src/hg/hgc/t2g.c 1.5

Index: src/hg/hgc/t2g.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/t2g.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/hgc/t2g.c	20 May 2010 21:07:27 -0000	1.4
+++ src/hg/hgc/t2g.c	20 May 2010 22:28:05 -0000	1.5
@@ -1,145 +1,143 @@
 /* t2g.c - display details of text2genome stuff */
 
 #include "common.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgc.h"
 #include "trackDb.h"
 #include "web.h"
 #include "hash.h"
+#include "obscure.h"
 
 void printPubmedLink(char* pmid) 
 {
     printf("<B>PubMed:</B>&nbsp;<A HREF=\"http://www.ncbi.nlm.nih.gov/pubmed/%s\" TARGET=_blank>%s</A><BR>\n", pmid, pmid);
 }
 
 void printPmcLink(char* pmcId) 
 {
     printf("<B>PubMed&nbsp;Central:</B>&nbsp;<A HREF=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC%s/?tool=pubmed\" TARGET=_blank>%s</A><BR>\n", pmcId, pmcId);
 }
 
 void printT2gLink(char* pmcId) 
 {
     printf("<B>Text2Genome:</B>&nbsp;<A HREF=\"http://kumiho.smith.man.ac.uk/bergman/text2genome/inspector.cgi?pmcId=%s\" TARGET=_blank>%s</A><BR>\n", pmcId, pmcId);
 }
 
 void printLinks(char* pmid, char* pmcId) 
 {
     printT2gLink(pmcId);
     printPubmedLink(pmid);
     printPmcLink(pmcId);
     printf("<BR>\n");
 }
 
 char* printArticleInfo(struct sqlConnection *conn, struct trackDb* tdb, char* item) 
 /* Header with information about paper, return documentId */
 {
     char query[512];
     char* articleTable = hashMustFindVal(tdb->settingsHash, "articleTable");
 
     safef(query, sizeof(query), "SELECT pmid, pmcId, title,authors, abstract FROM %s WHERE displayId='%s'", articleTable, item);
     struct sqlResult *sr = sqlGetResult(conn, query);
     char **row;
     char *docId=0;
     if ((row = sqlNextRow(sr)) != NULL)
 	{
 	printLinks(row[0], row[1]);
 	printf("<b>%s</b>", row[2]);
 	printf("<p style=\"font-size:96%%\">%s</p>", row[3]);
 	printf("<p style=\"font-size:92%%\">%s</p>", row[4]);
         docId = row[1];
 	}
     sqlFreeResult(&sr);
     return docId;
 }
 
 void printSeqInfo(struct sqlConnection* conn, struct trackDb* tdb,  char* docId) {
     /* print table of sequences */
     char query[512];
     char* sequenceTable = hashMustFindVal(tdb->settingsHash, "sequenceTable");
     safef(query, sizeof(query), "SELECT seqId, sequence FROM %s WHERE pmcId='%s'", sequenceTable, docId);
     struct sqlResult *sr = sqlGetResult(conn, query);
     char **row;
 
     webNewSection("Sequences in article");
 	webPrintLinkTableStart();
     while ((row = sqlNextRow(sr)) != NULL)
 	{
         webPrintLinkCell(row[1]);
         webPrintLinkTableNewRow();
         //printf("%s<br>", row[1]);
 	}
 	webPrintLinkTableEnd();
 
     sqlFreeResult(&sr);
     printTrackHtml(tdb);
 }
 
 void doT2gDetails(struct trackDb *tdb, char *item)
 /* text2genome.org custom display */
 {
+int start = cgiInt("o");
+int end = cgiInt("t");
 char versionString[256];
 char dateReference[256];
 char headerTitle[512];
-char **row = NULL;
-char query[512];
-struct sqlResult *sr = NULL;
-struct sqlConnection *conn = hAllocConn(database); // where the heck does "database" come from?
-safef(query, sizeof(query), "select chrom,chromStart,chromEnd,strand from %s "
-      "where name = '%s'", tdb->table, item);
-sr = sqlGetResult(conn, query);
-row = sqlNextRow(sr);
-char *chr = cloneString(row[0]);
-int start = sqlUnsigned(row[1]);
-int end = sqlUnsigned(row[2]);
-char strand[2];
-strand[0] = row[3][0];
-strand[1] = (char)NULL;
-sqlFreeResult(&sr);
+struct sqlConnection *conn = hAllocConn(database);
 
 /* see if hgFixed.trackVersion exists */
 boolean trackVersionExists = hTableExists("hgFixed", "trackVersion");
 
 if (trackVersionExists)
     {
     char query[256];
     safef(query, sizeof(query), "select version,dateReference from hgFixed.trackVersion where db = '%s' AND name = 't2g' order by updateTime DESC limit 1", database);
     struct sqlResult *sr = sqlGetResult(conn, query);
     char **row;
 
     /* in case of NULL result from the table */
     versionString[0] = 0;
     while ((row = sqlNextRow(sr)) != NULL)
 	{
 	safef(versionString, sizeof(versionString), "version %s",
 		row[0]);
 	safef(dateReference, sizeof(dateReference), "%s",
 		row[1]);
 	}
     sqlFreeResult(&sr);
     }
 else
     {
     versionString[0] = 0;
     dateReference[0] = 0;
     }
 
 if (versionString[0])
     safef(headerTitle, sizeof(headerTitle), "%s - %s", item, versionString);
 else
     safef(headerTitle, sizeof(headerTitle), "%s", item);
 
 genericHeader(tdb, headerTitle);
-printPos(chr, start, end, strand, FALSE, item);
-freeMem(chr);
+
+printf("<B>Position:</B>&nbsp;"
+           "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">",
+                  hgTracksPathAndSettings(), database, seqName, start+1, end);
+char startBuf[64], endBuf[64];
+sprintLongWithCommas(startBuf, start + 1);
+sprintLongWithCommas(endBuf, end);
+printf("%s:%s-%s</A><BR>\n", seqName, startBuf, endBuf);
+long size = end - start;
+sprintLongWithCommas(startBuf, size);
+printf("<B>Genomic Size:</B>&nbsp;%s<BR>\n", startBuf);
 
 char* docId = printArticleInfo(conn, tdb, item);
 
 
 if (docId!=0) 
 {
     printSeqInfo(conn, tdb, docId);
 }
 hFreeConn(&conn);
 }