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package jalview.analysis; |
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import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE; |
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import jalview.datamodel.AlignedCodon; |
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import jalview.datamodel.AlignedCodonFrame; |
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import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.GeneLociI; |
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import jalview.datamodel.IncompleteCodonException; |
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import jalview.datamodel.Mapping; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.SequenceFeatures; |
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import jalview.io.gff.Gff3Helper; |
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import jalview.io.gff.SequenceOntologyI; |
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import jalview.schemes.ResidueProperties; |
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import jalview.util.Comparison; |
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import jalview.util.DBRefUtils; |
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import jalview.util.IntRangeComparator; |
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import jalview.util.MapList; |
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import jalview.util.MappingUtils; |
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import jalview.util.StringUtils; |
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import java.io.UnsupportedEncodingException; |
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import java.net.URLEncoder; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collection; |
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import java.util.Collections; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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import java.util.Iterator; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import java.util.NoSuchElementException; |
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import java.util.Set; |
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import java.util.SortedMap; |
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import java.util.TreeMap; |
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@author |
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| 84.3% |
Uncovered Elements: 214 (1,361) |
Complexity: 313 |
Complexity Density: 0.35 |
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public class AlignmentUtils |
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{ |
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private static final int CODON_LENGTH = 3; |
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private static final String SEQUENCE_VARIANT = "sequence_variant:"; |
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private static final String ID = "ID"; |
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| 64.3% |
Uncovered Elements: 5 (14) |
Complexity: 6 |
Complexity Density: 1 |
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static final class DnaVariant |
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{ |
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final String base; |
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SequenceFeature variant; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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DnaVariant(String nuc)... |
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{ |
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base = nuc; |
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variant = null; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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DnaVariant(String nuc, SequenceFeature var)... |
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{ |
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base = nuc; |
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variant = var; |
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} |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
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public String getSource()... |
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{ |
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return variant == null ? null : variant.getFeatureGroup(); |
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} |
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| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
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@Override... |
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public String toString() |
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{ |
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return base + ":" + (variant == null ? "" : variant.getDescription()); |
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} |
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} |
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@param |
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@param |
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@return |
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| 98.4% |
Uncovered Elements: 1 (62) |
Complexity: 10 |
Complexity Density: 0.22 |
|
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public static AlignmentI expandContext(AlignmentI core, int flankSize)... |
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{ |
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List<SequenceI> sq = new ArrayList<>(); |
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int maxoffset = 0; |
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for (SequenceI s : core.getSequences()) |
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{ |
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SequenceI newSeq = s.deriveSequence(); |
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final int newSeqStart = newSeq.getStart() - 1; |
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if (newSeqStart > maxoffset |
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&& newSeq.getDatasetSequence().getStart() < s.getStart()) |
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{ |
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maxoffset = newSeqStart; |
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} |
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sq.add(newSeq); |
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} |
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if (flankSize > -1) |
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{ |
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maxoffset = Math.min(maxoffset, flankSize); |
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} |
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for (SequenceI s : sq) |
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{ |
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SequenceI ds = s; |
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while (ds.getDatasetSequence() != null) |
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{ |
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ds = ds.getDatasetSequence(); |
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} |
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int s_end = s.findPosition(s.getStart() + s.getLength()); |
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int ustream_ds = s.getStart() - ds.getStart(); |
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int dstream_ds = ds.getEnd() - s_end; |
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int offset = maxoffset - ustream_ds; |
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if (flankSize >= 0) |
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{ |
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if (flankSize < ustream_ds) |
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{ |
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offset = maxoffset - flankSize; |
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ustream_ds = flankSize; |
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} |
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if (flankSize <= dstream_ds) |
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{ |
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dstream_ds = flankSize - 1; |
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} |
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} |
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char[] upstream = new String(ds |
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.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1)) |
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.toLowerCase().toCharArray(); |
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char[] downstream = new String( |
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ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase() |
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.toCharArray(); |
190 |
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char[] coreseq = s.getSequence(); |
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char[] nseq = new char[offset + upstream.length + downstream.length |
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+ coreseq.length]; |
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char c = core.getGapCharacter(); |
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|
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131 |
int p = 0; |
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for (; p < offset; p++) |
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{ |
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nseq[p] = c; |
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} |
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System.arraycopy(upstream, 0, nseq, p, upstream.length); |
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System.arraycopy(coreseq, 0, nseq, p + upstream.length, |
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coreseq.length); |
204 |
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System.arraycopy(downstream, 0, nseq, |
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p + coreseq.length + upstream.length, downstream.length); |
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s.setSequence(new String(nseq)); |
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s.setStart(s.getStart() - ustream_ds); |
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s.setEnd(s_end + downstream.length); |
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} |
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AlignmentI newAl = new jalview.datamodel.Alignment( |
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sq.toArray(new SequenceI[0])); |
212 |
27 |
for (SequenceI s : sq) |
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{ |
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if (s.getAnnotation() != null) |
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{ |
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for (AlignmentAnnotation aa : s.getAnnotation()) |
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{ |
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aa.adjustForAlignment(); |
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newAl.addAnnotation(aa); |
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} |
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} |
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} |
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newAl.setDataset(core.getDataset()); |
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return newAl; |
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} |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
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57660 |
public static int getSequenceIndex(AlignmentI al, SequenceI seq)... |
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{ |
237 |
57660 |
int result = -1; |
238 |
57660 |
int pos = 0; |
239 |
57660 |
for (SequenceI alSeq : al.getSequences()) |
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{ |
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125897562 |
if (alSeq == seq) |
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{ |
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57660 |
result = pos; |
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57660 |
break; |
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} |
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125839902 |
pos++; |
247 |
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} |
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57660 |
return result; |
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} |
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@see |
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| 92.9% |
Uncovered Elements: 1 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
|
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1 |
public static Map<String, List<SequenceI>> getSequencesByName(... |
259 |
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AlignmentI al) |
260 |
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{ |
261 |
1 |
Map<String, List<SequenceI>> theMap = new LinkedHashMap<>(); |
262 |
1 |
for (SequenceI seq : al.getSequences()) |
263 |
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{ |
264 |
3 |
String name = seq.getName(); |
265 |
3 |
if (name != null) |
266 |
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{ |
267 |
3 |
List<SequenceI> seqs = theMap.get(name); |
268 |
3 |
if (seqs == null) |
269 |
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{ |
270 |
2 |
seqs = new ArrayList<>(); |
271 |
2 |
theMap.put(name, seqs); |
272 |
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} |
273 |
3 |
seqs.add(seq); |
274 |
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} |
275 |
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} |
276 |
1 |
return theMap; |
277 |
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} |
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@param |
286 |
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@param |
287 |
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@return |
288 |
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| 77.8% |
Uncovered Elements: 2 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
289 |
4 |
public static boolean mapProteinAlignmentToCdna(... |
290 |
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final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment) |
291 |
|
{ |
292 |
4 |
if (proteinAlignment == null || cdnaAlignment == null) |
293 |
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{ |
294 |
0 |
return false; |
295 |
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} |
296 |
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297 |
4 |
Set<SequenceI> mappedDna = new HashSet<>(); |
298 |
4 |
Set<SequenceI> mappedProtein = new HashSet<>(); |
299 |
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300 |
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301 |
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302 |
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303 |
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304 |
4 |
boolean mappingPerformed = mapProteinToCdna(proteinAlignment, |
305 |
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cdnaAlignment, mappedDna, mappedProtein, true); |
306 |
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307 |
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308 |
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309 |
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310 |
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311 |
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312 |
4 |
mappingPerformed |= mapProteinToCdna(proteinAlignment, cdnaAlignment, |
313 |
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mappedDna, mappedProtein, false); |
314 |
4 |
return mappingPerformed; |
315 |
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} |
316 |
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317 |
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319 |
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320 |
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@param |
322 |
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@param |
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@param |
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@param |
326 |
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327 |
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@param |
328 |
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329 |
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@return |
330 |
|
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| 93.8% |
Uncovered Elements: 2 (32) |
Complexity: 9 |
Complexity Density: 0.41 |
|
331 |
8 |
protected static boolean mapProteinToCdna(... |
332 |
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final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment, |
333 |
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Set<SequenceI> mappedDna, Set<SequenceI> mappedProtein, |
334 |
|
boolean xrefsOnly) |
335 |
|
{ |
336 |
8 |
boolean mappingExistsOrAdded = false; |
337 |
8 |
List<SequenceI> thisSeqs = proteinAlignment.getSequences(); |
338 |
8 |
for (SequenceI aaSeq : thisSeqs) |
339 |
|
{ |
340 |
22 |
boolean proteinMapped = false; |
341 |
22 |
AlignedCodonFrame acf = new AlignedCodonFrame(); |
342 |
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|
343 |
22 |
for (SequenceI cdnaSeq : cdnaAlignment.getSequences()) |
344 |
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{ |
345 |
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346 |
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347 |
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348 |
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349 |
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350 |
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351 |
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352 |
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353 |
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354 |
86 |
if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq)) |
355 |
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{ |
356 |
39 |
continue; |
357 |
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} |
358 |
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359 |
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360 |
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361 |
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362 |
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363 |
47 |
if (!xrefsOnly && (mappedProtein.contains(aaSeq) |
364 |
|
|| mappedDna.contains(cdnaSeq))) |
365 |
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{ |
366 |
29 |
continue; |
367 |
|
} |
368 |
18 |
if (mappingExists(proteinAlignment.getCodonFrames(), |
369 |
|
aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence())) |
370 |
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{ |
371 |
0 |
mappingExistsOrAdded = true; |
372 |
|
} |
373 |
|
else |
374 |
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{ |
375 |
18 |
MapList map = mapCdnaToProtein(aaSeq, cdnaSeq); |
376 |
18 |
if (map != null) |
377 |
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{ |
378 |
12 |
acf.addMap(cdnaSeq, aaSeq, map); |
379 |
12 |
mappingExistsOrAdded = true; |
380 |
12 |
proteinMapped = true; |
381 |
12 |
mappedDna.add(cdnaSeq); |
382 |
12 |
mappedProtein.add(aaSeq); |
383 |
|
} |
384 |
|
} |
385 |
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} |
386 |
22 |
if (proteinMapped) |
387 |
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{ |
388 |
11 |
proteinAlignment.addCodonFrame(acf); |
389 |
|
} |
390 |
|
} |
391 |
8 |
return mappingExistsOrAdded; |
392 |
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} |
393 |
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394 |
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395 |
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396 |
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397 |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
398 |
18 |
protected static boolean mappingExists(List<AlignedCodonFrame> mappings,... |
399 |
|
SequenceI aaSeq, SequenceI cdnaSeq) |
400 |
|
{ |
401 |
18 |
if (mappings != null) |
402 |
|
{ |
403 |
18 |
for (AlignedCodonFrame acf : mappings) |
404 |
|
{ |
405 |
14 |
if (cdnaSeq == acf.getDnaForAaSeq(aaSeq)) |
406 |
|
{ |
407 |
0 |
return true; |
408 |
|
} |
409 |
|
} |
410 |
|
} |
411 |
18 |
return false; |
412 |
|
} |
413 |
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414 |
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415 |
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416 |
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417 |
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418 |
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419 |
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420 |
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421 |
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422 |
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423 |
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424 |
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425 |
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@param |
426 |
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|
427 |
|
@param |
428 |
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|
429 |
|
@return |
430 |
|
|
|
|
| 95.2% |
Uncovered Elements: 2 (42) |
Complexity: 12 |
Complexity Density: 0.43 |
|
431 |
25 |
public static MapList mapCdnaToProtein(SequenceI proteinSeq,... |
432 |
|
SequenceI cdnaSeq) |
433 |
|
{ |
434 |
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|
435 |
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|
436 |
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|
437 |
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|
438 |
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|
439 |
25 |
final SequenceI proteinDataset = proteinSeq.getDatasetSequence(); |
440 |
25 |
char[] aaSeqChars = proteinDataset != null |
441 |
|
? proteinDataset.getSequence() |
442 |
|
: proteinSeq.getSequence(); |
443 |
25 |
final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence(); |
444 |
25 |
char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence() |
445 |
|
: cdnaSeq.getSequence(); |
446 |
25 |
if (aaSeqChars == null || cdnaSeqChars == null) |
447 |
|
{ |
448 |
0 |
return null; |
449 |
|
} |
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
25 |
final int mappedLength = CODON_LENGTH * aaSeqChars.length; |
455 |
25 |
int cdnaLength = cdnaSeqChars.length; |
456 |
25 |
int cdnaStart = cdnaSeq.getStart(); |
457 |
25 |
int cdnaEnd = cdnaSeq.getEnd(); |
458 |
25 |
final int proteinStart = proteinSeq.getStart(); |
459 |
25 |
final int proteinEnd = proteinSeq.getEnd(); |
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
25 |
if (cdnaLength != mappedLength && cdnaLength > 2) |
465 |
|
{ |
466 |
10 |
String lastCodon = String.valueOf(cdnaSeqChars, |
467 |
|
cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(); |
468 |
10 |
for (String stop : ResidueProperties.STOP_CODONS) |
469 |
|
{ |
470 |
27 |
if (lastCodon.equals(stop)) |
471 |
|
{ |
472 |
3 |
cdnaEnd -= CODON_LENGTH; |
473 |
3 |
cdnaLength -= CODON_LENGTH; |
474 |
3 |
break; |
475 |
|
} |
476 |
|
} |
477 |
|
} |
478 |
|
|
479 |
|
|
480 |
|
|
481 |
|
|
482 |
25 |
int startOffset = 0; |
483 |
25 |
if (cdnaLength != mappedLength && cdnaLength > 2 |
484 |
|
&& String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase() |
485 |
|
.equals(ResidueProperties.START)) |
486 |
|
{ |
487 |
5 |
startOffset += CODON_LENGTH; |
488 |
5 |
cdnaStart += CODON_LENGTH; |
489 |
5 |
cdnaLength -= CODON_LENGTH; |
490 |
|
} |
491 |
|
|
492 |
25 |
if (translatesAs(cdnaSeqChars, startOffset, aaSeqChars)) |
493 |
|
{ |
494 |
|
|
495 |
|
|
496 |
|
|
497 |
15 |
MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, |
498 |
|
new int[] |
499 |
|
{ proteinStart, proteinEnd }, CODON_LENGTH, 1); |
500 |
15 |
return map; |
501 |
|
} |
502 |
|
|
503 |
|
|
504 |
|
|
505 |
|
|
506 |
10 |
return mapCdsToProtein(cdnaSeq, proteinSeq); |
507 |
|
} |
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
@param |
515 |
|
@param |
516 |
|
@param |
517 |
|
@return |
518 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (37) |
Complexity: 14 |
Complexity Density: 0.67 |
|
519 |
45 |
protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,... |
520 |
|
char[] aaSeqChars) |
521 |
|
{ |
522 |
45 |
if (cdnaSeqChars == null || aaSeqChars == null) |
523 |
|
{ |
524 |
3 |
return false; |
525 |
|
} |
526 |
|
|
527 |
42 |
int aaPos = 0; |
528 |
42 |
int dnaPos = cdnaStart; |
529 |
155 |
for (; dnaPos < cdnaSeqChars.length - 2 |
530 |
|
&& aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++) |
531 |
|
{ |
532 |
124 |
String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); |
533 |
124 |
final String translated = ResidueProperties.codonTranslate(codon); |
534 |
|
|
535 |
|
|
536 |
|
|
537 |
|
|
538 |
124 |
final char aaRes = aaSeqChars[aaPos]; |
539 |
124 |
if ((translated == null || ResidueProperties.STOP.equals(translated)) |
540 |
|
&& aaRes == '*') |
541 |
|
{ |
542 |
4 |
continue; |
543 |
|
} |
544 |
120 |
if (translated == null || !(aaRes == translated.charAt(0))) |
545 |
|
{ |
546 |
|
|
547 |
|
|
548 |
|
|
549 |
11 |
return false; |
550 |
|
} |
551 |
|
} |
552 |
|
|
553 |
|
|
554 |
|
|
555 |
|
|
556 |
31 |
if (aaPos != aaSeqChars.length) |
557 |
|
{ |
558 |
2 |
return false; |
559 |
|
} |
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
29 |
if (dnaPos == cdnaSeqChars.length) |
566 |
|
{ |
567 |
17 |
return true; |
568 |
|
} |
569 |
12 |
if (dnaPos == cdnaSeqChars.length - CODON_LENGTH) |
570 |
|
{ |
571 |
11 |
String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); |
572 |
11 |
if (ResidueProperties.STOP |
573 |
|
.equals(ResidueProperties.codonTranslate(codon))) |
574 |
|
{ |
575 |
9 |
return true; |
576 |
|
} |
577 |
|
} |
578 |
3 |
return false; |
579 |
|
} |
580 |
|
|
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
@param |
586 |
|
|
587 |
|
@param |
588 |
|
|
589 |
|
@param |
590 |
|
|
591 |
|
@param |
592 |
|
@param |
593 |
|
@return |
594 |
|
|
|
|
| 90% |
Uncovered Elements: 2 (20) |
Complexity: 5 |
Complexity Density: 0.36 |
|
595 |
8 |
public static boolean alignSequenceAs(SequenceI seq, AlignmentI al,... |
596 |
|
String gap, boolean preserveMappedGaps, |
597 |
|
boolean preserveUnmappedGaps) |
598 |
|
{ |
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
|
603 |
|
|
604 |
|
|
605 |
8 |
List<AlignedCodonFrame> mappings = al.getCodonFrame(seq); |
606 |
8 |
if (mappings == null || mappings.isEmpty()) |
607 |
|
{ |
608 |
0 |
return false; |
609 |
|
} |
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
|
|
616 |
8 |
SequenceI alignFrom = null; |
617 |
8 |
AlignedCodonFrame mapping = null; |
618 |
8 |
for (AlignedCodonFrame mp : mappings) |
619 |
|
{ |
620 |
8 |
alignFrom = mp.findAlignedSequence(seq, al); |
621 |
8 |
if (alignFrom != null) |
622 |
|
{ |
623 |
4 |
mapping = mp; |
624 |
4 |
break; |
625 |
|
} |
626 |
|
} |
627 |
|
|
628 |
8 |
if (alignFrom == null) |
629 |
|
{ |
630 |
4 |
return false; |
631 |
|
} |
632 |
4 |
alignSequenceAs(seq, alignFrom, mapping, gap, al.getGapCharacter(), |
633 |
|
preserveMappedGaps, preserveUnmappedGaps); |
634 |
4 |
return true; |
635 |
|
} |
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
@param |
644 |
|
@param |
645 |
|
@param |
646 |
|
@param |
647 |
|
@param |
648 |
|
@param |
649 |
|
@param |
650 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (88) |
Complexity: 20 |
Complexity Density: 0.33 |
|
651 |
19 |
public static void alignSequenceAs(SequenceI alignTo, SequenceI alignFrom,... |
652 |
|
AlignedCodonFrame mapping, String myGap, char sourceGap, |
653 |
|
boolean preserveMappedGaps, boolean preserveUnmappedGaps) |
654 |
|
{ |
655 |
|
|
656 |
|
|
657 |
|
|
658 |
19 |
int thisSeqPos = 0; |
659 |
19 |
int sourceDsPos = 0; |
660 |
|
|
661 |
19 |
int basesWritten = 0; |
662 |
19 |
char myGapChar = myGap.charAt(0); |
663 |
19 |
int ratio = myGap.length(); |
664 |
|
|
665 |
19 |
int fromOffset = alignFrom.getStart() - 1; |
666 |
19 |
int toOffset = alignTo.getStart() - 1; |
667 |
19 |
int sourceGapMappedLength = 0; |
668 |
19 |
boolean inExon = false; |
669 |
19 |
final int toLength = alignTo.getLength(); |
670 |
19 |
final int fromLength = alignFrom.getLength(); |
671 |
19 |
StringBuilder thisAligned = new StringBuilder(2 * toLength); |
672 |
|
|
673 |
|
|
674 |
|
|
675 |
|
|
676 |
205 |
for (int i = 0; i < fromLength; i++) |
677 |
|
{ |
678 |
186 |
char sourceChar = alignFrom.getCharAt(i); |
679 |
186 |
if (sourceChar == sourceGap) |
680 |
|
{ |
681 |
44 |
sourceGapMappedLength += ratio; |
682 |
44 |
continue; |
683 |
|
} |
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
|
688 |
142 |
sourceDsPos++; |
689 |
|
|
690 |
142 |
int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom, |
691 |
|
sourceDsPos + fromOffset); |
692 |
142 |
if (mappedPos == null) |
693 |
|
{ |
694 |
|
|
695 |
|
|
696 |
|
|
697 |
94 |
sourceGapMappedLength += ratio; |
698 |
|
|
699 |
|
|
700 |
|
|
701 |
94 |
continue; |
702 |
|
} |
703 |
|
|
704 |
48 |
int mappedCodonStart = mappedPos[0]; |
705 |
48 |
int mappedCodonEnd = mappedPos[mappedPos.length - 1]; |
706 |
48 |
StringBuilder trailingCopiedGap = new StringBuilder(); |
707 |
|
|
708 |
|
|
709 |
|
|
710 |
|
|
711 |
|
|
712 |
|
|
713 |
|
|
714 |
|
|
715 |
|
|
716 |
48 |
int intronLength = 0; |
717 |
294 |
while (basesWritten + toOffset < mappedCodonEnd |
718 |
|
&& thisSeqPos < toLength) |
719 |
|
{ |
720 |
246 |
final char c = alignTo.getCharAt(thisSeqPos++); |
721 |
246 |
if (c != myGapChar) |
722 |
|
{ |
723 |
146 |
basesWritten++; |
724 |
146 |
int sourcePosition = basesWritten + toOffset; |
725 |
146 |
if (sourcePosition < mappedCodonStart) |
726 |
|
{ |
727 |
|
|
728 |
|
|
729 |
|
|
730 |
|
|
731 |
48 |
if (preserveUnmappedGaps && trailingCopiedGap.length() > 0) |
732 |
|
{ |
733 |
17 |
thisAligned.append(trailingCopiedGap.toString()); |
734 |
17 |
intronLength += trailingCopiedGap.length(); |
735 |
17 |
trailingCopiedGap = new StringBuilder(); |
736 |
|
} |
737 |
48 |
intronLength++; |
738 |
48 |
inExon = false; |
739 |
|
} |
740 |
|
else |
741 |
|
{ |
742 |
98 |
final boolean startOfCodon = sourcePosition == mappedCodonStart; |
743 |
98 |
int gapsToAdd = calculateGapsToInsert(preserveMappedGaps, |
744 |
|
preserveUnmappedGaps, sourceGapMappedLength, inExon, |
745 |
|
trailingCopiedGap.length(), intronLength, startOfCodon); |
746 |
215 |
for (int k = 0; k < gapsToAdd; k++) |
747 |
|
{ |
748 |
117 |
thisAligned.append(myGapChar); |
749 |
|
} |
750 |
98 |
sourceGapMappedLength = 0; |
751 |
98 |
inExon = true; |
752 |
|
} |
753 |
146 |
thisAligned.append(c); |
754 |
146 |
trailingCopiedGap = new StringBuilder(); |
755 |
|
} |
756 |
|
else |
757 |
|
{ |
758 |
100 |
if (inExon && preserveMappedGaps) |
759 |
|
{ |
760 |
32 |
trailingCopiedGap.append(myGapChar); |
761 |
|
} |
762 |
68 |
else if (!inExon && preserveUnmappedGaps) |
763 |
|
{ |
764 |
27 |
trailingCopiedGap.append(myGapChar); |
765 |
|
} |
766 |
|
} |
767 |
|
} |
768 |
|
} |
769 |
|
|
770 |
|
|
771 |
|
|
772 |
|
|
773 |
|
|
774 |
129 |
while (thisSeqPos < toLength) |
775 |
|
{ |
776 |
110 |
final char c = alignTo.getCharAt(thisSeqPos++); |
777 |
110 |
if (c != myGapChar || preserveUnmappedGaps) |
778 |
|
{ |
779 |
102 |
thisAligned.append(c); |
780 |
|
} |
781 |
110 |
sourceGapMappedLength--; |
782 |
|
} |
783 |
|
|
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
|
788 |
19 |
if (preserveUnmappedGaps) |
789 |
|
{ |
790 |
24 |
while (sourceGapMappedLength > 0) |
791 |
|
{ |
792 |
12 |
thisAligned.append(myGapChar); |
793 |
12 |
sourceGapMappedLength--; |
794 |
|
} |
795 |
|
} |
796 |
|
|
797 |
|
|
798 |
|
|
799 |
|
|
800 |
19 |
alignTo.setSequence(new String(thisAligned)); |
801 |
|
} |
802 |
|
|
803 |
|
|
804 |
|
|
805 |
|
|
806 |
|
@param |
807 |
|
@param |
808 |
|
@param |
809 |
|
@param |
810 |
|
@param |
811 |
|
@param |
812 |
|
@param |
813 |
|
@return |
814 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 10 |
Complexity Density: 0.67 |
|
815 |
98 |
protected static int calculateGapsToInsert(boolean preserveMappedGaps,... |
816 |
|
boolean preserveUnmappedGaps, int sourceGapMappedLength, |
817 |
|
boolean inExon, int trailingGapLength, int intronLength, |
818 |
|
final boolean startOfCodon) |
819 |
|
{ |
820 |
98 |
int gapsToAdd = 0; |
821 |
98 |
if (startOfCodon) |
822 |
|
{ |
823 |
|
|
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
|
828 |
|
|
829 |
40 |
if (inExon && !preserveMappedGaps) |
830 |
|
{ |
831 |
4 |
trailingGapLength = 0; |
832 |
|
} |
833 |
40 |
if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps)) |
834 |
|
{ |
835 |
19 |
trailingGapLength = 0; |
836 |
|
} |
837 |
40 |
if (inExon) |
838 |
|
{ |
839 |
14 |
gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength); |
840 |
|
} |
841 |
|
else |
842 |
|
{ |
843 |
26 |
if (intronLength + trailingGapLength <= sourceGapMappedLength) |
844 |
|
{ |
845 |
20 |
gapsToAdd = sourceGapMappedLength - intronLength; |
846 |
|
} |
847 |
|
else |
848 |
|
{ |
849 |
6 |
gapsToAdd = Math.min( |
850 |
|
intronLength + trailingGapLength - sourceGapMappedLength, |
851 |
|
trailingGapLength); |
852 |
|
} |
853 |
|
} |
854 |
|
} |
855 |
|
else |
856 |
|
{ |
857 |
|
|
858 |
|
|
859 |
|
|
860 |
58 |
if (!preserveMappedGaps) |
861 |
|
{ |
862 |
32 |
trailingGapLength = 0; |
863 |
|
} |
864 |
58 |
gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength); |
865 |
|
} |
866 |
98 |
return gapsToAdd; |
867 |
|
} |
868 |
|
|
869 |
|
|
870 |
|
|
871 |
|
|
872 |
|
|
873 |
|
@param |
874 |
|
|
875 |
|
@param |
876 |
|
|
877 |
|
@return |
878 |
|
|
|
|
| 62.5% |
Uncovered Elements: 3 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
879 |
3 |
public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)... |
880 |
|
{ |
881 |
3 |
if (protein.isNucleotide() || !dna.isNucleotide()) |
882 |
|
{ |
883 |
0 |
System.err.println("Wrong alignment type in alignProteinAsDna"); |
884 |
0 |
return 0; |
885 |
|
} |
886 |
3 |
List<SequenceI> unmappedProtein = new ArrayList<>(); |
887 |
3 |
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap( |
888 |
|
protein, dna, unmappedProtein); |
889 |
3 |
return alignProteinAs(protein, alignedCodons, unmappedProtein); |
890 |
|
} |
891 |
|
|
892 |
|
|
893 |
|
|
894 |
|
|
895 |
|
|
896 |
|
|
897 |
|
|
898 |
|
@param |
899 |
|
|
900 |
|
@param |
901 |
|
|
902 |
|
@return |
903 |
|
|
|
|
| 83.3% |
Uncovered Elements: 4 (24) |
Complexity: 5 |
Complexity Density: 0.28 |
|
904 |
4 |
public static int alignCdsAsProtein(AlignmentI dna, AlignmentI protein)... |
905 |
|
{ |
906 |
4 |
if (protein.isNucleotide() || !dna.isNucleotide()) |
907 |
|
{ |
908 |
0 |
System.err.println("Wrong alignment type in alignProteinAsDna"); |
909 |
0 |
return 0; |
910 |
|
} |
911 |
|
|
912 |
4 |
List<AlignedCodonFrame> mappings = protein.getCodonFrames(); |
913 |
4 |
int alignedCount = 0; |
914 |
4 |
int width = 0; |
915 |
4 |
for (SequenceI dnaSeq : dna.getSequences()) |
916 |
|
{ |
917 |
5 |
if (alignCdsSequenceAsProtein(dnaSeq, protein, mappings, |
918 |
|
dna.getGapCharacter())) |
919 |
|
{ |
920 |
5 |
alignedCount++; |
921 |
|
} |
922 |
5 |
width = Math.max(dnaSeq.getLength(), width); |
923 |
|
} |
924 |
4 |
int oldwidth; |
925 |
4 |
int diff; |
926 |
4 |
for (SequenceI dnaSeq : dna.getSequences()) |
927 |
|
{ |
928 |
5 |
oldwidth = dnaSeq.getLength(); |
929 |
5 |
diff = width - oldwidth; |
930 |
5 |
if (diff > 0) |
931 |
|
{ |
932 |
1 |
dnaSeq.insertCharAt(oldwidth, diff, dna.getGapCharacter()); |
933 |
|
} |
934 |
|
} |
935 |
4 |
return alignedCount; |
936 |
|
} |
937 |
|
|
938 |
|
|
939 |
|
|
940 |
|
|
941 |
|
|
942 |
|
|
943 |
|
@param |
944 |
|
@param |
945 |
|
@param |
946 |
|
@param |
947 |
|
@return |
948 |
|
|
|
|
| 67.1% |
Uncovered Elements: 25 (76) |
Complexity: 16 |
Complexity Density: 0.33 |
|
949 |
5 |
static boolean alignCdsSequenceAsProtein(SequenceI cdsSeq,... |
950 |
|
AlignmentI protein, List<AlignedCodonFrame> mappings, |
951 |
|
char gapChar) |
952 |
|
{ |
953 |
5 |
SequenceI cdsDss = cdsSeq.getDatasetSequence(); |
954 |
5 |
if (cdsDss == null) |
955 |
|
{ |
956 |
0 |
System.err |
957 |
|
.println("alignCdsSequenceAsProtein needs aligned sequence!"); |
958 |
0 |
return false; |
959 |
|
} |
960 |
|
|
961 |
5 |
List<AlignedCodonFrame> dnaMappings = MappingUtils |
962 |
|
.findMappingsForSequence(cdsSeq, mappings); |
963 |
5 |
for (AlignedCodonFrame mapping : dnaMappings) |
964 |
|
{ |
965 |
5 |
SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein); |
966 |
5 |
if (peptide != null) |
967 |
|
{ |
968 |
5 |
final int peptideLength = peptide.getLength(); |
969 |
5 |
Mapping map = mapping.getMappingBetween(cdsSeq, peptide); |
970 |
5 |
if (map != null) |
971 |
|
{ |
972 |
5 |
MapList mapList = map.getMap(); |
973 |
5 |
if (map.getTo() == peptide.getDatasetSequence()) |
974 |
|
{ |
975 |
5 |
mapList = mapList.getInverse(); |
976 |
|
} |
977 |
5 |
final int cdsLength = cdsDss.getLength(); |
978 |
5 |
int mappedFromLength = MappingUtils.getLength(mapList |
979 |
|
.getFromRanges()); |
980 |
5 |
int mappedToLength = MappingUtils |
981 |
|
.getLength(mapList.getToRanges()); |
982 |
5 |
boolean addStopCodon = (cdsLength == mappedFromLength |
983 |
|
* CODON_LENGTH + CODON_LENGTH) |
984 |
|
|| (peptide.getDatasetSequence() |
985 |
|
.getLength() == mappedFromLength - 1); |
986 |
5 |
if (cdsLength != mappedToLength && !addStopCodon) |
987 |
|
{ |
988 |
0 |
System.err.println(String.format( |
989 |
|
"Can't align cds as protein (length mismatch %d/%d): %s", |
990 |
|
cdsLength, mappedToLength, cdsSeq.getName())); |
991 |
|
} |
992 |
|
|
993 |
|
|
994 |
|
|
995 |
|
|
996 |
5 |
char[] alignedCds = new char[peptideLength * CODON_LENGTH |
997 |
5 |
+ (addStopCodon ? CODON_LENGTH : 0)]; |
998 |
5 |
Arrays.fill(alignedCds, gapChar); |
999 |
|
|
1000 |
|
|
1001 |
|
|
1002 |
|
|
1003 |
|
|
1004 |
5 |
int copiedBases = 0; |
1005 |
5 |
int cdsStart = cdsDss.getStart(); |
1006 |
5 |
int proteinPos = peptide.getStart() - 1; |
1007 |
5 |
int cdsCol = 0; |
1008 |
|
|
1009 |
33 |
for (int col = 0; col < peptideLength; col++) |
1010 |
|
{ |
1011 |
28 |
char residue = peptide.getCharAt(col); |
1012 |
|
|
1013 |
28 |
if (Comparison.isGap(residue)) |
1014 |
|
{ |
1015 |
13 |
cdsCol += CODON_LENGTH; |
1016 |
|
} |
1017 |
|
else |
1018 |
|
{ |
1019 |
15 |
proteinPos++; |
1020 |
15 |
int[] codon = mapList.locateInTo(proteinPos, proteinPos); |
1021 |
15 |
if (codon == null) |
1022 |
|
{ |
1023 |
|
|
1024 |
0 |
cdsCol += CODON_LENGTH; |
1025 |
|
} |
1026 |
|
else |
1027 |
|
{ |
1028 |
60 |
for (int j = codon[0]; j <= codon[1]; j++) |
1029 |
|
{ |
1030 |
45 |
char mappedBase = cdsDss.getCharAt(j - cdsStart); |
1031 |
45 |
alignedCds[cdsCol++] = mappedBase; |
1032 |
45 |
copiedBases++; |
1033 |
|
} |
1034 |
|
} |
1035 |
|
} |
1036 |
|
} |
1037 |
|
|
1038 |
|
|
1039 |
|
|
1040 |
|
|
1041 |
|
|
1042 |
5 |
if (copiedBases == cdsLength - CODON_LENGTH) |
1043 |
|
{ |
1044 |
0 |
for (int i = alignedCds.length - 1; i >= 0; i--) |
1045 |
|
{ |
1046 |
0 |
if (!Comparison.isGap(alignedCds[i])) |
1047 |
|
{ |
1048 |
0 |
cdsCol = i + 1; |
1049 |
0 |
break; |
1050 |
|
} |
1051 |
|
} |
1052 |
0 |
for (int i = cdsLength - CODON_LENGTH; i < cdsLength; i++) |
1053 |
|
{ |
1054 |
0 |
alignedCds[cdsCol++] = cdsDss.getCharAt(i); |
1055 |
|
} |
1056 |
|
} |
1057 |
5 |
cdsSeq.setSequence(new String(alignedCds)); |
1058 |
5 |
return true; |
1059 |
|
} |
1060 |
|
} |
1061 |
|
} |
1062 |
0 |
return false; |
1063 |
|
} |
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
|
1069 |
|
|
1070 |
|
|
1071 |
|
|
1072 |
|
@param |
1073 |
|
|
1074 |
|
@param |
1075 |
|
|
1076 |
|
@param |
1077 |
|
|
1078 |
|
@return |
1079 |
|
|
|
|
| 93.3% |
Uncovered Elements: 1 (15) |
Complexity: 2 |
Complexity Density: 0.15 |
|
1080 |
3 |
protected static Map<AlignedCodon, Map<SequenceI, AlignedCodon>> buildCodonColumnsMap(... |
1081 |
|
AlignmentI protein, AlignmentI dna, |
1082 |
|
List<SequenceI> unmappedProtein) |
1083 |
|
{ |
1084 |
|
|
1085 |
|
|
1086 |
|
|
1087 |
|
|
1088 |
3 |
unmappedProtein.addAll(protein.getSequences()); |
1089 |
|
|
1090 |
3 |
List<AlignedCodonFrame> mappings = protein.getCodonFrames(); |
1091 |
|
|
1092 |
|
|
1093 |
|
|
1094 |
|
|
1095 |
|
|
1096 |
|
|
1097 |
3 |
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<>( |
1098 |
|
new CodonComparator()); |
1099 |
|
|
1100 |
3 |
for (SequenceI dnaSeq : dna.getSequences()) |
1101 |
|
{ |
1102 |
8 |
for (AlignedCodonFrame mapping : mappings) |
1103 |
|
{ |
1104 |
10 |
SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein); |
1105 |
10 |
if (prot != null) |
1106 |
|
{ |
1107 |
10 |
Mapping seqMap = mapping.getMappingForSequence(dnaSeq); |
1108 |
10 |
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap, |
1109 |
|
alignedCodons); |
1110 |
10 |
unmappedProtein.remove(prot); |
1111 |
|
} |
1112 |
|
} |
1113 |
|
} |
1114 |
|
|
1115 |
|
|
1116 |
|
|
1117 |
|
|
1118 |
|
|
1119 |
|
|
1120 |
3 |
int mappedSequenceCount = protein.getHeight() - unmappedProtein.size(); |
1121 |
3 |
addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount); |
1122 |
|
|
1123 |
3 |
return alignedCodons; |
1124 |
|
} |
1125 |
|
|
1126 |
|
|
1127 |
|
|
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
|
@param |
1132 |
|
|
1133 |
|
@param |
1134 |
|
|
1135 |
|
|
|
|
| 93.9% |
Uncovered Elements: 2 (33) |
Complexity: 6 |
Complexity Density: 0.26 |
|
1136 |
3 |
protected static void addUnmappedPeptideStarts(... |
1137 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons, |
1138 |
|
int mappedSequenceCount) |
1139 |
|
{ |
1140 |
|
|
1141 |
|
|
1142 |
|
|
1143 |
3 |
List<SequenceI> sequencesChecked = new ArrayList<>(); |
1144 |
3 |
AlignedCodon lastCodon = null; |
1145 |
3 |
Map<SequenceI, AlignedCodon> toAdd = new HashMap<>(); |
1146 |
|
|
1147 |
3 |
for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons |
1148 |
|
.entrySet()) |
1149 |
|
{ |
1150 |
21 |
for (Entry<SequenceI, AlignedCodon> sequenceCodon : entry.getValue() |
1151 |
|
.entrySet()) |
1152 |
|
{ |
1153 |
25 |
SequenceI seq = sequenceCodon.getKey(); |
1154 |
25 |
if (sequencesChecked.contains(seq)) |
1155 |
|
{ |
1156 |
17 |
continue; |
1157 |
|
} |
1158 |
8 |
sequencesChecked.add(seq); |
1159 |
8 |
AlignedCodon codon = sequenceCodon.getValue(); |
1160 |
8 |
if (codon.peptideCol > 1) |
1161 |
|
{ |
1162 |
0 |
System.err.println( |
1163 |
|
"Problem mapping protein with >1 unmapped start positions: " |
1164 |
|
+ seq.getName()); |
1165 |
|
} |
1166 |
8 |
else if (codon.peptideCol == 1) |
1167 |
|
{ |
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
2 |
if (lastCodon != null) |
1172 |
|
{ |
1173 |
1 |
AlignedCodon firstPeptide = new AlignedCodon(lastCodon.pos1, |
1174 |
|
lastCodon.pos2, lastCodon.pos3, |
1175 |
|
String.valueOf(seq.getCharAt(0)), 0); |
1176 |
1 |
toAdd.put(seq, firstPeptide); |
1177 |
|
} |
1178 |
|
else |
1179 |
|
{ |
1180 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
|
1184 |
1 |
AlignedCodon firstPeptide = new AlignedCodon(0, 0, 0, |
1185 |
|
String.valueOf(seq.getCharAt(0)), 0); |
1186 |
1 |
toAdd.put(seq, firstPeptide); |
1187 |
|
} |
1188 |
|
} |
1189 |
8 |
if (sequencesChecked.size() == mappedSequenceCount) |
1190 |
|
{ |
1191 |
|
|
1192 |
3 |
break; |
1193 |
|
} |
1194 |
|
} |
1195 |
21 |
lastCodon = entry.getKey(); |
1196 |
|
} |
1197 |
|
|
1198 |
|
|
1199 |
|
|
1200 |
|
|
1201 |
3 |
for (Entry<SequenceI, AlignedCodon> startCodon : toAdd.entrySet()) |
1202 |
|
{ |
1203 |
2 |
addCodonToMap(alignedCodons, startCodon.getValue(), |
1204 |
|
startCodon.getKey()); |
1205 |
|
} |
1206 |
|
} |
1207 |
|
|
1208 |
|
|
1209 |
|
|
1210 |
|
|
1211 |
|
|
1212 |
|
@param |
1213 |
|
@param |
1214 |
|
|
1215 |
|
|
1216 |
|
@param |
1217 |
|
@return |
1218 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 2 |
Complexity Density: 0.12 |
|
1219 |
3 |
protected static int alignProteinAs(AlignmentI protein,... |
1220 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons, |
1221 |
|
List<SequenceI> unmappedProtein) |
1222 |
|
{ |
1223 |
|
|
1224 |
|
|
1225 |
|
|
1226 |
3 |
int alignedWidth = alignedCodons.size(); |
1227 |
3 |
char[] gaps = new char[alignedWidth]; |
1228 |
3 |
Arrays.fill(gaps, protein.getGapCharacter()); |
1229 |
3 |
Map<SequenceI, char[]> peptides = new HashMap<>(); |
1230 |
3 |
for (SequenceI seq : protein.getSequences()) |
1231 |
|
{ |
1232 |
9 |
if (!unmappedProtein.contains(seq)) |
1233 |
|
{ |
1234 |
8 |
peptides.put(seq, Arrays.copyOf(gaps, gaps.length)); |
1235 |
|
} |
1236 |
|
} |
1237 |
|
|
1238 |
|
|
1239 |
|
|
1240 |
|
|
1241 |
|
|
1242 |
|
|
1243 |
|
|
1244 |
3 |
int column = 0; |
1245 |
3 |
for (AlignedCodon codon : alignedCodons.keySet()) |
1246 |
|
{ |
1247 |
22 |
final Map<SequenceI, AlignedCodon> columnResidues = alignedCodons |
1248 |
|
.get(codon); |
1249 |
22 |
for (Entry<SequenceI, AlignedCodon> entry : columnResidues.entrySet()) |
1250 |
|
{ |
1251 |
28 |
char residue = entry.getValue().product.charAt(0); |
1252 |
28 |
peptides.get(entry.getKey())[column] = residue; |
1253 |
|
} |
1254 |
22 |
column++; |
1255 |
|
} |
1256 |
|
|
1257 |
|
|
1258 |
|
|
1259 |
|
|
1260 |
3 |
for (Entry<SequenceI, char[]> entry : peptides.entrySet()) |
1261 |
|
{ |
1262 |
8 |
entry.getKey().setSequence(new String(entry.getValue())); |
1263 |
|
} |
1264 |
|
|
1265 |
3 |
return 0; |
1266 |
|
} |
1267 |
|
|
1268 |
|
|
1269 |
|
|
1270 |
|
|
1271 |
|
|
1272 |
|
|
1273 |
|
@param |
1274 |
|
|
1275 |
|
@param |
1276 |
|
|
1277 |
|
@param |
1278 |
|
|
1279 |
|
@param |
1280 |
|
|
1281 |
|
@param |
1282 |
|
|
1283 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 4 |
Complexity Density: 0.8 |
|
1284 |
10 |
static void addCodonPositions(SequenceI dna, SequenceI protein,... |
1285 |
|
char gapChar, Mapping seqMap, |
1286 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons) |
1287 |
|
{ |
1288 |
10 |
Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar); |
1289 |
|
|
1290 |
|
|
1291 |
|
|
1292 |
|
|
1293 |
|
|
1294 |
44 |
while (codons.hasNext()) |
1295 |
|
{ |
1296 |
34 |
try |
1297 |
|
{ |
1298 |
34 |
AlignedCodon codon = codons.next(); |
1299 |
34 |
addCodonToMap(alignedCodons, codon, protein); |
1300 |
|
} catch (IncompleteCodonException e) |
1301 |
|
{ |
1302 |
|
|
1303 |
|
} catch (NoSuchElementException e) |
1304 |
|
{ |
1305 |
|
|
1306 |
|
} |
1307 |
|
} |
1308 |
|
} |
1309 |
|
|
1310 |
|
|
1311 |
|
|
1312 |
|
|
1313 |
|
@param |
1314 |
|
@param |
1315 |
|
@param |
1316 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1317 |
36 |
protected static void addCodonToMap(... |
1318 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons, |
1319 |
|
AlignedCodon codon, SequenceI protein) |
1320 |
|
{ |
1321 |
36 |
Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon); |
1322 |
36 |
if (seqProduct == null) |
1323 |
|
{ |
1324 |
22 |
seqProduct = new HashMap<>(); |
1325 |
22 |
alignedCodons.put(codon, seqProduct); |
1326 |
|
} |
1327 |
36 |
seqProduct.put(protein, codon); |
1328 |
|
} |
1329 |
|
|
1330 |
|
|
1331 |
|
|
1332 |
|
|
1333 |
|
|
1334 |
|
|
1335 |
|
|
1336 |
|
|
1337 |
|
|
1338 |
|
|
1339 |
|
|
1340 |
|
|
1341 |
|
|
1342 |
|
|
1343 |
|
@param |
1344 |
|
@param |
1345 |
|
@return |
1346 |
|
|
|
|
| 90.9% |
Uncovered Elements: 2 (22) |
Complexity: 7 |
Complexity Density: 0.58 |
|
1347 |
8 |
public static boolean isMappable(AlignmentI al1, AlignmentI al2)... |
1348 |
|
{ |
1349 |
8 |
if (al1 == null || al2 == null) |
1350 |
|
{ |
1351 |
3 |
return false; |
1352 |
|
} |
1353 |
|
|
1354 |
|
|
1355 |
|
|
1356 |
|
|
1357 |
5 |
if (al1.isNucleotide() == al2.isNucleotide()) |
1358 |
|
{ |
1359 |
3 |
return false; |
1360 |
|
} |
1361 |
2 |
AlignmentI dna = al1.isNucleotide() ? al1 : al2; |
1362 |
2 |
AlignmentI protein = dna == al1 ? al2 : al1; |
1363 |
2 |
List<AlignedCodonFrame> mappings = protein.getCodonFrames(); |
1364 |
2 |
for (SequenceI dnaSeq : dna.getSequences()) |
1365 |
|
{ |
1366 |
2 |
for (SequenceI proteinSeq : protein.getSequences()) |
1367 |
|
{ |
1368 |
2 |
if (isMappable(dnaSeq, proteinSeq, mappings)) |
1369 |
|
{ |
1370 |
2 |
return true; |
1371 |
|
} |
1372 |
|
} |
1373 |
|
} |
1374 |
0 |
return false; |
1375 |
|
} |
1376 |
|
|
1377 |
|
|
1378 |
|
|
1379 |
|
|
1380 |
|
|
1381 |
|
@param |
1382 |
|
@param |
1383 |
|
@param |
1384 |
|
@return |
1385 |
|
|
|
|
| 50% |
Uncovered Elements: 8 (16) |
Complexity: 6 |
Complexity Density: 0.75 |
|
1386 |
2 |
protected static boolean isMappable(SequenceI dnaSeq,... |
1387 |
|
SequenceI proteinSeq, List<AlignedCodonFrame> mappings) |
1388 |
|
{ |
1389 |
2 |
if (dnaSeq == null || proteinSeq == null) |
1390 |
|
{ |
1391 |
0 |
return false; |
1392 |
|
} |
1393 |
|
|
1394 |
2 |
SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq |
1395 |
|
: dnaSeq.getDatasetSequence(); |
1396 |
2 |
SequenceI proteinDs = proteinSeq.getDatasetSequence() == null |
1397 |
|
? proteinSeq |
1398 |
|
: proteinSeq.getDatasetSequence(); |
1399 |
|
|
1400 |
2 |
for (AlignedCodonFrame mapping : mappings) |
1401 |
|
{ |
1402 |
0 |
if (proteinDs == mapping.getAaForDnaSeq(dnaDs)) |
1403 |
|
{ |
1404 |
|
|
1405 |
|
|
1406 |
|
|
1407 |
0 |
return true; |
1408 |
|
} |
1409 |
|
} |
1410 |
|
|
1411 |
|
|
1412 |
|
|
1413 |
|
|
1414 |
|
|
1415 |
2 |
return mapCdnaToProtein(proteinDs, dnaDs) != null; |
1416 |
|
} |
1417 |
|
|
1418 |
|
|
1419 |
|
|
1420 |
|
|
1421 |
|
|
1422 |
|
|
1423 |
|
|
1424 |
|
@param |
1425 |
|
|
1426 |
|
@param |
1427 |
|
|
1428 |
|
@param |
1429 |
|
|
1430 |
|
@param |
1431 |
|
|
1432 |
|
|
|
|
| 90% |
Uncovered Elements: 3 (30) |
Complexity: 7 |
Complexity Density: 0.39 |
|
1433 |
42 |
public static void findAddableReferenceAnnotations(... |
1434 |
|
List<SequenceI> sequenceScope, Map<String, String> labelForCalcId, |
1435 |
|
final Map<SequenceI, List<AlignmentAnnotation>> candidates, |
1436 |
|
AlignmentI al) |
1437 |
|
{ |
1438 |
42 |
if (sequenceScope == null) |
1439 |
|
{ |
1440 |
1 |
return; |
1441 |
|
} |
1442 |
|
|
1443 |
|
|
1444 |
|
|
1445 |
|
|
1446 |
|
|
1447 |
|
|
1448 |
|
|
1449 |
41 |
for (SequenceI seq : sequenceScope) |
1450 |
|
{ |
1451 |
25 |
SequenceI dataset = seq.getDatasetSequence(); |
1452 |
25 |
if (dataset == null) |
1453 |
|
{ |
1454 |
0 |
continue; |
1455 |
|
} |
1456 |
25 |
AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); |
1457 |
25 |
if (datasetAnnotations == null) |
1458 |
|
{ |
1459 |
19 |
continue; |
1460 |
|
} |
1461 |
6 |
final List<AlignmentAnnotation> result = new ArrayList<>(); |
1462 |
6 |
for (AlignmentAnnotation dsann : datasetAnnotations) |
1463 |
|
{ |
1464 |
|
|
1465 |
|
|
1466 |
|
|
1467 |
|
|
1468 |
|
|
1469 |
9 |
final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al |
1470 |
|
.findAnnotations(seq, dsann.getCalcId(), dsann.label); |
1471 |
9 |
if (!matchedAlignmentAnnotations.iterator().hasNext()) |
1472 |
|
{ |
1473 |
6 |
result.add(dsann); |
1474 |
6 |
if (labelForCalcId != null) |
1475 |
|
{ |
1476 |
6 |
labelForCalcId.put(dsann.getCalcId(), dsann.label); |
1477 |
|
} |
1478 |
|
} |
1479 |
|
} |
1480 |
|
|
1481 |
|
|
1482 |
|
|
1483 |
6 |
if (!result.isEmpty()) |
1484 |
|
{ |
1485 |
4 |
candidates.put(seq, result); |
1486 |
|
} |
1487 |
|
} |
1488 |
|
} |
1489 |
|
|
1490 |
|
|
1491 |
|
|
1492 |
|
|
1493 |
|
|
1494 |
|
@param |
1495 |
|
|
1496 |
|
@param |
1497 |
|
|
1498 |
|
@param |
1499 |
|
|
1500 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
|
1501 |
0 |
public static void addReferenceAnnotations(... |
1502 |
|
Map<SequenceI, List<AlignmentAnnotation>> annotations, |
1503 |
|
final AlignmentI alignment, final SequenceGroup selectionGroup) |
1504 |
|
{ |
1505 |
0 |
for (SequenceI seq : annotations.keySet()) |
1506 |
|
{ |
1507 |
0 |
for (AlignmentAnnotation ann : annotations.get(seq)) |
1508 |
|
{ |
1509 |
0 |
AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); |
1510 |
0 |
int startRes = 0; |
1511 |
0 |
int endRes = ann.annotations.length; |
1512 |
0 |
if (selectionGroup != null) |
1513 |
|
{ |
1514 |
0 |
startRes = selectionGroup.getStartRes(); |
1515 |
0 |
endRes = selectionGroup.getEndRes(); |
1516 |
|
} |
1517 |
0 |
copyAnn.restrict(startRes, endRes); |
1518 |
|
|
1519 |
|
|
1520 |
|
|
1521 |
|
|
1522 |
|
|
1523 |
0 |
if (!seq.hasAnnotation(ann)) |
1524 |
|
{ |
1525 |
0 |
seq.addAlignmentAnnotation(copyAnn); |
1526 |
|
} |
1527 |
|
|
1528 |
0 |
copyAnn.adjustForAlignment(); |
1529 |
|
|
1530 |
0 |
alignment.addAnnotation(copyAnn); |
1531 |
0 |
copyAnn.visible = true; |
1532 |
|
} |
1533 |
|
} |
1534 |
|
} |
1535 |
|
|
1536 |
|
|
1537 |
|
|
1538 |
|
|
1539 |
|
|
1540 |
|
|
1541 |
|
|
1542 |
|
@param |
1543 |
|
|
1544 |
|
@param |
1545 |
|
|
1546 |
|
|
1547 |
|
@param |
1548 |
|
|
1549 |
|
@param |
1550 |
|
|
1551 |
|
|
|
|
| 91.7% |
Uncovered Elements: 1 (12) |
Complexity: 7 |
Complexity Density: 1.17 |
|
1552 |
5 |
public static void showOrHideSequenceAnnotations(AlignmentI al,... |
1553 |
|
Collection<String> types, List<SequenceI> forSequences, |
1554 |
|
boolean anyType, boolean doShow) |
1555 |
|
{ |
1556 |
5 |
AlignmentAnnotation[] anns = al.getAlignmentAnnotation(); |
1557 |
5 |
if (anns != null) |
1558 |
|
{ |
1559 |
5 |
for (AlignmentAnnotation aa : anns) |
1560 |
|
{ |
1561 |
30 |
if (anyType || types.contains(aa.label)) |
1562 |
|
{ |
1563 |
21 |
if ((aa.sequenceRef != null) && (forSequences == null |
1564 |
|
|| forSequences.contains(aa.sequenceRef))) |
1565 |
|
{ |
1566 |
11 |
aa.visible = doShow; |
1567 |
|
} |
1568 |
|
} |
1569 |
|
} |
1570 |
|
} |
1571 |
|
} |
1572 |
|
|
1573 |
|
|
1574 |
|
|
1575 |
|
|
1576 |
|
@param |
1577 |
|
@param |
1578 |
|
@return |
1579 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1580 |
52 |
public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)... |
1581 |
|
{ |
1582 |
|
|
1583 |
|
|
1584 |
52 |
return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1); |
1585 |
|
} |
1586 |
|
|
1587 |
|
|
1588 |
|
|
1589 |
|
|
1590 |
|
|
1591 |
|
@param |
1592 |
|
@param |
1593 |
|
@return |
1594 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (16) |
Complexity: 5 |
Complexity Density: 0.5 |
|
1595 |
108 |
public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)... |
1596 |
|
{ |
1597 |
108 |
if (seq1 == null || seq2 == null) |
1598 |
|
{ |
1599 |
8 |
return false; |
1600 |
|
} |
1601 |
100 |
String name = seq2.getName(); |
1602 |
100 |
final DBRefEntry[] xrefs = seq1.getDBRefs(); |
1603 |
100 |
if (xrefs != null) |
1604 |
|
{ |
1605 |
22 |
for (DBRefEntry xref : xrefs) |
1606 |
|
{ |
1607 |
24 |
String xrefName = xref.getSource() + "|" + xref.getAccessionId(); |
1608 |
|
|
1609 |
24 |
if (xrefName.equalsIgnoreCase(name)) |
1610 |
|
{ |
1611 |
12 |
return true; |
1612 |
|
} |
1613 |
|
} |
1614 |
|
} |
1615 |
88 |
return false; |
1616 |
|
} |
1617 |
|
|
1618 |
|
|
1619 |
|
|
1620 |
|
|
1621 |
|
|
1622 |
|
|
1623 |
|
|
1624 |
|
|
1625 |
|
@param |
1626 |
|
|
1627 |
|
@param |
1628 |
|
|
1629 |
|
@param |
1630 |
|
|
1631 |
|
|
1632 |
|
@return |
1633 |
|
|
1634 |
|
|
|
|
| 76.1% |
Uncovered Elements: 21 (88) |
Complexity: 15 |
Complexity Density: 0.23 |
|
1635 |
4 |
public static AlignmentI makeCdsAlignment(SequenceI[] dna,... |
1636 |
|
AlignmentI dataset, SequenceI[] products) |
1637 |
|
{ |
1638 |
4 |
if (dataset == null || dataset.getDataset() != null) |
1639 |
|
{ |
1640 |
0 |
throw new IllegalArgumentException( |
1641 |
|
"IMPLEMENTATION ERROR: dataset.getDataset() must be null!"); |
1642 |
|
} |
1643 |
4 |
List<SequenceI> foundSeqs = new ArrayList<>(); |
1644 |
4 |
List<SequenceI> cdsSeqs = new ArrayList<>(); |
1645 |
4 |
List<AlignedCodonFrame> mappings = dataset.getCodonFrames(); |
1646 |
4 |
HashSet<SequenceI> productSeqs = null; |
1647 |
4 |
if (products != null) |
1648 |
|
{ |
1649 |
1 |
productSeqs = new HashSet<>(); |
1650 |
1 |
for (SequenceI seq : products) |
1651 |
|
{ |
1652 |
2 |
productSeqs.add(seq.getDatasetSequence() == null ? seq : seq |
1653 |
|
.getDatasetSequence()); |
1654 |
|
} |
1655 |
|
} |
1656 |
|
|
1657 |
|
|
1658 |
|
|
1659 |
|
|
1660 |
|
|
1661 |
|
|
1662 |
|
|
1663 |
|
|
1664 |
|
|
1665 |
|
|
1666 |
|
|
1667 |
|
|
1668 |
4 |
for (SequenceI dnaSeq : dna) |
1669 |
|
{ |
1670 |
8 |
SequenceI dnaDss = dnaSeq.getDatasetSequence() == null ? dnaSeq |
1671 |
|
: dnaSeq.getDatasetSequence(); |
1672 |
|
|
1673 |
8 |
List<AlignedCodonFrame> seqMappings = MappingUtils |
1674 |
|
.findMappingsForSequence(dnaSeq, mappings); |
1675 |
8 |
for (AlignedCodonFrame mapping : seqMappings) |
1676 |
|
{ |
1677 |
9 |
List<Mapping> mappingsFromSequence = mapping |
1678 |
|
.getMappingsFromSequence(dnaSeq); |
1679 |
|
|
1680 |
9 |
for (Mapping aMapping : mappingsFromSequence) |
1681 |
|
{ |
1682 |
11 |
MapList mapList = aMapping.getMap(); |
1683 |
11 |
if (mapList.getFromRatio() == 1) |
1684 |
|
{ |
1685 |
|
|
1686 |
|
|
1687 |
|
|
1688 |
0 |
continue; |
1689 |
|
} |
1690 |
|
|
1691 |
|
|
1692 |
|
|
1693 |
|
|
1694 |
11 |
SequenceI proteinProduct = aMapping.getTo(); |
1695 |
11 |
if (productSeqs != null && !productSeqs.contains(proteinProduct)) |
1696 |
|
{ |
1697 |
2 |
continue; |
1698 |
|
} |
1699 |
|
|
1700 |
|
|
1701 |
|
|
1702 |
|
|
1703 |
|
|
1704 |
|
|
1705 |
9 |
SequenceI cdsSeq = findCdsForProtein(mappings, dnaSeq, |
1706 |
|
seqMappings, aMapping); |
1707 |
9 |
if (cdsSeq != null) |
1708 |
|
{ |
1709 |
0 |
if (!foundSeqs.contains(cdsSeq)) |
1710 |
|
{ |
1711 |
0 |
foundSeqs.add(cdsSeq); |
1712 |
0 |
SequenceI derivedSequence = cdsSeq.deriveSequence(); |
1713 |
0 |
cdsSeqs.add(derivedSequence); |
1714 |
0 |
if (!dataset.getSequences().contains(cdsSeq)) |
1715 |
|
{ |
1716 |
0 |
dataset.addSequence(cdsSeq); |
1717 |
|
} |
1718 |
|
} |
1719 |
0 |
continue; |
1720 |
|
} |
1721 |
|
|
1722 |
|
|
1723 |
|
|
1724 |
|
|
1725 |
|
|
1726 |
9 |
cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping, |
1727 |
|
dataset).deriveSequence(); |
1728 |
|
|
1729 |
|
|
1730 |
|
|
1731 |
|
|
1732 |
9 |
SequenceI cdsSeqDss = cdsSeq.getDatasetSequence(); |
1733 |
|
|
1734 |
9 |
cdsSeqs.add(cdsSeq); |
1735 |
|
|
1736 |
9 |
if (!dataset.getSequences().contains(cdsSeqDss)) |
1737 |
|
{ |
1738 |
|
|
1739 |
|
|
1740 |
9 |
dataset.addSequence(cdsSeqDss); |
1741 |
|
} |
1742 |
|
|
1743 |
|
|
1744 |
|
|
1745 |
|
|
1746 |
9 |
List<int[]> cdsRange = Collections.singletonList(new int[] { 1, |
1747 |
|
cdsSeq.getLength() }); |
1748 |
9 |
MapList cdsToProteinMap = new MapList(cdsRange, |
1749 |
|
mapList.getToRanges(), mapList.getFromRatio(), |
1750 |
|
mapList.getToRatio()); |
1751 |
9 |
AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame(); |
1752 |
9 |
cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct, |
1753 |
|
cdsToProteinMap); |
1754 |
|
|
1755 |
|
|
1756 |
|
|
1757 |
|
|
1758 |
9 |
if (!mappings.contains(cdsToProteinMapping)) |
1759 |
|
{ |
1760 |
9 |
mappings.add(cdsToProteinMapping); |
1761 |
|
} |
1762 |
|
|
1763 |
9 |
propagateDBRefsToCDS(cdsSeqDss, dnaSeq.getDatasetSequence(), |
1764 |
|
proteinProduct, aMapping); |
1765 |
|
|
1766 |
|
|
1767 |
|
|
1768 |
9 |
AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame(); |
1769 |
9 |
final MapList dnaToCdsMap = new MapList(mapList.getFromRanges(), |
1770 |
|
cdsRange, 1, 1); |
1771 |
9 |
dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss, |
1772 |
|
dnaToCdsMap); |
1773 |
9 |
if (!mappings.contains(dnaToCdsMapping)) |
1774 |
|
{ |
1775 |
9 |
mappings.add(dnaToCdsMapping); |
1776 |
|
} |
1777 |
|
|
1778 |
|
|
1779 |
|
|
1780 |
|
|
1781 |
|
|
1782 |
9 |
final MapList cdsToDnaMap = dnaToCdsMap.getInverse(); |
1783 |
9 |
transferGeneLoci(dnaSeq, cdsToDnaMap, cdsSeq); |
1784 |
|
|
1785 |
|
|
1786 |
|
|
1787 |
|
|
1788 |
|
|
1789 |
|
|
1790 |
|
|
1791 |
|
|
1792 |
|
|
1793 |
|
|
1794 |
|
|
1795 |
|
|
1796 |
|
|
1797 |
|
|
1798 |
|
|
1799 |
|
|
1800 |
|
|
1801 |
|
|
1802 |
9 |
for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs()) |
1803 |
|
{ |
1804 |
|
|
1805 |
|
|
1806 |
|
|
1807 |
|
|
1808 |
2 |
String source = primRef.getSource(); |
1809 |
2 |
String version = primRef.getVersion(); |
1810 |
2 |
DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":" |
1811 |
|
+ version, primRef.getAccessionId()); |
1812 |
2 |
cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap))); |
1813 |
2 |
cdsSeqDss.addDBRef(cdsCrossRef); |
1814 |
|
|
1815 |
2 |
dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq |
1816 |
|
.getName(), new Mapping(cdsSeqDss, dnaToCdsMap))); |
1817 |
|
|
1818 |
|
|
1819 |
|
|
1820 |
|
|
1821 |
|
|
1822 |
|
|
1823 |
2 |
DBRefEntry proteinToCdsRef = new DBRefEntry(source, version, |
1824 |
|
cdsSeq.getName()); |
1825 |
|
|
1826 |
2 |
proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap |
1827 |
|
.getInverse())); |
1828 |
2 |
proteinProduct.addDBRef(proteinToCdsRef); |
1829 |
|
} |
1830 |
|
|
1831 |
|
|
1832 |
|
|
1833 |
|
|
1834 |
9 |
transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null, |
1835 |
|
SequenceOntologyI.CDS); |
1836 |
|
} |
1837 |
|
} |
1838 |
|
} |
1839 |
|
|
1840 |
4 |
AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs |
1841 |
|
.size()])); |
1842 |
4 |
cds.setDataset(dataset); |
1843 |
|
|
1844 |
4 |
return cds; |
1845 |
|
} |
1846 |
|
|
1847 |
|
|
1848 |
|
|
1849 |
|
|
1850 |
|
|
1851 |
|
@param |
1852 |
|
@param |
1853 |
|
|
1854 |
|
@param |
1855 |
|
|
|
|
| 92.9% |
Uncovered Elements: 1 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
1856 |
12 |
protected static void transferGeneLoci(SequenceI fromSeq,... |
1857 |
|
MapList targetToFrom, SequenceI targetSeq) |
1858 |
|
{ |
1859 |
12 |
if (targetSeq.getGeneLoci() != null) |
1860 |
|
{ |
1861 |
|
|
1862 |
1 |
return; |
1863 |
|
} |
1864 |
11 |
GeneLociI fromLoci = fromSeq.getGeneLoci(); |
1865 |
11 |
if (fromLoci == null) |
1866 |
|
{ |
1867 |
10 |
return; |
1868 |
|
} |
1869 |
|
|
1870 |
1 |
MapList newMap = targetToFrom.traverse(fromLoci.getMap()); |
1871 |
|
|
1872 |
1 |
if (newMap != null) |
1873 |
|
{ |
1874 |
1 |
targetSeq.setGeneLoci(fromLoci.getSpeciesId(), |
1875 |
|
fromLoci.getAssemblyId(), fromLoci.getChromosomeId(), newMap); |
1876 |
|
} |
1877 |
|
} |
1878 |
|
|
1879 |
|
|
1880 |
|
|
1881 |
|
|
1882 |
|
|
1883 |
|
|
1884 |
|
@param |
1885 |
|
|
1886 |
|
@param |
1887 |
|
|
1888 |
|
@param |
1889 |
|
|
1890 |
|
@param |
1891 |
|
|
1892 |
|
@return |
1893 |
|
|
|
|
| 45.2% |
Uncovered Elements: 17 (31) |
Complexity: 11 |
Complexity Density: 0.58 |
|
1894 |
9 |
static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,... |
1895 |
|
SequenceI dnaSeq, List<AlignedCodonFrame> seqMappings, |
1896 |
|
Mapping aMapping) |
1897 |
|
{ |
1898 |
|
|
1899 |
|
|
1900 |
|
|
1901 |
|
|
1902 |
9 |
SequenceI seqDss = dnaSeq.getDatasetSequence() == null ? dnaSeq |
1903 |
|
: dnaSeq.getDatasetSequence(); |
1904 |
9 |
SequenceI proteinProduct = aMapping.getTo(); |
1905 |
|
|
1906 |
|
|
1907 |
|
|
1908 |
|
|
1909 |
|
|
1910 |
9 |
int mappedFromLength = MappingUtils |
1911 |
|
.getLength(aMapping.getMap().getFromRanges()); |
1912 |
9 |
int dnaLength = seqDss.getLength(); |
1913 |
9 |
if (mappedFromLength == dnaLength |
1914 |
|
|| mappedFromLength == dnaLength - CODON_LENGTH) |
1915 |
|
{ |
1916 |
|
|
1917 |
|
|
1918 |
|
|
1919 |
|
|
1920 |
0 |
if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS) |
1921 |
|
.isEmpty()) |
1922 |
|
{ |
1923 |
0 |
return seqDss; |
1924 |
|
} |
1925 |
|
} |
1926 |
|
|
1927 |
|
|
1928 |
|
|
1929 |
|
|
1930 |
|
|
1931 |
9 |
List<AlignedCodonFrame> mappingsToPeptide = MappingUtils |
1932 |
|
.findMappingsForSequence(proteinProduct, mappings); |
1933 |
9 |
for (AlignedCodonFrame acf : mappingsToPeptide) |
1934 |
|
{ |
1935 |
9 |
for (SequenceToSequenceMapping map : acf.getMappings()) |
1936 |
|
{ |
1937 |
11 |
Mapping mapping = map.getMapping(); |
1938 |
11 |
if (mapping != aMapping |
1939 |
|
&& mapping.getMap().getFromRatio() == CODON_LENGTH |
1940 |
|
&& proteinProduct == mapping.getTo() |
1941 |
|
&& seqDss != map.getFromSeq()) |
1942 |
|
{ |
1943 |
0 |
mappedFromLength = MappingUtils |
1944 |
|
.getLength(mapping.getMap().getFromRanges()); |
1945 |
0 |
if (mappedFromLength == map.getFromSeq().getLength()) |
1946 |
|
{ |
1947 |
|
|
1948 |
|
|
1949 |
|
|
1950 |
|
|
1951 |
|
|
1952 |
0 |
SequenceI cdsSeq = map.getFromSeq(); |
1953 |
|
|
1954 |
|
|
1955 |
0 |
List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils |
1956 |
|
.findMappingsForSequence(cdsSeq, seqMappings); |
1957 |
0 |
if (!dnaToCdsMaps.isEmpty()) |
1958 |
|
{ |
1959 |
0 |
return cdsSeq; |
1960 |
|
} |
1961 |
|
} |
1962 |
|
} |
1963 |
|
} |
1964 |
|
} |
1965 |
9 |
return null; |
1966 |
|
} |
1967 |
|
|
1968 |
|
|
1969 |
|
|
1970 |
|
|
1971 |
|
|
1972 |
|
|
1973 |
|
@param |
1974 |
|
@param |
1975 |
|
@param |
1976 |
|
|
1977 |
|
|
1978 |
|
|
1979 |
|
@return |
1980 |
|
|
|
|
| 61.2% |
Uncovered Elements: 19 (49) |
Complexity: 10 |
Complexity Density: 0.32 |
|
1981 |
9 |
static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping,... |
1982 |
|
AlignmentI dataset) |
1983 |
|
{ |
1984 |
9 |
char[] seqChars = seq.getSequence(); |
1985 |
9 |
List<int[]> fromRanges = mapping.getMap().getFromRanges(); |
1986 |
9 |
int cdsWidth = MappingUtils.getLength(fromRanges); |
1987 |
9 |
char[] newSeqChars = new char[cdsWidth]; |
1988 |
|
|
1989 |
9 |
int newPos = 0; |
1990 |
9 |
for (int[] range : fromRanges) |
1991 |
|
{ |
1992 |
21 |
if (range[0] <= range[1]) |
1993 |
|
{ |
1994 |
|
|
1995 |
21 |
int length = range[1] - range[0] + 1; |
1996 |
21 |
System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos, |
1997 |
|
length); |
1998 |
21 |
newPos += length; |
1999 |
|
} |
2000 |
|
else |
2001 |
|
{ |
2002 |
|
|
2003 |
0 |
for (int i = range[0]; i >= range[1]; i--) |
2004 |
|
{ |
2005 |
0 |
newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]); |
2006 |
|
} |
2007 |
|
} |
2008 |
|
} |
2009 |
|
|
2010 |
|
|
2011 |
|
|
2012 |
|
|
2013 |
|
|
2014 |
9 |
String mapFromId = mapping.getMappedFromId(); |
2015 |
9 |
String seqId = "CDS|" + (mapFromId != null ? mapFromId : seq.getName()); |
2016 |
9 |
SequenceI newSeq = new Sequence(seqId, newSeqChars, 1, newPos); |
2017 |
9 |
if (dataset != null) |
2018 |
|
{ |
2019 |
9 |
SequenceI[] matches = dataset.findSequenceMatch(newSeq.getName()); |
2020 |
9 |
if (matches != null) |
2021 |
|
{ |
2022 |
9 |
boolean matched = false; |
2023 |
9 |
for (SequenceI mtch : matches) |
2024 |
|
{ |
2025 |
3 |
if (mtch.getStart() != newSeq.getStart()) |
2026 |
|
{ |
2027 |
0 |
continue; |
2028 |
|
} |
2029 |
3 |
if (mtch.getEnd() != newSeq.getEnd()) |
2030 |
|
{ |
2031 |
0 |
continue; |
2032 |
|
} |
2033 |
3 |
if (!Arrays.equals(mtch.getSequence(), newSeq.getSequence())) |
2034 |
|
{ |
2035 |
3 |
continue; |
2036 |
|
} |
2037 |
0 |
if (!matched) |
2038 |
|
{ |
2039 |
0 |
matched = true; |
2040 |
0 |
newSeq = mtch; |
2041 |
|
} |
2042 |
|
else |
2043 |
|
{ |
2044 |
0 |
System.err.println( |
2045 |
|
"JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):" |
2046 |
|
+ mtch.toString()); |
2047 |
|
} |
2048 |
|
} |
2049 |
|
} |
2050 |
|
} |
2051 |
|
|
2052 |
|
|
2053 |
9 |
return newSeq; |
2054 |
|
} |
2055 |
|
|
2056 |
|
|
2057 |
|
|
2058 |
|
|
2059 |
|
|
2060 |
|
@param |
2061 |
|
@param |
2062 |
|
@param |
2063 |
|
@param |
2064 |
|
@return |
2065 |
|
|
|
|
| 88.9% |
Uncovered Elements: 4 (36) |
Complexity: 9 |
Complexity Density: 0.38 |
|
2066 |
9 |
protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,... |
2067 |
|
SequenceI contig, SequenceI proteinProduct, Mapping mapping) |
2068 |
|
{ |
2069 |
|
|
2070 |
|
|
2071 |
9 |
List<DBRefEntry> direct = new ArrayList<>(); |
2072 |
9 |
HashSet<String> directSources = new HashSet<>(); |
2073 |
|
|
2074 |
9 |
if (contig.getDBRefs() != null) |
2075 |
|
{ |
2076 |
2 |
for (DBRefEntry dbr : contig.getDBRefs()) |
2077 |
|
{ |
2078 |
4 |
if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap()) |
2079 |
|
{ |
2080 |
2 |
MapList map = dbr.getMap().getMap(); |
2081 |
|
|
2082 |
2 |
if (mapping.getMap().equals(map)) |
2083 |
|
{ |
2084 |
2 |
direct.add(dbr); |
2085 |
2 |
directSources.add(dbr.getSource()); |
2086 |
|
} |
2087 |
|
} |
2088 |
|
} |
2089 |
|
} |
2090 |
9 |
DBRefEntry[] onSource = DBRefUtils.selectRefs( |
2091 |
|
proteinProduct.getDBRefs(), |
2092 |
|
directSources.toArray(new String[0])); |
2093 |
9 |
List<DBRefEntry> propagated = new ArrayList<>(); |
2094 |
|
|
2095 |
|
|
2096 |
9 |
for (DBRefEntry cdsref : direct) |
2097 |
|
{ |
2098 |
|
|
2099 |
2 |
MapList cdsposmap = new MapList( |
2100 |
|
Arrays.asList(new int[][] |
2101 |
|
{ new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }), |
2102 |
|
cdsref.getMap().getMap().getToRanges(), 3, 1); |
2103 |
2 |
Mapping cdsmap = new Mapping(cdsref.getMap().getTo(), |
2104 |
|
cdsref.getMap().getMap()); |
2105 |
|
|
2106 |
|
|
2107 |
2 |
DBRefEntry newref = new DBRefEntry(cdsref.getSource(), |
2108 |
|
cdsref.getVersion(), cdsref.getAccessionId(), |
2109 |
|
new Mapping(cdsmap.getTo(), cdsposmap)); |
2110 |
|
|
2111 |
|
|
2112 |
|
|
2113 |
|
|
2114 |
2 |
if (cdsmap.getTo() == null && onSource != null) |
2115 |
|
{ |
2116 |
2 |
List<DBRefEntry> sourceRefs = DBRefUtils.searchRefs(onSource, |
2117 |
|
cdsref.getAccessionId()); |
2118 |
2 |
if (sourceRefs != null) |
2119 |
|
{ |
2120 |
2 |
for (DBRefEntry srcref : sourceRefs) |
2121 |
|
{ |
2122 |
2 |
if (srcref.getSource().equalsIgnoreCase(cdsref.getSource())) |
2123 |
|
{ |
2124 |
|
|
2125 |
|
|
2126 |
2 |
newref.getMap().setTo(proteinProduct); |
2127 |
|
} |
2128 |
|
} |
2129 |
|
} |
2130 |
|
} |
2131 |
2 |
cdsSeq.addDBRef(newref); |
2132 |
2 |
propagated.add(newref); |
2133 |
|
} |
2134 |
9 |
return propagated; |
2135 |
|
} |
2136 |
|
|
2137 |
|
|
2138 |
|
|
2139 |
|
|
2140 |
|
|
2141 |
|
|
2142 |
|
@param |
2143 |
|
@param |
2144 |
|
@param |
2145 |
|
|
2146 |
|
@param |
2147 |
|
|
2148 |
|
|
2149 |
|
@param |
2150 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (49) |
Complexity: 10 |
Complexity Density: 0.32 |
|
2151 |
19 |
protected static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,... |
2152 |
|
MapList mapping, String select, String... omitting) |
2153 |
|
{ |
2154 |
19 |
SequenceI copyTo = toSeq; |
2155 |
28 |
while (copyTo.getDatasetSequence() != null) |
2156 |
|
{ |
2157 |
9 |
copyTo = copyTo.getDatasetSequence(); |
2158 |
|
} |
2159 |
|
|
2160 |
|
|
2161 |
|
|
2162 |
|
|
2163 |
19 |
List<SequenceFeature> sfs = select == null ? fromSeq.getFeatures() |
2164 |
|
.getPositionalFeatures() : fromSeq.getFeatures() |
2165 |
|
.getFeaturesByOntology(select); |
2166 |
|
|
2167 |
19 |
int count = 0; |
2168 |
19 |
for (SequenceFeature sf : sfs) |
2169 |
|
{ |
2170 |
14 |
String type = sf.getType(); |
2171 |
14 |
boolean omit = false; |
2172 |
14 |
for (String toOmit : omitting) |
2173 |
|
{ |
2174 |
7 |
if (type.equals(toOmit)) |
2175 |
|
{ |
2176 |
2 |
omit = true; |
2177 |
|
} |
2178 |
|
} |
2179 |
14 |
if (omit) |
2180 |
|
{ |
2181 |
2 |
continue; |
2182 |
|
} |
2183 |
|
|
2184 |
|
|
2185 |
|
|
2186 |
|
|
2187 |
|
|
2188 |
12 |
int start = sf.getBegin(); |
2189 |
12 |
int end = sf.getEnd(); |
2190 |
12 |
int[] mappedTo = mapping.locateInTo(start, end); |
2191 |
|
|
2192 |
|
|
2193 |
|
|
2194 |
|
|
2195 |
12 |
if (mappedTo == null) |
2196 |
|
{ |
2197 |
5 |
mappedTo = mapping.locateInTo(end, end); |
2198 |
5 |
if (mappedTo != null) |
2199 |
|
{ |
2200 |
|
|
2201 |
|
|
2202 |
|
|
2203 |
|
|
2204 |
1 |
mappedTo[0] = 1; |
2205 |
|
} |
2206 |
|
} |
2207 |
12 |
if (mappedTo == null) |
2208 |
|
{ |
2209 |
4 |
mappedTo = mapping.locateInTo(start, start); |
2210 |
4 |
if (mappedTo != null) |
2211 |
|
{ |
2212 |
|
|
2213 |
|
|
2214 |
|
|
2215 |
|
|
2216 |
1 |
mappedTo[1] = toSeq.getLength(); |
2217 |
|
} |
2218 |
|
} |
2219 |
12 |
if (mappedTo != null) |
2220 |
|
{ |
2221 |
9 |
int newBegin = Math.min(mappedTo[0], mappedTo[1]); |
2222 |
9 |
int newEnd = Math.max(mappedTo[0], mappedTo[1]); |
2223 |
9 |
SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, |
2224 |
|
sf.getFeatureGroup(), sf.getScore()); |
2225 |
9 |
copyTo.addSequenceFeature(copy); |
2226 |
9 |
count++; |
2227 |
|
} |
2228 |
|
} |
2229 |
19 |
return count; |
2230 |
|
} |
2231 |
|
|
2232 |
|
|
2233 |
|
|
2234 |
|
|
2235 |
|
|
2236 |
|
|
2237 |
|
|
2238 |
|
|
2239 |
|
@param |
2240 |
|
@param |
2241 |
|
@return |
2242 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (30) |
Complexity: 5 |
Complexity Density: 0.23 |
|
2243 |
16 |
public static MapList mapCdsToProtein(SequenceI dnaSeq,... |
2244 |
|
SequenceI proteinSeq) |
2245 |
|
{ |
2246 |
16 |
List<int[]> ranges = findCdsPositions(dnaSeq); |
2247 |
16 |
int mappedDnaLength = MappingUtils.getLength(ranges); |
2248 |
|
|
2249 |
|
|
2250 |
|
|
2251 |
|
|
2252 |
16 |
int codonRemainder = mappedDnaLength % CODON_LENGTH; |
2253 |
16 |
if (codonRemainder > 0) |
2254 |
|
{ |
2255 |
2 |
mappedDnaLength -= codonRemainder; |
2256 |
2 |
MappingUtils.removeEndPositions(codonRemainder, ranges); |
2257 |
|
} |
2258 |
|
|
2259 |
16 |
int proteinLength = proteinSeq.getLength(); |
2260 |
16 |
int proteinStart = proteinSeq.getStart(); |
2261 |
16 |
int proteinEnd = proteinSeq.getEnd(); |
2262 |
|
|
2263 |
|
|
2264 |
|
|
2265 |
|
|
2266 |
|
|
2267 |
16 |
if (proteinSeq.getCharAt(0) == 'X') |
2268 |
|
{ |
2269 |
|
|
2270 |
1 |
proteinStart++; |
2271 |
1 |
proteinLength--; |
2272 |
|
} |
2273 |
16 |
List<int[]> proteinRange = new ArrayList<>(); |
2274 |
|
|
2275 |
|
|
2276 |
|
|
2277 |
|
|
2278 |
16 |
int codesForResidues = mappedDnaLength / CODON_LENGTH; |
2279 |
16 |
if (codesForResidues == (proteinLength + 1)) |
2280 |
|
{ |
2281 |
|
|
2282 |
|
|
2283 |
2 |
codesForResidues--; |
2284 |
2 |
mappedDnaLength -= CODON_LENGTH; |
2285 |
2 |
MappingUtils.removeEndPositions(CODON_LENGTH, ranges); |
2286 |
|
} |
2287 |
|
|
2288 |
16 |
if (codesForResidues == proteinLength) |
2289 |
|
{ |
2290 |
6 |
proteinRange.add(new int[] { proteinStart, proteinEnd }); |
2291 |
6 |
return new MapList(ranges, proteinRange, CODON_LENGTH, 1); |
2292 |
|
} |
2293 |
10 |
return null; |
2294 |
|
} |
2295 |
|
|
2296 |
|
|
2297 |
|
|
2298 |
|
|
2299 |
|
|
2300 |
|
|
2301 |
|
|
2302 |
|
|
2303 |
|
@param |
2304 |
|
@return |
2305 |
|
|
|
|
| 91.7% |
Uncovered Elements: 2 (24) |
Complexity: 6 |
Complexity Density: 0.33 |
|
2306 |
18 |
protected static List<int[]> findCdsPositions(SequenceI dnaSeq)... |
2307 |
|
{ |
2308 |
18 |
List<int[]> result = new ArrayList<>(); |
2309 |
|
|
2310 |
18 |
List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology( |
2311 |
|
SequenceOntologyI.CDS); |
2312 |
18 |
if (sfs.isEmpty()) |
2313 |
|
{ |
2314 |
8 |
return result; |
2315 |
|
} |
2316 |
10 |
SequenceFeatures.sortFeatures(sfs, true); |
2317 |
|
|
2318 |
10 |
for (SequenceFeature sf : sfs) |
2319 |
|
{ |
2320 |
19 |
int phase = 0; |
2321 |
19 |
try |
2322 |
|
{ |
2323 |
19 |
phase = Integer.parseInt(sf.getPhase()); |
2324 |
|
} catch (NumberFormatException e) |
2325 |
|
{ |
2326 |
|
|
2327 |
|
} |
2328 |
|
|
2329 |
|
|
2330 |
|
|
2331 |
|
|
2332 |
19 |
int begin = sf.getBegin(); |
2333 |
19 |
int end = sf.getEnd(); |
2334 |
19 |
if (result.isEmpty() && phase > 0) |
2335 |
|
{ |
2336 |
2 |
begin += phase; |
2337 |
2 |
if (begin > end) |
2338 |
|
{ |
2339 |
|
|
2340 |
0 |
System.err |
2341 |
|
.println("Error: start phase extends beyond start CDS in " |
2342 |
|
+ dnaSeq.getName()); |
2343 |
|
} |
2344 |
|
} |
2345 |
19 |
result.add(new int[] { begin, end }); |
2346 |
|
} |
2347 |
|
|
2348 |
|
|
2349 |
|
|
2350 |
|
|
2351 |
|
|
2352 |
|
|
2353 |
|
|
2354 |
|
|
2355 |
10 |
Collections.sort(result, IntRangeComparator.ASCENDING); |
2356 |
10 |
return result; |
2357 |
|
} |
2358 |
|
|
2359 |
|
|
2360 |
|
|
2361 |
|
|
2362 |
|
|
2363 |
|
|
2364 |
|
|
2365 |
|
@param |
2366 |
|
@param |
2367 |
|
@param |
2368 |
|
|
|
|
| 87.5% |
Uncovered Elements: 2 (16) |
Complexity: 3 |
Complexity Density: 0.25 |
|
2369 |
7 |
public static int computeProteinFeatures(SequenceI dnaSeq,... |
2370 |
|
SequenceI peptide, MapList dnaToProtein) |
2371 |
|
{ |
2372 |
12 |
while (dnaSeq.getDatasetSequence() != null) |
2373 |
|
{ |
2374 |
5 |
dnaSeq = dnaSeq.getDatasetSequence(); |
2375 |
|
} |
2376 |
7 |
while (peptide.getDatasetSequence() != null) |
2377 |
|
{ |
2378 |
0 |
peptide = peptide.getDatasetSequence(); |
2379 |
|
} |
2380 |
|
|
2381 |
7 |
transferFeatures(dnaSeq, peptide, dnaToProtein, SequenceOntologyI.EXON); |
2382 |
|
|
2383 |
|
|
2384 |
|
|
2385 |
|
|
2386 |
|
|
2387 |
|
|
2388 |
|
|
2389 |
|
|
2390 |
|
|
2391 |
|
|
2392 |
|
|
2393 |
|
|
2394 |
7 |
LinkedHashMap<Integer, List<DnaVariant>[]> variants = buildDnaVariantsMap( |
2395 |
|
dnaSeq, dnaToProtein); |
2396 |
|
|
2397 |
|
|
2398 |
|
|
2399 |
|
|
2400 |
7 |
int count = 0; |
2401 |
7 |
for (Entry<Integer, List<DnaVariant>[]> variant : variants.entrySet()) |
2402 |
|
{ |
2403 |
6 |
int peptidePos = variant.getKey(); |
2404 |
6 |
List<DnaVariant>[] codonVariants = variant.getValue(); |
2405 |
6 |
count += computePeptideVariants(peptide, peptidePos, codonVariants); |
2406 |
|
} |
2407 |
|
|
2408 |
7 |
return count; |
2409 |
|
} |
2410 |
|
|
2411 |
|
|
2412 |
|
|
2413 |
|
|
2414 |
|
|
2415 |
|
|
2416 |
|
|
2417 |
|
@param |
2418 |
|
|
2419 |
|
@param |
2420 |
|
|
2421 |
|
@param |
2422 |
|
|
2423 |
|
@return |
2424 |
|
|
|
|
| 90% |
Uncovered Elements: 6 (60) |
Complexity: 13 |
Complexity Density: 0.36 |
|
2425 |
9 |
static int computePeptideVariants(SequenceI peptide, int peptidePos,... |
2426 |
|
List<DnaVariant>[] codonVariants) |
2427 |
|
{ |
2428 |
9 |
String residue = String.valueOf(peptide.getCharAt(peptidePos - 1)); |
2429 |
9 |
int count = 0; |
2430 |
9 |
String base1 = codonVariants[0].get(0).base; |
2431 |
9 |
String base2 = codonVariants[1].get(0).base; |
2432 |
9 |
String base3 = codonVariants[2].get(0).base; |
2433 |
|
|
2434 |
|
|
2435 |
|
|
2436 |
|
|
2437 |
9 |
for (DnaVariant dnavar : codonVariants[0]) |
2438 |
|
{ |
2439 |
11 |
if (dnavar.variant != null) |
2440 |
|
{ |
2441 |
3 |
String alleles = (String) dnavar.variant.getValue(Gff3Helper.ALLELES); |
2442 |
3 |
if (alleles != null) |
2443 |
|
{ |
2444 |
3 |
for (String base : alleles.split(",")) |
2445 |
|
{ |
2446 |
6 |
if (!base1.equalsIgnoreCase(base)) |
2447 |
|
{ |
2448 |
3 |
String codon = base.toUpperCase() + base2.toLowerCase() |
2449 |
|
+ base3.toLowerCase(); |
2450 |
3 |
String canonical = base1.toUpperCase() + base2.toLowerCase() |
2451 |
|
+ base3.toLowerCase(); |
2452 |
3 |
if (addPeptideVariant(peptide, peptidePos, residue, dnavar, |
2453 |
|
codon, canonical)) |
2454 |
|
{ |
2455 |
3 |
count++; |
2456 |
|
} |
2457 |
|
} |
2458 |
|
} |
2459 |
|
} |
2460 |
|
} |
2461 |
|
} |
2462 |
|
|
2463 |
|
|
2464 |
|
|
2465 |
|
|
2466 |
9 |
for (DnaVariant var : codonVariants[1]) |
2467 |
|
{ |
2468 |
9 |
if (var.variant != null) |
2469 |
|
{ |
2470 |
6 |
String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES); |
2471 |
6 |
if (alleles != null) |
2472 |
|
{ |
2473 |
6 |
for (String base : alleles.split(",")) |
2474 |
|
{ |
2475 |
13 |
if (!base2.equalsIgnoreCase(base)) |
2476 |
|
{ |
2477 |
7 |
String codon = base1.toLowerCase() + base.toUpperCase() |
2478 |
|
+ base3.toLowerCase(); |
2479 |
7 |
String canonical = base1.toLowerCase() + base2.toUpperCase() |
2480 |
|
+ base3.toLowerCase(); |
2481 |
7 |
if (addPeptideVariant(peptide, peptidePos, residue, var, |
2482 |
|
codon, canonical)) |
2483 |
|
{ |
2484 |
7 |
count++; |
2485 |
|
} |
2486 |
|
} |
2487 |
|
} |
2488 |
|
} |
2489 |
|
} |
2490 |
|
} |
2491 |
|
|
2492 |
|
|
2493 |
|
|
2494 |
|
|
2495 |
9 |
for (DnaVariant var : codonVariants[2]) |
2496 |
|
{ |
2497 |
10 |
if (var.variant != null) |
2498 |
|
{ |
2499 |
4 |
String alleles = (String) var.variant.getValue(Gff3Helper.ALLELES); |
2500 |
4 |
if (alleles != null) |
2501 |
|
{ |
2502 |
4 |
for (String base : alleles.split(",")) |
2503 |
|
{ |
2504 |
8 |
if (!base3.equalsIgnoreCase(base)) |
2505 |
|
{ |
2506 |
4 |
String codon = base1.toLowerCase() + base2.toLowerCase() |
2507 |
|
+ base.toUpperCase(); |
2508 |
4 |
String canonical = base1.toLowerCase() + base2.toLowerCase() |
2509 |
|
+ base3.toUpperCase(); |
2510 |
4 |
if (addPeptideVariant(peptide, peptidePos, residue, var, |
2511 |
|
codon, canonical)) |
2512 |
|
{ |
2513 |
4 |
count++; |
2514 |
|
} |
2515 |
|
} |
2516 |
|
} |
2517 |
|
} |
2518 |
|
} |
2519 |
|
} |
2520 |
|
|
2521 |
9 |
return count; |
2522 |
|
} |
2523 |
|
|
2524 |
|
|
2525 |
|
|
2526 |
|
|
2527 |
|
|
2528 |
|
|
2529 |
|
@param |
2530 |
|
@param |
2531 |
|
@param |
2532 |
|
@param |
2533 |
|
@param |
2534 |
|
|
2535 |
|
@param |
2536 |
|
|
2537 |
|
@return |
2538 |
|
|
|
|
| 92.2% |
Uncovered Elements: 4 (51) |
Complexity: 11 |
Complexity Density: 0.33 |
|
2539 |
14 |
static boolean addPeptideVariant(SequenceI peptide, int peptidePos,... |
2540 |
|
String residue, DnaVariant var, String codon, String canonical) |
2541 |
|
{ |
2542 |
|
|
2543 |
|
|
2544 |
|
|
2545 |
|
|
2546 |
|
|
2547 |
|
|
2548 |
14 |
String trans = codon.contains("-") ? null |
2549 |
14 |
: (codon.length() > CODON_LENGTH ? null |
2550 |
|
: ResidueProperties.codonTranslate(codon)); |
2551 |
14 |
if (trans == null) |
2552 |
|
{ |
2553 |
0 |
return false; |
2554 |
|
} |
2555 |
14 |
String desc = canonical + "/" + codon; |
2556 |
14 |
String featureType = ""; |
2557 |
14 |
if (trans.equals(residue)) |
2558 |
|
{ |
2559 |
3 |
featureType = SequenceOntologyI.SYNONYMOUS_VARIANT; |
2560 |
|
} |
2561 |
11 |
else if (ResidueProperties.STOP.equals(trans)) |
2562 |
|
{ |
2563 |
1 |
featureType = SequenceOntologyI.STOP_GAINED; |
2564 |
|
} |
2565 |
|
else |
2566 |
|
{ |
2567 |
10 |
String residue3Char = StringUtils |
2568 |
|
.toSentenceCase(ResidueProperties.aa2Triplet.get(residue)); |
2569 |
10 |
String trans3Char = StringUtils |
2570 |
|
.toSentenceCase(ResidueProperties.aa2Triplet.get(trans)); |
2571 |
10 |
desc = "p." + residue3Char + peptidePos + trans3Char; |
2572 |
10 |
featureType = SequenceOntologyI.NONSYNONYMOUS_VARIANT; |
2573 |
|
} |
2574 |
14 |
SequenceFeature sf = new SequenceFeature(featureType, desc, peptidePos, |
2575 |
|
peptidePos, var.getSource()); |
2576 |
|
|
2577 |
14 |
StringBuilder attributes = new StringBuilder(32); |
2578 |
14 |
String id = (String) var.variant.getValue(ID); |
2579 |
14 |
if (id != null) |
2580 |
|
{ |
2581 |
8 |
if (id.startsWith(SEQUENCE_VARIANT)) |
2582 |
|
{ |
2583 |
1 |
id = id.substring(SEQUENCE_VARIANT.length()); |
2584 |
|
} |
2585 |
8 |
sf.setValue(ID, id); |
2586 |
8 |
attributes.append(ID).append("=").append(id); |
2587 |
|
|
2588 |
8 |
StringBuilder link = new StringBuilder(32); |
2589 |
8 |
try |
2590 |
|
{ |
2591 |
8 |
link.append(desc).append(" ").append(id).append( |
2592 |
|
"|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=") |
2593 |
|
.append(URLEncoder.encode(id, "UTF-8")); |
2594 |
8 |
sf.addLink(link.toString()); |
2595 |
|
} catch (UnsupportedEncodingException e) |
2596 |
|
{ |
2597 |
|
|
2598 |
|
} |
2599 |
|
} |
2600 |
14 |
String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE); |
2601 |
14 |
if (clinSig != null) |
2602 |
|
{ |
2603 |
6 |
sf.setValue(CLINICAL_SIGNIFICANCE, clinSig); |
2604 |
6 |
attributes.append(";").append(CLINICAL_SIGNIFICANCE).append("=") |
2605 |
|
.append(clinSig); |
2606 |
|
} |
2607 |
14 |
peptide.addSequenceFeature(sf); |
2608 |
14 |
if (attributes.length() > 0) |
2609 |
|
{ |
2610 |
8 |
sf.setAttributes(attributes.toString()); |
2611 |
|
} |
2612 |
14 |
return true; |
2613 |
|
} |
2614 |
|
|
2615 |
|
|
2616 |
|
|
2617 |
|
|
2618 |
|
|
2619 |
|
|
2620 |
|
|
2621 |
|
|
2622 |
|
@param |
2623 |
|
@param |
2624 |
|
@return |
2625 |
|
|
|
|
| 91.3% |
Uncovered Elements: 6 (69) |
Complexity: 14 |
Complexity Density: 0.31 |
|
2626 |
9 |
@SuppressWarnings("unchecked")... |
2627 |
|
static LinkedHashMap<Integer, List<DnaVariant>[]> buildDnaVariantsMap( |
2628 |
|
SequenceI dnaSeq, MapList dnaToProtein) |
2629 |
|
{ |
2630 |
|
|
2631 |
|
|
2632 |
|
|
2633 |
|
|
2634 |
9 |
LinkedHashMap<Integer, List<DnaVariant>[]> variants = new LinkedHashMap<>(); |
2635 |
|
|
2636 |
9 |
List<SequenceFeature> dnaFeatures = dnaSeq.getFeatures() |
2637 |
|
.getFeaturesByOntology(SequenceOntologyI.SEQUENCE_VARIANT); |
2638 |
9 |
if (dnaFeatures.isEmpty()) |
2639 |
|
{ |
2640 |
3 |
return variants; |
2641 |
|
} |
2642 |
|
|
2643 |
6 |
int dnaStart = dnaSeq.getStart(); |
2644 |
6 |
int[] lastCodon = null; |
2645 |
6 |
int lastPeptidePostion = 0; |
2646 |
|
|
2647 |
|
|
2648 |
|
|
2649 |
|
|
2650 |
6 |
for (SequenceFeature sf : dnaFeatures) |
2651 |
|
{ |
2652 |
18 |
int dnaCol = sf.getBegin(); |
2653 |
18 |
if (dnaCol != sf.getEnd()) |
2654 |
|
{ |
2655 |
|
|
2656 |
0 |
continue; |
2657 |
|
} |
2658 |
|
|
2659 |
|
|
2660 |
|
|
2661 |
|
|
2662 |
18 |
String alls = (String) sf.getValue(Gff3Helper.ALLELES); |
2663 |
18 |
if (alls == null) |
2664 |
|
{ |
2665 |
0 |
continue; |
2666 |
|
} |
2667 |
|
|
2668 |
18 |
String[] alleles = alls.toUpperCase().split(","); |
2669 |
18 |
boolean isSnp = true; |
2670 |
18 |
for (String allele : alleles) |
2671 |
|
{ |
2672 |
33 |
if (allele.trim().length() > 1) |
2673 |
|
{ |
2674 |
5 |
isSnp = false; |
2675 |
|
} |
2676 |
|
} |
2677 |
18 |
if (!isSnp) |
2678 |
|
{ |
2679 |
5 |
continue; |
2680 |
|
} |
2681 |
|
|
2682 |
13 |
int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol); |
2683 |
13 |
if (mapsTo == null) |
2684 |
|
{ |
2685 |
|
|
2686 |
0 |
continue; |
2687 |
|
} |
2688 |
13 |
int peptidePosition = mapsTo[0]; |
2689 |
13 |
List<DnaVariant>[] codonVariants = variants.get(peptidePosition); |
2690 |
13 |
if (codonVariants == null) |
2691 |
|
{ |
2692 |
10 |
codonVariants = new ArrayList[CODON_LENGTH]; |
2693 |
10 |
codonVariants[0] = new ArrayList<>(); |
2694 |
10 |
codonVariants[1] = new ArrayList<>(); |
2695 |
10 |
codonVariants[2] = new ArrayList<>(); |
2696 |
10 |
variants.put(peptidePosition, codonVariants); |
2697 |
|
} |
2698 |
|
|
2699 |
|
|
2700 |
|
|
2701 |
|
|
2702 |
13 |
int[] codon = peptidePosition == lastPeptidePostion ? lastCodon |
2703 |
|
: MappingUtils.flattenRanges(dnaToProtein.locateInFrom( |
2704 |
|
peptidePosition, peptidePosition)); |
2705 |
13 |
lastPeptidePostion = peptidePosition; |
2706 |
13 |
lastCodon = codon; |
2707 |
|
|
2708 |
|
|
2709 |
|
|
2710 |
|
|
2711 |
52 |
for (int codonPos = 0; codonPos < CODON_LENGTH; codonPos++) |
2712 |
|
{ |
2713 |
39 |
String nucleotide = String.valueOf( |
2714 |
|
dnaSeq.getCharAt(codon[codonPos] - dnaStart)).toUpperCase(); |
2715 |
39 |
List<DnaVariant> codonVariant = codonVariants[codonPos]; |
2716 |
39 |
if (codon[codonPos] == dnaCol) |
2717 |
|
{ |
2718 |
13 |
if (!codonVariant.isEmpty() |
2719 |
|
&& codonVariant.get(0).variant == null) |
2720 |
|
{ |
2721 |
|
|
2722 |
|
|
2723 |
|
|
2724 |
3 |
codonVariant.get(0).variant = sf; |
2725 |
|
} |
2726 |
|
else |
2727 |
|
{ |
2728 |
|
|
2729 |
|
|
2730 |
|
|
2731 |
10 |
codonVariant.add(new DnaVariant(nucleotide, sf)); |
2732 |
|
} |
2733 |
|
} |
2734 |
26 |
else if (codonVariant.isEmpty()) |
2735 |
|
{ |
2736 |
|
|
2737 |
|
|
2738 |
|
|
2739 |
20 |
codonVariant.add(new DnaVariant(nucleotide)); |
2740 |
|
} |
2741 |
|
} |
2742 |
|
} |
2743 |
6 |
return variants; |
2744 |
|
} |
2745 |
|
|
2746 |
|
|
2747 |
|
|
2748 |
|
|
2749 |
|
|
2750 |
|
|
2751 |
|
@param |
2752 |
|
@param |
2753 |
|
@param |
2754 |
|
|
2755 |
|
@return |
2756 |
|
|
|
|
| 0% |
Uncovered Elements: 25 (25) |
Complexity: 7 |
Complexity Density: 0.41 |
|
2757 |
0 |
public static AlignmentI makeCopyAlignment(SequenceI[] seqs,... |
2758 |
|
SequenceI[] xrefs, AlignmentI dataset) |
2759 |
|
{ |
2760 |
0 |
AlignmentI copy = new Alignment(new Alignment(seqs)); |
2761 |
0 |
copy.setDataset(dataset); |
2762 |
0 |
boolean isProtein = !copy.isNucleotide(); |
2763 |
0 |
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs); |
2764 |
0 |
if (xrefs != null) |
2765 |
|
{ |
2766 |
0 |
for (SequenceI xref : xrefs) |
2767 |
|
{ |
2768 |
0 |
DBRefEntry[] dbrefs = xref.getDBRefs(); |
2769 |
0 |
if (dbrefs != null) |
2770 |
|
{ |
2771 |
0 |
for (DBRefEntry dbref : dbrefs) |
2772 |
|
{ |
2773 |
0 |
if (dbref.getMap() == null || dbref.getMap().getTo() == null |
2774 |
|
|| dbref.getMap().getTo().isProtein() != isProtein) |
2775 |
|
{ |
2776 |
0 |
continue; |
2777 |
|
} |
2778 |
0 |
SequenceI mappedTo = dbref.getMap().getTo(); |
2779 |
0 |
SequenceI match = matcher.findIdMatch(mappedTo); |
2780 |
0 |
if (match == null) |
2781 |
|
{ |
2782 |
0 |
matcher.add(mappedTo); |
2783 |
0 |
copy.addSequence(mappedTo); |
2784 |
|
} |
2785 |
|
} |
2786 |
|
} |
2787 |
|
} |
2788 |
|
} |
2789 |
0 |
return copy; |
2790 |
|
} |
2791 |
|
|
2792 |
|
|
2793 |
|
|
2794 |
|
|
2795 |
|
|
2796 |
|
|
2797 |
|
|
2798 |
|
|
2799 |
|
|
2800 |
|
@param |
2801 |
|
|
2802 |
|
@param |
2803 |
|
|
2804 |
|
@return |
2805 |
|
|
|
|
| 88.2% |
Uncovered Elements: 4 (34) |
Complexity: 5 |
Complexity Density: 0.19 |
|
2806 |
2 |
public static int alignAs(AlignmentI unaligned, AlignmentI aligned)... |
2807 |
|
{ |
2808 |
|
|
2809 |
|
|
2810 |
|
|
2811 |
2 |
if (alignAsSameSequences(unaligned, aligned)) |
2812 |
|
{ |
2813 |
0 |
return unaligned.getHeight(); |
2814 |
|
} |
2815 |
|
|
2816 |
|
|
2817 |
|
|
2818 |
|
|
2819 |
2 |
List<SequenceI> unmapped = new ArrayList<>(); |
2820 |
2 |
Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap( |
2821 |
|
unaligned, aligned, unmapped); |
2822 |
2 |
int width = columnMap.size(); |
2823 |
2 |
char gap = unaligned.getGapCharacter(); |
2824 |
2 |
int realignedCount = 0; |
2825 |
|
|
2826 |
|
|
2827 |
2 |
for (SequenceI seq : unaligned.getSequences()) |
2828 |
|
{ |
2829 |
4 |
if (!unmapped.contains(seq)) |
2830 |
|
{ |
2831 |
4 |
char[] newSeq = new char[width]; |
2832 |
4 |
Arrays.fill(newSeq, gap); |
2833 |
|
|
2834 |
4 |
int newCol = 0; |
2835 |
4 |
int lastCol = 0; |
2836 |
|
|
2837 |
|
|
2838 |
|
|
2839 |
|
|
2840 |
|
|
2841 |
4 |
for (Integer column : columnMap.keySet()) |
2842 |
|
{ |
2843 |
60 |
Character c = columnMap.get(column).get(seq); |
2844 |
60 |
if (c != null) |
2845 |
|
{ |
2846 |
|
|
2847 |
|
|
2848 |
|
|
2849 |
|
|
2850 |
36 |
newSeq[newCol] = c; |
2851 |
36 |
lastCol = newCol; |
2852 |
|
} |
2853 |
60 |
newCol++; |
2854 |
|
} |
2855 |
|
|
2856 |
|
|
2857 |
|
|
2858 |
|
|
2859 |
4 |
if (lastCol < width) |
2860 |
|
{ |
2861 |
4 |
char[] tmp = new char[lastCol + 1]; |
2862 |
4 |
System.arraycopy(newSeq, 0, tmp, 0, lastCol + 1); |
2863 |
4 |
newSeq = tmp; |
2864 |
|
} |
2865 |
|
|
2866 |
4 |
seq.setSequence(String.valueOf(newSeq)); |
2867 |
4 |
realignedCount++; |
2868 |
|
} |
2869 |
|
} |
2870 |
2 |
return realignedCount; |
2871 |
|
} |
2872 |
|
|
2873 |
|
|
2874 |
|
|
2875 |
|
|
2876 |
|
|
2877 |
|
|
2878 |
|
@param |
2879 |
|
|
2880 |
|
@param |
2881 |
|
|
2882 |
|
|
2883 |
|
@return |
2884 |
|
|
|
|
| 88% |
Uncovered Elements: 3 (25) |
Complexity: 6 |
Complexity Density: 0.35 |
|
2885 |
6 |
static boolean alignAsSameSequences(AlignmentI unaligned,... |
2886 |
|
AlignmentI aligned) |
2887 |
|
{ |
2888 |
6 |
if (aligned.getDataset() == null || unaligned.getDataset() == null) |
2889 |
|
{ |
2890 |
0 |
return false; |
2891 |
|
} |
2892 |
|
|
2893 |
|
|
2894 |
6 |
Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<>(); |
2895 |
6 |
for (SequenceI seq : aligned.getSequences()) |
2896 |
|
{ |
2897 |
15 |
SequenceI ds = seq.getDatasetSequence(); |
2898 |
15 |
if (alignedDatasets.get(ds) == null) |
2899 |
|
{ |
2900 |
14 |
alignedDatasets.put(ds, new ArrayList<SequenceI>()); |
2901 |
|
} |
2902 |
15 |
alignedDatasets.get(ds).add(seq); |
2903 |
|
} |
2904 |
|
|
2905 |
|
|
2906 |
|
|
2907 |
|
|
2908 |
|
|
2909 |
6 |
for (SequenceI seq : unaligned.getSequences()) |
2910 |
|
{ |
2911 |
12 |
if (!alignedDatasets.containsKey(seq.getDatasetSequence())) |
2912 |
|
{ |
2913 |
3 |
return false; |
2914 |
|
} |
2915 |
|
} |
2916 |
|
|
2917 |
|
|
2918 |
|
|
2919 |
|
|
2920 |
|
|
2921 |
|
|
2922 |
3 |
for (SequenceI seq : unaligned.getSequences()) |
2923 |
|
{ |
2924 |
7 |
List<SequenceI> alignedSequences = alignedDatasets |
2925 |
|
.get(seq.getDatasetSequence()); |
2926 |
|
|
2927 |
|
|
2928 |
7 |
seq.setSequence(alignedSequences.get(0).getSequenceAsString()); |
2929 |
7 |
if (alignedSequences.size() > 0) |
2930 |
|
{ |
2931 |
|
|
2932 |
7 |
alignedSequences.remove(0); |
2933 |
|
} |
2934 |
|
} |
2935 |
|
|
2936 |
3 |
return true; |
2937 |
|
} |
2938 |
|
|
2939 |
|
|
2940 |
|
|
2941 |
|
|
2942 |
|
|
2943 |
|
@param |
2944 |
|
@param |
2945 |
|
@param |
2946 |
|
@return |
2947 |
|
|
|
|
| 86.7% |
Uncovered Elements: 2 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
2948 |
2 |
static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(... |
2949 |
|
AlignmentI unaligned, AlignmentI aligned, |
2950 |
|
List<SequenceI> unmapped) |
2951 |
|
{ |
2952 |
|
|
2953 |
|
|
2954 |
|
|
2955 |
|
|
2956 |
|
|
2957 |
2 |
SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<>(); |
2958 |
|
|
2959 |
|
|
2960 |
|
|
2961 |
|
|
2962 |
2 |
unmapped.addAll(unaligned.getSequences()); |
2963 |
|
|
2964 |
2 |
List<AlignedCodonFrame> mappings = aligned.getCodonFrames(); |
2965 |
|
|
2966 |
2 |
for (SequenceI seq : unaligned.getSequences()) |
2967 |
|
{ |
2968 |
4 |
for (AlignedCodonFrame mapping : mappings) |
2969 |
|
{ |
2970 |
4 |
SequenceI fromSeq = mapping.findAlignedSequence(seq, aligned); |
2971 |
4 |
if (fromSeq != null) |
2972 |
|
{ |
2973 |
4 |
Mapping seqMap = mapping.getMappingBetween(fromSeq, seq); |
2974 |
4 |
if (addMappedPositions(seq, fromSeq, seqMap, map)) |
2975 |
|
{ |
2976 |
4 |
unmapped.remove(seq); |
2977 |
|
} |
2978 |
|
} |
2979 |
|
} |
2980 |
|
} |
2981 |
2 |
return map; |
2982 |
|
} |
2983 |
|
|
2984 |
|
|
2985 |
|
|
2986 |
|
|
2987 |
|
|
2988 |
|
|
2989 |
|
|
2990 |
|
|
2991 |
|
@param |
2992 |
|
|
2993 |
|
@param |
2994 |
|
|
2995 |
|
@param |
2996 |
|
|
2997 |
|
@param |
2998 |
|
|
2999 |
|
|
3000 |
|
@return |
3001 |
|
|
|
|
| 80% |
Uncovered Elements: 8 (40) |
Complexity: 11 |
Complexity Density: 0.46 |
|
3002 |
6 |
static boolean addMappedPositions(SequenceI seq, SequenceI fromSeq,... |
3003 |
|
Mapping seqMap, Map<Integer, Map<SequenceI, Character>> map) |
3004 |
|
{ |
3005 |
6 |
if (seqMap == null) |
3006 |
|
{ |
3007 |
0 |
return false; |
3008 |
|
} |
3009 |
|
|
3010 |
|
|
3011 |
|
|
3012 |
|
|
3013 |
6 |
if (seqMap.getTo() == fromSeq.getDatasetSequence()) |
3014 |
|
{ |
3015 |
0 |
seqMap = new Mapping(seq.getDatasetSequence(), |
3016 |
|
seqMap.getMap().getInverse()); |
3017 |
|
} |
3018 |
|
|
3019 |
6 |
int toStart = seq.getStart(); |
3020 |
|
|
3021 |
|
|
3022 |
|
|
3023 |
|
|
3024 |
6 |
for (int[] fromRange : seqMap.getMap().getFromRanges()) |
3025 |
|
{ |
3026 |
18 |
for (int i = 0; i < fromRange.length - 1; i += 2) |
3027 |
|
{ |
3028 |
9 |
boolean forward = fromRange[i + 1] >= fromRange[i]; |
3029 |
|
|
3030 |
|
|
3031 |
|
|
3032 |
|
|
3033 |
9 |
int[] range = seqMap.locateMappedRange(fromRange[i], |
3034 |
|
fromRange[i + 1]); |
3035 |
9 |
if (range == null) |
3036 |
|
{ |
3037 |
0 |
System.err.println("Error in mapping " + seqMap + " from " |
3038 |
|
+ fromSeq.getName()); |
3039 |
0 |
return false; |
3040 |
|
} |
3041 |
9 |
int fromCol = fromSeq.findIndex(fromRange[i]); |
3042 |
9 |
int mappedCharPos = range[0]; |
3043 |
|
|
3044 |
|
|
3045 |
|
|
3046 |
|
|
3047 |
|
|
3048 |
|
|
3049 |
|
|
3050 |
70 |
while (mappedCharPos <= range[1] && fromCol <= fromSeq.getLength() |
3051 |
|
&& fromCol >= 0) |
3052 |
|
{ |
3053 |
61 |
if (!Comparison.isGap(fromSeq.getCharAt(fromCol - 1))) |
3054 |
|
{ |
3055 |
|
|
3056 |
|
|
3057 |
|
|
3058 |
|
|
3059 |
48 |
Map<SequenceI, Character> seqsMap = map.get(fromCol); |
3060 |
48 |
if (seqsMap == null) |
3061 |
|
{ |
3062 |
42 |
seqsMap = new HashMap<>(); |
3063 |
42 |
map.put(fromCol, seqsMap); |
3064 |
|
} |
3065 |
48 |
seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart)); |
3066 |
48 |
mappedCharPos++; |
3067 |
|
} |
3068 |
61 |
fromCol += (forward ? 1 : -1); |
3069 |
|
} |
3070 |
|
} |
3071 |
|
} |
3072 |
6 |
return true; |
3073 |
|
} |
3074 |
|
|
3075 |
|
|
3076 |
|
|
|
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
|
3077 |
0 |
public static boolean looksLikeEnsembl(AlignmentI alignment)... |
3078 |
|
{ |
3079 |
0 |
for (SequenceI seq : alignment.getSequences()) |
3080 |
|
{ |
3081 |
0 |
String name = seq.getName(); |
3082 |
0 |
if (!name.startsWith("ENSG") && !name.startsWith("ENST")) |
3083 |
|
{ |
3084 |
0 |
return false; |
3085 |
|
} |
3086 |
|
} |
3087 |
0 |
return true; |
3088 |
|
} |
3089 |
|
} |