*/
package jalview.analysis;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
import jalview.ws.seqfetcher.ASequenceFetcher;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
/**
* Functions for cross-referencing sequence databases. user must first specify
* if cross-referencing from protein or dna (set dna==true)
for (int rs = 0; rs < retrieved.length; rs++)
{
// TODO: examine each sequence for 'redundancy'
- jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
+ DBRefEntry[] dbr = retrieved[rs]
.getDBRef();
if (dbr != null && dbr.length > 0)
{
{
// find any entry where we should put in the sequence being
// cross-referenced into the map
- jalview.datamodel.Mapping map = dbr[di].getMap();
+ Mapping map = dbr[di].getMap();
if (map != null)
{
if (map.getTo() != null && map.getMap() != null)
// check if this is the correct sequence type
{
typer[0] = nxt;
- boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+ boolean isDna = Comparison.isNucleotide(typer);
if ((direct && isDna == dna) || (!direct && isDna != dna))
{
// skip this sequence because it is same molecule type
DBRefEntry[] poss = nxt.getDBRef(), cands = null;
if (direct)
{
- cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+ cands = DBRefUtils.searchRefs(poss, xrf);
}
else
{
poss = CrossRef.findXDbRefs(dna, poss); //
- cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+ cands = DBRefUtils.searchRefs(poss, xrf);
}
if (cands != null)
{