0b69879792272a9ebc910a90be65a9c31dab2329 max Mon Jan 22 05:59:38 2024 -0800 adding menu entry and button for highlight here feature, refs #32892 diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c index 979bf17..dbc19a1 100644 --- src/hg/hgTracks/menu.c +++ src/hg/hgTracks/menu.c @@ -1,434 +1,436 @@ // Code to create hgTracks menu bar /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "dystring.h" #include "ensFace.h" #include "agpFrag.h" #include "ctgPos.h" #include "hCommon.h" #include "htmshell.h" #include "hash.h" #include "wikiLink.h" #include "web.h" #include "geoMirror.h" #include "hgTracks.h" #include "trackHub.h" #include "extTools.h" #include "trackVersion.h" #include "chromAlias.h" /* list of links to display in a menu */ /* a link with an empty name is displayed as a horizontal separator line */ struct hotLink { struct hotLink *next; char *name; char *url; char *id; char *mouseOver; char *onClick; char *shortcut; boolean inactive; /* greyed out */ boolean external; }; static void appendLink(struct hotLink **links, char *url, char *name, char *id, boolean external) { // append to list of links for later printing and/or communication with javascript client struct hotLink *link; AllocVar(link); link->name = cloneString(name); link->url = cloneString(url); link->id = cloneString(id); link->external = external; link->inactive = FALSE; slAddTail(links, link); } static void appendLinkMaybeInactive(struct hotLink **links, char *url, char *name, char *id, char *mouseOver, boolean external, boolean inactive) { appendLink(links, url, name, id, external); struct hotLink *le = slLastEl(links); le->inactive=inactive; le->mouseOver=mouseOver; } static void appendLinkWithOnclick(struct hotLink **links, char *url, char *name, char *id, char *mouseOver, char *onClick, char *shortcut, boolean external, boolean inactive) { appendLinkMaybeInactive(links, url, name, id, mouseOver, external, inactive); struct hotLink *le = slLastEl(links); le->onClick=onClick; le->shortcut=shortcut; } static void appendLinkWithShortcut(struct hotLink **links, char *url, char *name, char *id, char *mouseOver, char *shortcut, boolean external, boolean inactive) { appendLinkMaybeInactive(links, url, name, id, mouseOver, external, inactive); struct hotLink *le = slLastEl(links); le->shortcut=shortcut; } static void printEnsemblAnchor(char *database, char* archive, char *chrName, int start, int end, struct hotLink **links) /* Print anchor to Ensembl display on same window. */ { char *scientificName = hScientificName(database); char *dir = ensOrgNameFromScientificName(scientificName); struct dyString *ensUrl; char *name; int localStart, localEnd; name = chrName; if (sameWord(scientificName, "Takifugu rubripes")) { /* for Fugu, must give scaffold, not chr coordinates */ /* Also, must give "chrom" as "scaffold_N", name below. */ if (differentWord(chromName,"chrM") && !hScaffoldPos(database, chromName, winStart, winEnd, &name, &localStart, &localEnd)) /* position doesn't appear on Ensembl browser. * Ensembl doesn't show scaffolds < 2K */ return; } else if (sameWord(scientificName, "Gasterosteus aculeatus")) { if (differentWord("chrM", chrName)) { char *fixupName = replaceChars(chrName, "chr", "group"); name = fixupName; } } else if (sameWord(scientificName, "Ciona intestinalis")) { if (stringIn("chr0", chrName)) { char *fixupName = replaceChars(chrName, "chr0", "chr"); name = fixupName; } } else if (sameWord(scientificName, "Saccharomyces cerevisiae")) { if (stringIn("2micron", chrName)) { char *fixupName = replaceChars(chrName, "2micron", "2-micron"); name = fixupName; } } if (sameWord(chrName, "chrM")) name = "chrMt"; ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, start+1, end, archive); appendLink(links, ensUrl->string, "Ensembl", "ensemblLink", TRUE); /* NOTE: you can not freeMem(dir) because sometimes it is a literal * constant */ freeMem(scientificName); dyStringFree(&ensUrl); } static void fr2ScaffoldEnsemblLink(char *archive, struct hotLink **links) /* print out Ensembl link to appropriate scaffold there */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; char query[256]; sqlSafef(query, sizeof(query), "select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u", chromName, winEnd, winStart); sr = sqlGetResult(conn, query); int itemCount = 0; struct agpFrag *agpItem = NULL; while ((row = sqlNextRow(sr)) != NULL) { agpFragFree(&agpItem); // if there is a second one agpItem = agpFragLoad(row+1); ++itemCount; if (itemCount > 1) break; } sqlFreeResult(&sr); hFreeConn(&conn); if (1 == itemCount) { // verify *entirely* within single contig if ((winEnd <= agpItem->chromEnd) && (winStart >= agpItem->chromStart)) { int agpStart = winStart - agpItem->chromStart; int agpEnd = agpStart + winEnd - winStart; printEnsemblAnchor(database, archive, agpItem->frag, agpStart, agpEnd, links); } } agpFragFree(&agpItem); // the one we maybe used } void freeLinksAndConvert(struct hotLink *links, struct dyString *menuHtml) /* convert the links to html strings and append to the dyString "menu", destroying the links */ { int len = slCount(links); int i = 0; struct hotLink *link = NULL; for(i = 0, link = links; link != NULL; i++, link = link->next) { char class[100]; if(i == 0) safef(class, sizeof(class), "first"); else if (i + 1 == len) safef(class, sizeof(class), "last"); else if (isEmpty(link->name)) safef(class, sizeof(class), "horizSep"); else class[0] = 0; dyStringAppend(menuHtml, "<li"); char *encodedName = htmlEncode(link->name); if(*class) dyStringPrintf(menuHtml, " class='%s'", class); dyStringPrintf(menuHtml, ">\n"); if (!isEmpty(link->name)) { dyStringPrintf(menuHtml, "<a href='%s'", link->url); if (link->mouseOver) dyStringPrintf(menuHtml, " title='%s'", link->mouseOver); if (link->onClick) { jsOnEventById("click", link->id, link->onClick); } dyStringPrintf(menuHtml, " id='%s'", link->id); if (link->external) dyStringAppend(menuHtml, " TARGET='_blank'"); dyStringPrintf(menuHtml, ">%s</a>\n", encodedName); } if (!isEmpty(link->shortcut)) dyStringPrintf(menuHtml, "<span class='shortcut'>%s</span>", link->shortcut); dyStringPrintf(menuHtml, "</li>\n"); freez(&encodedName); freez(&link->name); freez(&link->url); freez(&link->id); } slFreeList(links); } void printMenuBar() /* Put up the special menu bar for hgTracks. */ { struct hotLink *links = NULL; struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConn(database); char *menuStr, buf[4096], uiVars[1024]; safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart)); menuStr = menuBar(cart, database); /* hide Projects dropdown (just used by static and gateway pages */ menuStr = replaceChars(menuStr, "<!-- OPTIONAL_PROJECT_MENU_START -->", "<!-- OPTIONAL_PROJECT_MENU_START"); menuStr = replaceChars(menuStr, "<!--OPTIONAL_PROJECT_MENU_END -->", "OPTIONAL_PROJECT_MENU_END -->"); // Add Recommended Track Sets to Genome Browser menu (if any for this assembly) // TODO: consider splitting the recommended track sets config file into separate files by database, // so we don't need to read file to see whether to add menu item if (recTrackSetsEnabled() && recTrackSetsForDb()) { #define recTrackSetsMenuItemId "recTrackSetsMenuItem" struct dyString *menuItemDs = dyStringCreate("<li><a href='#' id='%s'>Recommended Track Sets</a></li>", recTrackSetsMenuItemId); menuStr = replaceChars(menuStr, "<!-- OPTIONAL_RECOMMENDED_TRACK_SETS_MENU -->", dyStringCannibalize(&menuItemDs)); if (stringIn(recTrackSetsMenuItemId, menuStr)) jsOnEventById("click", recTrackSetsMenuItemId, "showRecTrackSetsPopup(); return false;"); } // Create top items in view menu safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.psOutput=on", uiVars); appendLink(&links, buf, "PDF", "pdfLink", FALSE); safef(buf, sizeof(buf), "%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s", hgcNameAndSettings(), winStart, chromName, winStart, winEnd, database, uiVars); //appendLink(&links, buf, "DNA", "dnaLink", FALSE); appendLinkWithShortcut(&links, buf, "DNA", "dnaLink", "Show DNA sequence in view", "v d", FALSE, FALSE); safef(buf, sizeof(buf), "../cgi-bin/hgConvert?hgsid=%s&db=%s", cartSessionId(cart), database); appendLink(&links, buf, "In Other Genomes (Convert)", "convertMenuLink", FALSE); // add the sendTo menu if (fileExists("extTools.ra")) { appendLinkWithOnclick(&links, "#", "In External Tools", "extToolLink", "Show current sequence on a third-party website", "showExtToolDialog(); return false;", "s t", FALSE, FALSE); } // Add link-outs to other dbs as appropriate for this assembly if (differentWord(database,"susScr2")) { /* Print Ensembl anchor for latest assembly of organisms we have * supported by Ensembl == if versionString from trackVersion exists */ struct trackVersion *trackVersion = getTrackVersion(database, "ensGene"); if ((conn != NULL) && sqlTableExists(conn, UCSC_TO_ENSEMBL)) printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); else if (sameWord(database,"hg19")) { printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); } else if (sameWord(database,"hg18")) { printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd, &links); } else if (sameWord(database,"oryCun2") || sameWord(database,"anoCar2") || sameWord(database,"calJac3")) { printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); } else if ((trackVersion != NULL) && !isEmpty(trackVersion->version)) { char *archive = NULL; if (!isEmpty(trackVersion->dateReference) && differentWord("current", trackVersion->dateReference)) archive = cloneString(trackVersion->dateReference); /* Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */ if (isUnknownChrom(database, chromName)) { // which table to check char *ctgPos = "ctgPos"; if (sameWord(database,"fr2")) fr2ScaffoldEnsemblLink(archive, &links); else if (hTableExists(database, UCSC_TO_ENSEMBL)) printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links); else if (hTableExists(database, ctgPos)) /* see if we are entirely within a single contig */ { struct sqlResult *sr = NULL; char **row = NULL; char query[256]; sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u", ctgPos, chromName, winEnd, winStart); sr = sqlGetResult(conn, query); int itemCount = 0; struct ctgPos *ctgItem = NULL; while ((row = sqlNextRow(sr)) != NULL) { ctgPosFree(&ctgItem); // if there is a second one ctgItem = ctgPosLoad(row); ++itemCount; if (itemCount > 1) break; } sqlFreeResult(&sr); if (1 == itemCount) { // verify *entirely* within single contig if ((winEnd <= ctgItem->chromEnd) && (winStart >= ctgItem->chromStart)) { int ctgStart = winStart - ctgItem->chromStart; int ctgEnd = ctgStart + winEnd - winStart; printEnsemblAnchor(database, archive, ctgItem->contig, ctgStart, ctgEnd, &links); } } ctgPosFree(&ctgItem); // the one we maybe used } } else { printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links); } } } hFreeConn(&conn); char *gcfId = hNcbiGcfId(database); char *gcaId = hNcbiGcaId(database); if (isNotEmpty(gcfId)) /* GCF has priority over GCA */ { char *ncbiChr = chromAliasNCBI(database, chromName, gcfId); safef(buf, sizeof(buf), "https://www.ncbi.nlm.nih.gov/genome/gdv/browser/" "?context=genome&acc=%s&chr=%s&from=%d&to=%d", gcfId, ncbiChr, winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (isNotEmpty(gcaId)) { char *ncbiChr = chromAliasNCBI(database, chromName, gcaId); safef(buf, sizeof(buf), "https://www.ncbi.nlm.nih.gov/genome/gdv/browser/" "?context=genome&acc=%s&chr=%s&from=%d&to=%d", gcaId, ncbiChr, winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (startsWith("oryLat", database)) { safef(buf, sizeof(buf), "http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "UTGB", "medakaLink", TRUE); } else if (sameString(database, "cb3")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "cb4")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_briggsae?name=%s:%d-%d", chromName, winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "ce10")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "ce4")) { safef(buf, sizeof(buf), "http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "ce2")) { safef(buf, sizeof(buf), "http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } // finish View menu appendLink(&links, "", "", "", FALSE); // separator line safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgTracksConfigPage=configure", uiVars); appendLinkWithShortcut(&links, buf, "Configure Browser", "configureMenuLink", "Open configuration menu", "c f", FALSE, FALSE); // multi-region appendLinkWithOnclick(&links, "#", "Multi-Region", "multiRegionLink", "Show multi-region options", "popUpHgt.hgTracks('multi-region config'); return false;", "", FALSE, FALSE); safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.reset=on", uiVars); appendLinkWithShortcut(&links, buf, "Default Tracks", "defaultTracksMenuLink", "Show only default tracks", "d t", FALSE, FALSE); safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.defaultImgOrder=on", uiVars); appendLinkWithShortcut(&links, buf, "Default Track Order", "defaultTrackOrderMenuLink", "Re-order tracks to be in default order", "d o", FALSE, FALSE); appendLinkWithOnclick(&links, "#", "Remove all highlights", "cleaerHighlightLink", "Remove all highlights on all genomes", "highlightCurrentPosition('clear'); $('ul.nice-menu li ul').hide();", "h c", FALSE, FALSE); -appendLinkWithShortcut(&links, "../cgi-bin/cartReset", "Reset All User Settings", "cartResetMenuLink", "Clear user data, e.g. active tracks, track configuration, custom data, ...", "c r", FALSE, FALSE); +appendLinkWithOnclick(&links, "#", "Highlight here", "highlightHereMenu", "Add a highlight that covers the entire currently shown region, using the default color. Keyboard shortcut memo is 'highlight mark here'", "highlightCurrentPosition('add'); $('ul.nice-menu li ul').hide();", "h m", FALSE, FALSE); + +appendLinkWithShortcut(&links, "../cgi-bin/cartReset?skipLs=1", "Reset All User Settings", "cartResetMenuLink", "Clear user data, e.g. active tracks, track configuration, custom data, ...", "c r", FALSE, FALSE); struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul>\n"); freeLinksAndConvert(links, viewMenu); dyStringAppend(viewMenu, "</ul>\n</li>\n"); menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu)); menuStr = replaceChars(menuStr, "id=\"main-menu-whole\"", "id=\"hgTracks-main-menu-whole\""); menuStr = replaceChars(menuStr, "id=\"home-link\"", "id=\"hgTracks-home-link\""); hPuts(menuStr); freez(&menuStr); }