![\"%s\"](\"../images/%s\"){kind=small}
\n"
//#define DEF_BUTTON "\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 "\n"
#define DEF_BUTTON "\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
+#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 (!sameString(tdb->table, tdb->track))
{
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,
@@ -119,65 +119,113 @@
if (hTableOrSplitExists(db, tdb->table))
{
char *tbOff = trackDbSetting(tdb, "tableBrowser");
if (isNotEmpty(tbOff) && sameString(nextWord(&tbOff), "off"))
return FALSE;
char *hint = " title='Open table schema in new window'";
if( label == NULL)
label = " View table schema";
struct trackDb *topLevel = trackDbTopLevelSelfOrParent(tdb);
printf(SCHEMA_LINKED, db, topLevel->grp, topLevel->track, tdb->table, hint, label);
return TRUE;
}
return FALSE;
}
+char *controlledVocabLink(char *file,char *term,char *value,char *title, char *label,char *suffix)
+// returns allocated string of HTML link to controlled vocabulary term
+{
+#define VOCAB_LINK "%s"
+char *encFile = cgiEncode(file);
+char *encTerm = cgiEncode(term);
+char *encValue = cgiEncode(value);
+struct dyString *dyLink = dyStringCreate(VOCAB_LINK,encFile,encTerm,encValue,title,label);
+if (suffix != NULL)
+ dyStringAppend(dyLink,suffix); // Don't encode since this may contain HTML
+
+freeMem(encFile);
+freeMem(encTerm);
+freeMem(encValue);
+return dyStringCannibalize(&dyLink);
+}
+
char *metadataAsHtmlTable(char *db,struct trackDb *tdb,boolean showLongLabel,boolean showShortLabel, struct hash *trackHash)
/* If metadata from metaDb exists, return string of html with table definition */
{
const struct mdbObj *safeObj = metadataForTable(db,tdb,NULL);
if (safeObj == NULL || safeObj->vars == NULL)
return NULL;
//struct dyString *dyTable = dyStringCreate("| %s | |
| shortLabel: | %s |
| %s: | ",mdbVar->var); dyStringAppend(dyTable,htmlStringForDownloadsLink(db, tdb, mdbVar->val, TRUE, trackHash)); dyStringAppend(dyTable," |
| %s: | %s |
| %s: | %s |
Color track by codons or bases:");
cgiMakeDropListFull(var, baseColorDrawAllOptionLabels,
baseColorDrawAllOptionValues,
ArraySize(baseColorDrawAllOptionLabels),
curValue, NULL);
#ifndef BAM_CFG_UI_CHANGES
printf("
");
#endif///ndef BAM_CFG_UI_CHANGES
printf("Help on mRNA coloring
",
CDS_MRNA_HELP_PAGE);
}
@@ -997,162 +1045,176 @@
cgiMakeDropListFull(var, baseColorDrawItemOptionLabels,
baseColorDrawItemOptionValues,
ArraySize(baseColorDrawItemOptionLabels),
curValue, NULL);
#ifndef BAM_CFG_UI_CHANGES
printf("
");
#endif///ndef BAM_CFG_UI_CHANGES
printf("Help on base coloring
",
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);
+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. */
{
char *stringVal = NULL;
assert(cart);
assert(tdb);
/* trackDb can override default of OFF; cart can override trackDb. */
stringVal = trackDbSettingClosestToHomeOrDefault(tdb, BASE_COLOR_DEFAULT,
BASE_COLOR_DRAW_OFF);
stringVal = cartUsualStringClosestToHome(cart, tdb, FALSE, BASE_COLOR_VAR_SUFFIX,stringVal);
return baseColorDrawOptStringToEnum(stringVal);
}
/*** Control of fancy indel display code: ***/
+static boolean tdbOrCartBoolean(struct cart *cart, struct trackDb *tdb,
+ char *settingName, char *defaultOnOff)
+/* Query cart & trackDb to determine if a boolean variable is set. */
+{
+boolean alreadySet;
+alreadySet = !sameString("off",trackDbSettingOrDefault(tdb, settingName, defaultOnOff));
+alreadySet = cartUsualBooleanClosestToHome(cart, tdb, FALSE, settingName, alreadySet); // NOTE: compositeLevel=FALSE because tdb param already is at appropriate level
+return alreadySet;
+}
+
static boolean indelAppropriate(struct trackDb *tdb)
/* Return true if it makes sense to offer indel display options for tdb. */
{
return (tdb && (startsWith("psl", tdb->type) || sameString("bam", tdb->type)) &&
(cfgOptionDefault("browser.indelOptions", NULL) != NULL));
}
-void indelShowOptions(struct cart *cart, struct trackDb *tdb)
+static void indelEnabledByName(struct cart *cart, struct trackDb *tdb, char *name,
+ float basesPerPixel, boolean *retDoubleInsert, boolean *retQueryInsert,
+ 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. */
+{
+struct trackDb *tdbLevel = tdb;
+if (differentString(tdb->track, name) && tdb->parent != NULL)
+ tdbLevel = tdb->parent;
+
+boolean apropos = indelAppropriate(tdb);
+if (apropos && (basesPerPixel > 0.0))
+ {
+ // check indel max zoom
+ float showIndelMaxZoom = trackDbFloatSettingOrDefault(tdbLevel, "showIndelMaxZoom", -1.0);
+ if ((showIndelMaxZoom >= 0)
+ && ((basesPerPixel > showIndelMaxZoom) || (showIndelMaxZoom == 0.0)))
+ apropos = FALSE;
+ }
+
+if (retDoubleInsert)
+ *retDoubleInsert = apropos &&
+ tdbOrCartBoolean(cart, tdbLevel, INDEL_DOUBLE_INSERT, "off");
+if (retQueryInsert)
+ *retQueryInsert = apropos &&
+ tdbOrCartBoolean(cart, tdbLevel, INDEL_QUERY_INSERT, "off");
+if (retPolyA)
+ *retPolyA = apropos &&
+ tdbOrCartBoolean(cart, tdbLevel, INDEL_POLY_A, "off");
+}
+
+void indelEnabled(struct cart *cart, struct trackDb *tdb, float basesPerPixel,
+ boolean *retDoubleInsert, boolean *retQueryInsert,
+ 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];
- indelEnabled(cart, tdb, 0.0, &showDoubleInsert, &showQueryInsert, &showPolyA);
+ indelEnabledByName(cart, tdb, name, 0.0, &showDoubleInsert, &showQueryInsert, &showPolyA);
#ifdef BAM_CFG_UI_CHANGES
printf("
| Alignment Gap/Insertion Display Options"); printf(" Help on display options\n | |
| ", INDEL_HELP_PAGE); - safef(var, sizeof(var), "%s_%s", INDEL_DOUBLE_INSERT, tdb->track); + safef(var, sizeof(var), "%s_%s", INDEL_DOUBLE_INSERT, name); cgiMakeCheckBox(var, showDoubleInsert); printf(" | Draw double horizontal lines when both genome and query have " "an insertion |
| "); - safef(var, sizeof(var), "%s_%s", INDEL_QUERY_INSERT, tdb->track); + safef(var, sizeof(var), "%s_%s", INDEL_QUERY_INSERT, name); 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 |
| "); - safef(var, sizeof(var), "%s_%s", INDEL_POLY_A, tdb->track); + safef(var, sizeof(var), "%s_%s", INDEL_POLY_A, name); /* 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 |
Alignment Gap/Insertion Display Options
\n");
- safef(var, sizeof(var), "%s_%s", INDEL_DOUBLE_INSERT, tdb->track);
+ safef(var, sizeof(var), "%s_%s", INDEL_DOUBLE_INSERT, name);
cgiMakeCheckBox(var, showDoubleInsert);
printf("Draw double horizontal lines when both genome and query have "
"an insertion "
"
\n");
- safef(var, sizeof(var), "%s_%s", INDEL_QUERY_INSERT, tdb->track);
+ safef(var, sizeof(var), "%s_%s", INDEL_QUERY_INSERT, name);
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"
"
\n");
- safef(var, sizeof(var), "%s_%s", INDEL_POLY_A, tdb->track);
+ safef(var, sizeof(var), "%s_%s", INDEL_POLY_A, name);
/* 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"
"
\n");
}
printf("Help on alignment gap/insertion display options"
"
\n",
INDEL_HELP_PAGE);
#endif///ndef BAM_CFG_UI_CHANGES
}
}
-static boolean tdbOrCartBoolean(struct cart *cart, struct trackDb *tdb,
- char *settingName, char *defaultOnOff)
-/* Query cart & trackDb to determine if a boolean variable is set. */
-{
-boolean alreadySet;
-char optionStr[512];
-alreadySet = !sameString("off",
- trackDbSettingOrDefault(tdb, settingName, defaultOnOff));
-safef(optionStr, sizeof(optionStr), "%s_%s",
- settingName, tdb->track);
-alreadySet = cartUsualBoolean(cart, optionStr, alreadySet);
-return alreadySet;
-}
-
-void indelEnabled(struct cart *cart, struct trackDb *tdb, float basesPerPixel,
- boolean *retDoubleInsert, boolean *retQueryInsert,
- 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. */
-{
-boolean apropos = indelAppropriate(tdb);
-if (apropos && (basesPerPixel > 0.0))
+void indelShowOptions(struct cart *cart, struct trackDb *tdb)
+/* Make HTML inputs for indel display options if any are applicable. */
{
- // check indel max zoom
- float showIndelMaxZoom = trackDbFloatSettingOrDefault(tdb, "showIndelMaxZoom", -1.0);
- if ((showIndelMaxZoom >= 0)
- && ((basesPerPixel > showIndelMaxZoom) || (showIndelMaxZoom == 0.0)))
- apropos = FALSE;
- }
-
-if (retDoubleInsert)
- *retDoubleInsert = apropos &&
- tdbOrCartBoolean(cart, tdb, INDEL_DOUBLE_INSERT, "off");
-if (retQueryInsert)
- *retQueryInsert = apropos &&
- tdbOrCartBoolean(cart, tdb, INDEL_QUERY_INSERT, "off");
-if (retPolyA)
- *retPolyA = apropos &&
- tdbOrCartBoolean(cart, tdb, INDEL_POLY_A, "off");
+indelShowOptionsWithName(cart, tdb, tdb->track);
}
-
/****** base position (ruler) controls *******/
static char *zoomOptions[] = {
ZOOM_1PT5X,
ZOOM_3X,
ZOOM_10X,
ZOOM_BASE
};
void zoomRadioButtons(char *var, char *curVal)
/* Make a list of radio buttons for all zoom options */
{
int i;
int size = ArraySize(zoomOptions);
for (i = 0; i < size; i++)
@@ -4537,36 +4599,36 @@
cgiMakeCheckBox(option, doScoreCtFilter);
safef(option, sizeof(option), "%s.filterTopScorersCt", name);
scoreFilterCt = cartUsualStringClosestToHome(cart, tdb, compositeLevel, "filterTopScorersCt", words[1]);
puts(" Show only items in top-scoring ");
cgiMakeIntVarWithLimits(option,atoi(scoreFilterCt),"Top-scoring count",0,1,100000);
/* Only check size of table if track does not have subtracks */
if ( !compositeLevel && hTableExists(db, tdb->table))
printf(" (range: 1 to 100,000 total items: %d)\n",getTableSize(db, tdb->table));
else
printf(" (range: 1 to 100,000)\n");
}
cfgEndBox(boxed);
}
-void pslCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed)
+void pslCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
/* Put up UI for psl tracks */
{
boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
-baseColorDropLists(cart, tdb);
-indelShowOptions(cart, tdb);
+baseColorDropLists(cart, tdb, name);
+indelShowOptionsWithName(cart, tdb, name);
cfgEndBox(boxed);
}
void netAlignCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *prefix, char *title, boolean boxed)
/* Put up UI for net tracks */
{
boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
boolean compositeLevel = isNameAtCompositeLevel(tdb,prefix);
enum netColorEnum netColor = netFetchColorOption(cart, tdb, compositeLevel);
char optString[256]; /* our option strings here */
safef(optString, ArraySize(optString), "%s.%s", prefix, NET_COLOR );
@@ -4942,31 +5004,31 @@
printf("%s ", "none");
}
if(trackDbSettingClosestToHomeOn(tdb, "nmdFilter"))
{
boolean nmdDefault = FALSE;
safef(varName, sizeof(varName), "hgt.%s.nmdFilter", name);
nmdDefault = cartUsualBoolean(cart,varName, FALSE); // TODO: var name (hgt prefix) needs changing before ClosesToHome can be used
printf("
Filter out NMD targets.");
cgiMakeCheckBox(varName, nmdDefault);
}
if(!sameString(tdb->track, "tigrGeneIndex")
&& !sameString(tdb->track, "ensGeneNonCoding")
&& !sameString(tdb->track, "encodeGencodeRaceFrags"))
- baseColorDrawOptDropDown(cart, tdb);
+ baseColorDropLists(cart, tdb, name);
filterBy_t *filterBySet = filterBySetGet(tdb,cart,name);
if(filterBySet != NULL)
{
filterBySetCfgUi(tdb,filterBySet);
filterBySetFree(&filterBySet);
}
cfgEndBox(boxed);
}
static boolean isSpeciesOn(struct cart *cart, struct trackDb *tdb, char *species, char *option, int optionSize, boolean defaultState)
/* check the cart to see if species is turned off or on (default is defaultState) */
{
boolean ret = defaultState;
safef(option, optionSize, "%s.%s", tdb->track, species);
@@ -5497,35 +5559,35 @@
printf("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);
puts("
");
#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"));
}
-baseColorDrawOptDropDown(cart, tdb);
+baseColorDropLists(cart, tdb, name);
#ifdef BAM_CFG_UI_CHANGES
puts("
");
#endif///def BAM_CFG_UI_CHANGES
-indelShowOptions(cart, tdb);
+indelShowOptionsWithName(cart, tdb, name);
printf("
\n");
printf("Additional coloring modes:
\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 -)
\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));
char onChange[2048];
@@ -5746,58 +5808,45 @@
(void)metadataForTable(db,childTdb,NULL);
if(vocab == NULL)
return cloneString(label); // No wrapping!
char *words[15];
int count,ix;
boolean found=FALSE;
if((count = chopByWhite(cloneString(vocab), words,15)) <= 1)
return cloneString(label);
char *suffix=NULL;
char *rootLabel = labelRoot(label,&suffix);
for(ix=1;ix