da2e00021362a366f2f3b17b238305ca7981c7d2 tdreszer Thu Dec 15 12:44:34 2011 -0800 Some older composites have packable children which are seen in rightClick as unpackable. The mixed case that gives rise to this should not be allowed now, but we can support it for those older composites. The rule is, if any single subtrack is packable, then the whole tree is. diff --git src/hg/hgTracks/config.c src/hg/hgTracks/config.c index ad45869..4ac5bdc 100644 --- src/hg/hgTracks/config.c +++ src/hg/hgTracks/config.c @@ -1,579 +1,579 @@ /* 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" #include "hubConnect.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"); 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); hPrintf("<TABLE BORDER='1' CELLSPACING='0' style='background-color:#%s; width:54em;'>\n",HG_COL_INSIDE); hPrintf("<TR NOWRAP class='blueToggleBar'>"); hPrintf("<TH NOWRAP align='left' colspan=3>"); hPrintf("<table style='width:100%%;'><tr><td style='text-align:left;'>"); hPrintf("\n<A NAME='%sGroup'></A>",group->name); hPrintf("<input type=hidden name='%s' id='%s' value=%d>", collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1)); //#define BUTTONS_BY_CSS_NOT_HERE #ifdef BUTTONS_BY_CSS_NOT_HERE hPrintf("<span class='pmButton toggleButton' onclick=\"vis.toggleForGroup(this,'%s')\" id='%s_button' title='%s this group'>%s</span> ", group->name, group->name, isOpen?"Collapse":"Expand", indicator); #else///ifndef BUTTONS_BY_CSS_NOT_HERE hPrintf("<IMG class='toggleButton' onclick=\"return vis.toggleForGroup(this,'%s');\" id='%s_button' src='%s' alt='%s' title='%s this group'> ", group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand"); #endif///ndef BUTTONS_BY_CSS_NOT_HERE hPrintf("<B> %s</B> ", group->label); hPrintf(" "); hPrintf("</td><td style='text-align:right;'>\n"); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" " "onClick=\"document.mainForm.%s.value='%s'; %s\" title='Hide all tracks in this groups'>", configHideAll, "hide all", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" " "onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show all tracks in this groups'>", configShowAll, "show all", configGroupTarget, group->name, jsSetVerticalPosition("mainForm")); hPrintf(" "); hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" " "onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show default tracks in this group'>", 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("</td></tr></table>\n"); hPrintf("</TH>\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("<TH>\n"); safef(pname, sizeof(pname), "%s.priority",group->name); hDoubleVar(pname, (double)group->priority, 4); hPrintf("</TH>\n"); if (isOpen) hPrintf("<TH align=CENTER BGCOLOR='#536ED3'><B> %s</B></TH> ", wrapWhiteFont("Group")); hPrintf("\n"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TR>\n"); /* First non-CT, non-hub group gets ruler. */ if (!showedRuler && !isHubTrack(group->name) && differentString(group->name, "user")) { showedRuler = TRUE; hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name); hPrintf("<TD>"); hPrintf("<A HREF=\"%s?%s=%u&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, RULER_TRACK_NAME); hPrintf("%s</A>", RULER_TRACK_LABEL); hPrintf("</TD>"); hPrintf("<TD>"); hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText"); hPrintf("</TD>"); hPrintf("<TD>"); hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)"); hPrintf("</TD>"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("<TD>"); hPrintf("</TD>"); hPrintf("<TD>"); hPrintf("</TD>"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TR>\n"); } /* 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("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none'"),group->name, rowCount++); hPrintf("<TD NOWRAP>"); 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("<A TITLE='%s%s...' HREF='%s?%s=%u&g=%s&hgTracksConfigPage=configure'>", 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("</A>"); hPrintf("</TD>"); hPrintf("<TD NOWRAP>"); 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("<A TITLE='Downloadable files...' HREF='%s?%s=%u&g=%s'>Downloads</A>", // 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) ? + rTdbTreeCanPack(track->tdb), (track->visibility == tvHide) ? "hiddenText" : "normalText", trackDbSetting(track->tdb, "onlyVisibility")); } } else hPrintf("[No data-%s]", chromName); hPrintf("</TD>"); hPrintf("<TD NOWRAP>"); hPrintf("%s", tdb->longLabel); hPrintf("</TD>"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI if (withPriorityOverride) { hPrintf("<TD>"); #ifdef DOWNLOADS_ONLY_TRACKS_INCLUDED if (tdbIsDownloadsOnly(tdb)) hPrintf(" </TD><TD>\n "); else #endif///def DOWNLOADS_ONLY_TRACKS_INCLUDED { safef(pname, sizeof(pname), "%s.priority",track->track); hDoubleVar(pname, (double)track->priority, 4); hPrintf("</TD>"); hPrintf("<TD>\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("</TD>"); } #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("</TR>\n"); } hPrintf("</TABLE>\n"); cgiDown(0.9); } } #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); if (trackHash == NULL) trackHash = makeGlobalTrackHash(trackList); parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated #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("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(), cartUsualString(cart, "formMethod", "POST")); webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); cartSaveSession(cart); hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">"); /* do not want all the submit buttons named the same thing, this one is: */ cgiMakeButton("topSubmit", "submit"); // 3 column table hPrintf("<TABLE style=\"border:0px; \">\n"); hPrintf("<TR><TD>image width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("pix", tl.picWidth, 4); hPrintf("<TD>pixels</TR>"); hPrintf("<TR><TD>label area width:"); hPrintf("<TD style=\"text-align: right\">"); hIntVar("hgt.labelWidth", leftLabelWidthChars, 2); hPrintf("<TD>characters<TD></TR>"); hPrintf("<TR><TD>text size:"); hPrintf("<TD style=\"text-align: right\">"); textSizeDropDown(); hPrintf("<TD>"); 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("<TR><BR>"); hTableStart(); if (ideoTrack != NULL) { hPrintf("<TR><TD>"); hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display chromosome ideogram above main graphic"); hPrintf("</TD></TR>\n"); } hPrintf("<TR><TD>"); hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show light blue vertical guidelines"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display labels to the left of items in tracks"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE)); hPrintf("</TD><TD>"); hPrintf("Display description above each track"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE)); hPrintf("</TD><TD>"); hPrintf("Show track controls under main graphic"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE)); hPrintf("</TD><TD>"); hPrintf("Next/previous item navigation"); hPrintf("</TD></TR>\n"); hPrintf("<TR><TD>"); hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE)); hPrintf("</TD><TD>"); hPrintf("Next/previous exon navigation"); hPrintf("</TD></TR>\n"); #ifdef PRIORITY_CHANGES_IN_CONFIG_UI hPrintf("<TR><TD>"); char *javascript="onClick=\"document.mainForm.hgTracksConfigPage.value='configure';document.mainForm.submit();\""; hCheckBoxJS(configPriorityOverride, cartUsualBoolean(cart, configPriorityOverride , FALSE), javascript); hPrintf("</TD><TD>"); hPrintf("Enable track re-ordering"); hPrintf("</TD></TR>\n"); #endif///def PRIORITY_CHANGES_IN_CONFIG_UI hTableEnd(); cgiDown(0.9); 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 vis.expandAllGroups(false)"); hPrintf(" "); hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return vis.expandAllGroups(true)"); hPrintf("<div style='margin-top:.2em; margin-bottom:.9em;'>Control track and group visibility more selectively below.</div>"); trackConfig(trackList, groupList, groupTarget, vis); dyStringFree(&title); freez(&groupTarget); webEndSectionTables(); hPrintf("</FORM>"); } void configPage() /* Put up configuration page. */ { configPageSetTrackVis(-2); }