/**
* Updates Interaction Data.
*
* @param searchHit Search Hit Object.
* @param interactionBundleModel Interaction Bundle Model.
*/
private void updateInteractionData(
ExtendedRecordType searchHit, InteractionBundleModel interactionBundleModel) {
RecordList recordList = parentRecordsMap.get(searchHit.getPrimaryId());
if (recordList != null) {
interactionBundleModel.setRecordList(recordList);
} else {
SummaryResponseType summaryResponseType = new SummaryResponseType();
recordList = new RecordList(summaryResponseType);
interactionBundleModel.setRecordList(recordList);
}
interactionBundleModel.setPhysicalEntityName(searchHit.getName());
}
/**
* Updates Pathway Data.
*
* @param searchHit SearchHit Object.
* @param pathwayTableModel Pathway Table Model.
*/
private void updatePathwayData(
ExtendedRecordType searchHit, PathwayTableModel pathwayTableModel) {
List<PathwayType> pathwayList = searchHit.getPathwayList().getPathway();
Vector dataVector = pathwayTableModel.getDataVector();
dataVector.removeAllElements();
if (pathwayList != null) {
pathwayTableModel.setRowCount(pathwayList.size());
pathwayTableModel.resetInternalIds(pathwayList.size());
// Only set the column count, if it is not already set.
// If we reset the column count, the user-modified column widths are lost.
if (pathwayTableModel.getColumnCount() != 2) {
pathwayTableModel.setColumnCount(2);
}
if (pathwayList.size() == 0) {
pathwayTableModel.setRowCount(1);
pathwayTableModel.setValueAt("No pathways found.", 0, 0);
} else {
for (int i = 0; i < pathwayList.size(); i++) {
PathwayType pathway = pathwayList.get(i);
pathwayTableModel.setValueAt(pathway.getName(), i, 0);
pathwayTableModel.setValueAt(pathway.getDataSource().getName(), i, 1);
pathwayTableModel.setInternalId(i, pathway.getPrimaryId());
}
}
}
}
/**
* Select the Phsyical Entity specified by the selected index.
*
* @param peSearchResponse SearchResponseType peSearchResponse.
* @param selectedIndex Selected Index.
* @param interactionBundleModel Interaction Table Model.
* @param pathwayTableModel Pathway Table Model.
* @param summaryDocumentModel Summary Document Model.
*/
public void selectPhysicalEntity(
SearchResponseType peSearchResponse,
int selectedIndex,
InteractionBundleModel interactionBundleModel,
PathwayTableModel pathwayTableModel,
Document summaryDocumentModel,
JTextPane textPane,
JComponent textPaneOwner) {
if (peSearchResponse != null) {
java.util.List<ExtendedRecordType> searchHits = peSearchResponse.getSearchHit();
ExtendedRecordType searchHit = searchHits.get(selectedIndex);
StringBuffer html = new StringBuffer();
html.append("<html>");
html.append("<h2>" + searchHit.getName() + "</h2>");
OrganismType organism = searchHit.getOrganism();
if (organism != null) {
String speciesName = organism.getSpeciesName();
html.append("<H3>" + speciesName + "</H3>");
}
// Next, add synonyms
List<String> synList = searchHit.getSynonym();
StringBuffer synBuffer = new StringBuffer();
if (synList != null && synList.size() > 0) {
for (String synonym : synList) {
if (!synonym.equalsIgnoreCase(searchHit.getName())) {
synBuffer.append("<LI>- " + synonym + "</LI>");
}
}
if (synBuffer.length() > 0) {
html.append("<h4>Synonyms:</h4>");
html.append("<UL>");
html.append(synBuffer.toString());
html.append("</UL>");
}
}
// Next, add XRefs
List<XRefType> xrefList = searchHit.getXref();
if (xrefList != null && xrefList.size() > 0) {
html.append("<H4>Links:</H4>");
html.append("<UL>");
for (XRefType xref : xrefList) {
String url = xref.getUrl();
if (url != null && url.length() > 0) {
html.append(
"<LI>- <a class=\"link\" href=\""
+ url
+ "\">"
+ xref.getDb()
+ ": "
+ xref.getId()
+ "</a></LI>");
} else {
html.append("<LI>- " + xref.getDb() + ": " + xref.getId() + "</LI>");
}
}
html.append("</UL>");
}
List<String> excerptList = searchHit.getExcerpt();
if (excerptList != null && excerptList.size() > 0) {
String primeExcerpt = null;
for (String excerpt : excerptList) {
if (primeExcerpt == null || excerpt.length() > primeExcerpt.length()) {
if (!excerpt.equalsIgnoreCase(searchHit.getName())) {
primeExcerpt = excerpt;
}
}
}
if (primeExcerpt != null) {
html.append("<H4>Matching Excerpt(s):</H4>");
html.append("<span class='excerpt'>" + primeExcerpt + "</span><BR>");
}
}
// Temporarily removed comments.
// java.util.List<String> commentList = searchHit.getComment();
// if (commentList != null) {
// html.append("<BR><B>Description:</B>");
// for (int i = commentList.size() - 1; i >= 0; i--) {
// html.append("<BR>" + commentList.get(i) + "<BR>");
// }
// }
html.append("</html>");
textPane.setText(html.toString());
textPane.setCaretPosition(0);
updatePathwayData(searchHit, pathwayTableModel);
updateInteractionData(searchHit, interactionBundleModel);
textPaneOwner.repaint();
}
}
