");
printf(
"
",
hgTracksPathAndSettings(), database, seqName, start+1, end, articleId, pslTrack, dispId);
printf("Show these sequence matches individually on genome browser (activates track \""
"Individual matches for article\")
");
@@ -458,58 +460,64 @@
articleSource = row[7];
extId = row[8];
url = mangleUrl(url);
if (strlen(abstract)==0)
abstract = "(No abstract available for this article. "
"Please follow the link to the fulltext above by clicking on the titel or the fulltext image.)";
if (stringIn("sciencedirect.com", url))
{
pubsHasSupp = FALSE;
pubsIsElsevier = TRUE;
}
// authors title
-printf("
\n");
+printf("
\n");
printf("
%s
\n", authors);
-printf("
%s\n", url, title);
-
+//
// logo of publisher
char *logoUrl = urlToLogoUrl(conn, pubsArticleTable, articleId, url);
if (logoUrl)
printf("
![](\"%s\")
\n", url, logoUrl);
freeMem(logoUrl);
+
+printf("
\n", url, title);
+printf("
\n");
printf("
\n");
-printf("
%s", cit);
+
+printf("
%s", cit);
if (strlen(pmid)!=0 && strcmp(pmid, "0"))
printf(", PMID%s\n", pmid, pmid);
printf("
\n");
-printf("
%s
\n", abstract);
+printf("
%s
\n", abstract);
if (pubsIsElsevier)
printf("
Copyright 2012 Elsevier B.V. All rights reserved.
");
sqlFreeResult(&sr);
return articleId;
}
static struct hash *getSeqIdHash(struct sqlConnection *conn, char *trackTable, \
char *articleId, char *item, char *seqName, int start)
/* return a hash with the sequence IDs for a given chain of BLAT matches */
{
+if (start==-1)
+ return NULL;
char query[512];
/* check first if the column exists (some debugging tables on hgwdev don't have seqIds) */
safef(query, sizeof(query), "SHOW COLUMNS FROM %s LIKE 'seqIds';", trackTable);
char *seqIdPresent = sqlQuickString(conn, query);
if (!seqIdPresent) {
return NULL;
}
/* get sequence-Ids for feature that was clicked (item&startPos are unique) and return as hash*/
safef(query, sizeof(query), "SELECT seqIds,'' FROM %s WHERE name='%s' "
"and chrom='%s' and chromStart=%d;", trackTable, item, seqName, start);
if (pubsDebug)
printf("%s
", query);
// split comma-sep list into parts
@@ -537,31 +545,31 @@
web2StartTableC("stdTbl centeredStdTbl");
web2StartTheadC("stdTblHead");
if (showDesc)
web2PrintHeaderCell("Article file", 10);
// yif sequences have no flanking text at M. Krauthammer's request
if (stringIn("yif", articleSource))
web2PrintHeaderCell("Matching sequences", 60);
else
web2PrintHeaderCell("One row per sequence, with flanking text, sequence in bold", 60);
if (pubsDebug)
web2PrintHeaderCell("Identifiers", 30);
if (!isClickedSection && !pubsDebug)
- web2PrintHeaderCell("Chained matches with this sequence", 20);
+ web2PrintHeaderCell("Link to matching genomic location", 20);
web2EndThead();
web2StartTbodyS("font-family: Arial, Helvetica, sans-serif; line-height: 1.5em; font-size: 0.9em;");
}
static void printAddWbr(char *text, int distance)
/* a crazy hack for firefox/mozilla that is unable to break long words in tables
* We need to add a
tag every x characters in the text to make text breakable.
*/
{
int i;
i = 0;
char *c;
c = text;
bool doNotBreak = FALSE;
while (*c != 0)
@@ -683,31 +691,31 @@
"FROM %s WHERE articleId='%s';", pubsSequenceTable, articleId);
if (pubsDebug)
puts(query);
struct sqlResult *sr = sqlGetResult(conn, query);
// construct title for section
char *otherFormat = NULL;
if (fasta)
otherFormat = "table";
else
otherFormat = "fasta";
char fullTitle[5000];
safef(fullTitle, sizeof(fullTitle),
"%s (%s format)\n",
-title, cartSidUrlString(cart), cgiString("o"), cgiString("t"), cgiString("g"), cgiString("i"),
+title, cartSidUrlString(cart), cgiOptionalString("o"), cgiOptionalString("t"), cgiString("g"), cgiString("i"),
!fasta, otherFormat);
web2StartSection("pubsSection", "%s", fullTitle);
// print filtering link at start of table & table headers
if (isClickedSection) {
printFilterLink(pslTable, articleId, articleTable);
}
if (!fasta)
printSeqHeaders(showDesc, isClickedSection);
// output rows
char **row;
@@ -832,31 +840,36 @@
bool skippedRows;
if (clickedSeqs)
skippedRows = printSeqSection(articleId, "Sequences matching here", \
fileDesc, conn, clickedSeqs, 1, fasta, pslTable, articleTable);
else
skippedRows=1;
if (skippedRows)
{
// the section title should change if the data comes from the yale image finder = a figure
char* docType = "article";
if (stringIn("yif", articleSource))
docType = "figure";
char title[1024];
+ if (clickedSeqs)
safef(title, sizeof(title), "Other Sequences in this %s", docType);
+ // NO clicked seqs can happen if the hgc was called with no o or t parameters
+ // from somewhere outside the browser, like elsevier or europmc
+ else
+ safef(title, sizeof(title), "Sequences in this %s", docType);
printSeqSection(articleId, title, \
fileDesc, conn, clickedSeqs, 0, fasta, pslTable, articleTable);
}
freeHash(&clickedSeqs);
}
static void printTrackVersion(struct trackDb *tdb, struct sqlConnection *conn, char *item)
{
char versionString[256];
char dateReference[256];
char headerTitle[512];
/* see if hgFixed.trackVersion exists */
boolean trackVersionExists = hTableExists("hgFixed", "trackVersion");
@@ -961,32 +974,32 @@
}
psl->blockSizes[i] = bs/3;
}
}
else
qt = gftDna;
showSomeAlignment(psl, oSeq, qt, 0, oSeq->size, NULL, 0, 0);
}
void doPubsDetails(struct trackDb *tdb, char *item)
/* publications custom display */
{
-int start = cgiInt("o");
-int end = cgiOptionalInt("t", 0);
+int start = cgiOptionalInt("o", -1);
+int end = cgiOptionalInt("t", -1);
char *trackTable = cgiString("g");
char *aliTable = cgiOptionalString("aliTable");
int fasta = cgiOptionalInt("fasta", 0);
pubsDebug = cgiOptionalInt("debug", 0);
struct sqlConnection *conn = hAllocConn(database);
char *articleTable = trackDbRequiredSetting(tdb, "pubsArticleTable");
if (stringIn("Psl", trackTable))
{
if (aliTable!=NULL)
{
pubsSequenceTable = trackDbRequiredSetting(tdb, "pubsSequenceTable");
pubsAli(conn, trackTable, pubsSequenceTable, item);
@@ -995,33 +1008,35 @@
else
{
genericHeader(tdb, item);
struct psl *psl = getAlignments(conn, trackTable, item);
printf("Genomic Alignment with sequence found in publication fulltext
");
printAlignmentsSimple(psl, start, trackTable, trackTable, item);
}
}
else
{
printTrackVersion(tdb, conn, item);
if (stringIn("Marker", trackTable))
{
char *markerTable = trackDbRequiredSetting(tdb, "pubsMarkerTable");
+ if (start!=-1)
printPositionAndSize(start, end, 0);
printMarkerSnippets(conn, articleTable, markerTable, item);
}
else
{
pubsSequenceTable = trackDbRequiredSetting(tdb, "pubsSequenceTable");
char *articleId = printArticleInfo(conn, item, articleTable);
if (articleId!=NULL)
{
char *pslTable = trackDbRequiredSetting(tdb, "pubsPslTrack");
- printSeqInfo(conn, trackTable, pslTable, articleId, item, seqName, start, pubsHasSupp, fasta, articleTable);
+ printSeqInfo(conn, trackTable, pslTable, articleId, item, \
+ seqName, start, pubsHasSupp, fasta, articleTable);
}
}
}
printTrackHtml(tdb);
hFreeConn(&conn);
}