c43463a089b13ab1ad705fc616f1e45c525fb9b9 angie Mon May 9 10:29:11 2011 -0700 Removing some old #ifndef code that has been unused for 6 months. diff --git src/hg/lib/hui.c src/hg/lib/hui.c index 9584bb8..7781368 100644 --- src/hg/lib/hui.c +++ src/hg/lib/hui.c @@ -39,31 +39,30 @@ //#define PM_BUTTON "<A NAME=\"%s\"></A><A HREF=\"#%s\"><IMG height=18 width=18 onclick=\"return (setCheckBoxesThatContain('%s',%s,true,'%s','','%s') == false);\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\"></A>\n" //#define DEF_BUTTON "<A NAME=\"%s\"></A><A HREF=\"#%s\"><IMG onclick=\"setCheckBoxesThatContain('%s',true,false,'%s','','%s'); return (setCheckBoxesThatContain('%s',false,false,'%s','_defOff','%s') == false);\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\"></A>\n" //#define DEFAULT_BUTTON(nameOrId,anc,beg,contains) printf(DEF_BUTTON,(anc),(anc),(nameOrId), (beg),(contains),(nameOrId),(beg),(contains),(anc),"defaults_sm.png","default") //#define PLUS_BUTTON(nameOrId,anc,beg,contains) printf(PM_BUTTON, (anc),(anc),(nameOrId),"true", (beg),(contains),(anc),"add_sm.gif", "+") //#define MINUS_BUTTON(nameOrId,anc,beg,contains) printf(PM_BUTTON, (anc),(anc),(nameOrId),"false",(beg),(contains),(anc),"remove_sm.gif","-") #define PM_BUTTON "<IMG height=18 width=18 onclick=\"setCheckBoxesThatContain('%s',%s,true,'%s','','%s');\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\">\n" #define DEF_BUTTON "<IMG onclick=\"setCheckBoxesThatContain('%s',true,false,'%s','','%s'); setCheckBoxesThatContain('%s',false,false,'%s','_defOff','%s');\" id=\"btn_%s\" src=\"../images/%s\" alt=\"%s\">\n" #define DEFAULT_BUTTON(nameOrId,anc,beg,contains) printf(DEF_BUTTON,(nameOrId), (beg),(contains),(nameOrId),(beg),(contains),(anc),"defaults_sm.png","default") #define PLUS_BUTTON(nameOrId,anc,beg,contains) printf(PM_BUTTON, (nameOrId),"true", (beg),(contains),(anc),"add_sm.gif", "+") #define MINUS_BUTTON(nameOrId,anc,beg,contains) printf(PM_BUTTON, (nameOrId),"false",(beg),(contains),(anc),"remove_sm.gif","-") #define ENCODE_DCC_DOWNLOADS "encodeDCC" //#define SUBTRACK_CFG_POPUP -#define BAM_CFG_UI_CHANGES struct trackDb *wgEncodeDownloadDirKeeper(char *db, struct trackDb *tdb, struct hash *trackHash) /* Look up through self and parents, looking for someone responsible for handling * where the downloads are. */ { if (!sameWord(tdb->type,"downloadsOnly") && !sameString(tdb->table, tdb->track) && trackHash) { tdb = hashFindVal(trackHash, tdb->table); if (tdb == NULL) errAbort("Can't find track for table %s in wgEncodeDownloadDirKeeper", tdb->table); } return trackDbTopLevelSelfOrParent(tdb); } static char *htmlStringForDownloadsLink(char *database, struct trackDb *tdb,char *name,boolean nameIsFile, @@ -1055,67 +1054,58 @@ /* draw the baseColor drop list options */ { enum baseColorDrawOpt curOpt = baseColorDrawOptEnabled(cart, tdb); char *curValue = baseColorDrawAllOptionValues[curOpt]; char var[512]; safef(var, sizeof(var), "%s." BASE_COLOR_VAR_SUFFIX, name); boolean gotCds = baseColorGotCds(tdb); boolean gotSeq = baseColorGotSequence(tdb); if (gotCds && gotSeq) { puts("<P><B>Color track by codons or bases:</B>"); cgiMakeDropListFull(var, baseColorDrawAllOptionLabels, baseColorDrawAllOptionValues, ArraySize(baseColorDrawAllOptionLabels), curValue, NULL); -#ifndef BAM_CFG_UI_CHANGES - printf("<BR>"); -#endif///ndef BAM_CFG_UI_CHANGES printf("<A HREF=\"%s\">Help on mRNA coloring</A><BR>", CDS_MRNA_HELP_PAGE); } else if (gotCds) { char buf[256]; char *disabled = NULL; safef(buf, sizeof(buf), "onchange='codonColoringChanged(\"%s\")'", name); puts("<P><B>Color track by codons:</B>"); cgiMakeDropListFull(var, baseColorDrawGenomicOptionLabels, baseColorDrawGenomicOptionValues, ArraySize(baseColorDrawGenomicOptionLabels), curValue, buf); -#ifndef BAM_CFG_UI_CHANGES - printf("<BR>"); -#endif///ndef BAM_CFG_UI_CHANGES printf("<A HREF=\"%s\">Help on codon coloring</A><BR>", CDS_HELP_PAGE); safef(buf, sizeof(buf), "%s.%s", name, CODON_NUMBERING_SUFFIX); puts("<br /><b>Show codon numbering</b>:\n"); if(curOpt == baseColorDrawOff) disabled = "disabled"; cgiMakeCheckBoxJS(buf, cartUsualBooleanClosestToHome(cart, tdb, FALSE, CODON_NUMBERING_SUFFIX, FALSE), disabled); } else if (gotSeq) { puts("<P><B>Color track by bases:</B>"); cgiMakeDropListFull(var, baseColorDrawItemOptionLabels, baseColorDrawItemOptionValues, ArraySize(baseColorDrawItemOptionLabels), curValue, NULL); -#ifndef BAM_CFG_UI_CHANGES - printf("<BR>"); -#endif///ndef BAM_CFG_UI_CHANGES printf("<A HREF=\"%s\">Help on base coloring</A><BR>", CDS_BASE_HELP_PAGE); } } void baseColorDrawOptDropDown(struct cart *cart, struct trackDb *tdb) /* Make appropriately labeled drop down of options if any are applicable.*/ { baseColorDropLists(cart, tdb, tdb->track); } enum baseColorDrawOpt baseColorDrawOptEnabled(struct cart *cart, struct trackDb *tdb) /* Query cart & trackDb to determine what drawing mode (if any) is enabled. */ { @@ -1187,80 +1177,52 @@ boolean *retPolyA) /* Query cart & trackDb to determine what indel display (if any) is enabled. Set * basesPerPixel to 0.0 to disable check for zoom level. */ { indelEnabledByName(cart,tdb,tdb->track,basesPerPixel,retDoubleInsert,retQueryInsert,retPolyA); } static void indelShowOptionsWithName(struct cart *cart, struct trackDb *tdb,char *name) /* Make HTML inputs for indel display options if any are applicable. */ { if (indelAppropriate(tdb)) { boolean showDoubleInsert, showQueryInsert, showPolyA; char var[512]; indelEnabledByName(cart, tdb, name, 0.0, &showDoubleInsert, &showQueryInsert, &showPolyA); -#ifdef BAM_CFG_UI_CHANGES printf("<TABLE><TR><TD colspan=2><B>Alignment Gap/Insertion Display Options</B>"); printf(" <A HREF=\"%s\">Help on display options</A>\n<TR valign='top'><TD>", INDEL_HELP_PAGE); safef(var, sizeof(var), "%s.%s", name, INDEL_DOUBLE_INSERT); cgiMakeCheckBox(var, showDoubleInsert); printf("</TD><TD>Draw double horizontal lines when both genome and query have " "an insertion</TD></TR>\n<TR valign='top'><TD>"); safef(var, sizeof(var), "%s.%s", name, INDEL_QUERY_INSERT); cgiMakeCheckBox(var, showQueryInsert); printf("</TD><TD>Draw a vertical purple line for an insertion at the beginning or " "end of the <BR>query, orange for insertion in the middle of the query</TD></TR>\n<TR valign='top'><TD>"); safef(var, sizeof(var), "%s.%s", name, INDEL_POLY_A); /* We can highlight valid polyA's only if we have query sequence -- * so indelPolyA code piggiebacks on baseColor code: */ if (baseColorGotSequence(tdb)) { cgiMakeCheckBox(var, showPolyA); printf("</TD><TD>Draw a vertical green line where query has a polyA tail " "insertion</TD></TR>\n"); } printf("</TABLE>\n"); -#else///ifndef BAM_CFG_UI_CHANGES - printf("<P><B>Alignment Gap/Insertion Display Options</B><BR>\n"); - safef(var, sizeof(var), "%s.%s", name, INDEL_DOUBLE_INSERT); - cgiMakeCheckBox(var, showDoubleInsert); - printf("Draw double horizontal lines when both genome and query have " - "an insertion " - "<BR>\n"); - safef(var, sizeof(var), "%s.%s", name, INDEL_QUERY_INSERT); - cgiMakeCheckBox(var, showQueryInsert); - printf("Draw a vertical purple line for an insertion at the beginning or " - "end of the query, orange for insertion in the middle of the query" - "<BR>\n"); - safef(var, sizeof(var), "%s.%s", name, INDEL_POLY_A); - /* We can highlight valid polyA's only if we have query sequence -- - * so indelPolyA code piggiebacks on baseColor code: */ - if (baseColorGotSequence(tdb)) - { - cgiMakeCheckBox(var, showPolyA); - printf("Draw a vertical green line where query has a polyA tail " - "insertion" - "<BR>\n"); - } - - printf("<A HREF=\"%s\">Help on alignment gap/insertion display options</A>" - "<BR>\n", - INDEL_HELP_PAGE); -#endif///ndef BAM_CFG_UI_CHANGES } } void indelShowOptions(struct cart *cart, struct trackDb *tdb) /* Make HTML inputs for indel display options if any are applicable. */ { indelShowOptionsWithName(cart, tdb, tdb->track); } /****** base position (ruler) controls *******/ static char *zoomOptions[] = { ZOOM_1PT5X, ZOOM_3X, ZOOM_10X, @@ -5844,89 +5806,65 @@ var inputs = document.getElementsByName('%s'); \ if (inputs) { \ for (var i=0; i < inputs.length; i++) { \ if (inputs[i].type == 'radio') { \ inputs[i].checked = (inputs[i].value == '%s'); \ } \ } \ }\"" void bamCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* BAM: short-read-oriented alignment file format. */ { boxed = cfgBeginBoxAndTitle(tdb, boxed, title); char cartVarName[1024]; -#ifdef BAM_CFG_UI_CHANGES printf("<TABLE%s><TR><TD>",boxed?" width='100%'":""); char *tdbShowNames = trackDbSetting(tdb, BAM_SHOW_NAMES); safef(cartVarName, sizeof(cartVarName), "%s.%s", name, BAM_SHOW_NAMES); cartMakeCheckBox(cart, cartVarName, !sameOk(tdbShowNames, "off")); printf("</TD><TD>Display read names</TD>"); if (boxed && fileExists(hHelpFile("hgBamTrackHelp"))) printf("<TD style='text-align:right'><A HREF=\"../goldenPath/help/hgBamTrackHelp.html\" TARGET=_BLANK>BAM " "configuration help</A></TD>"); printf("</TR>\n"); boolean canPair = (trackDbSetting(tdb, BAM_PAIR_ENDS_BY_NAME) != NULL); if (canPair) { printf("<TR><TD>"); safef(cartVarName, sizeof(cartVarName), "%s." BAM_PAIR_ENDS_BY_NAME, name); cartMakeCheckBox(cart, cartVarName, TRUE); printf("</TD><TD>Attempt to join paired end reads by name\n"); //puts("<BR>"); } printf("<TR><TD colspan=2>Minimum alignment quality:\n"); safef(cartVarName, sizeof(cartVarName), "%s." BAM_MIN_ALI_QUAL, name); cartMakeIntVar(cart, cartVarName, atoi(trackDbSettingOrDefault(tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT)), 4); printf("</TD></TR></TABLE>"); -#else///nef BAM_CFG_UI_CHANGES -puts("<BR>"); -printf("<B>Display read names:</B>\n"); -char *tdbShowNames = trackDbSetting(tdb, BAM_SHOW_NAMES); -safef(cartVarName, sizeof(cartVarName), "%s.%s", name, BAM_SHOW_NAMES); -cartMakeCheckBox(cart, cartVarName, !sameOk(tdbShowNames, "off")); -boolean canPair = (trackDbSetting(tdb, BAM_PAIR_ENDS_BY_NAME) != NULL); -puts("<BR>"); -if (canPair) - { - printf("<B>Attempt to join paired end reads by name:</B>\n"); - safef(cartVarName, sizeof(cartVarName), "%s." BAM_PAIR_ENDS_BY_NAME, name); - cartMakeCheckBox(cart, cartVarName, TRUE); - puts("<BR>"); - } -printf("<B>Minimum alignment quality:</B>\n"); -safef(cartVarName, sizeof(cartVarName), "%s." BAM_MIN_ALI_QUAL, name); -cartMakeIntVar(cart, cartVarName, - atoi(trackDbSettingOrDefault(tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT)), 4); -puts("<BR>"); -#endif///ndef BAM_CFG_UI_CHANGES if (isCustomTrack(name)) { // Auto-magic baseColor defaults for BAM, same as in hgTracks.c newCustomTrack hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra")); hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases")); hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString(".")); hashAdd(tdb->settingsHash, "showDiffBasesMaxZoom", cloneString("100")); } baseColorDropLists(cart, tdb, name); -#ifdef BAM_CFG_UI_CHANGES puts("<BR>"); -#endif///def BAM_CFG_UI_CHANGES indelShowOptionsWithName(cart, tdb, name); printf("<BR>\n"); printf("<B>Additional coloring modes:</B><BR>\n"); safef(cartVarName, sizeof(cartVarName), "%s." BAM_COLOR_MODE, name); char *selected = cartUsualString(cart, cartVarName, trackDbSettingOrDefault(tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT)); cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_STRAND, sameString(selected, BAM_COLOR_MODE_STRAND)); printf("Color by strand (blue for +, red for -)<BR>\n"); cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_GRAY, sameString(selected, BAM_COLOR_MODE_GRAY)); printf("Use gray for\n"); char cartVarName2[1024]; safef(cartVarName2, sizeof(cartVarName2), "%s." BAM_GRAY_MODE, name); int grayMenuSize = canPair ? ArraySize(grayLabels) : ArraySize(grayLabels)-1; char *sel2 = cartUsualString(cart, cartVarName2, trackDbSettingOrDefault(tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT)); @@ -5937,41 +5875,34 @@ printf("<BR>\n"); if (trackDbSetting(tdb, "noColorTag") == NULL) { cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_TAG, sameString(selected, BAM_COLOR_MODE_TAG)); printf("Use R,G,B colors specified in user-defined tag "); safef(cartVarName2, sizeof(cartVarName2), "%s." BAM_COLOR_TAG, name); sel2 = cartUsualString(cart, cartVarName2, trackDbSettingOrDefault(tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT)); safef(onChange, sizeof(onChange), UPDATE_RADIO_FORMAT, "onkeypress", cartVarName, BAM_COLOR_MODE_TAG); cgiMakeTextVarWithExtraHtml(cartVarName2, sel2, 30, onChange); printf("<BR>\n"); } cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_OFF, sameString(selected, BAM_COLOR_MODE_OFF)); printf("No additional coloring"); -#ifndef BAM_CFG_UI_CHANGES -printf("<BR>\n"); -#endif///ndef BAM_CFG_UI_CHANGES //TODO: include / exclude flags -#ifdef BAM_CFG_UI_CHANGES if (!boxed && fileExists(hHelpFile("hgBamTrackHelp"))) -#else///ifndef BAM_CFG_UI_CHANGES -if (fileExists(hHelpFile("hgBamTrackHelp"))) -#endif///ndef BAM_CFG_UI_CHANGES printf("<P><A HREF=\"../goldenPath/help/hgBamTrackHelp.html\" TARGET=_BLANK>BAM " "configuration help</A></P>"); cfgEndBox(boxed); } #endif//def USE_BAM struct trackDb *rFindViewInList(struct trackDb *tdbList, char *view) /* Return the trackDb on the list (or on any children of the list) that has matching view tag. */ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { char *viewSetting = trackDbSetting(tdb, "view"); if (sameOk(viewSetting, view))