*/
package jalview.datamodel;
+import jalview.datamodel.features.FeatureAttributeType;
import jalview.datamodel.features.FeatureLocationI;
+import jalview.datamodel.features.FeatureSourceI;
+import jalview.datamodel.features.FeatureSources;
import jalview.util.StringUtils;
import java.util.HashMap;
// 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>";
+ private static final String ROW_DATA = "<tr><td width=\"10%%\">%s</td><td width=\"50%%\">%s</td><td width=\"40%%\">%s</td></tr>";
/*
* map of otherDetails special keys, and their value fields' delimiter
public Vector<String> links;
+ /*
+ * the identifier (if known) for the FeatureSource held in FeatureSources,
+ * as a provider of metadata about feature attributes
+ */
+ private String source;
+
/**
* Constructs a duplicate feature. Note: Uses makes a shallow copy of the
* otherDetails map, so the new and original SequenceFeature may reference the
*/
public String getDetailsReport()
{
+ FeatureSourceI metadata = FeatureSources.getInstance()
+ .getSource(source);
+
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, "Type", type, ""));
sb.append(String.format(ROW_DATA, "Start/end", begin == end ? begin
- : begin + (isContactFeature() ? ":" : "-") + end));
+ : begin + (isContactFeature() ? ":" : "-") + end, ""));
String desc = StringUtils.stripHtmlTags(description);
- sb.append(String.format(ROW_DATA, "Description", desc));
+ sb.append(String.format(ROW_DATA, "Description", desc, ""));
if (!Float.isNaN(score) && score != 0f)
{
- sb.append(String.format(ROW_DATA, "Score", score));
+ sb.append(String.format(ROW_DATA, "Score", score, ""));
}
if (featureGroup != null)
{
- sb.append(String.format(ROW_DATA, "Group", featureGroup));
+ sb.append(String.format(ROW_DATA, "Group", featureGroup, ""));
}
if (otherDetails != null)
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>");
+ sb.append(String.format(ROW_DATA, key, "", value));
}
}
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>");
+ String attDesc = null;
+ if (metadata != null)
+ {
+ attDesc = metadata.getAttributeName(key);
+ }
+ String value = entry.getValue().toString();
+ if (isValueInteresting(key, value, metadata))
+ {
+ sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
+ : attDesc, value));
+ }
}
}
}
String text = sb.toString();
return text;
}
+
+ /**
+ * Answers true if we judge the value is worth displaying, by some heuristic
+ * rules, else false
+ *
+ * @param key
+ * @param value
+ * @param metadata
+ * @return
+ */
+ boolean isValueInteresting(String key, String value,
+ FeatureSourceI metadata)
+ {
+ /*
+ * currently suppressing zero values as well as null or empty
+ */
+ if (value == null || "".equals(value) || ".".equals(value)
+ || "0".equals(value))
+ {
+ return false;
+ }
+
+ if (metadata == null)
+ {
+ return true;
+ }
+
+ FeatureAttributeType attributeType = metadata.getAttributeType(key);
+ if (attributeType == FeatureAttributeType.Float
+ || attributeType.equals(FeatureAttributeType.Integer))
+ {
+ try
+ {
+ float fval = Float.valueOf(value);
+ if (fval == 0f)
+ {
+ return false;
+ }
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ }
+
+ return true; // default to interesting
+ }
+
+ /**
+ * Sets the feature source identifier
+ *
+ * @param theSource
+ */
+ public void setSource(String theSource)
+ {
+ source = theSource;
+ }
}