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/sageVisCGI/sageVisCGI.c src/hg/sageVisCGI/sageVisCGI.c
index 2d328a2..125f16d 100644
--- src/hg/sageVisCGI/sageVisCGI.c
+++ src/hg/sageVisCGI/sageVisCGI.c
@@ -1,277 +1,280 @@
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 /**
 
 \page sageVisCGI.doxp sageVisCGI cgi program for viewing graphs of sage data
 used standalone or called by the hgc.c program in ~kent/src/hg/hgc/.
 
 <p>sageVisCGI creates graphs on the fly for the sage data of different
 uniGene clusters. The clusters to be graphed are passed via cgi (or command
 line) in the form u=<uniGene number>. There is also an optional 'md' parameter
 which specifies a maximum tag count to go up to, default is 50.
 
 <p>Example
 <br><pre><code>
 sageVisCGI md=20 u=202 u=122566 > out.html
 </code></pre>
 or http://genome-test.cse.ucsc.edu/cgi-bin/sageVisCGI?md=20&u=202&u=122566 .
 
 \sa sageVisCGI.c
 
 */
 #include "common.h"
 #include "hCommon.h"
 #include "dystring.h"
 #include "sage.h"
 #include "sageExp.h"
 #include "gnuPlot2D.h"
 #include "portable.h"
 #include "jksql.h"
 #include "dnautil.h"
 #include "cheapcgi.h"
 #include "htmshell.h"
 #include "knownMore.h"
 #include "hdb.h"
 #include "genePred.h"
 #include "hgConfig.h"
 
 int maxDataVal =0;
 int dataValCeiling;
 
 /**
 Just prints out the <img> tag and filename
 */
 void doPlotPrintOut(char *fileName)
 {
 printf( "<img src=\"%s\">\n", fileName);
 }
 
 
 /**
  * Appends one string to another without having to
  * worry about going over. Assumes that the total length
  * of dest is the strlen(dest) + 1. Wasteful if you want to
  * use it lots of times in a row as it reallocates memory every time
  */
 void dynamicStrncat(char **dest, const char *src)
 {
 ExpandArray(*dest, (strlen(*dest)+1), (strlen(*dest) +strlen(src) + 1));
 strncat(*dest, src, strlen(src));
 }
 
 /**
 Construct a graphPoint from data in sage and current index.
 Assumes that the experiments are stored in order.
 */
 struct graphPoint2D*createSageGraphPoint(struct sage *sg, int i)
 {
 
 struct graphPoint2D *gp = NULL;
 char name[128];
 
 sprintf(name, "Hs.%d", sg->uni);
 AllocVar(gp);
 gp->y = sg->meds[i-1];
 if(gp->y > maxDataVal && gp->y < dataValCeiling)
     maxDataVal = gp->y;
 gp->x = i;
 gp->name = cloneString(name);
 gp->hName = cloneString(name);
 gp->groupName = cloneString(name);
 return gp;
 }
 
 /**
   Uses the sage experiment data (sageExp) and sage data itself (sage)
 to construct the basic gnuPlot2D data type, specifically creating the
 graphPoint2D data lists for each element in sgList */
 struct gnuPlot2D *createSagePlot(struct sageExp *seList, struct sage *sgList)
 {
 struct gnuPlot2D *gp = createGnuPlot2D();
 struct sage *sg = NULL;
 int i;
 for(sg = sgList; sg != NULL; sg = sg->next)
     {
     struct graphPoint2D *gList = NULL;
     for (i=0; i< sg->numExps; i++)
         {
         struct graphPoint2D *gTemp = NULL;
         gTemp = createSageGraphPoint(sg, i+1);
 	slAddHead(&gList, gTemp);
 	}
     gptAddGraphPointList(gp, gList, "linesp");
     }
 return gp;
 }
 
 /* Creates a string which tells gnuPlot what label to put on
    xTics and where to put them. Will Chop "SAGE" from name if present */
 char * constructXticsFromExps(struct sageExp *seList)
 {
 char *ret = cloneString("set xtics rotate(");
 static char buff[256];
 int count =1;
 struct sageExp *se;
 for(se = seList; se != NULL; se = se->next)
     {
     if(se->next == NULL)
 	sprintf(buff, " \"%d)%s\" %d ", count, strstr(se->exp,"SAGE_") ? strstr(se->exp,"_") : se->exp , count);
     else
 	sprintf(buff, " \"%d)%s\" %d, ", count, strstr(se->exp,"SAGE_") ? strstr(se->exp, "_") : se->exp, count);
     dynamicStrncat(&ret, buff);
     count++;
     }
 dynamicStrncat(&ret, ")\n");
 return ret;
 }
 
 /* Prints the header appropriate for the title
  * passed in. Links html to chucks stylesheet for
  * easier maintaince
  */
 void chuckHtmlStart(char *title)
 {
 printf("<html><head>");
 //FIXME blueStyle should not be absolute to genome-test and should bae called by:
 // webIncludeResourceFile("blueStyle.css");
 printf("<LINK REL=STYLESHEET TYPE=\"text/css\" href=\"http://genome-test.cse.ucsc.edu/style/blueStyle.css\" title=\"Chuck Style\">\n");
 printf("<title>%s</title>\n</head><body bgcolor=\"#f3f3ff\">",title);
 }
 
 /**
 Generates the data plot and associated html
 */
 void doCountsPage(struct sageExp *seList, struct sage *sgList)
 {
 struct gnuPlot2D *gp = needMem(sizeof(struct gnuPlot2D*));
 
 char *cmd = NULL;
 double xSize;
 double ySize;
 char *title = NULL;
 char *xTics = NULL;
 char plotSize[256]; // = cloneString("set size .75,.75\n");
 struct tempName pngTn;
 
 chuckHtmlStart("Sage Graph");
 printf("<center>");
 makeTempName(&pngTn, "sageDat", ".png");
 gp = createSagePlot(seList, sgList);
 gp->fileName = pngTn.forCgi;
 xTics = constructXticsFromExps(seList);
 title = cloneString("Sage Data for Unigene Clusters");
 xSize = 0.020*slCount(gp->gpList[0]);
 ySize = 0.075*slCount(sgList);
 if(ySize < 1.25) ySize = 1.25;
 if(xSize <.75) xSize = .75;
 sprintf(plotSize, "set size %g, %g\n", xSize,ySize);
 gp->other = cloneString(plotSize);
 dynamicStrncat(&gp->other, xTics);
 gp->ylabel = cloneString("Median Counts");
 gp->xlabel = cloneString("Experiment");
 gp->title = cloneString(title);
 gp->xMax = slCount(gp->gpList[0]);
 gp->yMax = maxDataVal;
 cmd = gptGenerateCmd(gp);
 gptPlotFromCmd(cmd);
 doPlotPrintOut(pngTn.forHtml);
 htmlEnd();
 }
 
 
 /** load the sage data by constructing a query based on the names in nmList
  */
 struct sage *loadSageData(char *table, struct slName *nmList)
 {
 char *user = cfgOption("db.user");
 char *password = cfgOption("db.password");
 struct sqlConnection *sc = NULL;
 struct dyString *query = newDyString(2048);
 struct sage *sgList = NULL, *sg=NULL;
 struct slName *nm =NULL;
 char *db = cgiUsualString("db", "hgFixed");
 char **row;
 int count=0;
 struct sqlResult *sr = NULL;
 sc = sqlConnectRemote("localhost", user, password, db);
 sqlDyStringPrintf(query, "select * from sage where ");
 for(nm=nmList;nm!=NULL;nm=nm->next)
     {
     if (count++)
         {
         sqlDyStringPrintf(query," or uni=%s ", nm->name );
         }
     else
 	{
 	sqlDyStringPrintf(query," uni=%s ", nm->name);
 	}
     }
 sr = sqlGetResult(sc,query->string);
 while((row = sqlNextRow(sr)) != NULL)
     {
     sg = sageLoad(row);
     slAddHead(&sgList,sg);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&sc);
 slReverse(&sgList);
 freeDyString(&query);
 return sgList;
 }
 
 /** load the sage experiment data
  */
 struct sageExp *loadSageExps(char *tableName, struct slName *nmList)
 {
 char *user = cfgOption("db.user");
 char *password = cfgOption("db.password");
 struct sqlConnection *sc = NULL;
 char query[256];
 struct sageExp *seList = NULL, *se=NULL;
 char **row;
 struct sqlResult *sr = NULL;
 char *db = cgiUsualString("db", "hgFixed");
 sc = sqlConnectRemote("localhost", user, password, db);
 sqlSafef(query, sizeof query, "select * from sageExp order by num");
 sr = sqlGetResult(sc,query);
 while((row = sqlNextRow(sr)) != NULL)
     {
     se = sageExpLoad(row);
     slAddHead(&seList,se);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&sc);
 slReverse(&seList);
 return seList;
 }
 
 /** print usage and quit */
 void usage()
 {
 errAbort("sageVisCGI - create a graph of median sage counts\n"
 	 "usage:\n\t sageVisCGI u=<uniGeneNum> u=<uniGeneNum2> u=<uniGeneNum3> etc. \n");
 }
 
 /** main html generating function for htmShell */
 void doHtml()
 {
 struct sageExp *seList;
 struct sage *sgList;
 struct slName *unis = cgiStringList("u");
 if(unis == NULL)
     usage();
 dataValCeiling = cgiOptionalInt("md",50);
 seList = loadSageExps("sageExp", unis);
 sgList = loadSageData("sage", unis);
 doCountsPage(seList, sgList);
 sageExpFreeList(&seList);
 sageFreeList(&sgList);
 slFreeList(&unis);
 }
 
 
 int main(int argc, char *argv[])
 {
 cgiSpoof(&argc, argv);
 printf("Content-Type: text/html\n\n");
 htmEmptyShell(doHtml, NULL);
 return 0;
 }