48de4e2ccfe829cfea8c38d9f1034aa217b04cf1 max Mon Jul 20 10:57:49 2020 -0700 Revert "fixing PDF output for new highlight cart variable format, also fixes a related problem that just came up on the ML, refs #25887" This reverts commit fb06bed25a9f45eaef8a875f3efbd45cfc14e804. diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c index afa6da8..7d44b40 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -2132,84 +2132,56 @@ } struct highlightVar // store highlight information { struct highlightVar *next; char *db; char *chrom; long chromStart; long chromEnd; char *hexColor; }; struct highlightVar *parseHighlightInfo() // Parse highlight info from cart var to a linked list of highlightVar structs -// Accepts three input formats for the highlight variable: -// 1) db.chrom:start-end (format in very old carts) -// 2) db.chrom:start-end#hexColor|db.chrom:start-end#hexColor|... (old format) -// 3) db#chrom#start#end#hexColor|db#chrom#start#end#hexColor|... (current format, to allow . in seq names) -// +// db.chrom:start-end#hexColor|db.chrom:start-end#hexColor|... { struct highlightVar *hlList = NULL; char *highlightDef = cartOptionalString(cart, "highlight"); if(highlightDef) { char *hlArr[256]; int hlCount = chopByChar(cloneString(highlightDef), '|', hlArr, ArraySize(hlArr)); int i; for (i=0; i<hlCount; i++) { char *oneHl = hlArr[i]; struct highlightVar *h; - char *chromStart, *chromEnd; AllocVar(h); - if (countSeparatedItems(oneHl, '#')==5) - // the new format: db#chrom#start#end#color - { - h->db = cloneNextWordByDelimiter(&oneHl,'#'); - h->chrom = cloneNextWordByDelimiter(&oneHl,'#'); - chromStart = cloneNextWordByDelimiter(&oneHl,'#'); - chromEnd = cloneNextWordByDelimiter(&oneHl,'#'); - h->hexColor = cloneString(oneHl); - } - else // the syntax only used in old saved sessions - // the old format: db.chr:start-end followed optionally by #color - { h->db = cloneNextWordByDelimiter(&oneHl,'.'); h->chrom = cloneNextWordByDelimiter(&oneHl,':'); - chromStart = cloneNextWordByDelimiter(&oneHl,'-'); - chromEnd = cloneNextWordByDelimiter(&oneHl,'#'); - if (oneHl && *oneHl != '\0') - h->hexColor = cloneString(oneHl); - } - - if (!isEmpty(chromStart) && !isEmpty(chromEnd) && - isNumericString(chromStart) && isNumericString(chromEnd) && - !isEmpty(h->db) && !isEmpty(h->chrom)) - { // long to handle virt chrom coordinates - h->chromStart = atol(chromStart); - h->chromEnd = atol(chromEnd); + h->chromStart = atol(cloneNextWordByDelimiter(&oneHl,'-')); + h->chromEnd = atol(cloneNextWordByDelimiter(&oneHl,'#')); h->chromStart--; // Not zero based + if (highlightDef && *highlightDef != '\0') + h->hexColor = cloneString(oneHl); slAddHead(&hlList, h); } - } - slReverse(&hlList); } - return hlList; } static void highlightRegions(struct cart *cart, struct hvGfx *hvg, int imagePixelHeight) // Highlights regions in the image. Only done if theImgBox is not defined. // Thus it is done for ps/pdf and view image but the hgTracks image is highlighted via js { struct highlightVar *hlList = parseHighlightInfo(); if(hlList && theImgBox == NULL) // Only highlight region when imgBox is not used. (pdf and show-image) { struct highlightVar *h; for (h=hlList; h; h=h->next) { if (virtualSingleChrom()) // DISGUISE VMODE @@ -8503,38 +8475,36 @@ * go along with this trick */ hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1 WIDTH=%d COLS=%d><TR>\n", tl.picWidth, 27); #ifndef USE_NAVIGATION_LINKS hPrintf("<TD COLSPAN=6 ALIGN=left NOWRAP>"); hPrintf("move start<BR>"); hButtonWithOnClick("hgt.dinkLL", " < ", "move start position to the left", "return imageV2.navigateButtonClick(this);"); hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3); hButtonWithOnClick("hgt.dinkLR", " > ", "move start position to the right", "return imageV2.navigateButtonClick(this);"); hPrintf("</TD>"); hPrintf("<td width='30'> </td>\n"); #endif//ndef USE_NAVIGATION_LINKS hPrintf("<TD class='infoText' COLSPAN=15 style=\"white-space:normal\">"); // allow this text to wrap - //hWrites("Click on a feature for details. "); - //hWrites("Click or drag in the base position track to zoom in. "); - //hWrites("Click side bars for track options. "); - //hWrites("Drag side bars or labels up or down to reorder tracks. "); - //hWrites("Drag tracks left or right to new position. "); - //hWrites("Press \"?\" for keyboard shortcuts. "); - hWrites("Unsure how to use the Genome Browser? "); - hWrites("Have a look at our <a href='../goldenPath/help/hgTracksHelp.html#FineTuning'>Tutorial</a>"); + hWrites("Click on a feature for details. "); + hWrites("Click or drag in the base position track to zoom in. "); + hWrites("Click side bars for track options. "); + hWrites("Drag side bars or labels up or down to reorder tracks. "); + hWrites("Drag tracks left or right to new position. "); + hWrites("Press \"?\" for keyboard shortcuts. "); hPrintf("</TD>"); #ifndef USE_NAVIGATION_LINKS hPrintf("<td width='30'> </td>\n"); hPrintf("<TD COLSPAN=6 ALIGN=right NOWRAP>"); hPrintf("move end<BR>"); hButtonWithOnClick("hgt.dinkRL", " < ", "move end position to the left", "return imageV2.navigateButtonClick(this);"); hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3); hButtonWithOnClick("hgt.dinkRR", " > ", "move end position to the right", "return imageV2.navigateButtonClick(this);"); hPrintf("</TD>"); #endif//ndef USE_NAVIGATION_LINKS hPrintf("</TR></TABLE>\n"); /* Display bottom control panel. */ @@ -8614,33 +8584,33 @@ if (showTrackControls) { /* Display viewing options for each track. */ /* Chuck: This is going to be wrapped in a table so that * the controls don't wrap around randomly */ hPrintf("<table border=0 cellspacing=1 cellpadding=1 width=%d>\n", CONTROL_TABLE_WIDTH); hPrintf("<tr><td align='left'>\n"); hButtonWithOnClick("hgt.collapseGroups", "collapse all", "collapse all track groups", "return vis.expandAllGroups(false)"); hPrintf("</td>"); hPrintf("<td colspan='%d' class='infoText' align='CENTER' nowrap>" "Use drop-down controls below and press refresh to alter tracks " - "displayed.<BR>", MAX_CONTROL_COLUMNS -2 ); - //"Tracks with lots of items will automatically be displayed in " - //"more compact modes.</td>\n", MAX_CONTROL_COLUMNS - 2); + "displayed.<BR>" + "Tracks with lots of items will automatically be displayed in " + "more compact modes.</td>\n", MAX_CONTROL_COLUMNS - 2); hPrintf("<td align='right'>"); hButtonWithOnClick("hgt.expandGroups", "expand all", "expand all track groups", "return vis.expandAllGroups(true)"); hPrintf("</td></tr>"); cg = startControlGrid(MAX_CONTROL_COLUMNS, "left"); for (group = groupList; group != NULL; group = group->next) { if (group->trackList == NULL) continue; struct trackRef *tr; /* check if group section should be displayed */