int[] to = new int[] { toStart, toEnd };
/*
- * Jalview always models from dna to protein, so switch values if the
- * GFF mapping is from protein to dna
+ * Jalview always models from dna to protein, so invert
+ * mapping if the GFF mapping is from protein to dna
*/
- if (mappingType == MappingType.PeptideToNucleotide)
+ if (MappingType.isPeptideToDna(mappingType))
{
int[] temp = from;
from = to;
to = temp;
- mappingType = mappingType.getInverse();
+ mappingType = MappingType.CdsToPeptide;
}
int fromRatio = mappingType.getFromRatio();
* 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>
String namesDelimiter, char nameValueSeparator,
String valuesDelimiter)
{
- Map<String, List<String>> map = new HashMap<String, List<String>>();
+ Map<String, List<String>> map = new HashMap<>();
if (text == null || text.trim().length() == 0)
{
return map;
List<String> vals = map.get(key);
if (vals == null)
{
- vals = new ArrayList<String>();
+ vals = new ArrayList<>();
map.put(key, vals);
}
for (String val : values.split(valuesDelimiter))
*/
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()))
{