6419fc05af66878081e2b7d4d944900ec42d7cb1
tdreszer
  Fri Jun 22 15:29:37 2012 -0700
First of many checkins as dictated by Jim's OCD.  Formatting space after if and limiting lines to 100 chars.  Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history.  None of these changes should affect executables in any way.  Only affect is to my sanity and Jim's.
diff --git src/hg/sageVisCGI/sageVisCGI.c src/hg/sageVisCGI/sageVisCGI.c
index 8e487ba..acffbec 100644
--- src/hg/sageVisCGI/sageVisCGI.c
+++ src/hg/sageVisCGI/sageVisCGI.c
@@ -1,278 +1,279 @@
 /**
 
 \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");
+//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);
 dyStringPrintf(query, "%s", "select * from sage where ");
 for(nm=nmList;nm!=NULL;nm=nm->next)
     {
     if(count++)
 	{
 	dyStringPrintf(query," or uni=%s ", nm->name );
 	}
     else
 	{
 	dyStringPrintf(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");
 char *tmp= cloneString("select * from sageExp order by num");
 sc = sqlConnectRemote("localhost", user, password, db);
 sprintf(query,"%s",tmp);
 sr = sqlGetResult(sc,query);
 while((row = sqlNextRow(sr)) != NULL)
     {
     se = sageExpLoad(row);
     slAddHead(&seList,se);
     }
 freez(&tmp);
 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;
 }