aab4f66a2aca5293f3536cc1d1438b17d2b09dfd tdreszer Thu May 5 16:14:15 2011 -0700 A large set of tiny changes. These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01. diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c index 5e487ba..54f72e5 100644 --- src/hg/hgTracks/config.c +++ src/hg/hgTracks/config.c @@ -1,575 +1,575 @@ /* config - put up track and display configuration page. */ #include "common.h" #include "dystring.h" #include "cheapcgi.h" #include "htmshell.h" #include "hdb.h" #include "hCommon.h" #include "cart.h" #include "web.h" #include "customTrack.h" #include "hgTracks.h" #include "hgConfig.h" #include "jsHelper.h" #include "imageV2.h" #include "search.h" #define DOWNLOADS_ONLY_TRACKS_INCLUDED #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED #include "fileUi.h" #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED static void textSizeDropDown() /* Create drop down for font size. */ { static char *sizes[] = {"6", "8", "10", "12", "14", "18", "24", "34"}; hDropList(textSizeVar, sizes, ArraySize(sizes), tl.textSize); } #ifdef PRIORITY_CHANGES_IN_CONFIG_UI static void printGroupListHtml(char *groupCgiName, struct group *groupList, char *defaultGroup) /* Make an HTML select input listing the groups. */ { char *groups[128]; char *labels[128]; char *defaultLabel = NULL; int numGroups = 0; struct group *group = NULL; for (group = groupList; group != NULL; group = group->next) { groups[numGroups] = group->name; labels[numGroups] = group->name; if (sameWord(defaultGroup, groups[numGroups])) defaultLabel = groups[numGroups]; numGroups++; if (numGroups >= ArraySize(groups)) internalErr(); } cgiMakeDropListFull(groupCgiName, labels, groups, numGroups, defaultLabel, NULL); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI static void trackConfig(struct track *trackList, struct group *groupList, char *groupTarget, int changeVis) /* Put up track configurations. If groupTarget is * NULL then set visibility for tracks in all groups. Otherwise, * just set it for the given group. If vis is -2, then visibility is * unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { #ifdef PRIORITY_CHANGES_IN_CONFIG_UI char pname[512]; char gname[512]; #endif///def PRIORITY_CHANGES_IN_CONFIG_UI struct group *group; boolean showedRuler = FALSE; setRulerMode(); changeTrackVis(groupList, groupTarget, changeVis); /* Set up ruler mode according to changeVis. */ #ifdef BOB_DOESNT_LIKE if (changeVis != -2) { if (groupTarget == NULL || (groupList != NULL && sameString(groupTarget, groupList->name))) { if (changeVis == -1) rulerMode = tvFull; else rulerMode = changeVis; } } #endif /* BOB_DOESNT_LIKE */ jsInit(); cgiMakeHiddenVar(configGroupTarget, "none"); boolean isFirstNotCtGroup = TRUE; for (group = groupList; group != NULL; group = group->next) { struct trackRef *tr; if (group->trackList == NULL) continue; /* check if group section should be displayed */ char *otherState; char *indicator; char *indicatorImg; boolean isOpen = !isCollapsedGroup(group); collapseGroupGoodies(isOpen, FALSE, &indicatorImg, &indicator, &otherState); hTableStart(); hPrintf(""); - hPrintf(""); + hPrintf(""); hPrintf("\n",group->name); hPrintf("", collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1)); hPrintf("%s  ", hgTracksName(), cartSidUrlString(cart),collapseGroupVar(group->name), otherState, group->name, group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand"); hPrintf(" %s ", wrapWhiteFont(group->label)); hPrintf("   "); hPrintf("", configHideAll, "hide all", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); hPrintf("", configShowAll, "show all", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); hPrintf("", configDefaultAll, "default", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); /* do not want all the submit buttons named the same. It is * confusing to the javascript submit() function. */ char submitName[256]; safef(submitName, sizeof(submitName), "%sSubmit", group->name); cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("      "); hPrintf("      "); hPrintf("      "); hPrintf("%s", wrapWhiteFont("Group Order: ")); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("\n"); safef(pname, sizeof(pname), "%s.priority",group->name); hDoubleVar(pname, (double)group->priority, 4); hPrintf("\n"); if (isOpen) - hPrintf(" %s ", wrapWhiteFont("Group")); + hPrintf(" %s ", wrapWhiteFont("Group")); hPrintf("\n"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("\n"); /* First non-CT group gets ruler. */ if (!showedRuler && isFirstNotCtGroup && differentString(group->name, "user")) { showedRuler = TRUE; hPrintf("",(isOpen ? "" : "style='display: none'"), group->name); hPrintf(""); hPrintf("", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, RULER_TRACK_NAME); hPrintf("%s", RULER_TRACK_LABEL); hPrintf(""); hPrintf(""); hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText"); hPrintf(""); hPrintf(""); hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)"); hPrintf(""); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf(""); hPrintf(""); hPrintf(""); hPrintf(""); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("\n"); } if (differentString(group->name, "user")) isFirstNotCtGroup = FALSE; /* Scan track list to determine which supertracks have visible member * tracks, and to insert a track in the list for the supertrack. * Sort tracks and supertracks together by priority */ makeGlobalTrackHash(trackList); groupTrackListAddSuper(cart, group); if (!withPriorityOverride) { /* sort hierarchically by priority, considering supertracks */ struct trackRef *refList = NULL, *ref; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; if (tdbIsSuperTrackChild(track->tdb)) /* ignore supertrack member tracks till supertrack is found */ continue; AllocVar(ref); ref->track = track; slAddTail(&refList, ref); if (tdbIsSuper(track->tdb)) { struct slRef *child = track->tdb->children; for (; child != NULL; child=child->next) { struct trackDb *childTdb = child->val; struct track *childTrack = hashFindVal(trackHash, childTdb->track); #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED // Try adding downloadsOnly track if (childTrack == NULL && tdbIsDownloadsOnly(childTdb)) { AllocVar(childTrack); // Fake a track! childTrack->tdb = childTdb; childTrack->hasUi = FALSE; } #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED if (childTrack != NULL) { AllocVar(ref); ref->track = childTrack; slAddTail(&refList, ref); } } } } group->trackList = refList; } /* Loop through this group and display */ int rowCount=1; for (tr = group->trackList; tr != NULL; tr = tr->next) { struct track *track = tr->track; struct trackDb *tdb = track->tdb; hPrintf("",(isOpen ? "" : "style='display: none'"),group->name, rowCount++); hPrintf(""); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf("    "); // Print an icon before the title when one is defined hPrintPennantIcon(tdb); if (track->hasUi) hPrintf("", tdb->parent ? "Part of super track: " : "Configure ", tdb->parent ? tdb->parent->shortLabel : tdb->shortLabel, hgTrackUiName(),cartSessionVarName(), cartSessionId(cart), track->track); hPrintf(" %s", tdb->shortLabel); if (tdbIsSuper(tdb)) hPrintf("..."); if (track->hasUi) hPrintf(""); hPrintf(""); hPrintf(""); if (tdbIsSuperTrackChild(tdb)) /* indent members of a supertrack */ hPrintf("    "); /* If track is not on this chrom print an informational message for the user. */ #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED if (tdbIsDownloadsOnly(tdb)) hPrintf("Downloads", // No vis display for downloadsOnly hgFileUiName(),cartSessionVarName(), cartSessionId(cart), tdb->track); else #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED if (hTrackOnChrom(track->tdb, chromName)) { if (tdbIsSuper(track->tdb)) { /* supertrack dropdown is hide/show */ superTrackDropDown(cart, track->tdb, 1); } else { /* check for option of limiting visibility to one mode */ hTvDropDownClassVisOnly(track->track, track->visibility, track->canPack, (track->visibility == tvHide) ? "hiddenText" : "normalText", trackDbSetting(track->tdb, "onlyVisibility")); } } else hPrintf("[No data-%s]", chromName); hPrintf(""); hPrintf(""); hPrintf("%s", tdb->longLabel); hPrintf(""); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf(""); #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED if (tdbIsDownloadsOnly(tdb)) hPrintf(" \n "); else #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED { safef(pname, sizeof(pname), "%s.priority",track->track); hDoubleVar(pname, (double)track->priority, 4); hPrintf(""); hPrintf("\n"); /* suppress group pull-down for supertrack members */ if (tdbIsSuperTrackChild(track->tdb)) hPrintf(" "); else { safef(gname, sizeof(gname), "%s.group",track->track); printGroupListHtml(gname, groupList, track->groupName); } } hPrintf(""); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("\n"); } hTableEnd(); hPrintf("
"); } } #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED static int addDownloadOnlyTracks(char *db,struct group **pGroupList,struct track **pTrackList) // Download only tracks are not normaly incorporated into the grou and track lists { int count = 0; struct track *track = NULL; struct group *group = NULL; struct trackDb *tdbList = hTrackDb(db); struct trackDb *tdb = tdbList; for(;tdb != NULL; tdb = tdb->next) { if (!tdbIsDownloadsOnly(tdb) || tdbIsFolderContent(tdb) || tdbIsCompositeChild(tdb)) continue; // Must find group if (tdb->grp == NULL) continue; for (group = *pGroupList;group != NULL; group = group->next) { if (sameWord(group->name,tdb->grp)) break; } if (group == NULL) continue; // Make the track track = trackFromTrackDb(tdb); track->group = group; track->groupName = cloneString(group->name); // Don't even bother looking in cart. That junk should be thrown out, now that we have dragReorder slAddHead(pTrackList,track); count++; } if (count > 0) { // Going to have to make all new group->trackLists slSort(pGroupList, gCmpPriority); for (group = *pGroupList;group != NULL; group = group->next) slFreeList(&group->trackList); // Sort the tracks anew and add each on into it's group. slSort(pTrackList, tgCmpPriority); for (track = *pTrackList; track != NULL; track = track->next) { struct trackRef *tr; AllocVar(tr); tr->track = track; slAddHead(&track->group->trackList, tr); } /* Straighten things out, clean up, and go home. */ for (group = *pGroupList;group != NULL; group = group->next) slReverse(&group->trackList); } return count; } #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED void configPageSetTrackVis(int vis) /* Do config page after setting track visibility. If vis is -2, then visibility * is unchanged. If -1 then set visibility to default, otherwise it should * be tvHide, tvDense, etc. */ { struct dyString *title = dyStringNew(0); char *groupTarget = NULL; struct track *trackList = NULL; struct track *ideoTrack = NULL; struct group *groupList = NULL; withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE); /* Get track list and group them. */ ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName); trackList = getTrackList(&groupList, vis); #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED addDownloadOnlyTracks(database,&groupList,&trackList); #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED /* The ideogram for some reason is considered a track. * We don't really want to process it as one though, so * we see if it's there, and if necessary remove it. */ ideoTrack = chromIdeoTrack(trackList); if (ideoTrack != NULL) removeTrackFromGroup(ideoTrack); /* Fetch group to change on if any from CGI, * and remove var so it doesn't get used again. */ groupTarget = cloneString(cartUsualString(cart, configGroupTarget, "")); cartRemove(cart, configGroupTarget); if (sameString(groupTarget, "none")) freez(&groupTarget); dyStringPrintf(title, "Configure Image"); hPrintf("
\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); cartSaveSession(cart); hPrintf(""); /* do not want all the submit buttons named the same thing, this one is: */ cgiMakeButton("topSubmit", "submit"); // 3 column table hPrintf("\n"); hPrintf(""); hPrintf(""); hPrintf("
"); hTableStart(); if (ideoTrack != NULL) { hPrintf("\n"); } hPrintf("\n"); hPrintf("\n"); hPrintf("\n"); hPrintf("\n"); hPrintf("\n"); hPrintf("\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("\n"); #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("\n"); hTableEnd(); puts("
"); char *freeze = hFreezeFromDb(database); char buf[128]; if (stringIn(database, freeze)) safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s", organization, browserName, organism, freeze); else safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)", organization, browserName, organism, freeze, database); webNewSection(buf); hPrintf("Tracks: "); if(isSearchTracksSupported(database,cart)) { cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT); hPrintf(" "); } cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly"); hPrintf(" "); cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks"); hPrintf("   Groups: "); hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return setAllTrackGroupVisibility(false)"); hPrintf(" "); hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return setAllTrackGroupVisibility(true)"); hPrintf("
Control track and group visibility more selectively below.
"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf(""); } void configPage() /* Put up configuration page. */ { configPageSetTrackVis(-2); }
image width:"); hPrintf(""); hIntVar("pix", tl.picWidth, 4); hPrintf("pixels
label area width:"); hPrintf(""); hIntVar("hgt.labelWidth", leftLabelWidthChars, 2); hPrintf("characters
text size:"); hPrintf(""); textSizeDropDown(); hPrintf(""); if (trackLayoutInclFontExtras()) { char *defaultStyle = cartUsualString(cart, "fontType", "medium"); cartMakeRadioButton(cart, "fontType", "medium", defaultStyle); hPrintf(" medium "); cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle); hPrintf(" fixed "); cartMakeRadioButton(cart, "fontType", "bold", defaultStyle); hPrintf(" bold "); hPrintf(" "); } hPrintf("
"); hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE)); hPrintf(""); hPrintf("Display chromosome ideogram above main graphic"); hPrintf("
"); hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE)); hPrintf(""); hPrintf("Show light blue vertical guidelines"); hPrintf("
"); hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE)); hPrintf(""); hPrintf("Display labels to the left of items in tracks"); hPrintf("
"); hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE)); hPrintf(""); hPrintf("Display description above each track"); hPrintf("
"); hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE)); hPrintf(""); hPrintf("Show track controls under main graphic"); hPrintf("
"); hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE)); hPrintf(""); hPrintf("Next/previous item navigation"); hPrintf("
"); hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE)); hPrintf(""); hPrintf("Next/previous exon navigation"); hPrintf("
"); char *javascript="onClick=\"document.mainForm.hgTracksConfigPage.value='configure';document.mainForm.submit();\""; hCheckBoxJS(configPriorityOverride, cartUsualBoolean(cart, configPriorityOverride , FALSE), javascript); hPrintf(""); hPrintf("Enable track re-ordering"); hPrintf("
"); hCheckBox("enableAdvancedJavascript", advancedJavascriptFeaturesEnabled(cart)); hPrintf(""); hPrintf("Enable advanced javascript features"); hPrintf("