import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntologyFactory;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.io.gff.SequenceOntologyI;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.DBRefUtils;
+import jalview.util.IntRangeComparator;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.StringUtils;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
-import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Map.Entry;
import java.util.NoSuchElementException;
import java.util.Set;
+import java.util.SortedMap;
import java.util.TreeMap;
/**
{
private static final int CODON_LENGTH = 3;
+
private static final String SEQUENCE_VARIANT = "sequence_variant:";
+
private static final String ID = "ID";
/**
*/
if (cdnaLength != mappedLength && cdnaLength > 2)
{
- String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - CODON_LENGTH, CODON_LENGTH)
- .toUpperCase();
+ String lastCodon = String.valueOf(cdnaSeqChars,
+ cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
for (String stop : ResidueProperties.STOP)
{
if (lastCodon.equals(stop))
int aaPos = 0;
int dnaPos = cdnaStart;
- for (; dnaPos < cdnaSeqChars.length - 2
- && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
+ for (; dnaPos < cdnaSeqChars.length - 2 && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
{
String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
final String translated = ResidueProperties.codonTranslate(codon);
int toOffset = alignTo.getStart() - 1;
int sourceGapMappedLength = 0;
boolean inExon = false;
- final char[] thisSeq = alignTo.getSequence();
- final char[] thatAligned = alignFrom.getSequence();
- StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
+ final int toLength = alignTo.getLength();
+ final int fromLength = alignFrom.getLength();
+ StringBuilder thisAligned = new StringBuilder(2 * toLength);
/*
* Traverse the 'model' aligned sequence
*/
- for (char sourceChar : thatAligned)
+ for (int i = 0; i < fromLength; i++)
{
+ char sourceChar = alignFrom.getCharAt(i);
if (sourceChar == sourceGap)
{
sourceGapMappedLength += ratio;
*/
int intronLength = 0;
while (basesWritten + toOffset < mappedCodonEnd
- && thisSeqPos < thisSeq.length)
+ && thisSeqPos < toLength)
{
- final char c = thisSeq[thisSeqPos++];
+ final char c = alignTo.getCharAt(thisSeqPos++);
if (c != myGapChar)
{
basesWritten++;
int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
preserveUnmappedGaps, sourceGapMappedLength, inExon,
trailingCopiedGap.length(), intronLength, startOfCodon);
- for (int i = 0; i < gapsToAdd; i++)
+ for (int k = 0; k < gapsToAdd; k++)
{
thisAligned.append(myGapChar);
}
* At end of model aligned sequence. Copy any remaining target sequence, optionally
* including (intron) gaps.
*/
- while (thisSeqPos < thisSeq.length)
+ while (thisSeqPos < toLength)
{
- final char c = thisSeq[thisSeqPos++];
+ final char c = alignTo.getCharAt(thisSeqPos++);
if (c != myGapChar || preserveUnmappedGaps)
{
thisAligned.append(c);
.println("alignCdsSequenceAsProtein needs aligned sequence!");
return false;
}
-
+
List<AlignedCodonFrame> dnaMappings = MappingUtils
.findMappingsForSequence(cdsSeq, mappings);
for (AlignedCodonFrame mapping : dnaMappings)
SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein);
if (peptide != null)
{
- int peptideLength = peptide.getLength();
+ final int peptideLength = peptide.getLength();
Mapping map = mapping.getMappingBetween(cdsSeq, peptide);
if (map != null)
{
{
mapList = mapList.getInverse();
}
- int cdsLength = cdsDss.getLength();
+ final int cdsLength = cdsDss.getLength();
int mappedFromLength = MappingUtils.getLength(mapList
.getFromRanges());
int mappedToLength = MappingUtils
.getLength(mapList.getToRanges());
- boolean addStopCodon = (cdsLength == mappedFromLength * CODON_LENGTH + CODON_LENGTH)
+ boolean addStopCodon = (cdsLength == mappedFromLength
+ * CODON_LENGTH + CODON_LENGTH)
|| (peptide.getDatasetSequence().getLength() == mappedFromLength - 1);
if (cdsLength != mappedToLength && !addStopCodon)
{
* walk over the aligned peptide sequence and insert mapped
* codons for residues in the aligned cds sequence
*/
- char[] alignedPeptide = peptide.getSequence();
- char[] nucleotides = cdsDss.getSequence();
int copiedBases = 0;
int cdsStart = cdsDss.getStart();
int proteinPos = peptide.getStart() - 1;
int cdsCol = 0;
- for (char residue : alignedPeptide)
+
+ for (int col = 0; col < peptideLength; col++)
{
+ char residue = peptide.getCharAt(col);
+
if (Comparison.isGap(residue))
{
cdsCol += CODON_LENGTH;
{
for (int j = codon[0]; j <= codon[1]; j++)
{
- char mappedBase = nucleotides[j - cdsStart];
+ char mappedBase = cdsDss.getCharAt(j - cdsStart);
alignedCds[cdsCol++] = mappedBase;
copiedBases++;
}
* append stop codon if not mapped from protein,
* closing it up to the end of the mapped sequence
*/
- if (copiedBases == nucleotides.length - CODON_LENGTH)
+ if (copiedBases == cdsLength - CODON_LENGTH)
{
for (int i = alignedCds.length - 1; i >= 0; i--)
{
break;
}
}
- for (int i = nucleotides.length - CODON_LENGTH; i < nucleotides.length; i++)
+ for (int i = cdsLength - CODON_LENGTH; i < cdsLength; i++)
{
- alignedCds[cdsCol++] = nucleotides[i];
+ alignedCds[cdsCol++] = cdsDss.getCharAt(i);
}
}
cdsSeq.setSequence(new String(alignedCds));
// TODO resolve JAL-2022 so this fudge can be removed
int mappedSequenceCount = protein.getHeight() - unmappedProtein.size();
addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount);
-
+
return alignedCodons;
}
List<SequenceI> unmappedProtein)
{
/*
- * Prefill aligned sequences with gaps before inserting aligned protein
- * residues.
+ * prefill peptide sequences with gaps
*/
int alignedWidth = alignedCodons.size();
char[] gaps = new char[alignedWidth];
Arrays.fill(gaps, protein.getGapCharacter());
- String allGaps = String.valueOf(gaps);
+ Map<SequenceI, char[]> peptides = new HashMap<>();
for (SequenceI seq : protein.getSequences())
{
if (!unmappedProtein.contains(seq))
{
- seq.setSequence(allGaps);
+ peptides.put(seq, Arrays.copyOf(gaps, gaps.length));
}
}
+ /*
+ * Traverse the codons left to right (as defined by CodonComparator)
+ * and insert peptides in each column where the sequence is mapped.
+ * This gives a peptide 'alignment' where residues are aligned if their
+ * corresponding codons occupy the same columns in the cdna alignment.
+ */
int column = 0;
for (AlignedCodon codon : alignedCodons.keySet())
{
.get(codon);
for (Entry<SequenceI, AlignedCodon> entry : columnResidues.entrySet())
{
- // place translated codon at its column position in sequence
- entry.getKey().getSequence()[column] = entry.getValue().product
- .charAt(0);
+ char residue = entry.getValue().product.charAt(0);
+ peptides.get(entry.getKey())[column] = residue;
}
column++;
}
+
+ /*
+ * and finally set the constructed sequences
+ */
+ for (Entry<SequenceI, char[]> entry : peptides.entrySet())
+ {
+ entry.getKey().setSequence(new String(entry.getValue()));
+ }
+
return 0;
}
*/
List<int[]> cdsRange = Collections.singletonList(new int[] { 1,
cdsSeq.getLength() });
- MapList cdsToProteinMap = new MapList(cdsRange, mapList.getToRanges(),
- mapList.getFromRatio(), mapList.getToRatio());
+ MapList cdsToProteinMap = new MapList(cdsRange,
+ mapList.getToRanges(), mapList.getFromRatio(),
+ mapList.getToRatio());
AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
cdsToProteinMap);
*/
AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
- cdsRange, 1,
- 1);
+ cdsRange, 1, 1);
dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
dnaToCdsMap);
if (!mappings.contains(dnaToCdsMapping))
* same source and accession, so need a different accession for
* the CDS from the dna sequence
*/
-
+
// specific use case:
// Genomic contig ENSCHR:1, contains coding regions for ENSG01,
// ENSG02, ENSG03, with transcripts and products similarly named.
// cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01
-
+
// JBPNote: ?? can't actually create an example that demonstrates we
// need to
// synthesize an xref.
-
+
for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
{
// creates a complementary cross-reference to the source sequence's
/*
* transfer any features on dna that overlap the CDS
*/
- transferFeatures(dnaSeq, cdsSeq, cdsToProteinMap, null,
+ transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
SequenceOntologyI.CDS);
}
}
int mappedFromLength = MappingUtils.getLength(aMapping.getMap()
.getFromRanges());
int dnaLength = seqDss.getLength();
- if (mappedFromLength == dnaLength || mappedFromLength == dnaLength - CODON_LENGTH)
+ if (mappedFromLength == dnaLength
+ || mappedFromLength == dnaLength - CODON_LENGTH)
{
return seqDss;
}
for (SequenceToSequenceMapping map : acf.getMappings())
{
Mapping mapping = map.getMapping();
- if (mapping != aMapping && mapping.getMap().getFromRatio() == CODON_LENGTH
+ if (mapping != aMapping
+ && mapping.getMap().getFromRatio() == CODON_LENGTH
&& proteinProduct == mapping.getTo()
&& seqDss != map.getFromSeq())
{
}
}
}
-
+
/*
* assign 'from id' held in the mapping if set (e.g. EMBL protein_id),
* else generate a sequence name
*
* @param fromSeq
* @param toSeq
+ * @param mapping
+ * the mapping from 'fromSeq' to 'toSeq'
* @param select
* if not null, only features of this type are copied (including
* subtypes in the Sequence Ontology)
- * @param mapping
- * the mapping from 'fromSeq' to 'toSeq'
* @param omitting
*/
public static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
copyTo = copyTo.getDatasetSequence();
}
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ /*
+ * get features, optionally restricted by an ontology term
+ */
+ List<SequenceFeature> sfs = select == null ? fromSeq.getFeatures()
+ .getPositionalFeatures() : fromSeq.getFeatures()
+ .getFeaturesByOntology(select);
+
int count = 0;
- SequenceFeature[] sfs = fromSeq.getSequenceFeatures();
- if (sfs != null)
+ for (SequenceFeature sf : sfs)
{
- for (SequenceFeature sf : sfs)
+ String type = sf.getType();
+ boolean omit = false;
+ for (String toOmit : omitting)
{
- String type = sf.getType();
- if (select != null && !so.isA(type, select))
+ if (type.equals(toOmit))
{
- continue;
- }
- boolean omit = false;
- for (String toOmit : omitting)
- {
- if (type.equals(toOmit))
- {
- omit = true;
- }
- }
- if (omit)
- {
- continue;
+ omit = true;
}
+ }
+ if (omit)
+ {
+ continue;
+ }
- /*
- * locate the mapped range - null if either start or end is
- * not mapped (no partial overlaps are calculated)
- */
- int start = sf.getBegin();
- int end = sf.getEnd();
- int[] mappedTo = mapping.locateInTo(start, end);
- /*
- * if whole exon range doesn't map, try interpreting it
- * as 5' or 3' exon overlapping the CDS range
- */
- if (mappedTo == null)
- {
- mappedTo = mapping.locateInTo(end, end);
- if (mappedTo != null)
- {
- /*
- * end of exon is in CDS range - 5' overlap
- * to a range from the start of the peptide
- */
- mappedTo[0] = 1;
- }
- }
- if (mappedTo == null)
+ /*
+ * locate the mapped range - null if either start or end is
+ * not mapped (no partial overlaps are calculated)
+ */
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ int[] mappedTo = mapping.locateInTo(start, end);
+ /*
+ * if whole exon range doesn't map, try interpreting it
+ * as 5' or 3' exon overlapping the CDS range
+ */
+ if (mappedTo == null)
+ {
+ mappedTo = mapping.locateInTo(end, end);
+ if (mappedTo != null)
{
- mappedTo = mapping.locateInTo(start, start);
- if (mappedTo != null)
- {
- /*
- * start of exon is in CDS range - 3' overlap
- * to a range up to the end of the peptide
- */
- mappedTo[1] = toSeq.getLength();
- }
+ /*
+ * end of exon is in CDS range - 5' overlap
+ * to a range from the start of the peptide
+ */
+ mappedTo[0] = 1;
}
+ }
+ if (mappedTo == null)
+ {
+ mappedTo = mapping.locateInTo(start, start);
if (mappedTo != null)
{
- SequenceFeature copy = new SequenceFeature(sf);
- copy.setBegin(Math.min(mappedTo[0], mappedTo[1]));
- copy.setEnd(Math.max(mappedTo[0], mappedTo[1]));
- copyTo.addSequenceFeature(copy);
- count++;
+ /*
+ * start of exon is in CDS range - 3' overlap
+ * to a range up to the end of the peptide
+ */
+ mappedTo[1] = toSeq.getLength();
}
}
+ if (mappedTo != null)
+ {
+ int newBegin = Math.min(mappedTo[0], mappedTo[1]);
+ int newEnd = Math.max(mappedTo[0], mappedTo[1]);
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ sf.getFeatureGroup(), sf.getScore());
+ copyTo.addSequenceFeature(copy);
+ count++;
+ }
}
return count;
}
public static List<int[]> findCdsPositions(SequenceI dnaSeq)
{
List<int[]> result = new ArrayList<int[]>();
- SequenceFeature[] sfs = dnaSeq.getSequenceFeatures();
- if (sfs == null)
+
+ List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology(
+ SequenceOntologyI.CDS);
+ if (sfs.isEmpty())
{
return result;
}
-
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceFeatures.sortFeatures(sfs, true);
int startPhase = 0;
for (SequenceFeature sf : sfs)
{
+ int phase = 0;
+ try
+ {
+ phase = Integer.parseInt(sf.getPhase());
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
/*
- * process a CDS feature (or a sub-type of CDS)
+ * phase > 0 on first codon means 5' incomplete - skip to the start
+ * of the next codon; example ENST00000496384
*/
- if (so.isA(sf.getType(), SequenceOntologyI.CDS))
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ if (result.isEmpty())
{
- int phase = 0;
- try
- {
- phase = Integer.parseInt(sf.getPhase());
- } catch (NumberFormatException e)
- {
- // ignore
- }
- /*
- * phase > 0 on first codon means 5' incomplete - skip to the start
- * of the next codon; example ENST00000496384
- */
- int begin = sf.getBegin();
- int end = sf.getEnd();
- if (result.isEmpty())
+ begin += phase;
+ if (begin > end)
{
- begin += phase;
- if (begin > end)
- {
- // shouldn't happen!
- System.err
- .println("Error: start phase extends beyond start CDS in "
- + dnaSeq.getName());
- }
+ // shouldn't happen!
+ System.err
+ .println("Error: start phase extends beyond start CDS in "
+ + dnaSeq.getName());
}
- result.add(new int[] { begin, end });
}
+ result.add(new int[] { begin, end });
}
/*
* ranges are assembled in order. Other cases should not use this method,
* but instead construct an explicit mapping for CDS (e.g. EMBL parsing).
*/
- Collections.sort(result, new Comparator<int[]>()
- {
- @Override
- public int compare(int[] o1, int[] o2)
- {
- return Integer.compare(o1[0], o2[0]);
- }
- });
+ Collections.sort(result, IntRangeComparator.ASCENDING);
return result;
}
count += computePeptideVariants(peptide, peptidePos, codonVariants);
}
- /*
- * sort to get sequence features in start position order
- * - would be better to store in Sequence as a TreeSet or NCList?
- */
- if (peptide.getSequenceFeatures() != null)
- {
- Arrays.sort(peptide.getSequenceFeatures(),
- new Comparator<SequenceFeature>()
- {
- @Override
- public int compare(SequenceFeature o1, SequenceFeature o2)
- {
- int c = Integer.compare(o1.getBegin(), o2.getBegin());
- return c == 0 ? Integer.compare(o1.getEnd(), o2.getEnd())
- : c;
- }
- });
- }
return count;
}
String trans3Char = StringUtils
.toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
String desc = "p." + residue3Char + peptidePos + trans3Char;
- // set score to 0f so 'graduated colour' option is offered! JAL-2060
SequenceFeature sf = new SequenceFeature(
SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
- peptidePos, 0f, var.getSource());
+ peptidePos, var.getSource());
StringBuilder attributes = new StringBuilder(32);
String id = (String) var.variant.getValue(ID);
if (id != null)
StringBuilder link = new StringBuilder(32);
try
{
- link.append(desc).append(" ").append(id)
+ link.append(desc)
+ .append(" ")
+ .append(id)
.append("|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
.append(URLEncoder.encode(id, "UTF-8"));
sf.addLink(link.toString());
// as if
}
}
- String clinSig = (String) var.variant
- .getValue(CLINICAL_SIGNIFICANCE);
+ String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
if (clinSig != null)
{
sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
* LinkedHashMap ensures we keep the peptide features in sequence order
*/
LinkedHashMap<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<Integer, List<DnaVariant>[]>();
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
- SequenceFeature[] dnaFeatures = dnaSeq.getSequenceFeatures();
- if (dnaFeatures == null)
+ List<SequenceFeature> dnaFeatures = dnaSeq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.SEQUENCE_VARIANT);
+ if (dnaFeatures.isEmpty())
{
return variants;
}
// not handling multi-locus variant features
continue;
}
- if (so.isA(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT))
+ int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
+ if (mapsTo == null)
{
- int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
- if (mapsTo == null)
- {
- // feature doesn't lie within coding region
- continue;
- }
- int peptidePosition = mapsTo[0];
- List<DnaVariant>[] codonVariants = variants.get(peptidePosition);
- if (codonVariants == null)
- {
- codonVariants = new ArrayList[CODON_LENGTH];
- codonVariants[0] = new ArrayList<DnaVariant>();
- codonVariants[1] = new ArrayList<DnaVariant>();
- codonVariants[2] = new ArrayList<DnaVariant>();
- variants.put(peptidePosition, codonVariants);
- }
+ // feature doesn't lie within coding region
+ continue;
+ }
+ int peptidePosition = mapsTo[0];
+ List<DnaVariant>[] codonVariants = variants.get(peptidePosition);
+ if (codonVariants == null)
+ {
+ codonVariants = new ArrayList[CODON_LENGTH];
+ codonVariants[0] = new ArrayList<DnaVariant>();
+ codonVariants[1] = new ArrayList<DnaVariant>();
+ codonVariants[2] = new ArrayList<DnaVariant>();
+ variants.put(peptidePosition, codonVariants);
+ }
- /*
- * extract dna variants to a string array
- */
- String alls = (String) sf.getValue("alleles");
- if (alls == null)
- {
- continue;
- }
- String[] alleles = alls.toUpperCase().split(",");
- int i = 0;
- for (String allele : alleles)
- {
- alleles[i++] = allele.trim(); // lose any space characters "A, G"
- }
+ /*
+ * extract dna variants to a string array
+ */
+ String alls = (String) sf.getValue("alleles");
+ if (alls == null)
+ {
+ continue;
+ }
+ String[] alleles = alls.toUpperCase().split(",");
+ int i = 0;
+ for (String allele : alleles)
+ {
+ alleles[i++] = allele.trim(); // lose any space characters "A, G"
+ }
- /*
- * get this peptide's codon positions e.g. [3, 4, 5] or [4, 7, 10]
- */
- int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
- : MappingUtils.flattenRanges(dnaToProtein.locateInFrom(
- peptidePosition, peptidePosition));
- lastPeptidePostion = peptidePosition;
- lastCodon = codon;
+ /*
+ * get this peptide's codon positions e.g. [3, 4, 5] or [4, 7, 10]
+ */
+ int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
+ : MappingUtils.flattenRanges(dnaToProtein.locateInFrom(
+ peptidePosition, peptidePosition));
+ lastPeptidePostion = peptidePosition;
+ lastCodon = codon;
- /*
- * save nucleotide (and any variant) for each codon position
- */
- for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++)
+ /*
+ * save nucleotide (and any variant) for each codon position
+ */
+ for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++)
+ {
+ String nucleotide = String.valueOf(
+ dnaSeq.getCharAt(codon[codonPos] - dnaStart)).toUpperCase();
+ List<DnaVariant> codonVariant = codonVariants[codonPos];
+ if (codon[codonPos] == dnaCol)
{
- String nucleotide = String.valueOf(
- dnaSeq.getCharAt(codon[codonPos] - dnaStart))
- .toUpperCase();
- List<DnaVariant> codonVariant = codonVariants[codonPos];
- if (codon[codonPos] == dnaCol)
+ if (!codonVariant.isEmpty()
+ && codonVariant.get(0).variant == null)
{
- if (!codonVariant.isEmpty()
- && codonVariant.get(0).variant == null)
- {
- /*
- * already recorded base value, add this variant
- */
- codonVariant.get(0).variant = sf;
- }
- else
- {
- /*
- * add variant with base value
- */
- codonVariant.add(new DnaVariant(nucleotide, sf));
- }
+ /*
+ * already recorded base value, add this variant
+ */
+ codonVariant.get(0).variant = sf;
}
- else if (codonVariant.isEmpty())
+ else
{
/*
- * record (possibly non-varying) base value
+ * add variant with base value
*/
- codonVariant.add(new DnaVariant(nucleotide));
+ codonVariant.add(new DnaVariant(nucleotide, sf));
}
}
+ else if (codonVariant.isEmpty())
+ {
+ /*
+ * record (possibly non-varying) base value
+ */
+ codonVariant.add(new DnaVariant(nucleotide));
+ }
}
}
return variants;
}
newCol++;
}
-
+
/*
* trim trailing gaps
*/
* @param unmapped
* @return
*/
- static Map<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
+ static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
{
/*
* {unalignedSequence, characterPerSequence} at that position.
* TreeMap keeps the entries in ascending column order.
*/
- Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
/*
* record any sequences that have no mapping so can't be realigned
.getInverse());
}
- char[] fromChars = fromSeq.getSequence();
int toStart = seq.getStart();
- char[] toChars = seq.getSequence();
/*
* traverse [start, end, start, end...] ranges in fromSeq
* of the next character of the mapped-to sequence; stop when all
* the characters of the range have been counted
*/
- while (mappedCharPos <= range[1] && fromCol <= fromChars.length
+ while (mappedCharPos <= range[1] && fromCol <= fromSeq.getLength()
&& fromCol >= 0)
{
- if (!Comparison.isGap(fromChars[fromCol - 1]))
+ if (!Comparison.isGap(fromSeq.getCharAt(fromCol - 1)))
{
/*
* mapped from sequence has a character in this column
seqsMap = new HashMap<SequenceI, Character>();
map.put(fromCol, seqsMap);
}
- seqsMap.put(seq, toChars[mappedCharPos - toStart]);
+ seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart));
mappedCharPos++;
}
fromCol += (forward ? 1 : -1);