1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c
kate
  Thu Nov 10 15:59:18 2016 -0800
Cleanup C code. refs #17369

diff --git src/hg/lib/gtexUi.c src/hg/lib/gtexUi.c
index fba09a2..8833fa3 100644
--- src/hg/lib/gtexUi.c
+++ src/hg/lib/gtexUi.c
@@ -1,418 +1,463 @@
 /* GTEx (Genotype Tissue Expression) track controls */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "cheapcgi.h"
 #include "cart.h"
 #include "hui.h"
 #include "trackDb.h"
 #include "jsHelper.h"
 #include "gtexTissue.h"
 #include "gtexInfo.h"
 #include "gtexUi.h"
 
 #define SYSTEM_BRAIN            "Brain"
 #define SYSTEM_REPRODUCTIVE     "Reproductive"
 #define SYSTEM_GASTRO           "Digestive"
 
 #define SYSTEM_ENDOCRINE        "Endocrine"
 #define SYSTEM_CARDIO           "Cardiovascular"
 #define SYSTEM_OTHER            "Other"
 
 
 /* Restrict features on right-click (popup) version */
 static boolean isPopup = FALSE;
 
 /* Convenience functions for tissue filter controls */
 
 static char *makeTissueColorPatch(struct gtexTissue *tis)
 /* Display a box colored by defined tissue color */
 {
 char buf[256];
 safef(buf, sizeof(buf), "<td bgcolor=#%06X></td>", tis->color);
 return(cloneString(buf));
 }
 
 static char *makeTissueLabel(struct gtexTissue *tis)
 {
 /* Display tissue color and label */
 char buf[256];
 safef(buf, sizeof(buf), "<td bgcolor=%X></td>"
                         "<td>&nbsp;%s</td>", 
                                 tis->color, tis->description);
 return(cloneString(buf));
 }
 
 static char *getSystem(struct gtexTissue *tis)
 /* Rough categorization of tissues for filter presentation */
 {
 if (startsWith("brain", tis->name))
     return(SYSTEM_BRAIN);
 else if (sameString(tis->name, "uterus") || sameString(tis->name, "testis") ||
         sameString(tis->name, "vagina") || sameString(tis->name, "prostate") ||
         sameString(tis->name, "ovary") ||
         sameString(tis->name, "breastMamTissue") || sameString(tis->name, "ectocervix") ||
         sameString(tis->name, "endocervix") || sameString(tis->name, "fallopianTube"))
     return(SYSTEM_REPRODUCTIVE);
 else if (startsWith("esophagus", tis->name) || startsWith("colon", tis->name) ||
         sameString(tis->name, "stomach") || sameString("smallIntestine", tis->name) ||
         sameString("pancreas", tis->name) || sameString("liver", tis->name))
     return(SYSTEM_GASTRO);
 else if (sameString("adrenalGland", tis->name) || sameString("pituitary", tis->name) ||
         sameString("thyroid", tis->name))
     return(SYSTEM_ENDOCRINE);
 else if (startsWith("heart", tis->name) || startsWith("artery", tis->name))
     return(SYSTEM_CARDIO);
 else
     return(SYSTEM_OTHER);
 }
 
 struct tissueSelect
     {
     struct tissueSelect *next;
     char *name;
     char *label;
     boolean checked;
     };
 
 static void makeGroupCheckboxes(char *name, char *title, struct tissueSelect *tisSelects)
 {
 if (title != NULL)
     printf("<tr><td colspan=10><i><b>%s</b></i></td></tr><tr>\n", title);
 int count = slCount(tisSelects);
 struct tissueSelect **tisArray;
 AllocArray(tisArray, count);
 int i=0;
 struct tissueSelect *tsel;
 for (i=0, tsel = tisSelects; tsel != NULL; tsel = tsel->next, i++)
     tisArray[i] = tsel;
 int col=0;
 int row=0;
 int tableColumns=3;
 for (i=0; i<count; i++)
     {
     int j = row + col*(count/tableColumns+1);
     if (j>=count)
         {
         printf("</tr><tr>");
         row++;
         col = 0;
         }
     j = row + col*(count/tableColumns+1);
     if (!isPopup)
         {
         printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s></td>" "<td>%s</td>\n",
                name, tisArray[j]->name, tisArray[j]->checked ? "checked" : "", tisArray[j]->label);
         }
     col++;
     }
 if ((i % tableColumns) != 0)
     while ((i++ % tableColumns) != 0)
         printf("<td></td>");
 printf("</tr><tr><td></td></tr>\n");
 }
 
 static void initTissueTableStyle()
 /* Reduce font in tissue table so more rows are visible.
  * Specify some colors.*/
 {
 puts("<style>\n"
         "#tissueTable th, #tissueTable td {font-size: 75%; margin: 0px; border: 0px; padding: 0px}\n"
         "#tissueTable input {margin: 0px .5ex; width: 8px; height: 8px}\n"
         "#gtexGeneControls div {margin-bottom: .3em;}\n"
         ".notSortable {font-color: black;}\n"
     "</style>\n");
 }
 
 static void makeTableTissueCheckboxes(char *name, struct gtexTissue *tissues, 
                         struct slName *checked, struct cart *cart, char *track, char *version)
 {
 initTissueTableStyle();
 char *onClick = "";
 // Sortable table can't be displayed when UI is activated from right-click (popup mode)
 if (!isPopup)
     {
     jsIncludeFile("hui.js", NULL);
     onClick = "'tableSortAtButtonPress(this);";
     }
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 //puts("<table borderwidth=0><tr>");
 puts("\n<table id='tissueTable' cellspacing='1' cellpadding='0' border='0' class='sortable'>");
 
 /* table header */
 char orderVar[256];
 safef(orderVar, sizeof(orderVar), "%s.sortOrder", name);
 char *sortOrder = cartCgiUsualString(cart, orderVar, "tissue=+ samples=+ organ=+ system=+");
 puts("\n<thead class='sortable'>");
 puts("\n<tr class='sortable'>");
 char *sortableClass = isPopup ? "notSortable" : "sortable";
 printf("\n<th>&nbsp;<input type=hidden name='%s' class='sortOrder' value='%s'></th>\n",
         orderVar, sortOrder);
 puts("<th>&nbsp;&nbsp;&nbsp;&nbsp;</th>");
 printf("<th id='tissue' class='%s sort1' %s align='left'>&nbsp;Tissue</th>", 
                sortableClass, onClick);
 printf("<th id='samples' abbr='use' class='%s sort2' %s align='left'>&nbsp;Samples</th>", 
                sortableClass, onClick);
 printf("<th id='organ' class='%s sort3' %s align='left'>&nbsp;Organ</th>", 
                sortableClass, onClick);
 printf("<th id='system' class='%s sort4' %s align='left'>&nbsp;System</th>", 
                sortableClass, onClick);
 puts("\n</tr>");
 puts("</thead>");
 
 /* table body */
 printf("<tbody class='sortable noAltColors initBySortOrder'>");
 struct hash *tscHash = gtexGetTissueSampleCount(version);
 struct gtexTissue *tis;
 boolean isChecked = FALSE;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     puts("\n<tr valign='top'>");
 
     // checkbox
     if (hashNumEntries(checkHash) == 0)
         isChecked = TRUE;
     else
         isChecked = (hashLookup(checkHash, tis->name) != NULL);
     printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s %s></td>",
            name, tis->name, isChecked ? "checked" : "", isPopup ? "disabled" : "");
     // color patch
     printf("\n%s", makeTissueColorPatch(tis));
     // tissue name
     printf("\n<td>&nbsp;%s</td>", tis->description);
     // sample count
     int samples = hashIntValDefault(tscHash, tis->name, 0);
     printf("\n<td abbr='%05d' style='text-align: right; padding-right: 8px'>&nbsp;%d</td>", samples, samples);
     // organ
     printf("\n<td style='padding-right: 8px'>&nbsp;%s</td>", tis->organ);
     // system
     printf("\n<td>&nbsp;%s</td>", getSystem(tis));
 
     puts("\n</tr>");
     }
 puts("</tbody>");
 puts("</table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 static void makeGroupedTissueCheckboxes(char *name, struct gtexTissue *tissues, struct slName *checked)
 {
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 puts("<table borderwidth=0><tr>");
 struct tissueSelect *brainTissues = NULL;
 struct tissueSelect *digestiveTissues = NULL;
 struct tissueSelect *reproductiveTissues = NULL;
 struct tissueSelect *otherTissues = NULL;
 struct tissueSelect *tsel;
 struct gtexTissue *tis;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     AllocVar(tsel);
     tsel->name = tis->name;
     tsel->label = makeTissueLabel(tis);
     if (hashNumEntries(checkHash) == 0)
         tsel->checked = TRUE;
     else
         tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
     char *system = getSystem(tis);
     if (sameString(SYSTEM_BRAIN, system))
         slAddHead(&brainTissues, tsel);
     else if (sameString(SYSTEM_REPRODUCTIVE, system))
         slAddHead(&reproductiveTissues, tsel);
     else if (sameString(SYSTEM_GASTRO, system))
         slAddHead(&digestiveTissues, tsel);
     else
         slAddHead(&otherTissues, tsel);
     }
 slReverse(&brainTissues);
 slReverse(&digestiveTissues);
 slReverse(&reproductiveTissues);
 slReverse(&otherTissues);
 makeGroupCheckboxes(name, "Brain", brainTissues);
 makeGroupCheckboxes(name, "Gastrointestinal", digestiveTissues);
 makeGroupCheckboxes(name, "Reproductive", reproductiveTissues);
 makeGroupCheckboxes(name, "Other", otherTissues);
 puts("</tr></table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 static void makeAllTissueCheckboxes(char *name, struct gtexTissue *tissues, 
                                         struct slName *checked)
 {
 struct hash *checkHash = hashNew(0);
 struct slName *sel;
 for (sel = checked; sel != NULL; sel = sel->next)
     hashAdd(checkHash, sel->name, sel->name);
 puts("<table borderwidth=0><tr>");
 struct tissueSelect *tsel;
 struct gtexTissue *tis;
 struct tissueSelect *allTissues = NULL;
 for (tis = tissues; tis != NULL; tis = tis->next)
     {
     AllocVar(tsel);
     tsel->name = tis->name;
     tsel->label = makeTissueLabel(tis);
     if (hashNumEntries(checkHash) == 0)
         tsel->checked = TRUE;
     else
         tsel->checked = (hashLookup(checkHash, tis->name) != NULL);
     slAddHead(&allTissues, tsel);
     }
 slReverse(&allTissues);
 makeGroupCheckboxes(name, NULL, allTissues);
 puts("</tr></table>");
 char buf[512];
 safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name);
 cgiMakeHiddenVar(buf, "0");
 }
 
 void gtexPortalLink(char *geneId)
 /* print URL to GTEX portal gene expression page using Ensembl Gene Id*/
 {
 printf("<a target='_blank' href='http://www.gtexportal.org/home/gene/%s'>"
         "View at GTEx portal</a>\n", geneId);
 }
 
-void gtexGeneUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed)
-/* GTEx (Genotype Tissue Expression) per gene data */
-{
-if (cartVarExists(cart, "ajax"))
-    isPopup = TRUE;
-
-boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
-printf("\n<table id=gtexGeneControls style='font-size:%d%%' %s>\n<tr><td>", 
-        isPopup ? 75 : 100, boxed ?" width='100%'":"");
+/* Convenience functions shared by hgTrackUi and hgGtexTrackSettings. hgTrackUi is for now still
+ * available from right-click */
 
+void gtexGeneUiGeneLabel(struct cart *cart, char *track, struct trackDb *tdb)
+/* Radio buttons to select format of gene label */
+{
 char cartVar[1024];
-char buf[512];
-
-/* Gene labels  */
-printf("<div>");
 char *geneLabel = cartUsualStringClosestToHome(cart, tdb, isNameAtParentLevel(tdb, track), 
                         GTEX_LABEL, GTEX_LABEL_DEFAULT);
 printf("<b>Label:</b> ");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LABEL);
 cgiMakeRadioButton(cartVar, GTEX_LABEL_SYMBOL , sameString(GTEX_LABEL_SYMBOL, geneLabel));
 printf("%s ", "gene symbol");
 cgiMakeRadioButton(cartVar, GTEX_LABEL_ACCESSION, sameString(GTEX_LABEL_ACCESSION, geneLabel));
 printf("%s ", "accession");
 cgiMakeRadioButton(cartVar, GTEX_LABEL_BOTH, sameString(GTEX_LABEL_BOTH, geneLabel));
 printf("%s ", "both");
-printf("</div>\n");
+}
 
-/* Filter on coding genes */
-printf("<div>");
-printf("<b>Limit to protein coding genes:</b>\n");
+void gtexGeneUiCodingFilter(struct cart *cart, char *track, struct trackDb *tdb)
+/* Checkbox to restrict display to protein coding genes */
+{
+char cartVar[1024];
+puts("<b>Limit to protein coding genes:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_CODING_GENE_FILTER);
 boolean isCodingOnly = cartCgiUsualBoolean(cart, cartVar, GTEX_CODING_GENE_FILTER_DEFAULT);
 cgiMakeCheckBox(cartVar, isCodingOnly);
+}
 
-/* Show exons in gene model */
-printf("&nbsp;&nbsp;<b>Show GTEx gene model</b>\n");
+void gtexGeneUiGeneModel(struct cart *cart, char *track, struct trackDb *tdb)
+/* Checkbox to enable display of GTEx gene model */
+{
+char cartVar[1024];
+puts("&nbsp;&nbsp;<b>Show GTEx gene model</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SHOW_EXONS);
 boolean showExons = cartCgiUsualBoolean(cart, cartVar, GTEX_SHOW_EXONS_DEFAULT);
 cgiMakeCheckBox(cartVar, showExons);
-printf("</div>");
+}
 
-/* Data transform. When selected, the next control (view limits max) is disabled */
-printf("<div><b>Log10 transform:</b>\n");
+void gtexGeneUiLogTransform(struct cart *cart, char *track, struct trackDb *tdb)
+/* Checkbox to select log-transformed RPKM values */
+{
+char cartVar[1024];
+char buf[512];
+puts("<b>Log10 transform:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_LOG_TRANSFORM);
 boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT);
 safef(buf, sizeof buf, "onchange='gtexTransformChanged(\"%s\")'", track);
 cgiMakeCheckBoxJS(cartVar, isLogTransform, buf);
+}
 
-/* Viewing limits max.  This control is disabled if log transform is selected */
-// construct class so JS can toggle
+void gtexGeneUiViewLimits(struct cart *cart, char *track, struct trackDb *tdb)
+/* Set viewing limits if log transform not checked */
+{
+char cartVar[1024];
+char buf[512];
+boolean isLogTransform = cartCgiUsualBoolean(cart, cartVar, GTEX_LOG_TRANSFORM_DEFAULT);
 safef(buf, sizeof buf, "%sViewLimitsMaxLabel %s", track, isLogTransform ? "disabled" : "");
-printf("&nbsp;&nbsp;<span class='%s'><b>View limits maximum:</b></span>\n", buf);
+printf("<span class='%s'><b>View limits maximum:</b></span>\n", buf);
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_MAX_LIMIT);
 int viewMax = cartCgiUsualInt(cart, cartVar, GTEX_MAX_LIMIT_DEFAULT);
 cgiMakeIntVarWithExtra(cartVar, viewMax, 4, isLogTransform ? "disabled" : "");
 char *version = gtexVersion(tdb->table);
 printf("<span class='%s'>  RPKM (range 0-%d)</span>\n", buf, round(gtexMaxMedianScore(version)));
-printf("</div>");
+}
+
+void gtexGeneUi(struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed)
+/* GTEx (Genotype Tissue Expression) per gene data */
+{
+if (cartVarExists(cart, "ajax"))
+    isPopup = TRUE;
+
+boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
+printf("\n<table id=gtexGeneControls style='font-size:%d%%' %s>\n<tr><td>", 
+        isPopup ? 75 : 100, boxed ?" width='100%'":"");
+
+char cartVar[1024];
+
+/* Gene labels  */
+puts("<div>");
+gtexGeneUiGeneLabel(cart, track, tdb);
+puts("</div>\n");
+
+/* Filter on coding genes */
+puts("<div>");
+gtexGeneUiCodingFilter(cart, track, tdb);
+
+/* Show exons in gene model */
+puts("&nbsp;&nbsp;");
+gtexGeneUiGeneModel(cart, track, tdb);
+puts("</div>");
+
+/* Data transform. When selected, the next control (view limits max) is disabled */
+
+puts("<div>");
+gtexGeneUiLogTransform(cart, track, tdb);
+
+/* Viewing limits max.  This control is disabled if log transform is selected */
+// construct class so JS can toggle
+puts("&nbsp;&nbsp;");
+gtexGeneUiViewLimits(cart, track, tdb);
+puts("</div>");
 
 #ifdef COMPARISON
 /* Sample selection */
 printf("<div><b>Samples:</b>&nbsp;");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_SAMPLES);
 char *selected = cartCgiUsualString(cart, cartVar, GTEX_SAMPLES_DEFAULT); 
 boolean isAllSamples = sameString(selected, GTEX_SAMPLES_ALL);
 safef(buf, sizeof buf, "onchange='gtexSamplesChanged(\"%s\")'", track);
 char *command = buf;
 cgiMakeOnClickRadioButton(cartVar, GTEX_SAMPLES_ALL, isAllSamples, command);
 printf("All\n");
 cgiMakeOnClickRadioButton(cartVar, GTEX_SAMPLES_COMPARE_SEX, !isAllSamples, command);
 printf("Compare by gender\n");
 printf("</div>");
 
 /* Comparison type. Disabled if All samples selected. */
 safef(buf, sizeof buf, "%sComparisonLabel %s", track, isAllSamples ? "disabled" : "");
 printf("<div><b><span class='%s'>Comparison display:</b></span>", buf);
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_COMPARISON_DISPLAY);
 selected = cartCgiUsualString(cart, cartVar, GTEX_COMPARISON_DEFAULT); 
 boolean isMirror = sameString(selected, GTEX_COMPARISON_MIRROR);
 
 cgiMakeRadioButton(cartVar, GTEX_COMPARISON_DIFF, !isMirror);
 printf("<span class='%s'>Difference graph</span>", buf);
 cgiMakeRadioButton(cartVar, GTEX_COMPARISON_MIRROR, isMirror);
 printf("<span class='%s'>Two graphs</span>\n", buf);
 printf("</div>");
 #endif
 
 /* Color scheme */
 // We don't need the rainbow color scheme, but may want another (e.g. different
 // colors for brain tissues), so leaving code in for now.
 #ifdef COLOR_SCHEME
 printf("<p><b>Tissue colors:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_COLORS);
 selected = cartCgiUsualString(cart, cartVar, GTEX_COLORS_DEFAULT); 
 boolean isGtexColors = sameString(selected, GTEX_COLORS_GTEX);
 cgiMakeRadioButton(cartVar, GTEX_COLORS_GTEX, isGtexColors);
 printf("GTEx\n");
 cgiMakeRadioButton(cartVar, GTEX_COLORS_RAINBOW, !isGtexColors);
 printf("Rainbow\n");
 printf("</p>");
 #endif
 
 /* Tissue filter */
 printf("<br>");
 printf("<div><b>Tissues:</b>\n");
 safef(cartVar, sizeof(cartVar), "%s.%s", track, GTEX_TISSUE_SELECT);
 if (isPopup)
     {
     printf("<a href='../cgi-bin/hgTrackUi?g=%s'><button type='button'>Change</button><a>", track);
     }
 else
     {
     jsMakeCheckboxGroupSetClearButton(cartVar, TRUE);
     puts("&nbsp;");
     jsMakeCheckboxGroupSetClearButton(cartVar, FALSE);
     }
 printf("</div>");
+char *version = gtexVersion(tdb->table);
 struct gtexTissue *tissues = gtexGetTissues(version);
 struct slName *selectedValues = NULL;
 if (cartListVarExistsAnyLevel(cart, tdb, FALSE, GTEX_TISSUE_SELECT))
     selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, GTEX_TISSUE_SELECT);
 char *selectType = cgiUsualString("tis", "table");
 if (sameString(selectType, "group"))
     makeGroupedTissueCheckboxes(cartVar, tissues, selectedValues);
 else if (sameString(selectType, "table"))
     makeTableTissueCheckboxes(cartVar, tissues, selectedValues, cart, track, version);
 else
     makeAllTissueCheckboxes(cartVar, tissues, selectedValues);
 
 puts("\n</table>\n");
 cfgEndBox(boxed);
 }