e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/hgGenome/configure.c src/hg/hgGenome/configure.c
index 92f24df..671eb9b 100644
--- src/hg/hgGenome/configure.c
+++ src/hg/hgGenome/configure.c
@@ -1,154 +1,157 @@
+/* Copyright (C) 2011 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hash.h"
 #include "jksql.h"
 #include "hCommon.h"
 #include "cart.h"
 #include "cheapcgi.h"
 #include "chromGraph.h"
 #include "web.h"
 #include "hPrint.h"
 #include "hui.h"
 #include "hgGenome.h"
 
 
 void makeNumMenu(char *varName, int minVal, int maxVal, int defaultVal)
 /* Make a drop down menu with a limited number of numerical choices. */
 {
 int choiceCount = maxVal - minVal + 1;
 int i;
 
 printf("<SELECT NAME=\"%s\">\n", varName);
 for (i=0; i<choiceCount; ++i)
     {
     int choice = i + minVal;
     char *selString = ((choice == defaultVal) ? " SELECTED" : "");
     hPrintf("<OPTION%s>%d</OPTION>\n", selString, choice);
     }
 printf("</SELECT>\n");
 }
 
 char *chromLayouts[] = {
     layTwoPerLine,
     layOnePerLine,
     layAllOneLine,
     };
 
 
 void configurePage()
 /* Put up configuration page. */
 {
 cartWebStart(cart, database, "Configure Genome Graphs");
 hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
 cartSaveSession(cart);
 hPrintf("<TABLE>\n");
 hPrintf("<TR>\n");
 hPrintf("<TD>\n");
 hPrintf("image width: ");
 cgiMakeIntVar(hggImageWidth, cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth), 4);
 hPrintf("</TD>\n");
 hPrintf("<TD>\n");
 hPrintf("graph height: ");
 cgiMakeIntVar(hggGraphHeight, graphHeight(), 3);
 hPrintf("</TD>\n");
 hPrintf("<TD>\n");
 hPrintf(" graphs per line: ");
 makeNumMenu(hggGraphsPerLine, minGraphsPerLine, maxGraphsPerLine, 
 	graphsPerLine());
 hPrintf("</TD>\n");
 hPrintf("<TD>\n");
 hPrintf(" lines of graphs: ");
 makeNumMenu(hggLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs, 
 	linesOfGraphs());
 hPrintf("</TD>\n");
 hPrintf("</TR>\n");
 hPrintf("</TABLE>\n");
 hPrintf("<TABLE><TR><TD>\n");
 hPrintf("chromosome layout: ");
 cgiMakeDropList(hggChromLayout, chromLayouts, ArraySize(chromLayouts), 
         chromLayout());
 hPrintf("</TD></TR></TABLE>\n");
 hPrintf("<TABLE><TR><TD>\n");
 hPrintf("numerical labels: ");
 cartMakeCheckBox(cart, hggLabels, TRUE);
 hPrintf(" <I>Label axis on left for first graph and on right for last graph</I>");
 hPrintf("</TD></TR></TABLE>\n");
 hPrintf("<TABLE><TR><TD>\n");
 hPrintf("highlight missing: ");
 cartMakeCheckBox(cart, hggYellowMissing, FALSE);
 hPrintf(" <I>Highlight background in yellow/gray if there is missing data in first graph</I>");
 hPrintf("</TD></TR></TABLE>\n");
 hPrintf("<TABLE><TR><TD>\n");
 hPrintf("region padding: ");
 cgiMakeIntVar(hggRegionPad, regionPad(), 6);
 hPrintf(" <I>Number of bases to add to either side of regions over threshold</I>");
 hPrintf("</TD></TR></TABLE>\n");
 hPrintf("<TABLE><TR><TD>\n");
 cgiMakeButton("submit", "submit");
 hPrintf("</TD></TR></TABLE>\n");
 hPrintf("</TD>\n");
 hPrintf("</FORM>\n");
 
 webNewSection("Configure Graphs");
 hPrintf("Click on the hyperlink by the graph name to configure it.");
 hTableStart();
 hPrintf("<TR><TH>name</TH>");
 hPrintf("<TH>description</TH></TR>");
 struct slRef *ref;
 for (ref = ggList; ref != NULL; ref = ref->next)
     {
     struct genoGraph *gg = ref->val;
     /* Only show custom graphs, stand-alone DB graphs, and composite */
     /* graphs.  Don't show subGraphs part of a composite. */
     if (gg->isSubGraph == FALSE)
 	{
 	char *tmp = cgiEncode(gg->name);
 	hPrintf("<TR><TD><A HREF=\"../cgi-bin/hgGenome?%s&%s=on&g=%s\">",
 		cartSidUrlString(cart), hggConfigureOne, tmp);
 	freeMem(tmp);
 	hPrintf("%s</A></TD>", gg->shortLabel);
 	hPrintf("<TD>%s</TD></TR>\n", gg->longLabel);
 	}
     }
 hTableEnd();
 cartWebEnd();
 }
 
 void configureOnePage()
 /* Put up configuration for one graph. */
 {
 /* Figure out which graph we're configuring. */
 char *graphName = cartString(cart, "g");
 struct genoGraph *gg = hashFindVal(ggHash, graphName);
 if (gg == NULL)
     {
     /* Warn/return rather than abort if have problems, so that 
      * cartRemovePrefix(hggDo) is executed to keep us from error
      * loop forever... */
     warn("Graph %s not found", graphName);
     return;
     }
 
 /* Put up web page with controls */
 cartWebStart(cart, database, "Configure %s", gg->shortLabel);
 hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
 cartSaveSession(cart);
 cgiMakeHiddenVar(hggConfigure, "on");
 struct chromGraphSettings *cgs = gg->settings;
 char varName[chromGraphVarNameMaxSize];
 chromGraphVarName(gg->name, "minVal", varName);
 hPrintf("display min value: ");
 cartMakeIntVar(cart, varName, cgs->minVal, 5);
 chromGraphVarName(gg->name, "maxVal", varName);
 hPrintf(" max value: ");
 cartMakeIntVar(cart, varName, cgs->maxVal, 5);
 hPrintf("<BR>\n");
 hPrintf("draw connecting lines between markers separated by up to ");
 chromGraphVarName(gg->name, "maxGapToFill", varName);
 cartMakeIntVar(cart, varName, cgs->maxGapToFill, 8);
 hPrintf(" bases.");
 hPrintf("<BR>\n");
 cgiMakeButton("submit", "submit");
 hPrintf("</FORM>\n");
 cartWebEnd();
 }