target = link.substring(0, sep);
sep = link.lastIndexOf("|");
label = link.substring(0, sep);
- url_prefix = link.substring(sep + 1);
+ url_prefix = link.substring(sep + 1).trim();
regexReplace = null; // implies we trim any prefix if necessary //
// regexReplace=".*\\|?(.*)";
url_suffix = null;
*/
protected void parseUrl(String link, String varName, int sqidPos, int sep)
{
- url_prefix = link.substring(sep + 1, sqidPos);
+ url_prefix = link.substring(sep + 1, sqidPos).trim();
// delimiter at start of regex: e.g. $SEQUENCE_ID=/
String startDelimiter = "$" + varName + "=/";
}
/**
+ * Create a set of URL links for a sequence
*
- * @param urlLink
* @param seq
+ * The sequence to create links for
* @param linkset
+ * Map of links: key = id | link, value = [target, label, id, link]
*/
public void createLinksFromSeq(final SequenceI seq,
Map<String, List<String>> linkset)
* Create a static URL link
*
* @param linkset
+ * Map of links: key = id | link, value = [target, label, id, link]
*/
- public void createStaticLink(Map<String, List<String>> linkset)
+ protected void createStaticLink(Map<String, List<String>> linkset)
{
if (!linkset.containsKey(label + "|" + getUrl_prefix()))
{
}
/**
- * Create a dynamic URL link
+ * Create dynamic URL links
*
* @param seq
+ * The sequence to create links for
* @param linkset
+ * Map of links: key = id | link, value = [target, label, id, link]
*/
- public void createDynamicLinks(final SequenceI seq,
+ protected void createDynamicLinks(final SequenceI seq,
Map<String, List<String>> linkset)
{
// collect id string too
for (int r = 0; r < dbr.length; r++)
{
// create Bare ID link for this URL
- createBareURLLink(dbr[r].getAccessionId(), linkset, true);
+ createBareURLLink(dbr[r].getAccessionId(), true, linkset);
}
}
}
else if (!usesSeqId() && id != null) // link is name
{
// create Bare ID link for this URL
- createBareURLLink(id, linkset, false);
+ createBareURLLink(id, false, linkset);
}
// Create urls from description but only for URL links which are regex
if (descr != null && getRegexReplace() != null)
{
// create link for this URL from description where regex matches
- createBareURLLink(descr, linkset, false);
+ createBareURLLink(descr, false, linkset);
}
}
/*
* Create a bare URL Link
+ * Returns map where key = id | link, and value = [target, label, id, link]
*/
- protected void createBareURLLink(String id,
- Map<String, List<String>> linkset, Boolean combineLabel)
+ protected void createBareURLLink(String id, Boolean combineLabel,
+ Map<String, List<String>> linkset)
{
String[] urls = makeUrls(id, true);
if (urls != null)
String thisLabel = label;
if (combineLabel)
{
+ // incorporate label with idstring
thisLabel = label + "|" + urls[u];
}