import java.util.Locale;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import jalview.bin.Console;
import jalview.commands.RemoveGapColCommand;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.util.MapList;
import jalview.util.MappingUtils;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
.toLowerCase(Locale.ROOT).toCharArray();
char[] downstream = new String(
- ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT)
- .toCharArray();
+ ds.getSequence(s_end - 1, s_end + dstream_ds))
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
+ coreseq.length];
if (cdnaLength != mappedLength && cdnaLength > 2)
{
String lastCodon = String.valueOf(cdnaSeqChars,
- cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT);
+ cdnaLength - CODON_LENGTH, CODON_LENGTH)
+ .toUpperCase(Locale.ROOT);
for (String stop : ResidueProperties.STOP_CODONS)
{
if (lastCodon.equals(stop))
*/
int startOffset = 0;
if (cdnaLength != mappedLength && cdnaLength > 2
- && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT)
+ && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH)
+ .toUpperCase(Locale.ROOT)
.equals(ResidueProperties.START))
{
startOffset += CODON_LENGTH;
mapList = mapList.getInverse();
}
final int cdsLength = cdsDss.getLength();
- int mappedFromLength = MappingUtils.getLength(mapList
- .getFromRanges());
+ int mappedFromLength = MappingUtils
+ .getLength(mapList.getFromRanges());
int mappedToLength = MappingUtils
.getLength(mapList.getToRanges());
boolean addStopCodon = (cdsLength == mappedFromLength
productSeqs = new HashSet<>();
for (SequenceI seq : products)
{
- productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
- .getDatasetSequence());
+ productSeqs.add(seq.getDatasetSequence() == null ? seq
+ : seq.getDatasetSequence());
}
}
dataset.addSequence(cdsSeqDss);
AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
- cdsToProteinMap);
+ cdsToProteinMap);
/*
* guard against duplicating the mapping if repeating this action
List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs();
for (int ip = 0, np = primrefs.size(); ip < np; ip++)
{
- DBRefEntry primRef = primrefs.get(ip);
+ DBRefEntry primRef = primrefs.get(ip);
/*
* create a cross-reference from CDS to the source sequence's
* primary reference and vice versa
*/
String source = primRef.getSource();
String version = primRef.getVersion();
- DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":"
- + version, primRef.getAccessionId());
- cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap)));
+ DBRefEntry cdsCrossRef = new DBRefEntry(source,
+ source + ":" + version, primRef.getAccessionId());
+ cdsCrossRef
+ .setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap)));
cdsSeqDss.addDBRef(cdsCrossRef);
- dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
- .getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
+ dnaSeq.addDBRef(new DBRefEntry(source, version,
+ cdsSeq.getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
// problem here is that the cross-reference is synthesized -
// cdsSeq.getName() may be like 'CDS|dnaaccession' or
// 'CDS|emblcdsacc'
DBRefEntry proteinToCdsRef = new DBRefEntry(source, version,
cdsSeq.getName());
//
- proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
- .getInverse()));
+ proteinToCdsRef.setMap(
+ new Mapping(cdsSeqDss, cdsToProteinMap.getInverse()));
proteinProduct.addDBRef(proteinToCdsRef);
}
/*
}
}
- AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
- .size()]));
+ AlignmentI cds = new Alignment(
+ cdsSeqs.toArray(new SequenceI[cdsSeqs.size()]));
cds.setDataset(dataset);
return cds;
SequenceI newSeq = null;
- final MapList maplist = mapping.getMap();
- if (maplist.isContiguous() && maplist.isFromForwardStrand())
- {
- /*
- * just a subsequence, keep same dataset sequence
- */
- int start = maplist.getFromLowest();
- int end = maplist.getFromHighest();
- newSeq = seq.getSubSequence(start - 1, end);
- newSeq.setName(seqId);
- }
- else
- {
- /*
- * construct by splicing mapped from ranges
- */
- char[] seqChars = seq.getSequence();
- List<int[]> fromRanges = maplist.getFromRanges();
- int cdsWidth = MappingUtils.getLength(fromRanges);
- char[] newSeqChars = new char[cdsWidth];
+ /*
+ * construct CDS sequence by splicing mapped from ranges
+ */
+ char[] seqChars = seq.getSequence();
+ List<int[]> fromRanges = mapping.getMap().getFromRanges();
+ int cdsWidth = MappingUtils.getLength(fromRanges);
+ char[] newSeqChars = new char[cdsWidth];
- int newPos = 0;
- for (int[] range : fromRanges)
+ int newPos = 0;
+ for (int[] range : fromRanges)
+ {
+ if (range[0] <= range[1])
{
- if (range[0] <= range[1])
- {
- // forward strand mapping - just copy the range
- int length = range[1] - range[0] + 1;
- System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
- length);
- newPos += length;
- }
- else
+ // forward strand mapping - just copy the range
+ int length = range[1] - range[0] + 1;
+ System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
+ length);
+ newPos += length;
+ }
+ else
+ {
+ // reverse strand mapping - copy and complement one by one
+ for (int i = range[0]; i >= range[1]; i--)
{
- // reverse strand mapping - copy and complement one by one
- for (int i = range[0]; i >= range[1]; i--)
- {
- newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
- }
+ newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
}
}
}
else
{
- System.err.println(
- "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
+ Console.error(
+ "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:"
+ mtch.toString());
}
}
/*
* get features, optionally restricted by an ontology term
*/
- List<SequenceFeature> sfs = select == null ? fromSeq.getFeatures()
- .getPositionalFeatures() : fromSeq.getFeatures()
- .getFeaturesByOntology(select);
+ List<SequenceFeature> sfs = select == null
+ ? fromSeq.getFeatures().getPositionalFeatures()
+ : fromSeq.getFeatures().getFeaturesByOntology(select);
int count = 0;
for (SequenceFeature sf : sfs)
{
List<int[]> result = new ArrayList<>();
- List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology(
- SequenceOntologyI.CDS);
+ List<SequenceFeature> sfs = dnaSeq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.CDS);
if (sfs.isEmpty())
{
return result;
int phase = 0;
try
{
- String s = sf.getPhase();
- if (s != null)
- {
- phase = Integer.parseInt(s);
- }
+ String s = sf.getPhase();
+ if (s != null)
+ {
+ phase = Integer.parseInt(s);
+ }
} catch (NumberFormatException e)
{
// leave as zero
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
- // BH 2019.01.25 recoded to remove iterators
-
+ // BH 2019.01.25 recoded to remove iterators
+
for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
{
- SequenceI xref = xrefs[ix];
+ SequenceI xref = xrefs[ix];
List<DBRefEntry> dbrefs = xref.getDBRefs();
if (dbrefs != null)
{
* true; else returns false
*
* @param unaligned
- * - sequences to be aligned based on aligned
+ * - sequences to be aligned based on aligned
* @param aligned
- * - 'guide' alignment containing sequences derived from same
- * dataset as unaligned
+ * - 'guide' alignment containing sequences derived from same dataset
+ * as unaligned
* @return
*/
static boolean alignAsSameSequences(AlignmentI unaligned,
{
return false;
}
- SequenceI alignedSeq = alignedDatasets.get(ds)
- .get(0);
+ SequenceI alignedSeq = alignedDatasets.get(ds).get(0);
int startCol = alignedSeq.findIndex(seq.getStart()); // 1..
leftmost = Math.min(leftmost, startCol);
}
git://source.jalview.org / jalview.git / blobdiff