src/hg/hgc/t2g.c 1.1

Index: src/hg/hgc/t2g.c
===================================================================
RCS file: src/hg/hgc/t2g.c
diff -N src/hg/hgc/t2g.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/hgc/t2g.c	20 May 2010 18:30:00 -0000	1.1
@@ -0,0 +1,112 @@
+/* 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"
+
+void printPubmedLink(char* pmid) 
+{
+    printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/pubmed/%s\">PubMed</A>", pmid);
+}
+
+void printPmcLink(char* pmcId) 
+{
+    printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC%s/?tool=pubmed\">PubmedCentral</A>", pmcId);
+}
+
+void printT2gLink(char* pmcId) 
+{
+    printf("<A HREF=\"http://kumiho.smith.man.ac.uk/bergman/text2genome/inspector.cgi?pmcId=%s\">text2genome</A>", pmcId);
+}
+
+void printLinks(char* pmid, char* pmcId) 
+{
+    printf("Links: ");
+    printf("<SMALL>");
+    printT2gLink(pmcId);
+    printf(", ");
+    printPubmedLink(pmid);
+    printf(", ");
+    printPmcLink(pmcId);
+    printf("</SMALL><P>");
+}
+
+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><p>", row[2]);
+	printf("<small>%s</small><p>", row[3]);
+	printf("<small>%s</small>", 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 */
+{
+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 = row[0];
+int start = sqlUnsigned(row[1]);
+int end = sqlUnsigned(row[2]);
+char strand[2];
+strand[0] = row[3][0];
+strand[1] = (char)NULL;
+//cartWebStart(cart, database, "Article information ");
+genericHeader(tdb, "Article information");
+printf("<B>Item:</B>&nbsp;%s<BR>\n", item);
+printPos(chr, start, end, strand, TRUE, item);
+sqlFreeResult(&sr);
+char* docId=0;
+docId = printArticleInfo(conn, tdb, item);
+
+if (docId!=0) 
+{
+    printSeqInfo(conn, tdb, docId);
+}
+hFreeConn(&conn);
+}