package jalview.datamodel;
import jalview.datamodel.features.FeatureLocationI;
+import jalview.util.StringUtils;
import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.TreeMap;
import java.util.Vector;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * A class that models a single contiguous feature on a sequence. If flag
+ * 'contactFeature' is true, the start and end positions are interpreted instead
+ * as two contact points.
*/
public class SequenceFeature implements FeatureLocationI
{
// private key for ENA location designed not to conflict with real GFF data
private static final String LOCATION = "!Location";
+ private static final String ROW_DATA = "<tr><td>%s</td><td>%s</td></tr>";
+
+ /*
+ * map of otherDetails special keys, and their value fields' delimiter
+ */
+ private static final Map<String, String> INFO_KEYS = new HashMap<>();
+
+ static
+ {
+ INFO_KEYS.put("CSQ", ",");
+ // todo capture second level metadata (CSQ FORMAT)
+ // and delimiter "|" so as to report in a table within a table?
+ }
+
/*
* ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
* name1=value1;name2=value2,value3;...etc
{
return begin == 0 && end == 0;
}
+
+ /**
+ * Answers an html-formatted report of feature details
+ *
+ * @return
+ */
+ public String getDetailsReport()
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("<br>");
+ sb.append("<table>");
+ sb.append(String.format(ROW_DATA, "Type", type));
+ sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
+ String desc = StringUtils.stripHtmlTags(description);
+ sb.append(String.format(ROW_DATA, "Description", desc));
+ if (!Float.isNaN(score) && score != 0f)
+ {
+ sb.append(String.format(ROW_DATA, "Score", score));
+ }
+ if (featureGroup != null)
+ {
+ sb.append(String.format(ROW_DATA, "Group", featureGroup));
+ }
+
+ if (otherDetails != null)
+ {
+ TreeMap<String, Object> ordered = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ ordered.putAll(otherDetails);
+
+ for (Entry<String, Object> entry : ordered.entrySet())
+ {
+ String key = entry.getKey();
+ if (ATTRIBUTES.equals(key))
+ {
+ continue; // to avoid double reporting
+ }
+ if (INFO_KEYS.containsKey(key))
+ {
+ /*
+ * split selected INFO data by delimiter over multiple lines
+ */
+ String delimiter = INFO_KEYS.get(key);
+ String[] values = entry.getValue().toString().split(delimiter);
+ for (String value : values)
+ {
+ sb.append("<tr><td>").append(key).append("</td><td>")
+ .append(value)
+ .append("</td></tr>");
+ }
+ }
+ else
+ { // tried <td title="key"> but it failed to provide a tooltip :-(
+ sb.append("<tr><td>").append(key).append("</td><td>");
+ sb.append(entry.getValue().toString()).append("</td></tr>");
+ }
+ }
+ }
+ sb.append("</table>");
+
+ String text = sb.toString();
+ return text;
+ }
}