aaf862066887971c08f4fb632fff365a2d453450 jcasper Tue Jan 13 23:09:13 2026 -0800 Changing Hi-C arc limit default to 10000 and turning it on by default, also correcting a typo. refs #36774 diff --git src/hg/inc/hicUi.h src/hg/inc/hicUi.h index 268a9285636..846f9c95aba 100644 --- src/hg/inc/hicUi.h +++ src/hg/inc/hicUi.h @@ -1,120 +1,126 @@ /* hic track UI */ /* Copyright (C) 2019 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HIC_UI_H #define HIC_UI_H #include "hic.h" /* Number of bins to split score values into, also the number of gradient * steps in the color values from lowest to highest. 1024 is already overkill * for hex-valued colors. */ #define HIC_SCORE_BINS 1024 /* hic-specific trackDb setting names */ #define HIC_TDB_DRAW_MODE "drawMode" #define HIC_TDB_NORMALIZATION "normalization" #define HIC_TDB_RESOLUTION "resolution" #define HIC_TDB_MAX_VALUE "saturationScore" #define HIC_TDB_AUTOSCALE "autoScale" #define HIC_TDB_COLOR "color" #define HIC_TDB_MAX_DISTANCE "hicDistanceMax" #define HIC_TDB_MIN_DISTANCE "hicDistanceMin" /* Cart variables */ #define HIC_DRAW_MODE "drawMode" #define HIC_DRAW_MODE_TRIANGLE "triangle" #define HIC_DRAW_MODE_SQUARE "square" #define HIC_DRAW_MODE_ARC "arc" #define HIC_DRAW_MODE_DEFAULT HIC_DRAW_MODE_TRIANGLE #define HIC_DRAW_INVERTED "inverted" #define HIC_NORMALIZATION "normalization" #define HIC_RESOLUTION "resolution" #define HIC_DRAW_AUTOSCALE "autoscale" #define HIC_DRAW_MAX_VALUE "max" #define HIC_DRAW_MAX_VALUE_DEFAULT 100 #define HIC_DRAW_COLOR "color" #define HIC_DRAW_BG_COLOR "bgColor" /* Default to drawing red on a white background */ #define HIC_DRAW_COLOR_DEFAULT "#ff0000" #define HIC_DRAW_BG_COLOR_DEFAULT "#ffffff" #define HIC_DRAW_MAX_DISTANCE "maxDistance" #define HIC_DRAW_MIN_DISTANCE "minDistance" #define HIC_ARC_LIMIT "hicArcLimit" #define HIC_ARC_LIMIT_CHECKBOX "hicArcLimitEnabled" void hicCfgUi(char *database, struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed); /* Draw the list of track configuration options for Hi-C tracks */ void hicCfgUiComposite(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed); /* Draw the (empty) list of track configuration options for a composite of Hi-C tracks */ char *hicUiFetchResolution(struct cart *cart, struct trackDb *tdb, struct hicMeta *meta); /* Return the current resolution selection, or the default if none * has been selected. */ void hicUiResolutionDropDown(struct cart *cart, struct trackDb *tdb, struct hicMeta *meta); /* Draw a dropdown menu in HTML to select which binSize to use for fetching data */ int hicUiFetchResolutionAsInt(struct cart *cart, struct trackDb *tdb, struct hicMeta *meta, int windowSize); /* Return the current resolution selection as an integer. If there is no selection, or if "Auto" * has been selected, return the largest available value that still partitions the window into at - * least 5000 bins. */ + * least 500 bins. */ char *hicUiFetchNormalization(struct cart *cart, struct trackDb *tdb, struct hicMeta *meta); /* Return the current normalization selection, or the default if none * has been selected. Right now this is a hard-coded set specifically for * .hic files, but in the future this list might be dynamically determined by * the contents and format of the Hi-C file. */ void hicUiNormalizationDropDown(struct cart *cart, struct trackDb *tdb, struct hicMeta *meta); /* Draw a dropdown menu in HTML to select the normalization method to use. */ char *hicUiFetchDrawMode(struct cart *cart, struct trackDb *tdb); /* Return the current draw mode selection, or the default if none * has been selected. */ boolean hicUiFetchInverted(struct cart *cart, struct trackDb *tdb); /* Check if the user has set this track to draw in inverted mode. * Ideally this would also be available via a trackDb setting, but * this is the first pass at this feature. */ char *hicUiFetchDrawColor(struct cart *cart, struct trackDb *tdb); /* Retrieve the HTML hex code for the color to draw the * track values in (e.g., #00ffa1) */ char *hicUiFetchBgColor(struct cart *cart, struct trackDb *tdb); /* Retrieve the HTML hex code of the background color for the * track. This is the color associated with scores at or close to 0. */ boolean hicUiFetchAutoScale(struct cart *cart, struct trackDb *tdb); /* Returns whether the track is configured to automatically scale its color range * depending on the scores present in the window (true), or if it should stick to a * gradient based on the user's selected maximum value (false). */ double hicUiFetchMaxValue(struct cart *cart, struct trackDb *tdb); /* Retrieve the score value at which the draw color reaches its * its maximum intensity. Any scores above this value will * share that same draw color. */ double hicUiMaxInteractionRange(struct cart *cart, struct trackDb *tdb); /* Retrieve the maximum range for an interaction to be drawn. Range is * calculated from the left-most start to the right-most end of the interaction. */ double hicUiMinInteractionRange(struct cart *cart, struct trackDb *tdb); /* Retrieve the minimum range for an interaction to be drawn. Range is * calculated from the left-most start to the right-most end of the interaction. */ int hicUiGetArcLimit(struct cart *cart, struct trackDb *tdb); +/* Returns the currently configured limit on the number of arcs drawn in arc mode. + * Defaults to 10000. + */ + boolean hicUiArcLimitEnabled(struct cart *cart, struct trackDb *tdb); +/* Returns true if the checkbox for limiting the number of displayed arcs is checked. + * Defaults to true. */ #endif