import java.util.HashMap;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
private static final String ROW_DATA = "<tr><td>%s</td><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
*/
if (sf.otherDetails != null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
for (Entry<String, Object> entry : sf.otherDetails.entrySet())
{
otherDetails.put(entry.getKey(), entry.getValue());
}
if (sf.links != null && sf.links.size() > 0)
{
- links = new Vector<String>();
+ links = new Vector<>();
for (int i = 0, iSize = sf.links.size(); i < iSize; i++)
{
links.addElement(sf.links.elementAt(i));
{
if (links == null)
{
- links = new Vector<String>();
+ links = new Vector<>();
}
if (!links.contains(labelLink))
/**
* Answers the value of the specified attribute as string, or null if no such
- * value
+ * value. If more than one attribute name is provided, tries to resolve as keys
+ * to nested maps. For example, if attribute "CSQ" holds a map of key-value
+ * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
+ * in that map.
*
* @param key
* @return
*/
- public String getValueAsString(String key)
+ public String getValueAsString(String... key)
{
if (otherDetails == null)
{
return null;
}
- Object value = otherDetails.get(key);
+ Object value = otherDetails.get(key[0]);
+ if (key.length > 1 && value instanceof Map<?, ?>)
+ {
+ value = ((Map) value).get(key[1]);
+ }
return value == null ? null : value.toString();
}
{
if (otherDetails == null)
{
- otherDetails = new HashMap<String, Object>();
+ otherDetails = new HashMap<>();
}
otherDetails.put(key, value);
- FeatureAttributes.getInstance().addAttribute(this.type, key);
+ recordAttribute(key, value);
}
}
+ /**
+ * Notifies the addition of a feature attribute. This lets us keep track of
+ * which attributes are present on each feature type, and also the range of
+ * numerical-valued attributes.
+ *
+ * @param key
+ * @param value
+ */
+ protected void recordAttribute(String key, Object value)
+ {
+ String attDesc = null;
+ if (source != null)
+ {
+ attDesc = FeatureSources.getInstance().getSource(source)
+ .getAttributeName(key);
+ }
+
+ FeatureAttributes.getInstance().addAttribute(this.type, attDesc, value,
+ key);
+ }
+
/*
* The following methods are added to maintain the castor Uniprot mapping file
* for the moment.
{
continue; // to avoid double reporting
}
- if (INFO_KEYS.containsKey(key))
+
+ Object value = entry.getValue();
+ if (value instanceof Map<?, ?>)
{
/*
- * split selected INFO data by delimiter over multiple lines
+ * expand values in a Map attribute across separate lines
+ * copy to a TreeMap for alphabetical ordering
*/
- String delimiter = INFO_KEYS.get(key);
- String[] values = entry.getValue().toString().split(delimiter);
- for (String value : values)
+ Map<String, Object> values = (Map<String, Object>) value;
+ SortedMap<String, Object> sm = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
+ sm.putAll(values);
+ for (Entry<?, ?> e : sm.entrySet())
{
- sb.append(String.format(ROW_DATA, key, "", value));
+ sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
+ .getValue().toString()));
}
}
else
- { // tried <td title="key"> but it failed to provide a tooltip :-(
+ {
+ // tried <td title="key"> but it failed to provide a tooltip :-(
String attDesc = null;
if (metadata != null)
{
attDesc = metadata.getAttributeName(key);
}
- String value = entry.getValue().toString();
- if (isValueInteresting(key, value, metadata))
+ String s = entry.getValue().toString();
+ if (isValueInteresting(key, s, metadata))
{
sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
- : attDesc, value));
+ : attDesc, s));
}
}
}