* restrict from range to make them match up
* it's kind of arbitrary which end we truncate - here it is the end
*/
- System.err.print("Truncating mapping from " + Arrays.toString(from)
- + " to ");
+ System.err.print(
+ "Truncating mapping from " + Arrays.toString(from) + " to ");
if (from[1] > from[0])
{
from[1] -= fromOverlap / toRatio;
/*
* restrict to range to make them match up
*/
- System.err.print("Truncating mapping to " + Arrays.toString(to)
- + " to ");
+ System.err.print(
+ "Truncating mapping to " + Arrays.toString(to) + " to ");
if (to[1] > to[0])
{
to[1] -= fromOverlap / fromRatio;
/**
* Parses the input line to a map of name / value(s) pairs. For example the
* line <br>
- * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal <br>
+ * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal
+ * <br>
* if parsed with delimiter=";" and separators {' ', '='} <br>
* would return a map with { Notes={Fe=S, Metal}, Method={manual curation,
* prediction}, source={Pfam}} <br>
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> attributes)
{
+ return buildSequenceFeature(gff, TYPE_COL, gff[SOURCE_COL], attributes);
+ }
+
+ /**
+ * @param gff
+ * @param typeColumn
+ * @param group
+ * @param attributes
+ * @return
+ */
+ protected SequenceFeature buildSequenceFeature(String[] gff,
+ int typeColumn, String group, Map<String, List<String>> attributes)
+ {
try
{
int start = Integer.parseInt(gff[START_COL]);
// e.g. '.' - leave as zero
}
- SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
- gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
+ SequenceFeature sf = new SequenceFeature(gff[typeColumn],
+ gff[SOURCE_COL], start, end, score, group);
sf.setStrand(gff[STRAND_COL]);
*/
for (Entry<String, List<String>> attr : attributes.entrySet())
{
- String values = StringUtils.listToDelimitedString(
- attr.getValue(), ",");
+ String values = StringUtils.listToDelimitedString(attr.getValue(),
+ ",");
sf.setValue(attr.getKey(), values);
if (NOTE.equals(attr.getKey()))
{