ff6ca2d3f51184034c9430ce91dd15773d2d661e tdreszer Wed Oct 5 09:20:07 2011 -0700 More screw tightening. Encode peaks are not configurable unless there are additional trackDb settings that say so. diff --git src/hg/lib/hui.c src/hg/lib/hui.c index defb9b3..942e1b4 100644 --- src/hg/lib/hui.c +++ src/hg/lib/hui.c @@ -4003,45 +4003,56 @@ puts("<TBODY>"); } // Finally the big "for loop" to list each subtrack as a table row. printf("\n<!-- ----- subtracks list ----- -->\n"); for (subtrackRef = subtrackRefList; subtrackRef != NULL; subtrackRef = subtrackRef->next) { subtrack = subtrackRef->val; int ix; // Determine whether subtrack is checked, visible, configurable, has group membership, etc. int fourState = subtrackFourStateChecked(subtrack,cart); boolean checkedCB = fourStateChecked(fourState); boolean enabledCB = fourStateEnabled(fourState); boolean visibleCB = fourStateVisible(fourState); + membership_t *membership = subgroupMembershipGet(subtrack); eCfgType cType = cfgTypeFromTdb(subtrack,FALSE); if (cType != cfgNone) { #ifdef SUBTRACK_CFG // Turn off configuring for certain track type or if explicitly turned off if (regexMatch(subtrack->track, "^snp[0-9]+") // Special cases to be removed || regexMatch(subtrack->track, "^cons[0-9]+way") // (matches logic in json setup in imageV2.c) || regexMatch(subtrack->track, "^multiz") || SETTING_IS_OFF(trackDbSettingClosestToHome(subtrack, "configureByPopup"))) + cType = cfgNone; + else if (membersForAll->members[dimV]) + { + if (-1 != (ix = stringArrayIx(membersForAll->members[dimV]->groupTag, membership->subgroups, membership->count))) + { // Don't make a configurable subtrack if there is only one in the view (assumes view is configurable) + if (slCount(membersForAll->members[dimV]->subtrackList[ix]) < 2) + cType = cfgNone; + } + } + else if (slCount(parentTdb->subtracks) < 2 && cfgTypeFromTdb(parentTdb,FALSE) != cfgNone) + cType = cfgNone; // don't bother if there is a single subtrack but the composite is configurable. #else///ifndef SUBTRACK_CFG if (trackDbSettingClosestToHomeOn(subtrack, "configurable") == FALSE) - #endif///ndef SUBTRACK_CFG cType = cfgNone; + #endif///ndef SUBTRACK_CFG } - membership_t *membership = subgroupMembershipGet(subtrack); if (sortOrder == NULL && !useDragAndDrop) { if ( divisionIfNeeded(lastDivide,dividers,membership) ) colorIx = (colorIx == COLOR_BG_DEFAULT_IX ? COLOR_BG_ALTDEFAULT_IX : COLOR_BG_DEFAULT_IX); } // Start the TR which must have an id that is directly related to the checkBox id char *id = checkBoxIdMakeForTrack(subtrack,membersForAll->members,membersForAll->dimMax,membership); // view is known tag printf("<TR valign='top' class='%s%s'",colors[colorIx],(useDragAndDrop?" trDraggable":"")); printf(" id=tr_%s%s>\n",id,(!visibleCB && !displayAll?" style='display:none'":"")); // Now the TD that holds the checkbox printf("<TD%s%s>", @@ -4801,49 +4812,48 @@ printf("<TD align='left'%s> (%d to %d)",altLabel,minLimit, maxLimit); else if(minLimit != NO_VALUE) printf("<TD align='left'%s> (minimum %d)",altLabel,minLimit); else if(maxLimit != NO_VALUE) printf("<TD align='left'%s> (maximum %d)",altLabel,maxLimit); else printf("<TD align='left'%s",altLabel); } puts("</TR>"); return TRUE; } return FALSE; } -#ifdef ALL_SCORE_FILTERS_LOGIC static int numericFiltersShowAll(struct cart *cart, struct trackDb *tdb, boolean *opened, boolean boxed, boolean compositeLevel,char *name, char *title) // Shows all *Filter style filters. Note that these are in random order and have no graceful title { int count = 0; struct slName *filterSettings = trackDbSettingsWildMatch(tdb, "*Filter"); if (filterSettings) { puts("<BR>"); struct slName *filter = NULL; struct slPair *extras = NULL; char *extraFields = trackDbSetting(tdb, "extraFields"); // TODo: seems like there should be a cleaner way if (extraFields != NULL) extras = slPairListFromString(extraFields,TRUE); // Quoted strings may be okay while ((filter = slPopHead(&filterSettings)) != NULL) { - if (differentString(filter->name,"noScoreFilter") && differentString(filter->name,"scoreFilter")) // TODO: scoreFilter could be included + if (differentString(filter->name,NO_SCORE_FILTER) && differentString(filter->name,SCORE_FILTER)) // TODO: scoreFilter could be included { char *field = cloneString(filter->name); int ix = strlen(field) - strlen("Filter"); assert(ix > 0); field[ix] = '\0'; // Could lookup extraFields // TODO: Should we be using extra fields? Could this be sorted by the order in extraFields? if (extras != NULL) { char *foundLabel = slPairFindVal(extras, field); if (foundLabel != NULL) { // Found label so replace field freeMem(field); field = strchr(foundLabel,']'); if (field == NULL) field = cloneString(foundLabel); @@ -4856,69 +4866,64 @@ safef(label,sizeof(label),"Minimum %s",field); freeMem(field); // Determine floating point or integer char *setting = trackDbSetting(tdb, filter->name); boolean isFloat = (strchr(setting,'.') != NULL); showScoreFilter(cart,tdb,opened,boxed,compositeLevel,name,title,label,filter->name,isFloat); count++; } slNameFree(&filter); } } if (count > 0) puts("</TABLE>"); return count; } -#endif///def ALL_SCORE_FILTERS_LOGIC void scoreCfgUi(char *db, struct cart *cart, struct trackDb *tdb, char *name, char *title, int maxScore, boolean boxed) /* Put up UI for filtering bed track based on a score */ { char option[256]; boolean compositeLevel = isNameAtCompositeLevel(tdb,name); boolean skipScoreFilter = FALSE; filterBy_t *filterBySet = filterBySetGet(tdb,cart,name); -#ifdef ALL_SCORE_FILTERS_LOGIC // Numeric filters are first boolean isBoxOpened = FALSE; if (numericFiltersShowAll(cart, tdb, &isBoxOpened, boxed, compositeLevel, name, title) > 0) skipScoreFilter = TRUE; -#endif///def ALL_SCORE_FILTERS_LOGIC // Add any multi-selects next if(filterBySet != NULL) { if(!tdbIsComposite(tdb) && cartOptionalString(cart, "ajax") == NULL) jsIncludeFile("hui.js",NULL); if (!isBoxOpened) // Note filterBy boxes are not double "boxed", if there are no other filters printf("<BR>"); filterBySetCfgUi(cart,tdb,filterBySet,TRUE); filterBySetFree(&filterBySet); skipScoreFilter = TRUE; } // For no good reason scoreFilter is incompatible with filterBy and or numericFilters // FIXME scoreFilter should be implemented inside numericFilters and is currently specificly excluded to avoid unexpected changes if (skipScoreFilter) { - #ifdef ALL_SCORE_FILTERS_LOGIC if (isBoxOpened) cfgEndBox(boxed); - #endif///def ALL_SCORE_FILTERS_LOGIC return; // Cannot have both '*filter' and 'scoreFilter' } boolean scoreFilterOk = (trackDbSettingClosestToHome(tdb, NO_SCORE_FILTER) == NULL); boolean glvlScoreMin = (trackDbSettingClosestToHome(tdb, GRAY_LEVEL_SCORE_MIN) != NULL); if (! (scoreFilterOk || glvlScoreMin)) return; boxed = cfgBeginBoxAndTitle(tdb, boxed, title); if (scoreFilterOk) { int minLimit=0,maxLimit=maxScore,minVal=0,maxVal=maxScore; getScoreIntRangeFromCart(cart,tdb,SCORE_FILTER,&minLimit,&maxLimit,&minVal,&maxVal); @@ -5262,31 +5267,30 @@ { if((int)max == NO_VALUE || ((int)maxLimit != NO_VALUE && maxLimit == max)) dyStringPrintf(extraWhere, "%s(%s >= %g)", (*and?" and ":""),field,min); // min only else if((int)min == NO_VALUE || ((int)minLimit != NO_VALUE && minLimit == min)) dyStringPrintf(extraWhere, "%s(%s <= %g)", (*and?" and ":""),field,max); // max only else dyStringPrintf(extraWhere, "%s(%s BETWEEN %g and %g)", (*and?" and ":""),field,min,max); // both min and max #endif//ndef FILTER_ASSUMES_RANGE_AT_LIMITS_IS_VALID_FILTER *and=TRUE; } } //if(dyStringLen(extraWhere)) warn("SELECT FROM %s WHERE %s",tdb->table,dyStringContents(extraWhere)); return extraWhere; } -#ifdef ALL_SCORE_FILTERS_LOGIC struct dyString *dyAddAllScoreFilters(struct cart *cart, struct trackDb *tdb, struct dyString *extraWhere,boolean *and) /* creates the where clause condition to gather together all random double filters Filters are expected to follow {fiterName}: trackDb min or min:max - default value(s); {filterName}Min or {filterName}: min (user supplied) cart variable; {filterName}Max: max (user supplied) cart variable; {filterName}Limits: trackDb allowed range "0.0:10.0" Optional uses: defaultLimits: function param if no tdb limits settings found) The 'and' param and dyString in/out allows stringing multiple where clauses together */ { struct slName *filterSettings = trackDbSettingsWildMatch(tdb, "*Filter"); if (filterSettings) { struct slName *filter = NULL; while ((filter = slPopHead(&filterSettings)) != NULL) @@ -5297,31 +5301,48 @@ int ix = strlen(field) - strlen("filter"); assert(ix > 0); field[ix] = '\0'; char *setting = trackDbSetting(tdb, filter->name); // How to determine float or int ? If actual tracDb setting has decimal places, then float! if (strchr(setting,'.') == NULL) extraWhere = dyAddFilterAsInt(cart,tdb,extraWhere,filter->name,"0:1000",field,and); else extraWhere = dyAddFilterAsDouble(cart,tdb,extraWhere,filter->name,NULL,field,and); } slNameFree(&filter); } } return extraWhere; } -#endif///def ALL_SCORE_FILTERS_LOGIC + +boolean encodePeakHasCfgUi(struct trackDb *tdb) +// Confirms that this track has encode Peak cfgUI +{ +if (sameWord("narrowPeak",tdb->type) +|| sameWord("broadPeak", tdb->type) +|| sameWord("encodePeak",tdb->type) +|| sameWord("gappedPeak",tdb->type)) + { + return (trackDbSettingClosestToHome(tdb, SCORE_FILTER ) + || trackDbSettingClosestToHome(tdb, SIGNAL_FILTER) + || trackDbSettingClosestToHome(tdb, PVALUE_FILTER) + || trackDbSettingClosestToHome(tdb, QVALUE_FILTER) + || trackDbSettingClosestToHome(tdb, SCORE_FILTER )); + } + return FALSE; +} + void encodePeakCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed) /* Put up UI for filtering wgEnocde peaks based on score, Pval and Qval */ { boolean compositeLevel = isNameAtCompositeLevel(tdb,name); boolean opened = FALSE; showScoreFilter(cart,tdb,&opened,boxed,compositeLevel,name,title,"Minimum Signal value", SIGNAL_FILTER,TRUE); showScoreFilter(cart,tdb,&opened,boxed,compositeLevel,name,title,"Minimum P-Value (<code>-log<sub>10</sub></code>)",PVALUE_FILTER,TRUE); showScoreFilter(cart,tdb,&opened,boxed,compositeLevel,name,title,"Minimum Q-Value (<code>-log<sub>10</sub></code>)",QVALUE_FILTER,TRUE); char *setting = trackDbSettingClosestToHomeOrDefault(tdb, SCORE_FILTER,NULL);//"0:1000"); if(setting) { if(!opened) {