void doControls(struct sqlConnection *conn)
/* Put up controls pane. */
{
char *listSpec = cartUsualString(cart, hgpListSpec, "");
htmlSetBgColor(0xD0FFE0);
// resource file link wrapped in html
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE);
if (link)
htmlSetStyle(link);
htmStart(stdout, "do controls");
printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" target=\"_parent\" METHOD=GET>\n",
hgVisiGeneCgiName());
cartSaveSession(cart);
printf("<TABLE WIDTH=100%%><TR>");
printf("<TD WIDTH=230 bgcolor=\"#"HG_COL_HOTLINKS"\">");
printf(" <B><A HREF=\"../index.html\" target=\"_parent\" class=\"topbar\">UCSC</A> ");
printf(" <A HREF=\"%s?%s=\" target=\"_parent\" class=\"topbar\">VisiGene</A></B> ",
hgVisiGeneCgiName(), hgpListSpec);
printf("</TD>");
printf("<TD>");
printf(" ");
cgiMakeTextVar(hgpListSpec, listSpec, 16);
cgiMakeButton(hgpDoSearch, "search");
printf("</TD>");
#ifdef SOON
printf("<TD>");
cgiMakeButton(hgpDoConfig, "configure");
printf("</TD>");
#endif /* SOON */
printf("<TD>");
printf("Zoom: ");
printf(
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmOut\" VALUE=\" out \""
" onclick=\"parent.image.bigImg.zoomer('out');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmIn\" VALUE=\" in \""
" onclick=\"parent.image.bigImg.zoomer('in');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFull\" VALUE=\" full \""
" onclick=\"parent.image.bigImg.zoomer('full');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFit\" VALUE=\" fit \""
" onclick=\"parent.image.bigImg.zoomer('fit');return false;\"> "
"\n");
printf("</TD>");
printf("<TD ALIGN=Right>");
printf("<A HREF=\"../goldenPath/help/hgTracksHelp.html#VisiGeneHelp\" target=_parent>");
printf("Help");
printf("</A> ");
printf("</TD>");
printf("</TR></TABLE>");
printf("</FORM>\n");
htmlEnd();
}
void doInitialPage()
/* Put up page with search box that explains program and
* some good things to search on. */
{
char *listSpec = NULL;
webStartWrapperDetailedNoArgs(cart, NULL, "", "VisiGene Image Browser",
FALSE, FALSE, FALSE, TRUE);
printf("<FORM ACTION=\"%s\" METHOD=GET>\n",
hgVisiGeneCgiName());
puts("<P>VisiGene is a virtual microscope for viewing <em>in situ</em> images. \n"
"These images show where a gene is used in an organism, sometimes down to \n"
"cellular resolution. With VisiGene users can retrieve images that meet specific "
"search criteria, then interactively zoom and scroll across the collection.</P>\n");
printf("<CENTER>");
listSpec = cartUsualString(cart, hgpListSpec, "");
cgiMakeTextVar(hgpListSpec, listSpec, 30);
cgiMakeButton(hgpDoSearch, "search");
printf("<BR>\n");
printf("</CENTER>");
puts(
"<P>Good search terms include gene symbols, authors, years, body parts,\n"
"organisms, GenBank and UniProt accessions, Known Gene descriptive terms,\n"
"<A HREF=\"http://genex.hgu.mrc.ac.uk/Atlas/intro.html\" \n"
"TARGET=_blank>Theiler</A> stages for mice, and \n"
"<A HREF=\"http://www.xenbase.org/atlas/NF/NF-all.html\" \n"
"TARGET=_blank>Nieuwkoop/Faber</A> stages for frogs. The wildcard characters\n"
"* and ? work with gene symbols; otherwise the full word must match.</P>\n"
"<P> \n"
"<H3>Sample queries</H3> \n"
"<TABLE border=0 CELLPADDING=0 CELLSPACING=0> \n"
" <TR><TD VALIGN=Top NOWRAP><B>Request:</B><BR></TD> \n"
" <TD VALIGN=Top COLSPAN=2><B> VisiGene Response:</B><BR></TD> \n"
" </TR> \n"
// " <TR><TD VALIGN=Top><BR></TD></TR> \n"
" <TR><TD VALIGN=Top NOWRAP>nkx2-2</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images associated with the gene nkx2-2</TD>\n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>hoxa*</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images of all genes in the Hox-A cluster (Note: * works only at the end of the word)</TD>\n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>NM_007492</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images associated with accession NM_007492</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>theiler 22</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all images that show Theiler stage 22</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>vgPrb_16</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images associated with VisiGene probe ID 16</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>allen institute</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all images from the Allen Brain Atlas</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>mouse</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all mouse images </TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>xenopus</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays all images associated with frogs of genus Xenopus </TD>\n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>mouse midbrain</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays mouse images that show expression in the "
"midbrain</TD> \n"
" </TR> \n"
" <TR><TD VALIGN=Top NOWRAP>smith jc 1994</TD> \n"
" <TD WIDTH=14></TD> \n"
" <TD VALIGN=Top>Displays images contributed by scientist J.C. Smith "
"in 1994</TD> \n"
" </TR> \n"
"</TABLE> \n"
);
printf("</FORM>\n");
doHelp();
webEnd();
}
void doFrame(struct sqlConnection *conn, boolean forceImageToList)
/* Make a html frame page. Fill frame with thumbnail, control bar,
* and image panes. */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char *sidUrl = cartSidUrlString(cart);
char *listSpec = cartUsualString(cart, hgpListSpec, "");
struct tempName matchTempName;
char *matchFile = NULL;
struct visiMatch *matchList = visiSearch(conn, listSpec);
#ifdef SOON
if (!cartUsualBoolean(cart, hgpIncludeMutants, FALSE))
matchList = removeMutants(conn, matchList);
#endif /* SOON */
matchList = onePerImageFile(conn, matchList);
weighMatches(conn, matchList);
slSort(&matchList, visiMatchCmpWeight);
if (forceImageToList)
{
if (matchList != NULL)
imageId = matchList->imageId;
else
imageId = 0;
}
trashDirFile(&matchTempName, "vg", "visiMatch", ".tab");
matchFile = matchTempName.forCgi;
saveMatchFile(matchFile, matchList);
cartSetString(cart, hgpMatchFile, matchFile);
cartSetInt(cart, hgpId, imageId);
//puts("\n");
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">");
printf("<HTML>\n");
printf("<HEAD>\n");
printf("<TITLE>\n");
printf("%s ", hgVisiGeneShortName());
printf("%s",titleMessage);
printf("</TITLE>\n");
printf("</HEAD>\n");
printf(" <frameset rows=\"27,*\">\n");
printf(" <frame name=\"controls\" src=\"%s?%s=go&%s&%s=%d\" noresize marginwidth=\"0\" marginheight=\"0\" frameborder=\"0\">\n",
hgVisiGeneCgiName(), hgpDoControls, sidUrl, hgpId, imageId);
printf(" <frameset cols=\"230,*\"> \n");
printf(" <frame src=\"%s?%s=go&%s&%s=%d\" noresize frameborder=\"0\" name=\"list\">\n",
hgVisiGeneCgiName(), hgpDoThumbnails, sidUrl, hgpId, imageId);
printf(" <frame src=\"%s?%s=go&%s&%s=%d\" name=\"image\" noresize frameborder=\"0\">\n",
hgVisiGeneCgiName(), hgpDoImage, sidUrl, hgpId, imageId);
printf(" </frameset>\n");
printf(" <noframes>\n");
printf(" <body>\n");
printf(" <p>This web page uses frames, but your browser doesn't support them.</p>\n");
printf(" </body>\n");
printf(" </noframes>\n");
printf("</frameset>\n");
printf("</HTML>\n");
}
void doImage(struct sqlConnection *conn)
/* Put up image page. */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char *sidUrl = cartSidUrlString(cart);
char buf[1024];
char url[1024];
char *p = NULL;
char dir[256];
char name[128];
char extension[64];
int w = 0, h = 0;
htmlSetBgColor(0xE0E0E0);
htmStart(stdout, "do image");
puts(
"<script type=\"text/JavaScript\">"
"document.getElementsByTagName('html')[0].style.height=\"100%\";"
"document.getElementsByTagName('body')[0].style.height=\"100%\";"
"</script>"
);
if (!visiGeneImageSize(conn, imageId, &w, &h))
imageId = 0;
if (imageId != 0)
{
printf("<B>");
smallCaption(conn, imageId);
printf(".</B> Click image to zoom in, drag or arrow keys to move. "
"Caption is below.<BR>\n");
p=visiGeneFullSizePath(conn, imageId);
splitPath(p, dir, name, extension);
#ifdef DEBUG
safef(buf,sizeof(buf),"../bigImageTest.html?url=%s%s/%s&w=%d&h=%d",
dir,name,name,w,h);
#else
safef(buf,sizeof(buf),"../bigImage.html?url=%s%s/%s&w=%d&h=%d",
dir,name,name,w,h);
#endif
printf("<IFRAME name=\"bigImg\" width=\"100%%\" height=\"90%%\" SRC=\"%s\"></IFRAME><BR>\n", buf);
fullCaption(conn, imageId);
safef(buf,sizeof(buf),"%s%s%s", dir, name, extension);
safef(url,sizeof(url),"%s?%s=go&%s&%s=%d",
hgVisiGeneCgiName(), hgpDoDownload, sidUrl, hgpId, imageId);
printf("<B>Full-size image:</B> %d x %d <A HREF='%s'> download </A> ", w, h, url);
/* Currently this is dangerous for users with less than 1 GB RAM to use
on large images, because their machines can thrash themselves into a coma.
X-windows (i.e. used by FireFox) will allocate 5 bytes per pixel.
If the image size in pixels times 5 exceeds real ram size, then
Linux thrashes incessantly. But you can hit ctrl-alt-F1 to
get a text only screen, then kill the bad processes (FF) and then
you can restore desktop with ctrl-alt-F7. Hiram says that's a
feature credited to SCO-Unix. On my 1GB machines at work/home,
I never encountered any problem what-so-ever, even with the
largest visiGene AllenBrain - about 19000x9000 pix.
printf(" <A HREF='%s'> view </A>\n", buf);
*/
printf("\n");
}
htmlEnd();
}
static void doThumbnails(struct sqlConnection *conn)
/* Write out list of thumbnail images. */
{
char *sidUrl = cartSidUrlString(cart);
char *listSpec = cartUsualString(cart, hgpListSpec, "");
char *matchFile = cartString(cart, hgpMatchFile);
struct visiMatch *matchList = NULL, *match;
int maxCount = 25, count = 0;
int startAt = cartUsualInt(cart, hgpStartAt, 0);
int imageCount;
htmlSetStyle(
"<STYLE TYPE=\"text/css\">\n"
" BODY {margin: 2px}\n"
" </STYLE>\n"
);
htmlSetBgColor(0xC0C0D6);
htmStart(stdout, "doThumbnails");
matchList = readMatchFile(matchFile);
imageCount = slCount(matchList);
if (imageCount > 0)
{
printf(
" <DIV"
" ID='perspClip'"
" STYLE='position:absolute;left:-1000px;top:-1000px;z-index:2;visibility:visible;overflow:hidden!important;'"
" onmouseover='this.style.left=\"-1000px\";' "
" >"
" <DIV"
" ID='perspective'"
" STYLE='position:absolute;left:0px;top:0px;'"
" >"
" <IMG ID='perspBox' SRC='../images/dot_clear.gif' STYLE='position:absolute;left:0px;top:0px;width:100px;height:100px;border-style:solid;border-color:#8080FF;border-width:1px' "
">"
" </DIV>"
" </DIV>"
);
printf("<TABLE>\n");
printf("<TR><TD><B>");
printf("%d images match<BR>\n", imageCount);
printf("</B></TD></TR>\n");
for (match = slElementFromIx(matchList, startAt);
match != NULL; match = match->next)
{
int id = match->imageId;
char *imageFile = visiGeneThumbSizePath(conn, id);
printf("<TR>");
printf("<TD>");
printf("<A HREF=\"%s?%s&%s=%d&%s=do\" target=\"image\" >",
hgVisiGeneCgiName(),
sidUrl, hgpId, id, hgpDoImage);
printf("<IMG SRC=\"%s\"></A><BR>\n", imageFile);
smallCaption(conn, id);
printf("<BR>\n");
printf("</TD>");
printf("</TR>");
if (++count >= maxCount)
break;
}
printf("</TABLE>\n");
printf("<HR>\n");
}
if (count != imageCount)
{
int start;
int page = 0;
printf("%d-%d of %d for:<BR>", startAt+1,
startAt+count, imageCount);
printf(" %s<BR>\n", listSpec);
printf("Page:\n");
for (start=0; start<imageCount; start += maxCount)
{
++page;
if (start != startAt)
{
printf("<A HREF=\"%s?", hgVisiGeneCgiName());
printf("%s&", sidUrl);
printf("%s=on&", hgpDoThumbnails);
printf("%s=%s&", hgpListSpec, listSpec);
if (start != 0)
printf("%s=%d", hgpStartAt, start);
printf("\">");
}
printf("%d", page);
if (start != startAt)
printf("</A>");
printf(" ");
}
}
else
{
printf("%d images for:<BR>", imageCount);
printf(" %s<BR>\n", listSpec);
}
cartRemove(cart, hgpStartAt);
htmlEnd();
}
static struct slName *getProbeList(struct sqlConnection *conn, int id)
/* Get list of probes with hyperlinks to probe info page. */
{
struct slName *returnList = NULL;
char query[256];
char *sidUrl = cartSidUrlString(cart);
struct dyString *dy = dyStringNew(0);
struct slInt *probeList = NULL, *probe;
int submissionSource = 0;
/* Make up a list of all probes in this image. */
safef(query, sizeof(query),
"select probe from imageProbe where image=%d", id);
probeList = sqlQuickNumList(conn, query);
safef(query, sizeof(query),
"select submissionSet.submissionSource from image, submissionSet"
" where image.submissionSet = submissionSet.id and image.id=%d", id);
submissionSource = sqlQuickNum(conn, query);
for (probe = probeList; probe != NULL; probe = probe->next)
{
char *type;
/* Create hyperlink to probe page around gene name. */
dyStringClear(dy);
dyStringPrintf(dy, "<A HREF=\"%s?%s&%s=%d&%s=%d\" target=_parent>",
hgVisiGeneCgiName(), sidUrl, hgpDoProbe, probe->val, hgpSs, submissionSource);
safef(query, sizeof(query),
"select probeType.name from probeType,probe where probe.id = %d "
"and probe.probeType = probeType.id",
probe->val);
type = sqlQuickString(conn, query);
dyStringPrintf(dy, "%s", naForEmpty(type));
if (sameWord(type, "antibody"))
{
char *abName;
safef(query, sizeof(query),
"select antibody.name from probe,antibody "
"where probe.id = %d and probe.antibody = antibody.id"
, probe->val);
abName = sqlQuickString(conn, query);
if (abName != NULL)
{
dyStringPrintf(dy, " %s", abName);
freeMem(abName);
}
}
else if (sameWord(type, "RNA"))
{
safef(query, sizeof(query),
"select length(seq) from probe where id=%d", probe->val);
if (sqlQuickNum(conn, query) > 0)
dyStringPrintf(dy, " sequenced");
else
{
safef(query, sizeof(query),
"select length(fPrimer) from probe where id=%d", probe->val);
if (sqlQuickNum(conn, query) > 0)
dyStringPrintf(dy, " from primers");
}
}
else if (sameWord(type, "BAC"))
{
char *name;
safef(query, sizeof(query),
"select bac.name from probe,bac "
"where probe.id = %d and probe.bac = bac.id"
, probe->val);
name = sqlQuickString(conn, query);
if (name != NULL)
{
dyStringPrintf(dy, " %s", name);
freeMem(name);
}
}
dyStringPrintf(dy, "</A>");
freez(&type);
/* Add to return list. */
slNameAddTail(&returnList, dy->string);
}
slFreeList(&probeList);
slReverse(&returnList);
return returnList;
}
