*/
public SequenceFeature(SequenceFeature cpy)
{
- this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
- .getScore());
+ this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(),
+ cpy.getScore());
}
/**
/**
* Answers the value of the specified attribute as string, or null if no such
- * 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.
+ * 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
sb.append("<br>");
sb.append("<table>");
String name = mf == null ? seqName : mf.getLinkedSequenceName();
- sb.append(String.format(ROW_DATA, "Location", name,
- begin == end ? begin
- : begin + (isContactFeature() ? ":" : "-") + end));
+ sb.append(String.format(ROW_DATA, "Location", name, begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
String consequence = "";
if (mf != null)
{
- int[] beginRange = mf.getMappedPositions(begin, begin);
- int[] endRange = mf.getMappedPositions(end, end);
- int from = beginRange[0];
- int to = endRange[endRange.length - 1];
+ int[] localRange = mf.getMappedPositions(begin, end);
+ int from = localRange[0];
+ int to = localRange[localRange.length - 1];
String s = mf.isFromCds() ? "Peptide Location" : "Coding location";
sb.append(String.format(ROW_DATA, s, seqName, from == to ? from
: from + (isContactFeature() ? ":" : "-") + to));
sm.putAll(values);
for (Entry<?, ?> e : sm.entrySet())
{
- sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
- .getValue().toString()));
+ sb.append(String.format(ROW_DATA, key, e.getKey().toString(),
+ e.getValue().toString()));
}
}
else
String s = entry.getValue().toString();
if (isValueInteresting(key, s, metadata))
{
- sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
- : attDesc, s));
+ sb.append(String.format(ROW_DATA, key,
+ attDesc == null ? "" : attDesc, s));
}
}
}
}
FeatureAttributeType attType = metadata.getAttributeType(key);
- if (attType != null
- && (attType == FeatureAttributeType.Float || attType
- .equals(FeatureAttributeType.Integer)))
+ if (attType != null && (attType == FeatureAttributeType.Float
+ || attType.equals(FeatureAttributeType.Integer)))
{
try
{