVPGEASLXZB"};
char *protSeq;
int protSeqLen;
char aaChar[20];
float aa_hydro[256];
int aa_attrib[256];
char aa[100000];
struct vGfx *g_vg;
MgFont *g_font;
Color pbRed, pbBlue;
int currentYoffset;
int pbScale = {6};
char pbScaleStr[5];
boolean scaleButtonPushed;
double tx[100000], ty[100000];
double xScale = 50.0;
double yScale = 100.0;
struct pbStampPict *stampPictPtr;
double avg[20];
double stddev[20];
int exStart[500], exEnd[500];
int exCount;
int aaStart[500], aaEnd[500];
char kgProtMapTableName[20] = {"kgProtMap"};
int blockSize[500], blockSizePositive[500];
int blockStart[500], blockStartPositive[500];
int blockEnd[500], blockEndPositive[500];
int blockGenomeStart[500], blockGenomeStartPositive[500];
int blockGenomeEnd[500], blockGenomeEndPositive[500];
int trackOrigOffset = 0; /* current track display origin offset */
int aaOrigOffset = 0; /* current track AA base origin offset */
boolean initialWindow = TRUE;
struct vGfx *vg, *vg2;
Color bkgColor;
Color abnormalColor;
Color normalColor;
void dvPrintf(char *format, va_list args)
/* Suppressable variable args hPrintf. */
{
char temp[1000];
safef(temp, sizeof(temp), "<br>%s", format);
vprintf(temp, args);
fflush(stdout);
}
/* used for debugging only */
/* #include "dPrint.c" */
void hvPrintf(char *format, va_list args)
/* Suppressable variable args hPrintf. */
{
if (!suppressHtml)
vprintf(format, args);
}
void hPrintf(char *format, ...)
/* Printf that can be suppressed if not making
* html. */
{
va_list(args);
va_start(args, format);
hvPrintf(format, args);
va_end(args);
}
void smallBreak()
/* Draw small horizontal break */
{
hPrintf("<FONT SIZE=1><BR></FONT>\n");
}
void makeActiveImagePB(char *psOutput, char *psOutput2)
/* Make image and image map. */
{
char *mapName = "map";
int pixWidth, pixHeight;
struct sqlConnection *conn;
int iypos;
char *spDisplayId;
hPrintf("<br><font size=4>");
hPrintf("%s protein: ", organism);
hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" TARGET=_blank><B>%s</B></A>\n",
proteinID, proteinID);
/* show SWISS-PROT display ID if it is different than the accession ID */
/* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
spDisplayId = spAccToId(spConn, proteinID);
if (strstr(spDisplayId, proteinID) == NULL)
{
hPrintf(" (aka %s", spDisplayId);
/* don't show 2nd aka if the new and old displayId are the same */
if (oldSpDisplayId(spDisplayId) != NULL)
{
if (!sameWord(spDisplayId, oldSpDisplayId(spDisplayId)))
{
hPrintf(" or %s", oldSpDisplayId(spDisplayId));
}
}
hPrintf(") ", oldSpDisplayId(spDisplayId));
}
hPrintf(" %s\n", description);
hPrintf("</font><br><br>");
protSeq = getAA(proteinID);
if (protSeq == NULL)
{
- errAbort("%s is not a current valid entry in UniProtKB\n", proteinID);
+ hUserAbort("%s is not a current valid entry in UniProtKB\n", proteinID);
}
protSeqLen = strlen(protSeq);
iypos = 15;
doTracks(proteinID, mrnaID, protSeq, &iypos, psOutput);
if (!hTableExists(database, "pbStamp")) goto histDone;
pbScale = 3;
pixWidth = 765;
insideWidth = pixWidth-gfxBorder;
pixHeight = 350;
if (psOutput2)
{
vg2 = vgOpenPostScript(pixWidth, pixHeight, psOutput2);
}
else
{
trashDirFile(&gifTn2, "pbt", "pbt", ".gif");
vg2 = vgOpenGif(pixWidth, pixHeight, gifTn2.forCgi);
}
g_vg = vg2;
pbRed = vgFindColorIx(vg2, 0xf9, 0x51, 0x59);
pbBlue = vgFindColorIx(g_vg, 0x00, 0x00, 0xd0);
normalColor = pbBlue;
abnormalColor = pbRed;
bkgColor = vgFindColorIx(vg2, 255, 254, 232);
vgBox(vg2, 0, 0, insideWidth, pixHeight, bkgColor);
/* Start up client side map. */
mapName=cloneString("pbStamps");
hPrintf("\n<MAP Name=%s>\n", mapName);
vgSetClip(vg2, 0, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
iypos = 15;
/* Draw stamps. */
doStamps(proteinID, mrnaID, protSeq, vg2, &iypos);
/* Finish map. */
hPrintf("</MAP>\n");
/* Save out picture and tell html file about it. */
vgClose(&vg2);
hPrintf("<P>");
hPrintf("\n<IMG SRC=\"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s><BR>",
gifTn2.forCgi, pixWidth, pixHeight, mapName);
hPrintf("\n<A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml#histograms\" TARGET=_blank>");
hPrintf("Explanation of Protein Property Histograms</A><BR>");
hPrintf("<P>");
histDone:
hPrintf("\n<B>UCSC Links:</B><BR>\n ");
hPrintf("<UL>\n");
doGenomeBrowserLink(proteinID, mrnaID, hgsidStr);
doGeneDetailsLink(proteinID, mrnaID, hgsidStr);
/* show Gene Sorter link only if it is valid for this genome */
if (hgNearOk(database))
{
doGeneSorterLink(protDisplayID, mrnaID, hgsidStr);
}
hPrintf("</UL><P>");
conn = sqlConnect(UNIPROT_DB_NAME);
domainsPrint(conn, proteinID);
hPrintf("<P>");
doPathwayLinks(protDisplayID, mrnaID);
printFASTA(proteinID, protSeq);
}
void doTrackForm(char *psOutput, char *psOutput2)
/* Make the tracks display form */
{
if (psOutput != NULL)
{
suppressHtml = TRUE;
hideControls = TRUE;
}
/* Tell browser where to go when they click on image. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" METHOD=POST>\n\n", "../cgi-bin/pbTracks");
cartSaveSession(cart);
hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#"HG_COL_HOTLINKS"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"2\"><TR>\n");
hPrintf("<TD ALIGN=LEFT><A HREF=\"../index.html\">%s</A></TD>", wrapWhiteFont("Home"));
hPrintf("<TD ALIGN=CENTER><FONT COLOR=\"#FFFFFF\" SIZE=4>%s</FONT></TD>",
"UCSC Proteome Browser");
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/pbTracks?%s=%u&pbt.psOutput=on\">%s</A></TD>\n",
cartSessionVarName(), cartSessionId(cart), wrapWhiteFont("PDF/PS"));
hPrintf("<TD ALIGN=Right><A HREF=\"../goldenPath/help/pbTracksHelpFiles/pbTracksHelp.shtml\" TARGET=_blank>%s</A></TD>",
wrapWhiteFont("Help"));
hPrintf("</TR></TABLE>");
fflush(stdout);
/* Make clickable image and map. */
makeActiveImagePB(psOutput, psOutput2);
if (psOutput == NULL) hPrintf("</FORM>");
}
void handlePostscript()
/* Deal with Postscript output. */
{
struct tempName psTn;
struct tempName psTn2;
char *pdfFile = NULL;
trashDirFile(&psTn, "pbt", "pbt", ".eps");
trashDirFile(&psTn2, "pbt", "pbt2", ".eps");
printf("<H1>PostScript/PDF Output</H1>\n");
printf("PostScript images can be printed at high resolution "
"and edited by many drawing programs such as Adobe Illustrator.");
printf(" PDF can be viewed with Adobe Acrobat Reader.<BR><BR>\n");
doTrackForm(psTn.forCgi, psTn2.forCgi);
printf("<A HREF=\"%s\">Click here to download</A> "
"the current protein tracks graphic in PostScript. ", psTn.forCgi);
pdfFile = convertEpsToPdf(psTn.forCgi);
if(pdfFile != NULL)
{
printf("<BR><A HREF=\"%s\">Click here to download</A> "
"the current protein tracks graphic in PDF", pdfFile);
}
else
printf("<BR><BR>PDF format not available");
printf("<BR><BR><A HREF=\"%s\">Click here to download</A> "
"the current protein histograms graphic in PostScript. ", psTn2.forCgi);
pdfFile = convertEpsToPdf(psTn2.forCgi);
if(pdfFile != NULL)
{
printf("<BR><A HREF=\"%s\">Click here to download</A> "
"the current protein histograms graphic in PDF", pdfFile);
}
else
printf("<BR><BR>PDF format not available");
freez(&pdfFile);
}
void doMiddle(struct cart *theCart)
/* Print the body of an html file. */
{
char cond_str[255];
struct sqlConnection *conn;
char *proteinAC;
char *chp, *chp1, *chp9;
char *debugTmp = NULL;
char *answer;
/* Initialize layout and database. */
cart = theCart;
/* Uncomment this to see parameters for debugging. */
/* Be careful though, it breaks if custom track is more than 4k */
/*
{ struct dyString *state = cgiUrlString();
hPrintf("State: %s\n", state->string); }
*/
getDbAndGenome(cart, &database, &organism, oldVars);
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2"))
{
kgVersion = KG_III;
strcpy(kgProtMapTableName, "kgProtMap2");
}
protDbName = hPdbFromGdb(database);
spConn = sqlConnect(UNIPROT_DB_NAME);
debugTmp = cartUsualString(cart, "hgDebug", "off");
if(sameString(debugTmp, "on"))
hgDebug = TRUE;
else
hgDebug = FALSE;
conn = hAllocConn(database);
hgsid = cartOptionalString(cart, "hgsid");
if (hgsid != NULL)
{
safef(hgsidStr, sizeof(hgsidStr), "&hgsid=%s", hgsid);
}
else
{
strcpy(hgsidStr, "");
}
proteinID = cartOptionalString(cart, "proteinID");
/* check proteinID to see if it is a valid SWISS-PROT/TrEMBL accession or display ID */
/* then assign the accession number to global variable proteinID */
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
if (proteinAC == NULL)
{
safef(cond_str, sizeof(cond_str), "displayID='%s'", proteinID);
proteinAC = sqlGetField(protDbName, "spXref3", "accession", cond_str);
if (proteinAC == NULL)
{
hUserAbort("'%s' does not seem to be a valid UniProtKB protein ID.", proteinID);
}
else
{
protDisplayID = proteinID;
proteinID = proteinAC;
}
}
else
{
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
protDisplayID = sqlGetField(protDbName, "spXref3", "displayID", cond_str);
}
if (spFindAcc(spConn, proteinID) == NULL)
{
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
answer = sqlGetField(protDbName, "spXref3", "biodatabaseID", cond_str);
if (sameWord(answer, "3"))
{
- errAbort("The corresponding protein %s is no longer available from UniProtKB.",
+ hUserAbort("The corresponding protein %s is no longer available from UniProtKB.",
proteinID);
}
else
{
- errAbort("%s seems not to be a valid protein ID.", proteinID);
+ hUserAbort("%s seems not to be a valid protein ID.", proteinID);
}
}
else
{
if (!sameWord(proteinID, spFindAcc(spConn, proteinID)))
{
hPrintf("%s seems to be an outdated protein ID.", proteinID);
printf("<BR><BR>Please try ");
hPrintf("<A HREF=\"../cgi-bin/pbGlobal?proteinID=%s\"> %s</A> instead.\n",
spFindAcc(spConn, proteinID), spFindAcc(spConn, proteinID));fflush(stdout);
- errAbort(" ");
+ hUserAbort(" ");
}
}
if (kgVersion == KG_III)
{
safef(cond_str, sizeof(cond_str), "spID='%s'", proteinID);
mrnaID = sqlGetField(database, "kgXref", "kgId", cond_str);
}
else
{
safef(cond_str, sizeof(cond_str), "proteinID='%s'", protDisplayID);
mrnaID = sqlGetField(database, "knownGene", "name", cond_str);
}
safef(cond_str, sizeof(cond_str), "accession='%s'", proteinID);
description = sqlGetField(protDbName, "spXref3", "description", cond_str);
/* obtain previous genome position range selected by the Genome Browser user */
positionStr = cloneString(cartOptionalString(cart, "position"));
if (positionStr != NULL)
{
chp = strstr(positionStr, ":");
*chp = '\0';
prevGBChrom = cloneString(positionStr);
chp1 = chp + 1;
chp9 = strstr(chp1, "-");
*chp9 = '\0';
prevGBStartPos = atoi(chp1);
chp1 = chp9 + 1;
prevGBEndPos = atoi(chp1);
}
else
{
prevGBChrom = NULL;
prevGBStartPos = -1;
prevGBEndPos = -1;
}
/* Do main display. */
if (cgiVarExists("pbt.psOutput"))
handlePostscript();
else
doTrackForm(NULL, NULL);
}
void doDown(struct cart *cart)
{
hPrintf("<H2>The Browser is Being Updated</H2>\n");
hPrintf("The browser is currently unavailable. We are in the process of\n");
hPrintf("updating the database and the display software.\n");
hPrintf("Please try again later.\n");
}
/* Other than submit and Submit all these vars should start with pbt.
* to avoid weeding things out of other program's namespaces.
* Because the browser is a central program, most of it's cart
* variables are not pbt. qualified. It's a good idea if other
* program's unique variables be qualified with a prefix though. */
char *excludeVars[] = { "submit", "Submit", "pbt.reset",
"pbt.in1", "pbt.in2", "pbt.in3", "pbt.inBase",
"pbt.out1", "pbt.out2", "pbt.out3",
"pbt.left1", "pbt.left2", "pbt.left3",
"pbt.right1", "pbt.right2", "pbt.right3",
"pbt.dinkLL", "pbt.dinkLR", "pbt.dinkRL", "pbt.dinkRR",
"pbt.tui", "pbt.hideAll", "pbt.psOutput", "hideControls",
NULL };
void resetVars()
/* Reset vars except for position and database. */
{
static char *except[] = {"db", "position", NULL};
char *cookieName = hUserCookie();
int sessionId = cgiUsualInt(cartSessionVarName(), 0);
char *hguidString = findCookieData(cookieName);
int userId = (hguidString == NULL ? 0 : atoi(hguidString));
struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL);
cartRemoveExcept(oldCart, except);
cartCheckout(&oldCart);
cgiVarExcludeExcept(except);
}
int main(int argc, char *argv[])
{
cgiSpoof(&argc, argv);
oldVars = hashNew(10);
htmlSetBackground(hBackgroundImage());
if (cgiVarExists("pbt.reset"))
resetVars();
cartHtmlShellPB("UCSC Proteome Browser", doMiddle, hUserCookie(), excludeVars, oldVars);
return 0;
}