import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.DynamicData;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.GffConstants;
-import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Comparator;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
void appendFeature(final StringBuilder sb, int rpos,
Map<String, float[][]> minmax, SequenceFeature feature)
{
- String tmpString;
- if (feature.getType().equals("disulfide bond"))
+ if (feature.isContactFeature())
{
if (feature.getBegin() == rpos || feature.getEnd() == rpos)
{
{
sb.append("<br>");
}
- sb.append("disulfide bond ").append(feature.getBegin()).append(":")
+ sb.append(feature.getType()).append(" ").append(feature.getBegin())
+ .append(":")
.append(feature.getEnd());
}
}
if (feature.getDescription() != null
&& !feature.description.equals(feature.getType()))
{
- tmpString = feature.getDescription();
+ String tmpString = feature.getDescription();
String tmp2up = tmpString.toUpperCase();
int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
// check score should be shown
if (!Float.isNaN(feature.getScore()))
{
- float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(feature.getType()));
+ float[][] rng = (minmax == null) ? null : minmax.get(feature
+ .getType());
if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
{
- sb.append(" Score=" + feature.getScore());
+ sb.append(" Score=").append(String.valueOf(feature.getScore()));
}
}
String status = (String) feature.getValue("status");
{
try
{
- for (String[] urllink : createLinksFrom(null, urlstring))
+ for (List<String> urllink : createLinksFrom(null, urlstring))
{
sb.append("<br/> <a href=\""
- + urllink[3]
+ + urllink.get(3)
+ "\" target=\""
- + urllink[0]
+ + urllink.get(0)
+ "\">"
- + (urllink[0].toLowerCase().equals(
- urllink[1].toLowerCase()) ? urllink[0]
- : (urllink[0] + ":" + urllink[1]))
+ + (urllink.get(0).toLowerCase()
+ .equals(urllink.get(1).toLowerCase()) ? urllink
+ .get(0) : (urllink.get(0) + ":" + urllink
+ .get(1)))
+ "</a></br>");
}
} catch (Exception x)
*
* @param seq
* @param link
- * @return String[][] { String[] { link target, link label, dynamic component
- * inserted (if any), url }}
+ * @return Collection< List<String> > { List<String> { link target, link
+ * label, dynamic component inserted (if any), url }}
*/
- String[][] createLinksFrom(SequenceI seq, String link)
+ Collection<List<String>> createLinksFrom(SequenceI seq, String link)
{
- List<String[]> urlSets = new ArrayList<String[]>();
- List<String> uniques = new ArrayList<String>();
+ Map<String, List<String>> urlSets = new LinkedHashMap<String, List<String>>();
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
System.err.println(urlLink.getInvalidMessage());
return null;
}
- final String target = urlLink.getTarget(); // link.substring(0,
- // link.indexOf("|"));
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
- {
- urlSets.addAll(createDynamicLinks(seq, urlLink, uniques));
- }
- else
- {
- String unq = label + "|" + urlLink.getUrl_prefix();
- if (!uniques.contains(unq))
- {
- uniques.add(unq);
- urlSets.add(new String[] { target, label, null,
- urlLink.getUrl_prefix() });
- }
- }
-
- return urlSets.toArray(new String[][] {});
- }
- /**
- * Formats and returns a list of dynamic href links
- *
- * @param seq
- * @param urlLink
- * @param uniques
- */
- List<String[]> createDynamicLinks(SequenceI seq, UrlLink urlLink,
- List<String> uniques)
- {
- List<String[]> result = new ArrayList<String[]>();
- final String target = urlLink.getTarget();
- final String label = urlLink.getLabel();
+ urlLink.createLinksFromSeq(seq, urlSets);
- // collect matching db-refs
- DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { target });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this URL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- String unq = urls[u] + "|" + urls[u + 1];
- if (!uniques.contains(unq))
- {
- result.add(new String[] { target, label, urls[u], urls[u + 1] });
- uniques.add(unq);
- }
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this URL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- String unq = urls[u] + "|" + urls[u + 1];
- if (!uniques.contains(unq))
- {
- result.add(new String[] { target, label, urls[u], urls[u + 1] });
- uniques.add(unq);
- }
- }
- }
- }
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description only if regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- String unq = urls[u] + "|" + urls[u + 1];
- if (!uniques.contains(unq))
- {
- result.add(new String[] { target, label, urls[u], urls[u + 1] });
- uniques.add(unq);
- }
- }
- }
- }
- return result;
+ return urlSets.values();
}
public void createSequenceAnnotationReport(final StringBuilder tip,
}
}
sb.append("</i>");
+ List<PDBEntry> pdbEntries = ds.getAllPDBEntries();
+ sb.append(getToolTipTextFromPDBEntries(pdbEntries));
return maxWidth;
}
+ private String getToolTipTextFromPDBEntries(List<PDBEntry> pdbEntries)
+ {
+ String tooltip = "";
+ if (pdbEntries.isEmpty())
+ {
+ return tooltip;
+ }
+ if (pdbEntries.size() > 1)
+ {
+ int x = 0;
+ PDBEntry bestRanked = null;
+ for (PDBEntry pdb : pdbEntries)
+ {
+ if (pdb.getProperty("DYNAMIC_DATA_PHYRE2") != null)
+ {
+ x++;
+ }
+ // best ranked entry must be from a Phyre
+ if (x > 0 && bestRanked == null)
+ {
+ bestRanked = pdb;
+ }
+ }
+ tooltip = (x > 0) ? "<table border=\"1\" width=100%><tr><td>Contains <b>"
+ + x
+ + "</b> Phyre2 model structure(s)</td></tr>"
+ + "<tr><td>Best ranked Phyre2 model is <b>"
+ + bestRanked.getId() + "</b></td></tr></table>"
+ : "";
+ }
+ else
+ {
+ PDBEntry pdb = pdbEntries.iterator().next();
+ if (pdb.getProperty("DYNAMIC_DATA_PHYRE2") != null)
+ {
+ tooltip = getPhyreToolTipFromDynamicData((List<DynamicData>) pdb
+ .getProperty("DYNAMIC_DATA_PHYRE2"));
+ }
+ }
+ return tooltip;
+ }
+
+ private String getPhyreToolTipFromDynamicData(
+ List<DynamicData> dynamicDataList)
+ {
+ StringBuilder phyre2InfoBuilder = new StringBuilder();
+ phyre2InfoBuilder
+ .append("<html><table border=\"1\" width=100%>")
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ for (DynamicData data : dynamicDataList)
+ {
+ if (data.isDisplay())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append(data.getFieldTitle())
+ .append("</td><td>").append(data.getFieldValue())
+ .append("</td></tr>");
+ }
+ }
+ phyre2InfoBuilder.append("</table></html>");
+ return phyre2InfoBuilder.toString();
+ }
+
public void createTooltipAnnotationReport(final StringBuilder tip,
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
Map<String, float[][]> minmax)
git://source.jalview.org / jalview.git / blobdiff