src/hg/lib/hgExp.c 1.18

Index: src/hg/lib/hgExp.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/hgExp.c,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 1000000 -r1.17 -r1.18
--- src/hg/lib/hgExp.c	31 Jan 2009 07:28:55 -0000	1.17
+++ src/hg/lib/hgExp.c	3 Mar 2009 23:29:06 -0000	1.18
@@ -1,320 +1,326 @@
 /* hgExp - help browse expression data. */
 
 #include "common.h"
 #include "hash.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "gifLabel.h"
 #include "cart.h"
 #include "cheapcgi.h"
 #include "hgExp.h"
 #include "portable.h"
 
 static char const rcsid[] = "$Id$";
 
 static int expSubcellWidth = 21;
 
 static char *colorSchemeVals[] = {
 /* Menu option for color scheme. */
    "red high/green low",
    "yellow high/blue low",
 };
 
 void hgExpColorDropDown(struct cart *cart, char *varName)
 /* Make color drop-down. */
 {
 char *checked = cartUsualString(cart, varName, colorSchemeVals[0]);
 cgiMakeDropList(varName, 
 	colorSchemeVals, ArraySize(colorSchemeVals), checked);
 }
 
 boolean hgExpRatioUseBlue(struct cart *cart, char *varName)
 /* Return TRUE if should use blue instead of red
  * in the expression ratios. */
 {
 char *val = cartUsualString(cart, varName, colorSchemeVals[0]);
 return !sameString(val, colorSchemeVals[0]);
 }
 
 char **hgExpGetNames(char *database, char *table, 
 	int expCount, int *expIds, int skipSize)
 /* Create array filled with experiment names. */
 {
 char **names, *name;
 int i;
 char *db = database;
 struct sqlConnection *conn;
 char query[256], nameBuf[128];
 int maxLen = 0, len;
 
 if (!hTableExists(database, table))
     db = "hgFixed";
 conn = sqlConnect(db);
 /* Read into array and figure out longest name. */
 AllocArray(names, expCount);
 for (i=0; i<expCount; ++i)
     {
     int ix = expIds[i];
     if (ix == -1)
         names[i] = NULL;
     else
 	{
 	safef(query, sizeof(query), "select name from %s where id = %d", 
 	    table, expIds[i]);
 	if ((name = sqlQuickQuery(conn, query, nameBuf, sizeof(nameBuf))) == NULL)
 	    name = "unknown";
 	else
 	    name += skipSize;
 	names[i] = cloneString(name);
 	len = strlen(name);
 	if (len > maxLen) maxLen = len;
 	}
     }
 sqlDisconnect(&conn);
 
 /* Right justify names. */
 for (i=0; i<expCount; ++i)
     {
     char *name = names[i];
     if (name != NULL)
         {
 	safef(nameBuf, sizeof(nameBuf), "%*s", maxLen, name);
 	freeMem(name);
 	names[i] = cloneString(nameBuf);
 	}
     }
 return names;
 }
 
 static int countNonNull(char **row, int maxCount)
 /* Count number of non-null rows. */
 {
 int i;
 for (i=0; i<maxCount; ++i)
     {
     if (row[i] == NULL)
         break;
     }
 return i;
 }
 
 void hgExpLabelPrint(char *database, char *colName, char *subName, int skipName,
 	char *url, int representativeCount, int *representatives,
 	char *expTable, int gifStart)
 /* Print out labels of various experiments. */
 {
 int i;
 int groupSize;
 char gifName[128];
 char **experiments = hgExpGetNames(database,
 	expTable, representativeCount, representatives, skipName);
 int height = gifLabelMaxWidth(experiments, representativeCount);
 
 for (i=0; i<representativeCount; i += groupSize+1)
     {
     printf("<TD VALIGN='BOTTOM' WIDTH=%d>", expSubcellWidth);
     groupSize = countNonNull(experiments+i, representativeCount-i);
     safef(gifName, sizeof(gifName), "../trash/nea_%s_%s%d.gif", 
     	colName, subName, ++gifStart);
     gifLabelVerticalText(gifName, experiments+i, groupSize, height);
     if (url != NULL)
        printf("<A HREF=\"%s\">", url); 
     printf("<IMG BORDER=0 SRC=\"%s\">", gifName);
     if (url != NULL)
 	printf("</A>");
     printf("</TD>");
     }
 
 /* Clean up */
 for (i=0; i<representativeCount; ++i)
    freeMem(experiments[i]);
 freeMem(experiments);
 }
 
 
 boolean hgExpLoadVals(struct sqlConnection *lookupConn,
 	struct sqlConnection *dataConn,
 	char *lookupTable, char *name, char *dataTable,
 	int *retValCount, float **retVals)
 /* Load up and return expression bed record.  Return NULL
  * if none of given name exist. */
 {
 char query[256];
 char expName[64];
 struct sqlResult *sr;
 char **row;
 boolean ok = FALSE;
-safef(query, sizeof(query), "select value from %s where name = '%s'", 
+if (!sameWord(lookupTable, "null"))
+    {
+    safef(query, sizeof(query), "select value from %s where name = '%s'", 
 	lookupTable, name);
-if (sqlQuickQuery(lookupConn, query, expName, sizeof(expName)) == NULL)
+    if (sqlQuickQuery(lookupConn, query, expName, sizeof(expName)) == NULL)
     return FALSE;
-safef(query, sizeof(query), "select expScores from %s where name = '%s'",
+    safef(query, sizeof(query), "select expScores from %s where name = '%s'",
 	dataTable, expName);
+    }
+else
+    safef(query, sizeof(query), "select expScores from %s where name = '%s'",
+	  dataTable, name);    
 sr = sqlGetResult(dataConn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     sqlFloatDynamicArray(row[0], retVals, retValCount);
     ok = TRUE;
     }
 sqlFreeResult(&sr);
 return ok;
 }
 
 
 static void hexOne(double val)
 /* Convert val 0.0-1.0 to hex 00 to FF */
 {
 int hex = val * 0xFF;
 if (hex > 0xFF) hex = 0xFF;
 printf("%02X", hex);
 }
 
 static void colorVal(double val, double scale, boolean useBlue, boolean useGrays, boolean logGrays)
 /* Val is -1.0 to 1.0.  Print color in form #FF0000, normally
  * using green for minus values, red for plus values, but
  * optionally using blue for minus values and yellow for plus values. */
 {
 if (useGrays)
     {
     if (val < 1)
         printf("000000");
     else
 	{
 	val = (logGrays) ? log(val) * scale : val * scale;
 	hexOne(val);
 	hexOne(val);
 	hexOne(val);
 	}
     }
 else 
     {
     val *= scale;
     if (useBlue)
 	{
 	if (val < 0)
 	    {
 	    val = -val;
 	    printf("00");
 	    printf("00");
 	    hexOne(val);
 	    }
 	else
 	    {
 	    val *= 0.7;
 	    hexOne(val);    /* Red */
 	    hexOne(val);     /* Green */
 	    printf("00");   /* Blue */
 	    }
 	}
     else 
 	{
 	if (val < 0)
 	    {
 	    printf("00");	    /* Red */
 	    hexOne(-val*0.8);    /* Green - brighter than red*/
 	    printf("00");      /* Blue */
 	    }
 	else
 	    {
 	    hexOne(val);
 	    printf("00");
 	    printf("00");
 	    }
 	}
     }
 }
 
 static void startExpCell()
 /* Print out start of expression cell, which contains a table. */
 {
 printf("<TD><TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0><TR>");
 }
 
 static void endExpCell()
 /* Print out end of expression cell, closing up internal table. */
 {
 printf("</TR></TABLE></TD>");
 }
 
 static void restartExpCell()
 /* End expression cell and begin a new one. */
 {
 endExpCell();
 startExpCell();
 }
 
 static void printRatioShades(char *colName, int repCount, 
 	int *reps, int valCount, float *vals, 
 	boolean colorBlindColors,
 	boolean useGrays, boolean logGrays, float scale)
 /* Print out representatives in shades of color in table background. */
 {
 int i;
 float val;
 startExpCell();
 for (i=0; i<repCount; ++i)
     {
     int ix = reps[i];
     if (ix > valCount)
         errAbort("Representative larger than biggest experiment in %s", colName);
     if (ix == -1)
         {
 	restartExpCell();
 	}
     else
 	{
 	val = vals[ix];
 	if (val <= -9999)
 	    printf("<TD WIDTH=%d>&nbsp;</TD>", expSubcellWidth);
 	else
 	    {
 	    printf("<TD WIDTH=%d BGCOLOR='#", expSubcellWidth);
 	    colorVal(val, scale, colorBlindColors, useGrays, logGrays);
 	    printf("'>&nbsp;</TD>");
 	    }
 	}
     }
 endExpCell();
 }
 
 static void replicate(char *s, int repCount, int *reps)
 /* Replicate s in cells of table */
 {
 int i;
 startExpCell();
 printf("%s", s);
 for (i=0; i<repCount; ++i)
     {
     int ix = reps[i];
     if (ix == -1)
         {
 	restartExpCell();
 	printf("%s", s);
 	}
     }
 endExpCell();
 }
 
 void hgExpCellPrint(char *colName, char *geneId, 
 	struct sqlConnection *lookupConn, char *lookupTable,
 	struct sqlConnection *dataConn, char *dataTable,
 	int representativeCount, int *representatives,
 	boolean useBlue, boolean useGrays, boolean logGrays, float scale)
 /* Print out html for expression cell in table. */
 {
 int valCount;
 float *vals = NULL;
 
 if (hgExpLoadVals(lookupConn, dataConn, lookupTable, geneId, dataTable, 
 	&valCount, &vals))
     {
     printRatioShades(colName, representativeCount, representatives, 
     	valCount, vals, useBlue, useGrays, logGrays, scale);
     freez(&vals);
     }
 else
     {
     replicate("<TD>n/a</TD>", representativeCount, representatives);
     }
 }