ff9313091f342ffe62a124427b5c9d6a516faaea
hiram
Thu Oct 15 15:03:07 2015 -0700
fixup gcc warnings for -Wunused-but-set-variable refs #16121
diff --git src/hg/hgc/lowelab.c src/hg/hgc/lowelab.c
index f865e17..a367911 100644
--- src/hg/hgc/lowelab.c
+++ src/hg/hgc/lowelab.c
@@ -989,162 +989,151 @@
hFreeConn(&conn);
}
/*Code to display Sargasso Sea Information*/
void doSargassoSea(struct trackDb *tdb, char *trnaName)
{
struct bed *cb=NULL;
struct sargassoSeaXra *cbs=NULL, *cbs2, *list=NULL;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char query[512];
char *dupe, *words[16];
char **row;
char tempstring[255]="";
-int flag, z, dashes, wordCount, rowOffset;
-int start = cartInt(cart, "o"), num = 0, flag2=0;
+int z, dashes, wordCount;
+int start = cartInt(cart, "o"), num = 0;
float sequenceLength, dashlength=60;
genericHeader(tdb,trnaName);
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
if (wordCount > 1)
num = atoi(words[1]);
if (num < 3) num = 3;
genericBedClick(conn, tdb, trnaName, start, num);
-rowOffset = hOffsetPastBin(database, seqName, tdb->table);
sqlSafef(query, sizeof query, "select * from %s where name = '%s'", tdb->table, trnaName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
cb=bedLoadN(row+1, 6);
sequenceLength=(cb->chromEnd - cb->chromStart);
if(sequenceLength<0){ sequenceLength=sequenceLength*-1;}
sequenceLength=sequenceLength/3;
dashlength=sequenceLength/60;
/*Query the database for the extrainfo file for sargassoSea*/
conn=hAllocConn(database);/*sqlConnect(dupe);*/
sqlSafef(tempstring, sizeof(tempstring),"select * from sargassoSeaXra where qname = '%s'", trnaName);
sr = sqlGetResult(conn, tempstring);
/*Load the required data from the database*/
while ((row = sqlNextRow(sr)) != NULL)
{
cbs=sargassoSeaXraLoad(row);
slAddHead(&list, cbs);
}
slReverse(&list);
-flag=0;
-flag2=0;
-
/*Print out table with Blast information*/
printf(" \n\n
");
printf("
Organism");
printf(" \n | \n ");
printf("Nucleotides \naligned begin");
printf(" \n | \n ");
printf("Nucelotides \naligned end");
printf(" \n | \n NCBI Link");
printf(" \n | \n ");
printf("Evalue");
printf(" \n | \n ");
printf("Percent Identity");
printf(" \n | \n ");
printf("Alignment Length");
printf(" \n | \n "); printf("Gap openings"); printf(" | \n
");
printf("",cbs2->GI);
printf("%s",cbs2->GI,cbs2->species);
printf(" \n | \n ");
printf("%i",cbs2->thisseqstart);
printf(" \n | \n ");
printf("%i",cbs2->thisseqend);
printf(" \n | \n ");
printf("NCBI Link",cbs2->GI);
printf(" \n | \n ");
printf("%s",cbs2->evalue);
printf(" \n | \n ");
printf("%.2f",cbs2->PI);
printf(" \n | \n ");
printf("%i",cbs2->length);
printf(" \n | \n ");
printf("%i",cbs2->gap);
printf(" | \n
Organism");
printf(" \n | \n Alignment"); printf(" | \n
%s where each plus(+) is approx. %.1f amino acids", trnaName, dashlength);
printf(" \n | \n ");
printf("\n");
for(z=0; z<60; z++)
{
printf("+");
}
printf(" ");
printf(" | \n
"); dashes=cbs2->queryseqstart-cbs2->queryseqend; if(dashes<0) dashes=dashes*-1; printf("",cbs2->GI); printf("%s, %s",cbs2->GI, cbs2->species,cbs2->qName); printf("\n | \n");
printf("\n");
dashes=dashes/dashlength;
if(cbs2->queryseqstart>cbs2->queryseqend)
for(z=0; z<((cbs2->queryseqend)/dashlength); z++)
{
printf(" ");
}
else
for(z=0; z<((cbs2->queryseqstart)/dashlength); z++)
{
printf(" ");
}
if(dashes<1) printf("+");
for(z=0; z | \n
\n");
trna = tRNAsLoad(row+rowOffset);
printf("tRNA name: %s \n",trna->name); printf("tRNA Isotype: %s \n",trna->aa); printf("tRNA anticodon: %s \n",trna->ac); printf("tRNAscan-SE score: %.2f \n",trna->trnaScore); @@ -1265,38 +1250,34 @@ printf(" |
%s\n",snorna->guideStr); printf("Possible sRNA homolog(s): %s
\n");
for(z=0; z<60; z++)
{
printf("+");
}
printf("
");
printf("