* @param ac2
* @return
*/
- public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+ public static final int compareCodonPos(AlignedCodon ac1,
+ AlignedCodon ac2)
{
return comparator.compare(ac1, ac2);
// return jalview_2_8_2compare(ac1, ac2);
mappedrefs.add(ref); // add translated protein maps
}
}
- dnarefs = mappedrefs;//.toArray(new DBRefEntry[mappedrefs.size()]);
+ dnarefs = mappedrefs;// .toArray(new DBRefEntry[mappedrefs.size()]);
for (int d = 0, nd = dnarefs.size(); d < nd; d++)
{
Mapping mp = dnarefs.get(d).getMap();
/*
* Filled up a reading frame...
*/
- AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+ cdp[2]);
String aa = codeTable.translate(new String(codon));
rf = 0;
final String gapString = String.valueOf(gapChar);
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
MapList map)
{
- // BH 2019.01.25 nop?
-// List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
-// DBRefSource.DNACODINGDBS);
-// if (dnarefs != null)
-// {
-// // intersect with pep
-// for (int d = 0, nd = dnarefs.size(); d < nd; d++)
-// {
-// Mapping mp = dnarefs.get(d).getMap();
-// if (mp != null)
-// {
-// }
-// }
-// }
+ // BH 2019.01.25 nop?
+ // List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+ // DBRefSource.DNACODINGDBS);
+ // if (dnarefs != null)
+ // {
+ // // intersect with pep
+ // for (int d = 0, nd = dnarefs.size(); d < nd; d++)
+ // {
+ // Mapping mp = dnarefs.get(d).getMap();
+ // if (mp != null)
+ // {
+ // }
+ // }
+ // }
for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
{
- if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ {
+ // if (map.intersectsFrom(sf[f].begin, sf[f].end))
{
- // if (map.intersectsFrom(sf[f].begin, sf[f].end))
- {
- }
}
+ }
}
}