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package jalview.analysis; |
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import jalview.commands.RemoveGapColCommand; |
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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.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 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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| 84.1% |
Uncovered Elements: 194 (1,219) |
Complexity: 284 |
Complexity Density: 0.36 |
|
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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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public static final String VARIANT_ID = "id"; |
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| 0% |
Uncovered Elements: 14 (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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| 0% |
Uncovered Elements: 2 (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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| 0% |
Uncovered Elements: 2 (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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| 0% |
Uncovered Elements: 3 (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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} |
140 |
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sq.add(newSeq); |
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} |
142 |
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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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168 |
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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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182 |
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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(); |
188 |
131 |
char[] coreseq = s.getSequence(); |
189 |
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char[] nseq = new char[offset + upstream.length + downstream.length |
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+ coreseq.length]; |
191 |
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char c = core.getGapCharacter(); |
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193 |
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int p = 0; |
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461 |
for (; p < offset; p++) |
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{ |
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nseq[p] = c; |
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} |
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199 |
131 |
System.arraycopy(upstream, 0, nseq, p, upstream.length); |
200 |
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System.arraycopy(coreseq, 0, nseq, p + upstream.length, |
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coreseq.length); |
202 |
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System.arraycopy(downstream, 0, nseq, |
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p + coreseq.length + upstream.length, downstream.length); |
204 |
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s.setSequence(new String(nseq)); |
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s.setStart(s.getStart() - ustream_ds); |
206 |
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s.setEnd(s_end + downstream.length); |
207 |
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} |
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27 |
AlignmentI newAl = new jalview.datamodel.Alignment( |
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sq.toArray(new SequenceI[0])); |
210 |
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for (SequenceI s : sq) |
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{ |
212 |
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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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1 |
aa.adjustForAlignment(); |
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1 |
newAl.addAnnotation(aa); |
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} |
219 |
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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 |
230 |
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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 |
|
233 |
57464 |
public static int getSequenceIndex(AlignmentI al, SequenceI seq)... |
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{ |
235 |
57464 |
int result = -1; |
236 |
57464 |
int pos = 0; |
237 |
57464 |
for (SequenceI alSeq : al.getSequences()) |
238 |
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{ |
239 |
126202503 |
if (alSeq == seq) |
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{ |
241 |
57462 |
result = pos; |
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57462 |
break; |
243 |
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} |
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126145041 |
pos++; |
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} |
246 |
57463 |
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(... |
257 |
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AlignmentI al) |
258 |
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{ |
259 |
1 |
Map<String, List<SequenceI>> theMap = new LinkedHashMap<>(); |
260 |
1 |
for (SequenceI seq : al.getSequences()) |
261 |
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{ |
262 |
3 |
String name = seq.getName(); |
263 |
3 |
if (name != null) |
264 |
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{ |
265 |
3 |
List<SequenceI> seqs = theMap.get(name); |
266 |
3 |
if (seqs == null) |
267 |
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{ |
268 |
2 |
seqs = new ArrayList<>(); |
269 |
2 |
theMap.put(name, seqs); |
270 |
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} |
271 |
3 |
seqs.add(seq); |
272 |
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} |
273 |
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} |
274 |
1 |
return theMap; |
275 |
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} |
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283 |
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@param |
284 |
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@param |
285 |
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@return |
286 |
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| 77.8% |
Uncovered Elements: 2 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
287 |
4 |
public static boolean mapProteinAlignmentToCdna(... |
288 |
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final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment) |
289 |
|
{ |
290 |
4 |
if (proteinAlignment == null || cdnaAlignment == null) |
291 |
|
{ |
292 |
0 |
return false; |
293 |
|
} |
294 |
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295 |
4 |
Set<SequenceI> mappedDna = new HashSet<>(); |
296 |
4 |
Set<SequenceI> mappedProtein = new HashSet<>(); |
297 |
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298 |
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299 |
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300 |
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301 |
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302 |
4 |
boolean mappingPerformed = mapProteinToCdna(proteinAlignment, |
303 |
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cdnaAlignment, mappedDna, mappedProtein, true); |
304 |
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305 |
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306 |
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307 |
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308 |
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309 |
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310 |
4 |
mappingPerformed |= mapProteinToCdna(proteinAlignment, cdnaAlignment, |
311 |
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mappedDna, mappedProtein, false); |
312 |
4 |
return mappingPerformed; |
313 |
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} |
314 |
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315 |
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317 |
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318 |
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319 |
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@param |
320 |
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@param |
321 |
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@param |
322 |
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323 |
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@param |
324 |
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325 |
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@param |
326 |
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327 |
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@return |
328 |
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| 93.8% |
Uncovered Elements: 2 (32) |
Complexity: 9 |
Complexity Density: 0.41 |
|
329 |
8 |
protected static boolean mapProteinToCdna(... |
330 |
|
final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment, |
331 |
|
Set<SequenceI> mappedDna, Set<SequenceI> mappedProtein, |
332 |
|
boolean xrefsOnly) |
333 |
|
{ |
334 |
8 |
boolean mappingExistsOrAdded = false; |
335 |
8 |
List<SequenceI> thisSeqs = proteinAlignment.getSequences(); |
336 |
8 |
for (SequenceI aaSeq : thisSeqs) |
337 |
|
{ |
338 |
22 |
boolean proteinMapped = false; |
339 |
22 |
AlignedCodonFrame acf = new AlignedCodonFrame(); |
340 |
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|
341 |
22 |
for (SequenceI cdnaSeq : cdnaAlignment.getSequences()) |
342 |
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{ |
343 |
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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 |
86 |
if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq)) |
353 |
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{ |
354 |
39 |
continue; |
355 |
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} |
356 |
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357 |
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358 |
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|
359 |
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|
360 |
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|
361 |
47 |
if (!xrefsOnly && (mappedProtein.contains(aaSeq) |
362 |
|
|| mappedDna.contains(cdnaSeq))) |
363 |
|
{ |
364 |
29 |
continue; |
365 |
|
} |
366 |
18 |
if (mappingExists(proteinAlignment.getCodonFrames(), |
367 |
|
aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence())) |
368 |
|
{ |
369 |
0 |
mappingExistsOrAdded = true; |
370 |
|
} |
371 |
|
else |
372 |
|
{ |
373 |
18 |
MapList map = mapCdnaToProtein(aaSeq, cdnaSeq); |
374 |
18 |
if (map != null) |
375 |
|
{ |
376 |
12 |
acf.addMap(cdnaSeq, aaSeq, map); |
377 |
12 |
mappingExistsOrAdded = true; |
378 |
12 |
proteinMapped = true; |
379 |
12 |
mappedDna.add(cdnaSeq); |
380 |
12 |
mappedProtein.add(aaSeq); |
381 |
|
} |
382 |
|
} |
383 |
|
} |
384 |
22 |
if (proteinMapped) |
385 |
|
{ |
386 |
11 |
proteinAlignment.addCodonFrame(acf); |
387 |
|
} |
388 |
|
} |
389 |
8 |
return mappingExistsOrAdded; |
390 |
|
} |
391 |
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392 |
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393 |
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394 |
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395 |
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| 66.7% |
Uncovered Elements: 3 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
396 |
18 |
protected static boolean mappingExists(List<AlignedCodonFrame> mappings,... |
397 |
|
SequenceI aaSeq, SequenceI cdnaSeq) |
398 |
|
{ |
399 |
18 |
if (mappings != null) |
400 |
|
{ |
401 |
18 |
for (AlignedCodonFrame acf : mappings) |
402 |
|
{ |
403 |
14 |
if (cdnaSeq == acf.getDnaForAaSeq(aaSeq)) |
404 |
|
{ |
405 |
0 |
return true; |
406 |
|
} |
407 |
|
} |
408 |
|
} |
409 |
18 |
return false; |
410 |
|
} |
411 |
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412 |
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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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@param |
424 |
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425 |
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@param |
426 |
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427 |
|
@return |
428 |
|
|
|
|
| 95.2% |
Uncovered Elements: 2 (42) |
Complexity: 12 |
Complexity Density: 0.43 |
|
429 |
21 |
public static MapList mapCdnaToProtein(SequenceI proteinSeq,... |
430 |
|
SequenceI cdnaSeq) |
431 |
|
{ |
432 |
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433 |
|
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434 |
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|
435 |
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|
436 |
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|
437 |
21 |
final SequenceI proteinDataset = proteinSeq.getDatasetSequence(); |
438 |
21 |
char[] aaSeqChars = proteinDataset != null |
439 |
|
? proteinDataset.getSequence() |
440 |
|
: proteinSeq.getSequence(); |
441 |
21 |
final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence(); |
442 |
21 |
char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence() |
443 |
|
: cdnaSeq.getSequence(); |
444 |
21 |
if (aaSeqChars == null || cdnaSeqChars == null) |
445 |
|
{ |
446 |
0 |
return null; |
447 |
|
} |
448 |
|
|
449 |
|
|
450 |
|
|
451 |
|
|
452 |
21 |
final int mappedLength = CODON_LENGTH * aaSeqChars.length; |
453 |
21 |
int cdnaLength = cdnaSeqChars.length; |
454 |
21 |
int cdnaStart = cdnaSeq.getStart(); |
455 |
21 |
int cdnaEnd = cdnaSeq.getEnd(); |
456 |
21 |
final int proteinStart = proteinSeq.getStart(); |
457 |
21 |
final int proteinEnd = proteinSeq.getEnd(); |
458 |
|
|
459 |
|
|
460 |
|
|
461 |
|
|
462 |
21 |
if (cdnaLength != mappedLength && cdnaLength > 2) |
463 |
|
{ |
464 |
6 |
String lastCodon = String.valueOf(cdnaSeqChars, |
465 |
|
cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(); |
466 |
6 |
for (String stop : ResidueProperties.STOP_CODONS) |
467 |
|
{ |
468 |
17 |
if (lastCodon.equals(stop)) |
469 |
|
{ |
470 |
2 |
cdnaEnd -= CODON_LENGTH; |
471 |
2 |
cdnaLength -= CODON_LENGTH; |
472 |
2 |
break; |
473 |
|
} |
474 |
|
} |
475 |
|
} |
476 |
|
|
477 |
|
|
478 |
|
|
479 |
|
|
480 |
21 |
int startOffset = 0; |
481 |
21 |
if (cdnaLength != mappedLength && cdnaLength > 2 |
482 |
|
&& String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase() |
483 |
|
.equals(ResidueProperties.START)) |
484 |
|
{ |
485 |
5 |
startOffset += CODON_LENGTH; |
486 |
5 |
cdnaStart += CODON_LENGTH; |
487 |
5 |
cdnaLength -= CODON_LENGTH; |
488 |
|
} |
489 |
|
|
490 |
21 |
if (translatesAs(cdnaSeqChars, startOffset, aaSeqChars)) |
491 |
|
{ |
492 |
|
|
493 |
|
|
494 |
|
|
495 |
15 |
MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, |
496 |
|
new int[] |
497 |
|
{ proteinStart, proteinEnd }, CODON_LENGTH, 1); |
498 |
15 |
return map; |
499 |
|
} |
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
6 |
return mapCdsToProtein(cdnaSeq, proteinSeq); |
505 |
|
} |
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
@param |
513 |
|
@param |
514 |
|
@param |
515 |
|
@return |
516 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (37) |
Complexity: 14 |
Complexity Density: 0.67 |
|
517 |
41 |
protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,... |
518 |
|
char[] aaSeqChars) |
519 |
|
{ |
520 |
41 |
if (cdnaSeqChars == null || aaSeqChars == null) |
521 |
|
{ |
522 |
3 |
return false; |
523 |
|
} |
524 |
|
|
525 |
38 |
int aaPos = 0; |
526 |
38 |
int dnaPos = cdnaStart; |
527 |
151 |
for (; dnaPos < cdnaSeqChars.length - 2 |
528 |
|
&& aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++) |
529 |
|
{ |
530 |
120 |
String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); |
531 |
120 |
final String translated = ResidueProperties.codonTranslate(codon); |
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
120 |
final char aaRes = aaSeqChars[aaPos]; |
537 |
120 |
if ((translated == null || ResidueProperties.STOP.equals(translated)) |
538 |
|
&& aaRes == '*') |
539 |
|
{ |
540 |
4 |
continue; |
541 |
|
} |
542 |
116 |
if (translated == null || !(aaRes == translated.charAt(0))) |
543 |
|
{ |
544 |
|
|
545 |
|
|
546 |
|
|
547 |
7 |
return false; |
548 |
|
} |
549 |
|
} |
550 |
|
|
551 |
|
|
552 |
|
|
553 |
|
|
554 |
31 |
if (aaPos != aaSeqChars.length) |
555 |
|
{ |
556 |
2 |
return false; |
557 |
|
} |
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
29 |
if (dnaPos == cdnaSeqChars.length) |
564 |
|
{ |
565 |
17 |
return true; |
566 |
|
} |
567 |
12 |
if (dnaPos == cdnaSeqChars.length - CODON_LENGTH) |
568 |
|
{ |
569 |
11 |
String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH); |
570 |
11 |
if (ResidueProperties.STOP |
571 |
|
.equals(ResidueProperties.codonTranslate(codon))) |
572 |
|
{ |
573 |
9 |
return true; |
574 |
|
} |
575 |
|
} |
576 |
3 |
return false; |
577 |
|
} |
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
|
582 |
|
|
583 |
|
@param |
584 |
|
|
585 |
|
@param |
586 |
|
|
587 |
|
@param |
588 |
|
|
589 |
|
@param |
590 |
|
@param |
591 |
|
@return |
592 |
|
|
|
|
| 90% |
Uncovered Elements: 2 (20) |
Complexity: 5 |
Complexity Density: 0.36 |
|
593 |
8 |
public static boolean alignSequenceAs(SequenceI seq, AlignmentI al,... |
594 |
|
String gap, boolean preserveMappedGaps, |
595 |
|
boolean preserveUnmappedGaps) |
596 |
|
{ |
597 |
|
|
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
|
603 |
8 |
List<AlignedCodonFrame> mappings = al.getCodonFrame(seq); |
604 |
8 |
if (mappings == null || mappings.isEmpty()) |
605 |
|
{ |
606 |
0 |
return false; |
607 |
|
} |
608 |
|
|
609 |
|
|
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
8 |
SequenceI alignFrom = null; |
615 |
8 |
AlignedCodonFrame mapping = null; |
616 |
8 |
for (AlignedCodonFrame mp : mappings) |
617 |
|
{ |
618 |
8 |
alignFrom = mp.findAlignedSequence(seq, al); |
619 |
8 |
if (alignFrom != null) |
620 |
|
{ |
621 |
4 |
mapping = mp; |
622 |
4 |
break; |
623 |
|
} |
624 |
|
} |
625 |
|
|
626 |
8 |
if (alignFrom == null) |
627 |
|
{ |
628 |
4 |
return false; |
629 |
|
} |
630 |
4 |
alignSequenceAs(seq, alignFrom, mapping, gap, al.getGapCharacter(), |
631 |
|
preserveMappedGaps, preserveUnmappedGaps); |
632 |
4 |
return true; |
633 |
|
} |
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
@param |
642 |
|
@param |
643 |
|
@param |
644 |
|
@param |
645 |
|
@param |
646 |
|
@param |
647 |
|
@param |
648 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (88) |
Complexity: 20 |
Complexity Density: 0.33 |
|
649 |
19 |
public static void alignSequenceAs(SequenceI alignTo, SequenceI alignFrom,... |
650 |
|
AlignedCodonFrame mapping, String myGap, char sourceGap, |
651 |
|
boolean preserveMappedGaps, boolean preserveUnmappedGaps) |
652 |
|
{ |
653 |
|
|
654 |
|
|
655 |
|
|
656 |
19 |
int thisSeqPos = 0; |
657 |
19 |
int sourceDsPos = 0; |
658 |
|
|
659 |
19 |
int basesWritten = 0; |
660 |
19 |
char myGapChar = myGap.charAt(0); |
661 |
19 |
int ratio = myGap.length(); |
662 |
|
|
663 |
19 |
int fromOffset = alignFrom.getStart() - 1; |
664 |
19 |
int toOffset = alignTo.getStart() - 1; |
665 |
19 |
int sourceGapMappedLength = 0; |
666 |
19 |
boolean inExon = false; |
667 |
19 |
final int toLength = alignTo.getLength(); |
668 |
19 |
final int fromLength = alignFrom.getLength(); |
669 |
19 |
StringBuilder thisAligned = new StringBuilder(2 * toLength); |
670 |
|
|
671 |
|
|
672 |
|
|
673 |
|
|
674 |
205 |
for (int i = 0; i < fromLength; i++) |
675 |
|
{ |
676 |
186 |
char sourceChar = alignFrom.getCharAt(i); |
677 |
186 |
if (sourceChar == sourceGap) |
678 |
|
{ |
679 |
44 |
sourceGapMappedLength += ratio; |
680 |
44 |
continue; |
681 |
|
} |
682 |
|
|
683 |
|
|
684 |
|
|
685 |
|
|
686 |
142 |
sourceDsPos++; |
687 |
|
|
688 |
142 |
int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom, |
689 |
|
sourceDsPos + fromOffset); |
690 |
142 |
if (mappedPos == null) |
691 |
|
{ |
692 |
|
|
693 |
|
|
694 |
|
|
695 |
94 |
sourceGapMappedLength += ratio; |
696 |
|
|
697 |
|
|
698 |
|
|
699 |
94 |
continue; |
700 |
|
} |
701 |
|
|
702 |
48 |
int mappedCodonStart = mappedPos[0]; |
703 |
48 |
int mappedCodonEnd = mappedPos[mappedPos.length - 1]; |
704 |
48 |
StringBuilder trailingCopiedGap = new StringBuilder(); |
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
|
709 |
|
|
710 |
|
|
711 |
|
|
712 |
|
|
713 |
|
|
714 |
48 |
int intronLength = 0; |
715 |
294 |
while (basesWritten + toOffset < mappedCodonEnd |
716 |
|
&& thisSeqPos < toLength) |
717 |
|
{ |
718 |
246 |
final char c = alignTo.getCharAt(thisSeqPos++); |
719 |
246 |
if (c != myGapChar) |
720 |
|
{ |
721 |
146 |
basesWritten++; |
722 |
146 |
int sourcePosition = basesWritten + toOffset; |
723 |
146 |
if (sourcePosition < mappedCodonStart) |
724 |
|
{ |
725 |
|
|
726 |
|
|
727 |
|
|
728 |
|
|
729 |
48 |
if (preserveUnmappedGaps && trailingCopiedGap.length() > 0) |
730 |
|
{ |
731 |
17 |
thisAligned.append(trailingCopiedGap.toString()); |
732 |
17 |
intronLength += trailingCopiedGap.length(); |
733 |
17 |
trailingCopiedGap = new StringBuilder(); |
734 |
|
} |
735 |
48 |
intronLength++; |
736 |
48 |
inExon = false; |
737 |
|
} |
738 |
|
else |
739 |
|
{ |
740 |
98 |
final boolean startOfCodon = sourcePosition == mappedCodonStart; |
741 |
98 |
int gapsToAdd = calculateGapsToInsert(preserveMappedGaps, |
742 |
|
preserveUnmappedGaps, sourceGapMappedLength, inExon, |
743 |
|
trailingCopiedGap.length(), intronLength, startOfCodon); |
744 |
215 |
for (int k = 0; k < gapsToAdd; k++) |
745 |
|
{ |
746 |
117 |
thisAligned.append(myGapChar); |
747 |
|
} |
748 |
98 |
sourceGapMappedLength = 0; |
749 |
98 |
inExon = true; |
750 |
|
} |
751 |
146 |
thisAligned.append(c); |
752 |
146 |
trailingCopiedGap = new StringBuilder(); |
753 |
|
} |
754 |
|
else |
755 |
|
{ |
756 |
100 |
if (inExon && preserveMappedGaps) |
757 |
|
{ |
758 |
32 |
trailingCopiedGap.append(myGapChar); |
759 |
|
} |
760 |
68 |
else if (!inExon && preserveUnmappedGaps) |
761 |
|
{ |
762 |
27 |
trailingCopiedGap.append(myGapChar); |
763 |
|
} |
764 |
|
} |
765 |
|
} |
766 |
|
} |
767 |
|
|
768 |
|
|
769 |
|
|
770 |
|
|
771 |
|
|
772 |
129 |
while (thisSeqPos < toLength) |
773 |
|
{ |
774 |
110 |
final char c = alignTo.getCharAt(thisSeqPos++); |
775 |
110 |
if (c != myGapChar || preserveUnmappedGaps) |
776 |
|
{ |
777 |
102 |
thisAligned.append(c); |
778 |
|
} |
779 |
110 |
sourceGapMappedLength--; |
780 |
|
} |
781 |
|
|
782 |
|
|
783 |
|
|
784 |
|
|
785 |
|
|
786 |
19 |
if (preserveUnmappedGaps) |
787 |
|
{ |
788 |
24 |
while (sourceGapMappedLength > 0) |
789 |
|
{ |
790 |
12 |
thisAligned.append(myGapChar); |
791 |
12 |
sourceGapMappedLength--; |
792 |
|
} |
793 |
|
} |
794 |
|
|
795 |
|
|
796 |
|
|
797 |
|
|
798 |
19 |
alignTo.setSequence(new String(thisAligned)); |
799 |
|
} |
800 |
|
|
801 |
|
|
802 |
|
|
803 |
|
|
804 |
|
@param |
805 |
|
@param |
806 |
|
@param |
807 |
|
@param |
808 |
|
@param |
809 |
|
@param |
810 |
|
@param |
811 |
|
@return |
812 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 10 |
Complexity Density: 0.67 |
|
813 |
98 |
protected static int calculateGapsToInsert(boolean preserveMappedGaps,... |
814 |
|
boolean preserveUnmappedGaps, int sourceGapMappedLength, |
815 |
|
boolean inExon, int trailingGapLength, int intronLength, |
816 |
|
final boolean startOfCodon) |
817 |
|
{ |
818 |
98 |
int gapsToAdd = 0; |
819 |
98 |
if (startOfCodon) |
820 |
|
{ |
821 |
|
|
822 |
|
|
823 |
|
|
824 |
|
|
825 |
|
|
826 |
|
|
827 |
40 |
if (inExon && !preserveMappedGaps) |
828 |
|
{ |
829 |
4 |
trailingGapLength = 0; |
830 |
|
} |
831 |
40 |
if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps)) |
832 |
|
{ |
833 |
19 |
trailingGapLength = 0; |
834 |
|
} |
835 |
40 |
if (inExon) |
836 |
|
{ |
837 |
14 |
gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength); |
838 |
|
} |
839 |
|
else |
840 |
|
{ |
841 |
26 |
if (intronLength + trailingGapLength <= sourceGapMappedLength) |
842 |
|
{ |
843 |
20 |
gapsToAdd = sourceGapMappedLength - intronLength; |
844 |
|
} |
845 |
|
else |
846 |
|
{ |
847 |
6 |
gapsToAdd = Math.min( |
848 |
|
intronLength + trailingGapLength - sourceGapMappedLength, |
849 |
|
trailingGapLength); |
850 |
|
} |
851 |
|
} |
852 |
|
} |
853 |
|
else |
854 |
|
{ |
855 |
|
|
856 |
|
|
857 |
|
|
858 |
58 |
if (!preserveMappedGaps) |
859 |
|
{ |
860 |
32 |
trailingGapLength = 0; |
861 |
|
} |
862 |
58 |
gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength); |
863 |
|
} |
864 |
98 |
return gapsToAdd; |
865 |
|
} |
866 |
|
|
867 |
|
|
868 |
|
|
869 |
|
|
870 |
|
|
871 |
|
@param |
872 |
|
|
873 |
|
@param |
874 |
|
|
875 |
|
@return |
876 |
|
|
|
|
| 62.5% |
Uncovered Elements: 3 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
877 |
5 |
public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)... |
878 |
|
{ |
879 |
5 |
if (protein.isNucleotide() || !dna.isNucleotide()) |
880 |
|
{ |
881 |
0 |
System.err.println("Wrong alignment type in alignProteinAsDna"); |
882 |
0 |
return 0; |
883 |
|
} |
884 |
5 |
List<SequenceI> unmappedProtein = new ArrayList<>(); |
885 |
5 |
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap( |
886 |
|
protein, dna, unmappedProtein); |
887 |
5 |
return alignProteinAs(protein, alignedCodons, unmappedProtein); |
888 |
|
} |
889 |
|
|
890 |
|
|
891 |
|
|
892 |
|
|
893 |
|
|
894 |
|
|
895 |
|
|
896 |
|
@param |
897 |
|
|
898 |
|
@param |
899 |
|
|
900 |
|
@return |
901 |
|
|
|
|
| 83.3% |
Uncovered Elements: 4 (24) |
Complexity: 5 |
Complexity Density: 0.28 |
|
902 |
4 |
public static int alignCdsAsProtein(AlignmentI dna, AlignmentI protein)... |
903 |
|
{ |
904 |
4 |
if (protein.isNucleotide() || !dna.isNucleotide()) |
905 |
|
{ |
906 |
0 |
System.err.println("Wrong alignment type in alignProteinAsDna"); |
907 |
0 |
return 0; |
908 |
|
} |
909 |
|
|
910 |
4 |
List<AlignedCodonFrame> mappings = protein.getCodonFrames(); |
911 |
4 |
int alignedCount = 0; |
912 |
4 |
int width = 0; |
913 |
4 |
for (SequenceI dnaSeq : dna.getSequences()) |
914 |
|
{ |
915 |
5 |
if (alignCdsSequenceAsProtein(dnaSeq, protein, mappings, |
916 |
|
dna.getGapCharacter())) |
917 |
|
{ |
918 |
5 |
alignedCount++; |
919 |
|
} |
920 |
5 |
width = Math.max(dnaSeq.getLength(), width); |
921 |
|
} |
922 |
4 |
int oldwidth; |
923 |
4 |
int diff; |
924 |
4 |
for (SequenceI dnaSeq : dna.getSequences()) |
925 |
|
{ |
926 |
5 |
oldwidth = dnaSeq.getLength(); |
927 |
5 |
diff = width - oldwidth; |
928 |
5 |
if (diff > 0) |
929 |
|
{ |
930 |
1 |
dnaSeq.insertCharAt(oldwidth, diff, dna.getGapCharacter()); |
931 |
|
} |
932 |
|
} |
933 |
4 |
return alignedCount; |
934 |
|
} |
935 |
|
|
936 |
|
|
937 |
|
|
938 |
|
|
939 |
|
|
940 |
|
|
941 |
|
@param |
942 |
|
@param |
943 |
|
@param |
944 |
|
@param |
945 |
|
@return |
946 |
|
|
|
|
| 67.1% |
Uncovered Elements: 25 (76) |
Complexity: 16 |
Complexity Density: 0.33 |
|
947 |
5 |
static boolean alignCdsSequenceAsProtein(SequenceI cdsSeq,... |
948 |
|
AlignmentI protein, List<AlignedCodonFrame> mappings, |
949 |
|
char gapChar) |
950 |
|
{ |
951 |
5 |
SequenceI cdsDss = cdsSeq.getDatasetSequence(); |
952 |
5 |
if (cdsDss == null) |
953 |
|
{ |
954 |
0 |
System.err |
955 |
|
.println("alignCdsSequenceAsProtein needs aligned sequence!"); |
956 |
0 |
return false; |
957 |
|
} |
958 |
|
|
959 |
5 |
List<AlignedCodonFrame> dnaMappings = MappingUtils |
960 |
|
.findMappingsForSequence(cdsSeq, mappings); |
961 |
5 |
for (AlignedCodonFrame mapping : dnaMappings) |
962 |
|
{ |
963 |
5 |
SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein); |
964 |
5 |
if (peptide != null) |
965 |
|
{ |
966 |
5 |
final int peptideLength = peptide.getLength(); |
967 |
5 |
Mapping map = mapping.getMappingBetween(cdsSeq, peptide); |
968 |
5 |
if (map != null) |
969 |
|
{ |
970 |
5 |
MapList mapList = map.getMap(); |
971 |
5 |
if (map.getTo() == peptide.getDatasetSequence()) |
972 |
|
{ |
973 |
5 |
mapList = mapList.getInverse(); |
974 |
|
} |
975 |
5 |
final int cdsLength = cdsDss.getLength(); |
976 |
5 |
int mappedFromLength = MappingUtils.getLength(mapList |
977 |
|
.getFromRanges()); |
978 |
5 |
int mappedToLength = MappingUtils |
979 |
|
.getLength(mapList.getToRanges()); |
980 |
5 |
boolean addStopCodon = (cdsLength == mappedFromLength |
981 |
|
* CODON_LENGTH + CODON_LENGTH) |
982 |
|
|| (peptide.getDatasetSequence() |
983 |
|
.getLength() == mappedFromLength - 1); |
984 |
5 |
if (cdsLength != mappedToLength && !addStopCodon) |
985 |
|
{ |
986 |
0 |
System.err.println(String.format( |
987 |
|
"Can't align cds as protein (length mismatch %d/%d): %s", |
988 |
|
cdsLength, mappedToLength, cdsSeq.getName())); |
989 |
|
} |
990 |
|
|
991 |
|
|
992 |
|
|
993 |
|
|
994 |
5 |
char[] alignedCds = new char[peptideLength * CODON_LENGTH |
995 |
5 |
+ (addStopCodon ? CODON_LENGTH : 0)]; |
996 |
5 |
Arrays.fill(alignedCds, gapChar); |
997 |
|
|
998 |
|
|
999 |
|
|
1000 |
|
|
1001 |
|
|
1002 |
5 |
int copiedBases = 0; |
1003 |
5 |
int cdsStart = cdsDss.getStart(); |
1004 |
5 |
int proteinPos = peptide.getStart() - 1; |
1005 |
5 |
int cdsCol = 0; |
1006 |
|
|
1007 |
33 |
for (int col = 0; col < peptideLength; col++) |
1008 |
|
{ |
1009 |
28 |
char residue = peptide.getCharAt(col); |
1010 |
|
|
1011 |
28 |
if (Comparison.isGap(residue)) |
1012 |
|
{ |
1013 |
13 |
cdsCol += CODON_LENGTH; |
1014 |
|
} |
1015 |
|
else |
1016 |
|
{ |
1017 |
15 |
proteinPos++; |
1018 |
15 |
int[] codon = mapList.locateInTo(proteinPos, proteinPos); |
1019 |
15 |
if (codon == null) |
1020 |
|
{ |
1021 |
|
|
1022 |
0 |
cdsCol += CODON_LENGTH; |
1023 |
|
} |
1024 |
|
else |
1025 |
|
{ |
1026 |
60 |
for (int j = codon[0]; j <= codon[1]; j++) |
1027 |
|
{ |
1028 |
45 |
char mappedBase = cdsDss.getCharAt(j - cdsStart); |
1029 |
45 |
alignedCds[cdsCol++] = mappedBase; |
1030 |
45 |
copiedBases++; |
1031 |
|
} |
1032 |
|
} |
1033 |
|
} |
1034 |
|
} |
1035 |
|
|
1036 |
|
|
1037 |
|
|
1038 |
|
|
1039 |
|
|
1040 |
5 |
if (copiedBases == cdsLength - CODON_LENGTH) |
1041 |
|
{ |
1042 |
0 |
for (int i = alignedCds.length - 1; i >= 0; i--) |
1043 |
|
{ |
1044 |
0 |
if (!Comparison.isGap(alignedCds[i])) |
1045 |
|
{ |
1046 |
0 |
cdsCol = i + 1; |
1047 |
0 |
break; |
1048 |
|
} |
1049 |
|
} |
1050 |
0 |
for (int i = cdsLength - CODON_LENGTH; i < cdsLength; i++) |
1051 |
|
{ |
1052 |
0 |
alignedCds[cdsCol++] = cdsDss.getCharAt(i); |
1053 |
|
} |
1054 |
|
} |
1055 |
5 |
cdsSeq.setSequence(new String(alignedCds)); |
1056 |
5 |
return true; |
1057 |
|
} |
1058 |
|
} |
1059 |
|
} |
1060 |
0 |
return false; |
1061 |
|
} |
1062 |
|
|
1063 |
|
|
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
|
|
1068 |
|
|
1069 |
|
|
1070 |
|
@param |
1071 |
|
|
1072 |
|
@param |
1073 |
|
|
1074 |
|
@param |
1075 |
|
|
1076 |
|
@return |
1077 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 2 |
Complexity Density: 0.15 |
|
1078 |
5 |
protected static Map<AlignedCodon, Map<SequenceI, AlignedCodon>> buildCodonColumnsMap(... |
1079 |
|
AlignmentI protein, AlignmentI dna, |
1080 |
|
List<SequenceI> unmappedProtein) |
1081 |
|
{ |
1082 |
|
|
1083 |
|
|
1084 |
|
|
1085 |
|
|
1086 |
5 |
unmappedProtein.addAll(protein.getSequences()); |
1087 |
|
|
1088 |
5 |
List<AlignedCodonFrame> mappings = protein.getCodonFrames(); |
1089 |
|
|
1090 |
|
|
1091 |
|
|
1092 |
|
|
1093 |
|
|
1094 |
|
|
1095 |
5 |
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<>( |
1096 |
|
new CodonComparator()); |
1097 |
|
|
1098 |
5 |
for (SequenceI dnaSeq : dna.getSequences()) |
1099 |
|
{ |
1100 |
30 |
for (AlignedCodonFrame mapping : mappings) |
1101 |
|
{ |
1102 |
274 |
SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein); |
1103 |
274 |
if (prot != null) |
1104 |
|
{ |
1105 |
32 |
Mapping seqMap = mapping.getMappingForSequence(dnaSeq); |
1106 |
32 |
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap, |
1107 |
|
alignedCodons); |
1108 |
32 |
unmappedProtein.remove(prot); |
1109 |
|
} |
1110 |
|
} |
1111 |
|
} |
1112 |
|
|
1113 |
|
|
1114 |
|
|
1115 |
|
|
1116 |
|
|
1117 |
|
|
1118 |
5 |
int mappedSequenceCount = protein.getHeight() - unmappedProtein.size(); |
1119 |
5 |
addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount); |
1120 |
|
|
1121 |
5 |
return alignedCodons; |
1122 |
|
} |
1123 |
|
|
1124 |
|
|
1125 |
|
|
1126 |
|
|
1127 |
|
|
1128 |
|
|
1129 |
|
@param |
1130 |
|
|
1131 |
|
@param |
1132 |
|
|
1133 |
|
|
|
|
| 93.9% |
Uncovered Elements: 2 (33) |
Complexity: 6 |
Complexity Density: 0.26 |
|
1134 |
5 |
protected static void addUnmappedPeptideStarts(... |
1135 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons, |
1136 |
|
int mappedSequenceCount) |
1137 |
|
{ |
1138 |
|
|
1139 |
|
|
1140 |
|
|
1141 |
5 |
List<SequenceI> sequencesChecked = new ArrayList<>(); |
1142 |
5 |
AlignedCodon lastCodon = null; |
1143 |
5 |
Map<SequenceI, AlignedCodon> toAdd = new HashMap<>(); |
1144 |
|
|
1145 |
5 |
for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons |
1146 |
|
.entrySet()) |
1147 |
|
{ |
1148 |
1913 |
for (Entry<SequenceI, AlignedCodon> sequenceCodon : entry.getValue() |
1149 |
|
.entrySet()) |
1150 |
|
{ |
1151 |
10661 |
SequenceI seq = sequenceCodon.getKey(); |
1152 |
10661 |
if (sequencesChecked.contains(seq)) |
1153 |
|
{ |
1154 |
10631 |
continue; |
1155 |
|
} |
1156 |
30 |
sequencesChecked.add(seq); |
1157 |
30 |
AlignedCodon codon = sequenceCodon.getValue(); |
1158 |
30 |
if (codon.peptideCol > 1) |
1159 |
|
{ |
1160 |
0 |
System.err.println( |
1161 |
|
"Problem mapping protein with >1 unmapped start positions: " |
1162 |
|
+ seq.getName()); |
1163 |
|
} |
1164 |
30 |
else if (codon.peptideCol == 1) |
1165 |
|
{ |
1166 |
|
|
1167 |
|
|
1168 |
|
|
1169 |
6 |
if (lastCodon != null) |
1170 |
|
{ |
1171 |
5 |
AlignedCodon firstPeptide = new AlignedCodon(lastCodon.pos1, |
1172 |
|
lastCodon.pos2, lastCodon.pos3, |
1173 |
|
String.valueOf(seq.getCharAt(0)), 0); |
1174 |
5 |
toAdd.put(seq, firstPeptide); |
1175 |
|
} |
1176 |
|
else |
1177 |
|
{ |
1178 |
|
|
1179 |
|
|
1180 |
|
|
1181 |
|
|
1182 |
1 |
AlignedCodon firstPeptide = new AlignedCodon(0, 0, 0, |
1183 |
|
String.valueOf(seq.getCharAt(0)), 0); |
1184 |
1 |
toAdd.put(seq, firstPeptide); |
1185 |
|
} |
1186 |
|
} |
1187 |
30 |
if (sequencesChecked.size() == mappedSequenceCount) |
1188 |
|
{ |
1189 |
|
|
1190 |
5 |
break; |
1191 |
|
} |
1192 |
|
} |
1193 |
1913 |
lastCodon = entry.getKey(); |
1194 |
|
} |
1195 |
|
|
1196 |
|
|
1197 |
|
|
1198 |
|
|
1199 |
5 |
for (Entry<SequenceI, AlignedCodon> startCodon : toAdd.entrySet()) |
1200 |
|
{ |
1201 |
6 |
addCodonToMap(alignedCodons, startCodon.getValue(), |
1202 |
|
startCodon.getKey()); |
1203 |
|
} |
1204 |
|
} |
1205 |
|
|
1206 |
|
|
1207 |
|
|
1208 |
|
|
1209 |
|
|
1210 |
|
@param |
1211 |
|
@param |
1212 |
|
|
1213 |
|
|
1214 |
|
@param |
1215 |
|
@return |
1216 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 2 |
Complexity Density: 0.12 |
|
1217 |
5 |
protected static int alignProteinAs(AlignmentI protein,... |
1218 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons, |
1219 |
|
List<SequenceI> unmappedProtein) |
1220 |
|
{ |
1221 |
|
|
1222 |
|
|
1223 |
|
|
1224 |
5 |
int alignedWidth = alignedCodons.size(); |
1225 |
5 |
char[] gaps = new char[alignedWidth]; |
1226 |
5 |
Arrays.fill(gaps, protein.getGapCharacter()); |
1227 |
5 |
Map<SequenceI, char[]> peptides = new HashMap<>(); |
1228 |
5 |
for (SequenceI seq : protein.getSequences()) |
1229 |
|
{ |
1230 |
31 |
if (!unmappedProtein.contains(seq)) |
1231 |
|
{ |
1232 |
30 |
peptides.put(seq, Arrays.copyOf(gaps, gaps.length)); |
1233 |
|
} |
1234 |
|
} |
1235 |
|
|
1236 |
|
|
1237 |
|
|
1238 |
|
|
1239 |
|
|
1240 |
|
|
1241 |
|
|
1242 |
5 |
int column = 0; |
1243 |
5 |
for (AlignedCodon codon : alignedCodons.keySet()) |
1244 |
|
{ |
1245 |
1914 |
final Map<SequenceI, AlignedCodon> columnResidues = alignedCodons |
1246 |
|
.get(codon); |
1247 |
1914 |
for (Entry<SequenceI, AlignedCodon> entry : columnResidues.entrySet()) |
1248 |
|
{ |
1249 |
10682 |
char residue = entry.getValue().product.charAt(0); |
1250 |
10682 |
peptides.get(entry.getKey())[column] = residue; |
1251 |
|
} |
1252 |
1914 |
column++; |
1253 |
|
} |
1254 |
|
|
1255 |
|
|
1256 |
|
|
1257 |
|
|
1258 |
5 |
for (Entry<SequenceI, char[]> entry : peptides.entrySet()) |
1259 |
|
{ |
1260 |
30 |
entry.getKey().setSequence(new String(entry.getValue())); |
1261 |
|
} |
1262 |
|
|
1263 |
5 |
return 0; |
1264 |
|
} |
1265 |
|
|
1266 |
|
|
1267 |
|
|
1268 |
|
|
1269 |
|
|
1270 |
|
|
1271 |
|
@param |
1272 |
|
|
1273 |
|
@param |
1274 |
|
|
1275 |
|
@param |
1276 |
|
|
1277 |
|
@param |
1278 |
|
|
1279 |
|
@param |
1280 |
|
|
1281 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 4 |
Complexity Density: 0.8 |
|
1282 |
32 |
static void addCodonPositions(SequenceI dna, SequenceI protein,... |
1283 |
|
char gapChar, Mapping seqMap, |
1284 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons) |
1285 |
|
{ |
1286 |
32 |
Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar); |
1287 |
|
|
1288 |
|
|
1289 |
|
|
1290 |
|
|
1291 |
|
|
1292 |
10716 |
while (codons.hasNext()) |
1293 |
|
{ |
1294 |
10684 |
try |
1295 |
|
{ |
1296 |
10684 |
AlignedCodon codon = codons.next(); |
1297 |
10684 |
addCodonToMap(alignedCodons, codon, protein); |
1298 |
|
} catch (IncompleteCodonException e) |
1299 |
|
{ |
1300 |
|
|
1301 |
|
} catch (NoSuchElementException e) |
1302 |
|
{ |
1303 |
|
|
1304 |
|
} |
1305 |
|
} |
1306 |
|
} |
1307 |
|
|
1308 |
|
|
1309 |
|
|
1310 |
|
|
1311 |
|
@param |
1312 |
|
@param |
1313 |
|
@param |
1314 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
1315 |
10690 |
protected static void addCodonToMap(... |
1316 |
|
Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons, |
1317 |
|
AlignedCodon codon, SequenceI protein) |
1318 |
|
{ |
1319 |
10690 |
Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon); |
1320 |
10690 |
if (seqProduct == null) |
1321 |
|
{ |
1322 |
1914 |
seqProduct = new HashMap<>(); |
1323 |
1914 |
alignedCodons.put(codon, seqProduct); |
1324 |
|
} |
1325 |
10690 |
seqProduct.put(protein, codon); |
1326 |
|
} |
1327 |
|
|
1328 |
|
|
1329 |
|
|
1330 |
|
|
1331 |
|
|
1332 |
|
|
1333 |
|
|
1334 |
|
|
1335 |
|
|
1336 |
|
|
1337 |
|
|
1338 |
|
|
1339 |
|
|
1340 |
|
|
1341 |
|
@param |
1342 |
|
@param |
1343 |
|
@return |
1344 |
|
|
|
|
| 90.9% |
Uncovered Elements: 2 (22) |
Complexity: 7 |
Complexity Density: 0.58 |
|
1345 |
8 |
public static boolean isMappable(AlignmentI al1, AlignmentI al2)... |
1346 |
|
{ |
1347 |
8 |
if (al1 == null || al2 == null) |
1348 |
|
{ |
1349 |
3 |
return false; |
1350 |
|
} |
1351 |
|
|
1352 |
|
|
1353 |
|
|
1354 |
|
|
1355 |
5 |
if (al1.isNucleotide() == al2.isNucleotide()) |
1356 |
|
{ |
1357 |
3 |
return false; |
1358 |
|
} |
1359 |
2 |
AlignmentI dna = al1.isNucleotide() ? al1 : al2; |
1360 |
2 |
AlignmentI protein = dna == al1 ? al2 : al1; |
1361 |
2 |
List<AlignedCodonFrame> mappings = protein.getCodonFrames(); |
1362 |
2 |
for (SequenceI dnaSeq : dna.getSequences()) |
1363 |
|
{ |
1364 |
2 |
for (SequenceI proteinSeq : protein.getSequences()) |
1365 |
|
{ |
1366 |
2 |
if (isMappable(dnaSeq, proteinSeq, mappings)) |
1367 |
|
{ |
1368 |
2 |
return true; |
1369 |
|
} |
1370 |
|
} |
1371 |
|
} |
1372 |
0 |
return false; |
1373 |
|
} |
1374 |
|
|
1375 |
|
|
1376 |
|
|
1377 |
|
|
1378 |
|
|
1379 |
|
@param |
1380 |
|
@param |
1381 |
|
@param |
1382 |
|
@return |
1383 |
|
|
|
|
| 50% |
Uncovered Elements: 8 (16) |
Complexity: 6 |
Complexity Density: 0.75 |
|
1384 |
2 |
protected static boolean isMappable(SequenceI dnaSeq,... |
1385 |
|
SequenceI proteinSeq, List<AlignedCodonFrame> mappings) |
1386 |
|
{ |
1387 |
2 |
if (dnaSeq == null || proteinSeq == null) |
1388 |
|
{ |
1389 |
0 |
return false; |
1390 |
|
} |
1391 |
|
|
1392 |
2 |
SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq |
1393 |
|
: dnaSeq.getDatasetSequence(); |
1394 |
2 |
SequenceI proteinDs = proteinSeq.getDatasetSequence() == null |
1395 |
|
? proteinSeq |
1396 |
|
: proteinSeq.getDatasetSequence(); |
1397 |
|
|
1398 |
2 |
for (AlignedCodonFrame mapping : mappings) |
1399 |
|
{ |
1400 |
0 |
if (proteinDs == mapping.getAaForDnaSeq(dnaDs)) |
1401 |
|
{ |
1402 |
|
|
1403 |
|
|
1404 |
|
|
1405 |
0 |
return true; |
1406 |
|
} |
1407 |
|
} |
1408 |
|
|
1409 |
|
|
1410 |
|
|
1411 |
|
|
1412 |
|
|
1413 |
2 |
return mapCdnaToProtein(proteinDs, dnaDs) != null; |
1414 |
|
} |
1415 |
|
|
1416 |
|
|
1417 |
|
|
1418 |
|
|
1419 |
|
|
1420 |
|
|
1421 |
|
|
1422 |
|
@param |
1423 |
|
|
1424 |
|
@param |
1425 |
|
|
1426 |
|
@param |
1427 |
|
|
1428 |
|
@param |
1429 |
|
|
1430 |
|
|
|
|
| 90% |
Uncovered Elements: 3 (30) |
Complexity: 7 |
Complexity Density: 0.39 |
|
1431 |
46 |
public static void findAddableReferenceAnnotations(... |
1432 |
|
List<SequenceI> sequenceScope, Map<String, String> labelForCalcId, |
1433 |
|
final Map<SequenceI, List<AlignmentAnnotation>> candidates, |
1434 |
|
AlignmentI al) |
1435 |
|
{ |
1436 |
46 |
if (sequenceScope == null) |
1437 |
|
{ |
1438 |
1 |
return; |
1439 |
|
} |
1440 |
|
|
1441 |
|
|
1442 |
|
|
1443 |
|
|
1444 |
|
|
1445 |
|
|
1446 |
|
|
1447 |
45 |
for (SequenceI seq : sequenceScope) |
1448 |
|
{ |
1449 |
41 |
SequenceI dataset = seq.getDatasetSequence(); |
1450 |
41 |
if (dataset == null) |
1451 |
|
{ |
1452 |
0 |
continue; |
1453 |
|
} |
1454 |
41 |
AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); |
1455 |
41 |
if (datasetAnnotations == null) |
1456 |
|
{ |
1457 |
35 |
continue; |
1458 |
|
} |
1459 |
6 |
final List<AlignmentAnnotation> result = new ArrayList<>(); |
1460 |
6 |
for (AlignmentAnnotation dsann : datasetAnnotations) |
1461 |
|
{ |
1462 |
|
|
1463 |
|
|
1464 |
|
|
1465 |
|
|
1466 |
|
|
1467 |
9 |
final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al |
1468 |
|
.findAnnotations(seq, dsann.getCalcId(), dsann.label); |
1469 |
9 |
if (!matchedAlignmentAnnotations.iterator().hasNext()) |
1470 |
|
{ |
1471 |
6 |
result.add(dsann); |
1472 |
6 |
if (labelForCalcId != null) |
1473 |
|
{ |
1474 |
6 |
labelForCalcId.put(dsann.getCalcId(), dsann.label); |
1475 |
|
} |
1476 |
|
} |
1477 |
|
} |
1478 |
|
|
1479 |
|
|
1480 |
|
|
1481 |
6 |
if (!result.isEmpty()) |
1482 |
|
{ |
1483 |
4 |
candidates.put(seq, result); |
1484 |
|
} |
1485 |
|
} |
1486 |
|
} |
1487 |
|
|
1488 |
|
|
1489 |
|
|
1490 |
|
|
1491 |
|
|
1492 |
|
@param |
1493 |
|
|
1494 |
|
@param |
1495 |
|
|
1496 |
|
@param |
1497 |
|
|
1498 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
|
1499 |
0 |
public static void addReferenceAnnotations(... |
1500 |
|
Map<SequenceI, List<AlignmentAnnotation>> annotations, |
1501 |
|
final AlignmentI alignment, final SequenceGroup selectionGroup) |
1502 |
|
{ |
1503 |
0 |
for (SequenceI seq : annotations.keySet()) |
1504 |
|
{ |
1505 |
0 |
for (AlignmentAnnotation ann : annotations.get(seq)) |
1506 |
|
{ |
1507 |
0 |
AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); |
1508 |
0 |
int startRes = 0; |
1509 |
0 |
int endRes = ann.annotations.length; |
1510 |
0 |
if (selectionGroup != null) |
1511 |
|
{ |
1512 |
0 |
startRes = selectionGroup.getStartRes(); |
1513 |
0 |
endRes = selectionGroup.getEndRes(); |
1514 |
|
} |
1515 |
0 |
copyAnn.restrict(startRes, endRes); |
1516 |
|
|
1517 |
|
|
1518 |
|
|
1519 |
|
|
1520 |
|
|
1521 |
0 |
if (!seq.hasAnnotation(ann)) |
1522 |
|
{ |
1523 |
0 |
seq.addAlignmentAnnotation(copyAnn); |
1524 |
|
} |
1525 |
|
|
1526 |
0 |
copyAnn.adjustForAlignment(); |
1527 |
|
|
1528 |
0 |
alignment.addAnnotation(copyAnn); |
1529 |
0 |
copyAnn.visible = true; |
1530 |
|
} |
1531 |
|
} |
1532 |
|
} |
1533 |
|
|
1534 |
|
|
1535 |
|
|
1536 |
|
|
1537 |
|
|
1538 |
|
|
1539 |
|
|
1540 |
|
@param |
1541 |
|
|
1542 |
|
@param |
1543 |
|
|
1544 |
|
|
1545 |
|
@param |
1546 |
|
|
1547 |
|
@param |
1548 |
|
|
1549 |
|
|
|
|
| 91.7% |
Uncovered Elements: 1 (12) |
Complexity: 7 |
Complexity Density: 1.17 |
|
1550 |
5 |
public static void showOrHideSequenceAnnotations(AlignmentI al,... |
1551 |
|
Collection<String> types, List<SequenceI> forSequences, |
1552 |
|
boolean anyType, boolean doShow) |
1553 |
|
{ |
1554 |
5 |
AlignmentAnnotation[] anns = al.getAlignmentAnnotation(); |
1555 |
5 |
if (anns != null) |
1556 |
|
{ |
1557 |
5 |
for (AlignmentAnnotation aa : anns) |
1558 |
|
{ |
1559 |
30 |
if (anyType || types.contains(aa.label)) |
1560 |
|
{ |
1561 |
21 |
if ((aa.sequenceRef != null) && (forSequences == null |
1562 |
|
|| forSequences.contains(aa.sequenceRef))) |
1563 |
|
{ |
1564 |
11 |
aa.visible = doShow; |
1565 |
|
} |
1566 |
|
} |
1567 |
|
} |
1568 |
|
} |
1569 |
|
} |
1570 |
|
|
1571 |
|
|
1572 |
|
|
1573 |
|
|
1574 |
|
@param |
1575 |
|
@param |
1576 |
|
@return |
1577 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1578 |
52 |
public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)... |
1579 |
|
{ |
1580 |
|
|
1581 |
|
|
1582 |
52 |
return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1); |
1583 |
|
} |
1584 |
|
|
1585 |
|
|
1586 |
|
|
1587 |
|
|
1588 |
|
|
1589 |
|
@param |
1590 |
|
@param |
1591 |
|
@return |
1592 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 6 |
Complexity Density: 0.55 |
|
1593 |
108 |
public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)... |
1594 |
|
{ |
1595 |
108 |
if (seq1 == null || seq2 == null) |
1596 |
|
{ |
1597 |
8 |
return false; |
1598 |
|
} |
1599 |
100 |
String name = seq2.getName(); |
1600 |
100 |
final List<DBRefEntry> xrefs = seq1.getDBRefs(); |
1601 |
100 |
if (xrefs != null) |
1602 |
|
{ |
1603 |
34 |
for (int ix = 0, nx = xrefs.size(); ix < nx; ix++) |
1604 |
|
{ |
1605 |
24 |
DBRefEntry xref = xrefs.get(ix); |
1606 |
24 |
String xrefName = xref.getSource() + "|" + xref.getAccessionId(); |
1607 |
|
|
1608 |
24 |
if (xrefName.equalsIgnoreCase(name)) |
1609 |
|
{ |
1610 |
12 |
return true; |
1611 |
|
} |
1612 |
|
} |
1613 |
|
} |
1614 |
88 |
return false; |
1615 |
|
} |
1616 |
|
|
1617 |
|
|
1618 |
|
|
1619 |
|
|
1620 |
|
|
1621 |
|
|
1622 |
|
|
1623 |
|
|
1624 |
|
@param |
1625 |
|
|
1626 |
|
@param |
1627 |
|
|
1628 |
|
@param |
1629 |
|
|
1630 |
|
|
1631 |
|
@return |
1632 |
|
|
1633 |
|
|
|
|
| 81.5% |
Uncovered Elements: 17 (92) |
Complexity: 16 |
Complexity Density: 0.24 |
|
1634 |
6 |
public static AlignmentI makeCdsAlignment(SequenceI[] dna,... |
1635 |
|
AlignmentI dataset, SequenceI[] products) |
1636 |
|
{ |
1637 |
6 |
if (dataset == null || dataset.getDataset() != null) |
1638 |
|
{ |
1639 |
0 |
throw new IllegalArgumentException( |
1640 |
|
"IMPLEMENTATION ERROR: dataset.getDataset() must be null!"); |
1641 |
|
} |
1642 |
6 |
List<SequenceI> foundSeqs = new ArrayList<>(); |
1643 |
6 |
List<SequenceI> cdsSeqs = new ArrayList<>(); |
1644 |
6 |
List<AlignedCodonFrame> mappings = dataset.getCodonFrames(); |
1645 |
6 |
HashSet<SequenceI> productSeqs = null; |
1646 |
6 |
if (products != null) |
1647 |
|
{ |
1648 |
3 |
productSeqs = new HashSet<>(); |
1649 |
3 |
for (SequenceI seq : products) |
1650 |
|
{ |
1651 |
24 |
productSeqs.add(seq.getDatasetSequence() == null ? seq : seq |
1652 |
|
.getDatasetSequence()); |
1653 |
|
} |
1654 |
|
} |
1655 |
|
|
1656 |
|
|
1657 |
|
|
1658 |
|
|
1659 |
|
|
1660 |
|
|
1661 |
|
|
1662 |
|
|
1663 |
|
|
1664 |
|
|
1665 |
|
|
1666 |
|
|
1667 |
6 |
for (SequenceI dnaSeq : dna) |
1668 |
|
{ |
1669 |
52 |
SequenceI dnaDss = dnaSeq.getDatasetSequence() == null ? dnaSeq |
1670 |
|
: dnaSeq.getDatasetSequence(); |
1671 |
|
|
1672 |
52 |
List<AlignedCodonFrame> seqMappings = MappingUtils |
1673 |
|
.findMappingsForSequence(dnaSeq, mappings); |
1674 |
52 |
for (AlignedCodonFrame mapping : seqMappings) |
1675 |
|
{ |
1676 |
42 |
List<Mapping> mappingsFromSequence = mapping |
1677 |
|
.getMappingsFromSequence(dnaSeq); |
1678 |
|
|
1679 |
42 |
for (Mapping aMapping : mappingsFromSequence) |
1680 |
|
{ |
1681 |
44 |
MapList mapList = aMapping.getMap(); |
1682 |
44 |
if (mapList.getFromRatio() == 1) |
1683 |
|
{ |
1684 |
|
|
1685 |
|
|
1686 |
|
|
1687 |
11 |
continue; |
1688 |
|
} |
1689 |
|
|
1690 |
|
|
1691 |
|
|
1692 |
|
|
1693 |
33 |
SequenceI proteinProduct = aMapping.getTo(); |
1694 |
33 |
if (productSeqs != null && !productSeqs.contains(proteinProduct)) |
1695 |
|
{ |
1696 |
2 |
continue; |
1697 |
|
} |
1698 |
|
|
1699 |
|
|
1700 |
|
|
1701 |
|
|
1702 |
|
|
1703 |
|
|
1704 |
31 |
SequenceI cdsSeq = findCdsForProtein(mappings, dnaSeq, |
1705 |
|
seqMappings, aMapping); |
1706 |
31 |
if (cdsSeq != null) |
1707 |
|
{ |
1708 |
0 |
if (!foundSeqs.contains(cdsSeq)) |
1709 |
|
{ |
1710 |
0 |
foundSeqs.add(cdsSeq); |
1711 |
0 |
SequenceI derivedSequence = cdsSeq.deriveSequence(); |
1712 |
0 |
cdsSeqs.add(derivedSequence); |
1713 |
0 |
if (!dataset.getSequences().contains(cdsSeq)) |
1714 |
|
{ |
1715 |
0 |
dataset.addSequence(cdsSeq); |
1716 |
|
} |
1717 |
|
} |
1718 |
0 |
continue; |
1719 |
|
} |
1720 |
|
|
1721 |
|
|
1722 |
|
|
1723 |
|
|
1724 |
|
|
1725 |
31 |
cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping, |
1726 |
|
dataset).deriveSequence(); |
1727 |
|
|
1728 |
|
|
1729 |
|
|
1730 |
|
|
1731 |
31 |
SequenceI cdsSeqDss = cdsSeq.getDatasetSequence(); |
1732 |
|
|
1733 |
31 |
cdsSeqs.add(cdsSeq); |
1734 |
|
|
1735 |
|
|
1736 |
|
|
1737 |
|
|
1738 |
31 |
List<int[]> cdsRange = Collections |
1739 |
|
.singletonList(new int[] |
1740 |
|
{ cdsSeq.getStart(), |
1741 |
|
cdsSeq.getLength() + cdsSeq.getStart() - 1 }); |
1742 |
31 |
MapList cdsToProteinMap = new MapList(cdsRange, |
1743 |
|
mapList.getToRanges(), mapList.getFromRatio(), |
1744 |
|
mapList.getToRatio()); |
1745 |
|
|
1746 |
31 |
if (!dataset.getSequences().contains(cdsSeqDss)) |
1747 |
|
{ |
1748 |
|
|
1749 |
|
|
1750 |
|
|
1751 |
|
|
1752 |
|
|
1753 |
9 |
dataset.addSequence(cdsSeqDss); |
1754 |
9 |
AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame(); |
1755 |
9 |
cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct, |
1756 |
|
cdsToProteinMap); |
1757 |
|
|
1758 |
|
|
1759 |
|
|
1760 |
|
|
1761 |
9 |
if (!mappings.contains(cdsToProteinMapping)) |
1762 |
|
{ |
1763 |
9 |
mappings.add(cdsToProteinMapping); |
1764 |
|
} |
1765 |
|
} |
1766 |
|
|
1767 |
31 |
propagateDBRefsToCDS(cdsSeqDss, dnaSeq.getDatasetSequence(), |
1768 |
|
proteinProduct, aMapping); |
1769 |
|
|
1770 |
|
|
1771 |
|
|
1772 |
31 |
AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame(); |
1773 |
31 |
final MapList dnaToCdsMap = new MapList(mapList.getFromRanges(), |
1774 |
|
cdsRange, 1, 1); |
1775 |
31 |
dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss, |
1776 |
|
dnaToCdsMap); |
1777 |
31 |
if (!mappings.contains(dnaToCdsMapping)) |
1778 |
|
{ |
1779 |
20 |
mappings.add(dnaToCdsMapping); |
1780 |
|
} |
1781 |
|
|
1782 |
|
|
1783 |
|
|
1784 |
|
|
1785 |
|
|
1786 |
31 |
final MapList cdsToDnaMap = dnaToCdsMap.getInverse(); |
1787 |
31 |
transferGeneLoci(dnaSeq, cdsToDnaMap, cdsSeq); |
1788 |
|
|
1789 |
|
|
1790 |
|
|
1791 |
|
|
1792 |
|
|
1793 |
|
|
1794 |
|
|
1795 |
|
|
1796 |
|
|
1797 |
|
|
1798 |
|
|
1799 |
|
|
1800 |
|
|
1801 |
|
|
1802 |
|
|
1803 |
|
|
1804 |
|
|
1805 |
|
|
1806 |
31 |
List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs(); |
1807 |
55 |
for (int ip = 0, np = primrefs.size(); ip < np; ip++) |
1808 |
|
{ |
1809 |
24 |
DBRefEntry primRef = primrefs.get(ip); |
1810 |
|
|
1811 |
|
|
1812 |
|
|
1813 |
|
|
1814 |
24 |
String source = primRef.getSource(); |
1815 |
24 |
String version = primRef.getVersion(); |
1816 |
24 |
DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":" |
1817 |
|
+ version, primRef.getAccessionId()); |
1818 |
24 |
cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap))); |
1819 |
24 |
cdsSeqDss.addDBRef(cdsCrossRef); |
1820 |
|
|
1821 |
24 |
dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq |
1822 |
|
.getName(), new Mapping(cdsSeqDss, dnaToCdsMap))); |
1823 |
|
|
1824 |
|
|
1825 |
|
|
1826 |
|
|
1827 |
|
|
1828 |
24 |
DBRefEntry proteinToCdsRef = new DBRefEntry(source, version, |
1829 |
|
cdsSeq.getName()); |
1830 |
|
|
1831 |
24 |
proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap |
1832 |
|
.getInverse())); |
1833 |
24 |
proteinProduct.addDBRef(proteinToCdsRef); |
1834 |
|
} |
1835 |
|
|
1836 |
|
|
1837 |
|
|
1838 |
31 |
transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null, |
1839 |
|
SequenceOntologyI.CDS); |
1840 |
|
} |
1841 |
|
} |
1842 |
|
} |
1843 |
|
|
1844 |
6 |
AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs |
1845 |
|
.size()])); |
1846 |
6 |
cds.setDataset(dataset); |
1847 |
|
|
1848 |
6 |
return cds; |
1849 |
|
} |
1850 |
|
|
1851 |
|
|
1852 |
|
|
1853 |
|
|
1854 |
|
|
1855 |
|
@param |
1856 |
|
@param |
1857 |
|
|
1858 |
|
@param |
1859 |
|
|
|
|
| 92.9% |
Uncovered Elements: 1 (14) |
Complexity: 4 |
Complexity Density: 0.5 |
|
1860 |
34 |
protected static void transferGeneLoci(SequenceI fromSeq,... |
1861 |
|
MapList targetToFrom, SequenceI targetSeq) |
1862 |
|
{ |
1863 |
34 |
if (targetSeq.getGeneLoci() != null) |
1864 |
|
{ |
1865 |
|
|
1866 |
23 |
return; |
1867 |
|
} |
1868 |
11 |
GeneLociI fromLoci = fromSeq.getGeneLoci(); |
1869 |
11 |
if (fromLoci == null) |
1870 |
|
{ |
1871 |
10 |
return; |
1872 |
|
} |
1873 |
|
|
1874 |
1 |
MapList newMap = targetToFrom.traverse(fromLoci.getMapping()); |
1875 |
|
|
1876 |
1 |
if (newMap != null) |
1877 |
|
{ |
1878 |
1 |
targetSeq.setGeneLoci(fromLoci.getSpeciesId(), |
1879 |
|
fromLoci.getAssemblyId(), fromLoci.getChromosomeId(), newMap); |
1880 |
|
} |
1881 |
|
} |
1882 |
|
|
1883 |
|
|
1884 |
|
|
1885 |
|
|
1886 |
|
|
1887 |
|
|
1888 |
|
@param |
1889 |
|
|
1890 |
|
@param |
1891 |
|
|
1892 |
|
@param |
1893 |
|
|
1894 |
|
@param |
1895 |
|
|
1896 |
|
@return |
1897 |
|
|
|
|
| 45.2% |
Uncovered Elements: 17 (31) |
Complexity: 11 |
Complexity Density: 0.58 |
|
1898 |
31 |
static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,... |
1899 |
|
SequenceI dnaSeq, List<AlignedCodonFrame> seqMappings, |
1900 |
|
Mapping aMapping) |
1901 |
|
{ |
1902 |
|
|
1903 |
|
|
1904 |
|
|
1905 |
|
|
1906 |
31 |
SequenceI seqDss = dnaSeq.getDatasetSequence() == null ? dnaSeq |
1907 |
|
: dnaSeq.getDatasetSequence(); |
1908 |
31 |
SequenceI proteinProduct = aMapping.getTo(); |
1909 |
|
|
1910 |
|
|
1911 |
|
|
1912 |
|
|
1913 |
|
|
1914 |
31 |
int mappedFromLength = MappingUtils |
1915 |
|
.getLength(aMapping.getMap().getFromRanges()); |
1916 |
31 |
int dnaLength = seqDss.getLength(); |
1917 |
31 |
if (mappedFromLength == dnaLength |
1918 |
|
|| mappedFromLength == dnaLength - CODON_LENGTH) |
1919 |
|
{ |
1920 |
|
|
1921 |
|
|
1922 |
|
|
1923 |
|
|
1924 |
0 |
if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS) |
1925 |
|
.isEmpty()) |
1926 |
|
{ |
1927 |
0 |
return seqDss; |
1928 |
|
} |
1929 |
|
} |
1930 |
|
|
1931 |
|
|
1932 |
|
|
1933 |
|
|
1934 |
|
|
1935 |
31 |
List<AlignedCodonFrame> mappingsToPeptide = MappingUtils |
1936 |
|
.findMappingsForSequence(proteinProduct, mappings); |
1937 |
31 |
for (AlignedCodonFrame acf : mappingsToPeptide) |
1938 |
|
{ |
1939 |
31 |
for (SequenceToSequenceMapping map : acf.getMappings()) |
1940 |
|
{ |
1941 |
253 |
Mapping mapping = map.getMapping(); |
1942 |
253 |
if (mapping != aMapping |
1943 |
|
&& mapping.getMap().getFromRatio() == CODON_LENGTH |
1944 |
|
&& proteinProduct == mapping.getTo() |
1945 |
|
&& seqDss != map.getFromSeq()) |
1946 |
|
{ |
1947 |
0 |
mappedFromLength = MappingUtils |
1948 |
|
.getLength(mapping.getMap().getFromRanges()); |
1949 |
0 |
if (mappedFromLength == map.getFromSeq().getLength()) |
1950 |
|
{ |
1951 |
|
|
1952 |
|
|
1953 |
|
|
1954 |
|
|
1955 |
|
|
1956 |
0 |
SequenceI cdsSeq = map.getFromSeq(); |
1957 |
|
|
1958 |
|
|
1959 |
0 |
List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils |
1960 |
|
.findMappingsForSequence(cdsSeq, seqMappings); |
1961 |
0 |
if (!dnaToCdsMaps.isEmpty()) |
1962 |
|
{ |
1963 |
0 |
return cdsSeq; |
1964 |
|
} |
1965 |
|
} |
1966 |
|
} |
1967 |
|
} |
1968 |
|
} |
1969 |
31 |
return null; |
1970 |
|
} |
1971 |
|
|
1972 |
|
|
1973 |
|
|
1974 |
|
|
1975 |
|
|
1976 |
|
|
1977 |
|
@param |
1978 |
|
@param |
1979 |
|
@param |
1980 |
|
|
1981 |
|
|
1982 |
|
|
1983 |
|
@return |
1984 |
|
|
|
|
| 67.2% |
Uncovered Elements: 19 (58) |
Complexity: 12 |
Complexity Density: 0.32 |
|
1985 |
31 |
static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping,... |
1986 |
|
AlignmentI dataset) |
1987 |
|
{ |
1988 |
|
|
1989 |
|
|
1990 |
|
|
1991 |
|
|
1992 |
31 |
String mapFromId = mapping.getMappedFromId(); |
1993 |
31 |
final String seqId = "CDS|" |
1994 |
31 |
+ (mapFromId != null ? mapFromId : seq.getName()); |
1995 |
|
|
1996 |
31 |
SequenceI newSeq = null; |
1997 |
|
|
1998 |
31 |
final MapList maplist = mapping.getMap(); |
1999 |
31 |
if (maplist.isContiguous() && maplist.isFromForwardStrand()) |
2000 |
|
{ |
2001 |
|
|
2002 |
|
|
2003 |
|
|
2004 |
22 |
int start = maplist.getFromLowest(); |
2005 |
22 |
int end = maplist.getFromHighest(); |
2006 |
22 |
newSeq = seq.getSubSequence(start - 1, end); |
2007 |
22 |
newSeq.setName(seqId); |
2008 |
|
} |
2009 |
|
else |
2010 |
|
{ |
2011 |
|
|
2012 |
|
|
2013 |
|
|
2014 |
9 |
char[] seqChars = seq.getSequence(); |
2015 |
9 |
List<int[]> fromRanges = maplist.getFromRanges(); |
2016 |
9 |
int cdsWidth = MappingUtils.getLength(fromRanges); |
2017 |
9 |
char[] newSeqChars = new char[cdsWidth]; |
2018 |
|
|
2019 |
9 |
int newPos = 0; |
2020 |
9 |
for (int[] range : fromRanges) |
2021 |
|
{ |
2022 |
21 |
if (range[0] <= range[1]) |
2023 |
|
{ |
2024 |
|
|
2025 |
21 |
int length = range[1] - range[0] + 1; |
2026 |
21 |
System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos, |
2027 |
|
length); |
2028 |
21 |
newPos += length; |
2029 |
|
} |
2030 |
|
else |
2031 |
|
{ |
2032 |
|
|
2033 |
0 |
for (int i = range[0]; i >= range[1]; i--) |
2034 |
|
{ |
2035 |
0 |
newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]); |
2036 |
|
} |
2037 |
|
} |
2038 |
|
} |
2039 |
|
|
2040 |
9 |
newSeq = new Sequence(seqId, newSeqChars, 1, newPos); |
2041 |
|
} |
2042 |
|
|
2043 |
31 |
if (dataset != null) |
2044 |
|
{ |
2045 |
31 |
SequenceI[] matches = dataset.findSequenceMatch(newSeq.getName()); |
2046 |
31 |
if (matches != null) |
2047 |
|
{ |
2048 |
31 |
boolean matched = false; |
2049 |
31 |
for (SequenceI mtch : matches) |
2050 |
|
{ |
2051 |
3 |
if (mtch.getStart() != newSeq.getStart()) |
2052 |
|
{ |
2053 |
0 |
continue; |
2054 |
|
} |
2055 |
3 |
if (mtch.getEnd() != newSeq.getEnd()) |
2056 |
|
{ |
2057 |
0 |
continue; |
2058 |
|
} |
2059 |
3 |
if (!Arrays.equals(mtch.getSequence(), newSeq.getSequence())) |
2060 |
|
{ |
2061 |
3 |
continue; |
2062 |
|
} |
2063 |
0 |
if (!matched) |
2064 |
|
{ |
2065 |
0 |
matched = true; |
2066 |
0 |
newSeq = mtch; |
2067 |
|
} |
2068 |
|
else |
2069 |
|
{ |
2070 |
0 |
System.err.println( |
2071 |
|
"JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):" |
2072 |
|
+ mtch.toString()); |
2073 |
|
} |
2074 |
|
} |
2075 |
|
} |
2076 |
|
} |
2077 |
|
|
2078 |
|
|
2079 |
31 |
return newSeq; |
2080 |
|
} |
2081 |
|
|
2082 |
|
|
2083 |
|
|
2084 |
|
|
2085 |
|
|
2086 |
|
@param |
2087 |
|
@param |
2088 |
|
@param |
2089 |
|
@param |
2090 |
|
@return |
2091 |
|
|
|
|
| 88.6% |
Uncovered Elements: 5 (44) |
Complexity: 11 |
Complexity Density: 0.39 |
|
2092 |
31 |
protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,... |
2093 |
|
SequenceI contig, SequenceI proteinProduct, Mapping mapping) |
2094 |
|
{ |
2095 |
|
|
2096 |
|
|
2097 |
31 |
List<DBRefEntry> direct = new ArrayList<>(); |
2098 |
31 |
HashSet<String> directSources = new HashSet<>(); |
2099 |
|
|
2100 |
31 |
List<DBRefEntry> refs = contig.getDBRefs(); |
2101 |
31 |
if (refs != null) |
2102 |
|
{ |
2103 |
600 |
for (int ib = 0, nb = refs.size(); ib < nb; ib++) |
2104 |
|
{ |
2105 |
576 |
DBRefEntry dbr = refs.get(ib); |
2106 |
576 |
MapList map; |
2107 |
? |
if (dbr.hasMap() && (map = dbr.getMap().getMap()).isTripletMap()) |
2108 |
|
{ |
2109 |
|
|
2110 |
46 |
if (mapping.getMap().equals(map)) |
2111 |
|
{ |
2112 |
46 |
direct.add(dbr); |
2113 |
46 |
directSources.add(dbr.getSource()); |
2114 |
|
} |
2115 |
|
} |
2116 |
|
} |
2117 |
|
} |
2118 |
31 |
List<DBRefEntry> onSource = DBRefUtils.selectRefs( |
2119 |
|
proteinProduct.getDBRefs(), |
2120 |
|
directSources.toArray(new String[0])); |
2121 |
31 |
List<DBRefEntry> propagated = new ArrayList<>(); |
2122 |
|
|
2123 |
|
|
2124 |
77 |
for (int ic = 0, nc = direct.size(); ic < nc; ic++) |
2125 |
|
{ |
2126 |
46 |
DBRefEntry cdsref = direct.get(ic); |
2127 |
46 |
Mapping m = cdsref.getMap(); |
2128 |
|
|
2129 |
46 |
MapList cdsposmap = new MapList( |
2130 |
|
Arrays.asList(new int[][] |
2131 |
|
{ new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }), |
2132 |
|
m.getMap().getToRanges(), 3, 1); |
2133 |
46 |
Mapping cdsmap = new Mapping(m.getTo(), m.getMap()); |
2134 |
|
|
2135 |
|
|
2136 |
46 |
DBRefEntry newref = new DBRefEntry(cdsref.getSource(), |
2137 |
|
cdsref.getVersion(), cdsref.getAccessionId(), |
2138 |
|
new Mapping(cdsmap.getTo(), cdsposmap)); |
2139 |
|
|
2140 |
|
|
2141 |
|
|
2142 |
|
|
2143 |
46 |
if (cdsmap.getTo() == null && onSource != null) |
2144 |
|
{ |
2145 |
2 |
List<DBRefEntry> sourceRefs = DBRefUtils.searchRefs(onSource, |
2146 |
|
cdsref.getAccessionId()); |
2147 |
2 |
if (sourceRefs != null) |
2148 |
|
{ |
2149 |
2 |
for (DBRefEntry srcref : sourceRefs) |
2150 |
|
{ |
2151 |
2 |
if (srcref.getSource().equalsIgnoreCase(cdsref.getSource())) |
2152 |
|
{ |
2153 |
|
|
2154 |
|
|
2155 |
2 |
newref.getMap().setTo(proteinProduct); |
2156 |
|
} |
2157 |
|
} |
2158 |
|
} |
2159 |
|
} |
2160 |
46 |
cdsSeq.addDBRef(newref); |
2161 |
46 |
propagated.add(newref); |
2162 |
|
} |
2163 |
31 |
return propagated; |
2164 |
|
} |
2165 |
|
|
2166 |
|
|
2167 |
|
|
2168 |
|
|
2169 |
|
|
2170 |
|
|
2171 |
|
@param |
2172 |
|
@param |
2173 |
|
@param |
2174 |
|
|
2175 |
|
@param |
2176 |
|
|
2177 |
|
|
2178 |
|
@param |
2179 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (53) |
Complexity: 12 |
Complexity Density: 0.36 |
|
2180 |
34 |
protected static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,... |
2181 |
|
MapList mapping, String select, String... omitting) |
2182 |
|
{ |
2183 |
34 |
SequenceI copyTo = toSeq; |
2184 |
65 |
while (copyTo.getDatasetSequence() != null) |
2185 |
|
{ |
2186 |
31 |
copyTo = copyTo.getDatasetSequence(); |
2187 |
|
} |
2188 |
34 |
if (fromSeq == copyTo || fromSeq.getDatasetSequence() == copyTo) |
2189 |
|
{ |
2190 |
22 |
return 0; |
2191 |
|
} |
2192 |
|
|
2193 |
|
|
2194 |
|
|
2195 |
|
|
2196 |
12 |
List<SequenceFeature> sfs = select == null ? fromSeq.getFeatures() |
2197 |
|
.getPositionalFeatures() : fromSeq.getFeatures() |
2198 |
|
.getFeaturesByOntology(select); |
2199 |
|
|
2200 |
12 |
int count = 0; |
2201 |
12 |
for (SequenceFeature sf : sfs) |
2202 |
|
{ |
2203 |
14 |
String type = sf.getType(); |
2204 |
14 |
boolean omit = false; |
2205 |
14 |
for (String toOmit : omitting) |
2206 |
|
{ |
2207 |
7 |
if (type.equals(toOmit)) |
2208 |
|
{ |
2209 |
2 |
omit = true; |
2210 |
|
} |
2211 |
|
} |
2212 |
14 |
if (omit) |
2213 |
|
{ |
2214 |
2 |
continue; |
2215 |
|
} |
2216 |
|
|
2217 |
|
|
2218 |
|
|
2219 |
|
|
2220 |
|
|
2221 |
12 |
int start = sf.getBegin(); |
2222 |
12 |
int end = sf.getEnd(); |
2223 |
12 |
int[] mappedTo = mapping.locateInTo(start, end); |
2224 |
|
|
2225 |
|
|
2226 |
|
|
2227 |
|
|
2228 |
12 |
if (mappedTo == null) |
2229 |
|
{ |
2230 |
5 |
mappedTo = mapping.locateInTo(end, end); |
2231 |
5 |
if (mappedTo != null) |
2232 |
|
{ |
2233 |
|
|
2234 |
|
|
2235 |
|
|
2236 |
|
|
2237 |
1 |
mappedTo[0] = 1; |
2238 |
|
} |
2239 |
|
} |
2240 |
12 |
if (mappedTo == null) |
2241 |
|
{ |
2242 |
4 |
mappedTo = mapping.locateInTo(start, start); |
2243 |
4 |
if (mappedTo != null) |
2244 |
|
{ |
2245 |
|
|
2246 |
|
|
2247 |
|
|
2248 |
|
|
2249 |
1 |
mappedTo[1] = toSeq.getLength(); |
2250 |
|
} |
2251 |
|
} |
2252 |
12 |
if (mappedTo != null) |
2253 |
|
{ |
2254 |
9 |
int newBegin = Math.min(mappedTo[0], mappedTo[1]); |
2255 |
9 |
int newEnd = Math.max(mappedTo[0], mappedTo[1]); |
2256 |
9 |
SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, |
2257 |
|
sf.getFeatureGroup(), sf.getScore()); |
2258 |
9 |
copyTo.addSequenceFeature(copy); |
2259 |
9 |
count++; |
2260 |
|
} |
2261 |
|
} |
2262 |
12 |
return count; |
2263 |
|
} |
2264 |
|
|
2265 |
|
|
2266 |
|
|
2267 |
|
|
2268 |
|
|
2269 |
|
|
2270 |
|
|
2271 |
|
|
2272 |
|
@param |
2273 |
|
@param |
2274 |
|
@return |
2275 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (30) |
Complexity: 5 |
Complexity Density: 0.23 |
|
2276 |
12 |
public static MapList mapCdsToProtein(SequenceI dnaSeq,... |
2277 |
|
SequenceI proteinSeq) |
2278 |
|
{ |
2279 |
12 |
List<int[]> ranges = findCdsPositions(dnaSeq); |
2280 |
12 |
int mappedDnaLength = MappingUtils.getLength(ranges); |
2281 |
|
|
2282 |
|
|
2283 |
|
|
2284 |
|
|
2285 |
12 |
int codonRemainder = mappedDnaLength % CODON_LENGTH; |
2286 |
12 |
if (codonRemainder > 0) |
2287 |
|
{ |
2288 |
2 |
mappedDnaLength -= codonRemainder; |
2289 |
2 |
MappingUtils.removeEndPositions(codonRemainder, ranges); |
2290 |
|
} |
2291 |
|
|
2292 |
12 |
int proteinLength = proteinSeq.getLength(); |
2293 |
12 |
int proteinStart = proteinSeq.getStart(); |
2294 |
12 |
int proteinEnd = proteinSeq.getEnd(); |
2295 |
|
|
2296 |
|
|
2297 |
|
|
2298 |
|
|
2299 |
|
|
2300 |
12 |
if (proteinSeq.getCharAt(0) == 'X') |
2301 |
|
{ |
2302 |
|
|
2303 |
1 |
proteinStart++; |
2304 |
1 |
proteinLength--; |
2305 |
|
} |
2306 |
12 |
List<int[]> proteinRange = new ArrayList<>(); |
2307 |
|
|
2308 |
|
|
2309 |
|
|
2310 |
|
|
2311 |
12 |
int codesForResidues = mappedDnaLength / CODON_LENGTH; |
2312 |
12 |
if (codesForResidues == (proteinLength + 1)) |
2313 |
|
{ |
2314 |
|
|
2315 |
|
|
2316 |
2 |
codesForResidues--; |
2317 |
2 |
mappedDnaLength -= CODON_LENGTH; |
2318 |
2 |
MappingUtils.removeEndPositions(CODON_LENGTH, ranges); |
2319 |
|
} |
2320 |
|
|
2321 |
12 |
if (codesForResidues == proteinLength) |
2322 |
|
{ |
2323 |
4 |
proteinRange.add(new int[] { proteinStart, proteinEnd }); |
2324 |
4 |
return new MapList(ranges, proteinRange, CODON_LENGTH, 1); |
2325 |
|
} |
2326 |
8 |
return null; |
2327 |
|
} |
2328 |
|
|
2329 |
|
|
2330 |
|
|
2331 |
|
|
2332 |
|
|
2333 |
|
|
2334 |
|
|
2335 |
|
|
2336 |
|
@param |
2337 |
|
@return |
2338 |
|
|
|
|
| 92.9% |
Uncovered Elements: 2 (28) |
Complexity: 7 |
Complexity Density: 0.35 |
|
2339 |
14 |
protected static List<int[]> findCdsPositions(SequenceI dnaSeq)... |
2340 |
|
{ |
2341 |
14 |
List<int[]> result = new ArrayList<>(); |
2342 |
|
|
2343 |
14 |
List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology( |
2344 |
|
SequenceOntologyI.CDS); |
2345 |
14 |
if (sfs.isEmpty()) |
2346 |
|
{ |
2347 |
6 |
return result; |
2348 |
|
} |
2349 |
8 |
SequenceFeatures.sortFeatures(sfs, true); |
2350 |
|
|
2351 |
8 |
for (SequenceFeature sf : sfs) |
2352 |
|
{ |
2353 |
16 |
int phase = 0; |
2354 |
16 |
try |
2355 |
|
{ |
2356 |
16 |
String s = sf.getPhase(); |
2357 |
16 |
if (s != null) |
2358 |
|
{ |
2359 |
2 |
phase = Integer.parseInt(s); |
2360 |
|
} |
2361 |
|
} catch (NumberFormatException e) |
2362 |
|
{ |
2363 |
|
|
2364 |
|
} |
2365 |
|
|
2366 |
|
|
2367 |
|
|
2368 |
|
|
2369 |
16 |
int begin = sf.getBegin(); |
2370 |
16 |
int end = sf.getEnd(); |
2371 |
16 |
if (result.isEmpty() && phase > 0) |
2372 |
|
{ |
2373 |
2 |
begin += phase; |
2374 |
2 |
if (begin > end) |
2375 |
|
{ |
2376 |
|
|
2377 |
0 |
System.err |
2378 |
|
.println("Error: start phase extends beyond start CDS in " |
2379 |
|
+ dnaSeq.getName()); |
2380 |
|
} |
2381 |
|
} |
2382 |
16 |
result.add(new int[] { begin, end }); |
2383 |
|
} |
2384 |
|
|
2385 |
|
|
2386 |
|
|
2387 |
|
|
2388 |
|
|
2389 |
|
|
2390 |
|
|
2391 |
|
|
2392 |
8 |
Collections.sort(result, IntRangeComparator.ASCENDING); |
2393 |
8 |
return result; |
2394 |
|
} |
2395 |
|
|
2396 |
|
|
2397 |
|
|
2398 |
|
|
2399 |
|
|
2400 |
|
|
2401 |
|
@param |
2402 |
|
@param |
2403 |
|
@param |
2404 |
|
|
2405 |
|
@return |
2406 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 9 |
Complexity Density: 0.43 |
|
2407 |
0 |
public static AlignmentI makeCopyAlignment(SequenceI[] seqs,... |
2408 |
|
SequenceI[] xrefs, AlignmentI dataset) |
2409 |
|
{ |
2410 |
0 |
AlignmentI copy = new Alignment(new Alignment(seqs)); |
2411 |
0 |
copy.setDataset(dataset); |
2412 |
0 |
boolean isProtein = !copy.isNucleotide(); |
2413 |
0 |
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs); |
2414 |
0 |
if (xrefs != null) |
2415 |
|
{ |
2416 |
|
|
2417 |
|
|
2418 |
0 |
for (int ix = 0, nx = xrefs.length; ix < nx; ix++) |
2419 |
|
{ |
2420 |
0 |
SequenceI xref = xrefs[ix]; |
2421 |
0 |
List<DBRefEntry> dbrefs = xref.getDBRefs(); |
2422 |
0 |
if (dbrefs != null) |
2423 |
|
{ |
2424 |
0 |
for (int ir = 0, nir = dbrefs.size(); ir < nir; ir++) |
2425 |
|
{ |
2426 |
0 |
DBRefEntry dbref = dbrefs.get(ir); |
2427 |
0 |
Mapping map = dbref.getMap(); |
2428 |
0 |
SequenceI mto; |
2429 |
0 |
if (map == null || (mto = map.getTo()) == null |
2430 |
|
|| mto.isProtein() != isProtein) |
2431 |
|
{ |
2432 |
0 |
continue; |
2433 |
|
} |
2434 |
0 |
SequenceI mappedTo = mto; |
2435 |
0 |
SequenceI match = matcher.findIdMatch(mappedTo); |
2436 |
0 |
if (match == null) |
2437 |
|
{ |
2438 |
0 |
matcher.add(mappedTo); |
2439 |
0 |
copy.addSequence(mappedTo); |
2440 |
|
} |
2441 |
|
} |
2442 |
|
} |
2443 |
|
} |
2444 |
|
} |
2445 |
0 |
return copy; |
2446 |
|
} |
2447 |
|
|
2448 |
|
|
2449 |
|
|
2450 |
|
|
2451 |
|
|
2452 |
|
|
2453 |
|
|
2454 |
|
|
2455 |
|
|
2456 |
|
@param |
2457 |
|
|
2458 |
|
@param |
2459 |
|
|
2460 |
|
@return |
2461 |
|
|
|
|
| 94.1% |
Uncovered Elements: 2 (34) |
Complexity: 5 |
Complexity Density: 0.19 |
|
2462 |
4 |
public static int alignAs(AlignmentI unaligned, AlignmentI aligned)... |
2463 |
|
{ |
2464 |
|
|
2465 |
|
|
2466 |
|
|
2467 |
4 |
if (alignAsSameSequences(unaligned, aligned)) |
2468 |
|
{ |
2469 |
2 |
return unaligned.getHeight(); |
2470 |
|
} |
2471 |
|
|
2472 |
|
|
2473 |
|
|
2474 |
|
|
2475 |
2 |
List<SequenceI> unmapped = new ArrayList<>(); |
2476 |
2 |
Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap( |
2477 |
|
unaligned, aligned, unmapped); |
2478 |
2 |
int width = columnMap.size(); |
2479 |
2 |
char gap = unaligned.getGapCharacter(); |
2480 |
2 |
int realignedCount = 0; |
2481 |
|
|
2482 |
|
|
2483 |
2 |
for (SequenceI seq : unaligned.getSequences()) |
2484 |
|
{ |
2485 |
4 |
if (!unmapped.contains(seq)) |
2486 |
|
{ |
2487 |
4 |
char[] newSeq = new char[width]; |
2488 |
4 |
Arrays.fill(newSeq, gap); |
2489 |
|
|
2490 |
4 |
int newCol = 0; |
2491 |
4 |
int lastCol = 0; |
2492 |
|
|
2493 |
|
|
2494 |
|
|
2495 |
|
|
2496 |
|
|
2497 |
4 |
for (Integer column : columnMap.keySet()) |
2498 |
|
{ |
2499 |
60 |
Character c = columnMap.get(column).get(seq); |
2500 |
60 |
if (c != null) |
2501 |
|
{ |
2502 |
|
|
2503 |
|
|
2504 |
|
|
2505 |
|
|
2506 |
36 |
newSeq[newCol] = c; |
2507 |
36 |
lastCol = newCol; |
2508 |
|
} |
2509 |
60 |
newCol++; |
2510 |
|
} |
2511 |
|
|
2512 |
|
|
2513 |
|
|
2514 |
|
|
2515 |
4 |
if (lastCol < width) |
2516 |
|
{ |
2517 |
4 |
char[] tmp = new char[lastCol + 1]; |
2518 |
4 |
System.arraycopy(newSeq, 0, tmp, 0, lastCol + 1); |
2519 |
4 |
newSeq = tmp; |
2520 |
|
} |
2521 |
|
|
2522 |
4 |
seq.setSequence(String.valueOf(newSeq)); |
2523 |
4 |
realignedCount++; |
2524 |
|
} |
2525 |
|
} |
2526 |
2 |
return realignedCount; |
2527 |
|
} |
2528 |
|
|
2529 |
|
|
2530 |
|
|
2531 |
|
|
2532 |
|
|
2533 |
|
|
2534 |
|
@param |
2535 |
|
|
2536 |
|
@param |
2537 |
|
|
2538 |
|
|
2539 |
|
@return |
2540 |
|
|
|
|
| 88.4% |
Uncovered Elements: 5 (43) |
Complexity: 7 |
Complexity Density: 0.21 |
|
2541 |
8 |
static boolean alignAsSameSequences(AlignmentI unaligned,... |
2542 |
|
AlignmentI aligned) |
2543 |
|
{ |
2544 |
8 |
if (aligned.getDataset() == null || unaligned.getDataset() == null) |
2545 |
|
{ |
2546 |
0 |
return false; |
2547 |
|
} |
2548 |
|
|
2549 |
|
|
2550 |
8 |
Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<>(); |
2551 |
8 |
for (SequenceI seq : aligned.getSequences()) |
2552 |
|
{ |
2553 |
59 |
SequenceI ds = seq.getDatasetSequence(); |
2554 |
59 |
if (alignedDatasets.get(ds) == null) |
2555 |
|
{ |
2556 |
58 |
alignedDatasets.put(ds, new ArrayList<SequenceI>()); |
2557 |
|
} |
2558 |
59 |
alignedDatasets.get(ds).add(seq); |
2559 |
|
} |
2560 |
|
|
2561 |
|
|
2562 |
|
|
2563 |
|
|
2564 |
|
|
2565 |
|
|
2566 |
8 |
int leftmost = Integer.MAX_VALUE; |
2567 |
8 |
for (SequenceI seq : unaligned.getSequences()) |
2568 |
|
{ |
2569 |
34 |
final SequenceI ds = seq.getDatasetSequence(); |
2570 |
34 |
if (!alignedDatasets.containsKey(ds)) |
2571 |
|
{ |
2572 |
3 |
return false; |
2573 |
|
} |
2574 |
31 |
SequenceI alignedSeq = alignedDatasets.get(ds) |
2575 |
|
.get(0); |
2576 |
31 |
int startCol = alignedSeq.findIndex(seq.getStart()); |
2577 |
31 |
leftmost = Math.min(leftmost, startCol); |
2578 |
|
} |
2579 |
|
|
2580 |
|
|
2581 |
|
|
2582 |
|
|
2583 |
|
|
2584 |
|
|
2585 |
5 |
final char gapCharacter = aligned.getGapCharacter(); |
2586 |
5 |
for (SequenceI seq : unaligned.getSequences()) |
2587 |
|
{ |
2588 |
29 |
List<SequenceI> alignedSequences = alignedDatasets |
2589 |
|
.get(seq.getDatasetSequence()); |
2590 |
29 |
if (alignedSequences.isEmpty()) |
2591 |
|
{ |
2592 |
|
|
2593 |
|
|
2594 |
|
|
2595 |
0 |
continue; |
2596 |
|
} |
2597 |
29 |
SequenceI alignedSeq = alignedSequences.get(0); |
2598 |
|
|
2599 |
|
|
2600 |
|
|
2601 |
|
|
2602 |
|
|
2603 |
29 |
int startCol = alignedSeq.findIndex(seq.getStart()); |
2604 |
29 |
int endCol = alignedSeq.findIndex(seq.getEnd()); |
2605 |
29 |
char[] seqchars = new char[endCol - leftmost + 1]; |
2606 |
29 |
Arrays.fill(seqchars, gapCharacter); |
2607 |
29 |
char[] toCopy = alignedSeq.getSequence(startCol - 1, endCol); |
2608 |
29 |
System.arraycopy(toCopy, 0, seqchars, startCol - leftmost, |
2609 |
|
toCopy.length); |
2610 |
29 |
seq.setSequence(String.valueOf(seqchars)); |
2611 |
29 |
if (alignedSequences.size() > 0) |
2612 |
|
{ |
2613 |
|
|
2614 |
29 |
alignedSequences.remove(0); |
2615 |
|
} |
2616 |
|
} |
2617 |
|
|
2618 |
|
|
2619 |
|
|
2620 |
|
|
2621 |
5 |
new RemoveGapColCommand("", unaligned.getSequencesArray(), 0, |
2622 |
|
unaligned.getWidth() - 1, unaligned); |
2623 |
|
|
2624 |
5 |
return true; |
2625 |
|
} |
2626 |
|
|
2627 |
|
|
2628 |
|
|
2629 |
|
|
2630 |
|
|
2631 |
|
@param |
2632 |
|
@param |
2633 |
|
@param |
2634 |
|
@return |
2635 |
|
|
|
|
| 86.7% |
Uncovered Elements: 2 (15) |
Complexity: 3 |
Complexity Density: 0.27 |
|
2636 |
2 |
static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(... |
2637 |
|
AlignmentI unaligned, AlignmentI aligned, |
2638 |
|
List<SequenceI> unmapped) |
2639 |
|
{ |
2640 |
|
|
2641 |
|
|
2642 |
|
|
2643 |
|
|
2644 |
|
|
2645 |
2 |
SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<>(); |
2646 |
|
|
2647 |
|
|
2648 |
|
|
2649 |
|
|
2650 |
2 |
unmapped.addAll(unaligned.getSequences()); |
2651 |
|
|
2652 |
2 |
List<AlignedCodonFrame> mappings = aligned.getCodonFrames(); |
2653 |
|
|
2654 |
2 |
for (SequenceI seq : unaligned.getSequences()) |
2655 |
|
{ |
2656 |
4 |
for (AlignedCodonFrame mapping : mappings) |
2657 |
|
{ |
2658 |
4 |
SequenceI fromSeq = mapping.findAlignedSequence(seq, aligned); |
2659 |
4 |
if (fromSeq != null) |
2660 |
|
{ |
2661 |
4 |
Mapping seqMap = mapping.getMappingBetween(fromSeq, seq); |
2662 |
4 |
if (addMappedPositions(seq, fromSeq, seqMap, map)) |
2663 |
|
{ |
2664 |
4 |
unmapped.remove(seq); |
2665 |
|
} |
2666 |
|
} |
2667 |
|
} |
2668 |
|
} |
2669 |
2 |
return map; |
2670 |
|
} |
2671 |
|
|
2672 |
|
|
2673 |
|
|
2674 |
|
|
2675 |
|
|
2676 |
|
|
2677 |
|
|
2678 |
|
|
2679 |
|
@param |
2680 |
|
|
2681 |
|
@param |
2682 |
|
|
2683 |
|
@param |
2684 |
|
|
2685 |
|
@param |
2686 |
|
|
2687 |
|
|
2688 |
|
@return |
2689 |
|
|
|
|
| 80% |
Uncovered Elements: 8 (40) |
Complexity: 11 |
Complexity Density: 0.46 |
|
2690 |
6 |
static boolean addMappedPositions(SequenceI seq, SequenceI fromSeq,... |
2691 |
|
Mapping seqMap, Map<Integer, Map<SequenceI, Character>> map) |
2692 |
|
{ |
2693 |
6 |
if (seqMap == null) |
2694 |
|
{ |
2695 |
0 |
return false; |
2696 |
|
} |
2697 |
|
|
2698 |
|
|
2699 |
|
|
2700 |
|
|
2701 |
6 |
if (seqMap.getTo() == fromSeq.getDatasetSequence()) |
2702 |
|
{ |
2703 |
0 |
seqMap = new Mapping(seq.getDatasetSequence(), |
2704 |
|
seqMap.getMap().getInverse()); |
2705 |
|
} |
2706 |
|
|
2707 |
6 |
int toStart = seq.getStart(); |
2708 |
|
|
2709 |
|
|
2710 |
|
|
2711 |
|
|
2712 |
6 |
for (int[] fromRange : seqMap.getMap().getFromRanges()) |
2713 |
|
{ |
2714 |
18 |
for (int i = 0; i < fromRange.length - 1; i += 2) |
2715 |
|
{ |
2716 |
9 |
boolean forward = fromRange[i + 1] >= fromRange[i]; |
2717 |
|
|
2718 |
|
|
2719 |
|
|
2720 |
|
|
2721 |
9 |
int[] range = seqMap.locateMappedRange(fromRange[i], |
2722 |
|
fromRange[i + 1]); |
2723 |
9 |
if (range == null) |
2724 |
|
{ |
2725 |
0 |
System.err.println("Error in mapping " + seqMap + " from " |
2726 |
|
+ fromSeq.getName()); |
2727 |
0 |
return false; |
2728 |
|
} |
2729 |
9 |
int fromCol = fromSeq.findIndex(fromRange[i]); |
2730 |
9 |
int mappedCharPos = range[0]; |
2731 |
|
|
2732 |
|
|
2733 |
|
|
2734 |
|
|
2735 |
|
|
2736 |
|
|
2737 |
|
|
2738 |
70 |
while (mappedCharPos <= range[1] && fromCol <= fromSeq.getLength() |
2739 |
|
&& fromCol >= 0) |
2740 |
|
{ |
2741 |
61 |
if (!Comparison.isGap(fromSeq.getCharAt(fromCol - 1))) |
2742 |
|
{ |
2743 |
|
|
2744 |
|
|
2745 |
|
|
2746 |
|
|
2747 |
48 |
Map<SequenceI, Character> seqsMap = map.get(fromCol); |
2748 |
48 |
if (seqsMap == null) |
2749 |
|
{ |
2750 |
42 |
seqsMap = new HashMap<>(); |
2751 |
42 |
map.put(fromCol, seqsMap); |
2752 |
|
} |
2753 |
48 |
seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart)); |
2754 |
48 |
mappedCharPos++; |
2755 |
|
} |
2756 |
61 |
fromCol += (forward ? 1 : -1); |
2757 |
|
} |
2758 |
|
} |
2759 |
|
} |
2760 |
6 |
return true; |
2761 |
|
} |
2762 |
|
|
2763 |
|
|
2764 |
|
|
|
|
| 71.4% |
Uncovered Elements: 2 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
|
2765 |
4 |
public static boolean looksLikeEnsembl(AlignmentI alignment)... |
2766 |
|
{ |
2767 |
4 |
for (SequenceI seq : alignment.getSequences()) |
2768 |
|
{ |
2769 |
88 |
String name = seq.getName(); |
2770 |
88 |
if (!name.startsWith("ENSG") && !name.startsWith("ENST")) |
2771 |
|
{ |
2772 |
0 |
return false; |
2773 |
|
} |
2774 |
|
} |
2775 |
4 |
return true; |
2776 |
|
} |
2777 |
|
} |