public class AlignedCodonFrame
{
- /*
- * Data bean to hold mappings from one sequence to another
- */
- public class SequenceToSequenceMapping
- {
- private SequenceI fromSeq;
-
- private Mapping mapping;
-
- SequenceToSequenceMapping(SequenceI from, Mapping map)
- {
- this.fromSeq = from;
- this.mapping = map;
- }
-
- /**
- * Readable representation for debugging only, not guaranteed not to change
- */
- @Override
- public String toString()
- {
- return String.format("From %s %s", fromSeq.getName(),
- mapping.toString());
- }
-
- /**
- * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
- *
- * @see SequenceToSequenceMapping#hashCode()
- */
- @Override
- public int hashCode()
- {
- return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
- + mapping.hashCode();
- }
-
- /**
- * Answers true if the objects hold the same mapping between the same two
- * sequences
- *
- * @see Mapping#equals
- */
- @Override
- public boolean equals(Object obj)
- {
- if (!(obj instanceof SequenceToSequenceMapping))
- {
- return false;
- }
- SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
- if (this.mapping == null)
- {
- return that.mapping == null;
- }
- // TODO: can simplify by asserting fromSeq is a dataset sequence
- return (this.fromSeq == that.fromSeq || (this.fromSeq != null
- && that.fromSeq != null
- && this.fromSeq.getDatasetSequence() != null && this.fromSeq
- .getDatasetSequence() == that.fromSeq
- .getDatasetSequence())) && this.mapping.equals(that.mapping);
- }
-
- public SequenceI getFromSeq()
- {
- return fromSeq;
- }
-
- public Mapping getMapping()
- {
- return mapping;
- }
- }
-
- private List<SequenceToSequenceMapping> mappings;
+ private List<SequenceMapping> mappings;
/**
* Constructor
*/
public AlignedCodonFrame()
{
- mappings = new ArrayList<SequenceToSequenceMapping>();
+ mappings = new ArrayList<>();
}
/**
SequenceI fromSeq = (dnaseq.getDatasetSequence() == null) ? dnaseq
: dnaseq.getDatasetSequence();
- SequenceI toSeq = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
- .getDatasetSequence();
+ SequenceI toSeq = (aaseq.getDatasetSequence() == null) ? aaseq
+ : aaseq.getDatasetSequence();
/*
* if we already hold a mapping between these sequences, just add to it
* note that 'adding' a duplicate map does nothing; this protects against
* creating duplicate mappings in AlignedCodonFrame
*/
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.fromSeq == fromSeq && ssm.mapping.to == toSeq)
{
*/
Mapping mp = new Mapping(toSeq, map);
mp.setMappedFromId(mapFromId);
- mappings.add(new SequenceToSequenceMapping(fromSeq, mp));
+ mappings.add(new SequenceMapping(fromSeq, mp));
}
public SequenceI[] getdnaSeqs()
{
// TODO return a list instead?
// return dnaSeqs;
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- for (SequenceToSequenceMapping ssm : mappings)
+ List<SequenceI> seqs = new ArrayList<>();
+ for (SequenceMapping ssm : mappings)
{
seqs.add(ssm.fromSeq);
}
public SequenceI[] getAaSeqs()
{
// TODO not used - remove?
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- for (SequenceToSequenceMapping ssm : mappings)
+ List<SequenceI> seqs = new ArrayList<>();
+ for (SequenceMapping ssm : mappings)
{
seqs.add(ssm.mapping.to);
}
public MapList[] getdnaToProt()
{
- List<MapList> maps = new ArrayList<MapList>();
- for (SequenceToSequenceMapping ssm : mappings)
+ List<MapList> maps = new ArrayList<>();
+ for (SequenceMapping ssm : mappings)
{
maps.add(ssm.mapping.map);
}
public Mapping[] getProtMappings()
{
- List<Mapping> maps = new ArrayList<Mapping>();
- for (SequenceToSequenceMapping ssm : mappings)
+ List<Mapping> maps = new ArrayList<>();
+ for (SequenceMapping ssm : mappings)
{
maps.add(ssm.mapping);
}
* @param seq
* @return
*/
- public Mapping getMappingForSequence(SequenceI seq)
+ public Mapping getMappingForSequence(SequenceI seq, boolean cdsOnly)
{
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.fromSeq == seqDs || ssm.mapping.to == seqDs)
{
- return ssm.mapping;
+ if (!cdsOnly || ssm.fromSeq.getName().startsWith("CDS")
+ || ssm.mapping.to.getName().startsWith("CDS"))
+ {
+ return ssm.mapping;
+ }
}
}
return null;
public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
{
SequenceI dnads = dnaSeqRef.getDatasetSequence();
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.fromSeq == dnaSeqRef || ssm.fromSeq == dnads)
{
public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
{
SequenceI aads = aaSeqRef.getDatasetSequence();
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.mapping.to == aaSeqRef || ssm.mapping.to == aads)
{
* where highlighted regions go
*/
public void markMappedRegion(SequenceI seq, int index,
- SearchResults results)
+ SearchResultsI results)
{
int[] codon;
SequenceI ds = seq.getDatasetSequence();
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.fromSeq == seq || ssm.fromSeq == ds)
{
*/
MapList ml = null;
int i = 0;
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.fromSeq == seq)
{
/*
* Search mapped protein ('to') sequences first.
*/
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
{
/*
* Then try mapped dna sequences.
*/
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.mapping.to == seq
|| ssm.mapping.to == seq.getDatasetSequence())
{
SequenceI targetDs = target.getDatasetSequence() == null ? target
: target.getDatasetSequence();
- SequenceI queryDs = query.getDatasetSequence() == null ? query : query
- .getDatasetSequence();
+ SequenceI queryDs = query.getDatasetSequence() == null ? query
+ : query.getDatasetSequence();
if (targetDs == null || queryDs == null /*|| dnaToProt == null*/)
{
return null;
}
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
/*
* try mapping from target to query
{
MapList ml = null;
SequenceI dnaSeq = null;
- List<char[]> result = new ArrayList<char[]>();
+ List<char[]> result = new ArrayList<>();
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
if (ssm.mapping.to == protein
&& ssm.mapping.getMap().getFromRatio() == 3)
* Read off the mapped nucleotides (converting to position base 0)
*/
codonPos = MappingUtils.flattenRanges(codonPos);
- char[] dna = dnaSeq.getSequence();
int start = dnaSeq.getStart();
- result.add(new char[] { dna[codonPos[0] - start],
- dna[codonPos[1] - start], dna[codonPos[2] - start] });
+ char c1 = dnaSeq.getCharAt(codonPos[0] - start);
+ char c2 = dnaSeq.getCharAt(codonPos[1] - start);
+ char c3 = dnaSeq.getCharAt(codonPos[2] - start);
+ result.add(new char[] { c1, c2, c3 });
}
}
return result.isEmpty() ? null : result;
*/
public List<Mapping> getMappingsFromSequence(SequenceI seq)
{
- List<Mapping> result = new ArrayList<Mapping>();
- List<SequenceI> related = new ArrayList<SequenceI>();
+ List<Mapping> result = new ArrayList<>();
+ List<SequenceI> related = new ArrayList<>();
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
final Mapping mapping = ssm.mapping;
if (ssm.fromSeq == seqDs)
*/
protected int realiseWith(SequenceI seq, boolean doUpdate)
{
- SequenceI ds = seq.getDatasetSequence() != null ? seq
- .getDatasetSequence() : seq;
+ SequenceI ds = seq.getDatasetSequence() != null
+ ? seq.getDatasetSequence()
+ : seq;
int count = 0;
/*
* check for replaceable DNA ('map from') sequences
*/
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
{
SequenceI dna = ssm.fromSeq;
if (dna instanceof SequenceDummy
{
int start = replacement.getStart();
int end = replacement.getEnd();
- boolean mappingOverlapsSequence = (mapStart >= start && mapStart <= end)
- || (mapEnd >= start && mapEnd <= end);
+ boolean mappingOverlapsSequence = (mapStart >= start
+ && mapStart <= end) || (mapEnd >= start && mapEnd <= end);
if (mappingOverlapsSequence)
{
return true;
}
SequenceI ds = seq.getDatasetSequence();
- for (SequenceToSequenceMapping ssm : mappings)
+ for (SequenceMapping ssm : mappings)
/*
* 'from' sequences
*/
}
/**
- * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or null
- * if none found
+ * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or
+ * null if none found
*
* @param fromSeq
* aligned or dataset sequence
{
SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
: fromSeq.getDatasetSequence();
- SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq : toSeq
- .getDatasetSequence();
+ SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq
+ : toSeq.getDatasetSequence();
- for (SequenceToSequenceMapping mapping : mappings)
+ for (SequenceMapping mapping : mappings)
{
SequenceI from = mapping.fromSeq;
SequenceI to = mapping.mapping.to;
/**
* Returns a hashcode derived from the list of sequence mappings
*
- * @see SequenceToSequenceMapping#hashCode()
+ * @see SequenceMapping#hashCode()
* @see AbstractList#hashCode()
*/
@Override
return this.mappings.equals(((AlignedCodonFrame) obj).mappings);
}
- public List<SequenceToSequenceMapping> getMappings()
+ public List<SequenceMapping> getMappings()
{
return mappings;
}