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package jalview.analysis; |
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import jalview.api.AlignViewportI; |
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import jalview.datamodel.AlignedCodon; |
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import jalview.datamodel.AlignedCodonFrame; |
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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.Annotation; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.FeatureProperties; |
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import jalview.datamodel.GraphLine; |
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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.SequenceI; |
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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.MapList; |
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import jalview.util.ShiftList; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Comparator; |
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import java.util.Iterator; |
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import java.util.List; |
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| 63.7% |
Uncovered Elements: 195 (537) |
Complexity: 138 |
Complexity Density: 0.37 |
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public class Dna |
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{ |
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private static final String STOP_ASTERIX = "*"; |
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private static final Comparator<AlignedCodon> comparator = new CodonComparator(); |
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private final List<SequenceI> selection; |
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private final String[] seqstring; |
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private final Iterator<int[]> contigs; |
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private final char gapChar; |
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private final AlignmentAnnotation[] annotations; |
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private final int dnaWidth; |
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private final AlignmentI dataset; |
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private ShiftList vismapping; |
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private int[] startcontigs; |
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private int aaWidth = 0; |
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private AlignedCodon[] alignedCodons; |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
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public Dna(AlignViewportI viewport, Iterator<int[]> visibleContigs)... |
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{ |
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this.selection = Arrays.asList(viewport.getSequenceSelection()); |
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this.seqstring = viewport.getViewAsString(true); |
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this.contigs = visibleContigs; |
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this.gapChar = viewport.getGapCharacter(); |
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this.annotations = viewport.getAlignment().getAlignmentAnnotation(); |
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this.dnaWidth = viewport.getAlignment().getWidth(); |
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this.dataset = viewport.getAlignment().getDataset(); |
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initContigs(); |
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} |
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| 100% |
Uncovered Elements: 0 (22) |
Complexity: 3 |
Complexity Density: 0.17 |
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private void initContigs()... |
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{ |
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vismapping = new ShiftList(); |
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int npos = 0; |
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int[] lastregion = null; |
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ArrayList<Integer> tempcontigs = new ArrayList<>(); |
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while (contigs.hasNext()) |
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{ |
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int[] region = contigs.next(); |
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if (lastregion == null) |
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{ |
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vismapping.addShift(npos, region[0]); |
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} |
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else |
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{ |
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vismapping.addShift(npos, region[0] - lastregion[1] + 1); |
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} |
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lastregion = region; |
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tempcontigs.add(region[0]); |
136 |
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tempcontigs.add(region[1]); |
137 |
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} |
138 |
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139 |
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startcontigs = new int[tempcontigs.size()]; |
140 |
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int i = 0; |
141 |
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for (Integer val : tempcontigs) |
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{ |
143 |
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startcontigs[i] = val; |
144 |
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i++; |
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} |
146 |
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tempcontigs = null; |
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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 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
166 |
3347 |
public static final int compareCodonPos(AlignedCodon ac1,... |
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AlignedCodon ac2) |
168 |
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{ |
169 |
3347 |
return comparator.compare(ac1, ac2); |
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} |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 7 |
Complexity Density: 1.4 |
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private static int jalview_2_8_2compare(AlignedCodon ac1,... |
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AlignedCodon ac2) |
183 |
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{ |
184 |
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if (ac1 == null || ac2 == null || (ac1.equals(ac2))) |
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{ |
186 |
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return 0; |
187 |
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} |
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if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3) |
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{ |
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return -1; |
192 |
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} |
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return 1; |
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} |
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@return |
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| 96.6% |
Uncovered Elements: 1 (29) |
Complexity: 5 |
Complexity Density: 0.24 |
|
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23 |
public AlignmentI translateCdna(GeneticCodeI codeTable)... |
203 |
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{ |
204 |
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AlignedCodonFrame acf = new AlignedCodonFrame(); |
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206 |
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alignedCodons = new AlignedCodon[dnaWidth]; |
207 |
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208 |
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int s; |
209 |
23 |
int sSize = selection.size(); |
210 |
23 |
List<SequenceI> pepseqs = new ArrayList<>(); |
211 |
240 |
for (s = 0; s < sSize; s++) |
212 |
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{ |
213 |
217 |
SequenceI newseq = translateCodingRegion(selection.get(s), |
214 |
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seqstring[s], acf, pepseqs, codeTable); |
215 |
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216 |
217 |
if (newseq != null) |
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{ |
218 |
217 |
pepseqs.add(newseq); |
219 |
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SequenceI ds = newseq; |
220 |
217 |
if (dataset != null) |
221 |
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{ |
222 |
2 |
while (ds.getDatasetSequence() != null) |
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{ |
224 |
1 |
ds = ds.getDatasetSequence(); |
225 |
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} |
226 |
1 |
dataset.addSequence(ds); |
227 |
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} |
228 |
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} |
229 |
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} |
230 |
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231 |
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SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]); |
232 |
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AlignmentI al = new Alignment(newseqs); |
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234 |
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al.padGaps(); |
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236 |
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al.setDataset(dataset); |
237 |
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translateAlignedAnnotations(al, acf); |
238 |
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al.addCodonFrame(acf); |
239 |
23 |
return al; |
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} |
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247 |
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@param |
248 |
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@param |
249 |
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@return |
250 |
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| 0% |
Uncovered Elements: 35 (35) |
Complexity: 12 |
Complexity Density: 0.63 |
|
251 |
0 |
public static boolean canTranslate(SequenceI[] selection,... |
252 |
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int viscontigs[]) |
253 |
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{ |
254 |
0 |
for (int gd = 0; gd < selection.length; gd++) |
255 |
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{ |
256 |
0 |
SequenceI dna = selection[gd]; |
257 |
0 |
List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(), |
258 |
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jalview.datamodel.DBRefSource.DNACODINGDBS); |
259 |
0 |
if (dnarefs != null) |
260 |
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{ |
261 |
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262 |
0 |
List<DBRefEntry> mappedrefs = new ArrayList<>(); |
263 |
0 |
List<DBRefEntry> refs = dna.getDBRefs(); |
264 |
0 |
for (int d = 0, nd = refs.size(); d < nd; d++) |
265 |
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{ |
266 |
0 |
DBRefEntry ref = refs.get(d); |
267 |
0 |
if (ref.getMap() != null && ref.getMap().getMap() != null |
268 |
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&& ref.getMap().getMap().getFromRatio() == 3 |
269 |
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&& ref.getMap().getMap().getToRatio() == 1) |
270 |
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{ |
271 |
0 |
mappedrefs.add(ref); |
272 |
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} |
273 |
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} |
274 |
0 |
dnarefs = mappedrefs; |
275 |
0 |
for (int d = 0, nd = dnarefs.size(); d < nd; d++) |
276 |
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{ |
277 |
0 |
Mapping mp = dnarefs.get(d).getMap(); |
278 |
0 |
if (mp != null) |
279 |
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{ |
280 |
0 |
for (int vc = 0, nv = viscontigs.length; vc < nv; vc += 2) |
281 |
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{ |
282 |
0 |
int[] mpr = mp.locateMappedRange(viscontigs[vc], |
283 |
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viscontigs[vc + 1]); |
284 |
0 |
if (mpr != null) |
285 |
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{ |
286 |
0 |
return true; |
287 |
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} |
288 |
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} |
289 |
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} |
290 |
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} |
291 |
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} |
292 |
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} |
293 |
0 |
return false; |
294 |
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} |
295 |
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296 |
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297 |
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298 |
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299 |
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300 |
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@param |
301 |
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302 |
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| 12.8% |
Uncovered Elements: 41 (47) |
Complexity: 15 |
Complexity Density: 0.56 |
|
303 |
23 |
protected void translateAlignedAnnotations(AlignmentI al,... |
304 |
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AlignedCodonFrame acf) |
305 |
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{ |
306 |
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307 |
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308 |
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309 |
23 |
if (annotations != null) |
310 |
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{ |
311 |
23 |
for (AlignmentAnnotation annotation : annotations) |
312 |
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{ |
313 |
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314 |
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315 |
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316 |
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317 |
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318 |
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319 |
318 |
if (annotation.autoCalculated || !annotation.isForDisplay() |
320 |
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|| annotation.isRNA()) |
321 |
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{ |
322 |
318 |
continue; |
323 |
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} |
324 |
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|
325 |
0 |
int aSize = aaWidth; |
326 |
0 |
Annotation[] anots = (annotation.annotations == null) ? null |
327 |
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: new Annotation[aSize]; |
328 |
0 |
if (anots != null) |
329 |
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{ |
330 |
0 |
for (int a = 0; a < aSize; a++) |
331 |
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{ |
332 |
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|
333 |
0 |
if (a < alignedCodons.length && alignedCodons[a] != null |
334 |
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&& alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2)) |
335 |
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{ |
336 |
0 |
anots[a] = getCodonAnnotation(alignedCodons[a], |
337 |
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annotation.annotations); |
338 |
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} |
339 |
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} |
340 |
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} |
341 |
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|
342 |
0 |
AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label, |
343 |
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annotation.description, anots); |
344 |
0 |
aa.graph = annotation.graph; |
345 |
0 |
aa.graphGroup = annotation.graphGroup; |
346 |
0 |
aa.graphHeight = annotation.graphHeight; |
347 |
0 |
if (annotation.getThreshold() != null) |
348 |
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{ |
349 |
0 |
aa.setThreshold(new GraphLine(annotation.getThreshold())); |
350 |
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} |
351 |
0 |
if (annotation.hasScore) |
352 |
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{ |
353 |
0 |
aa.setScore(annotation.getScore()); |
354 |
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} |
355 |
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|
356 |
0 |
final SequenceI seqRef = annotation.sequenceRef; |
357 |
0 |
if (seqRef != null) |
358 |
|
{ |
359 |
0 |
SequenceI aaSeq = acf.getAaForDnaSeq(seqRef); |
360 |
0 |
if (aaSeq != null) |
361 |
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{ |
362 |
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|
363 |
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|
364 |
0 |
aa.setSequenceRef(aaSeq); |
365 |
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|
366 |
0 |
aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true); |
367 |
0 |
aa.adjustForAlignment(); |
368 |
0 |
aaSeq.addAlignmentAnnotation(aa); |
369 |
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} |
370 |
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} |
371 |
0 |
al.addAnnotation(aa); |
372 |
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} |
373 |
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} |
374 |
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} |
375 |
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| 0% |
Uncovered Elements: 38 (38) |
Complexity: 10 |
Complexity Density: 0.45 |
|
376 |
0 |
private static Annotation getCodonAnnotation(AlignedCodon is,... |
377 |
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Annotation[] annotations) |
378 |
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{ |
379 |
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|
380 |
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|
381 |
0 |
int contrib = 0; |
382 |
0 |
Annotation annot = null; |
383 |
0 |
for (int p = 1; p <= 3; p++) |
384 |
|
{ |
385 |
0 |
int dnaCol = is.getBaseColumn(p); |
386 |
0 |
if (annotations[dnaCol] != null) |
387 |
|
{ |
388 |
0 |
if (annot == null) |
389 |
|
{ |
390 |
0 |
annot = new Annotation(annotations[dnaCol]); |
391 |
0 |
contrib = 1; |
392 |
|
} |
393 |
|
else |
394 |
|
{ |
395 |
|
|
396 |
0 |
Annotation cpy = new Annotation(annotations[dnaCol]); |
397 |
0 |
if (annot.colour == null) |
398 |
|
{ |
399 |
0 |
annot.colour = cpy.colour; |
400 |
|
} |
401 |
0 |
if (annot.description == null || annot.description.length() == 0) |
402 |
|
{ |
403 |
0 |
annot.description = cpy.description; |
404 |
|
} |
405 |
0 |
if (annot.displayCharacter == null) |
406 |
|
{ |
407 |
0 |
annot.displayCharacter = cpy.displayCharacter; |
408 |
|
} |
409 |
0 |
if (annot.secondaryStructure == 0) |
410 |
|
{ |
411 |
0 |
annot.secondaryStructure = cpy.secondaryStructure; |
412 |
|
} |
413 |
0 |
annot.value += cpy.value; |
414 |
0 |
contrib++; |
415 |
|
} |
416 |
|
} |
417 |
|
} |
418 |
0 |
if (contrib > 1) |
419 |
|
{ |
420 |
0 |
annot.value /= contrib; |
421 |
|
} |
422 |
0 |
return annot; |
423 |
|
} |
424 |
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425 |
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426 |
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427 |
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428 |
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@param |
429 |
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430 |
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@param |
431 |
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432 |
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@param |
433 |
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434 |
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@param |
435 |
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@param |
436 |
|
@return |
437 |
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|
|
|
| 73.3% |
Uncovered Elements: 50 (187) |
Complexity: 38 |
Complexity Density: 0.3 |
|
438 |
217 |
protected SequenceI translateCodingRegion(SequenceI selection,... |
439 |
|
String seqstring, AlignedCodonFrame acf, |
440 |
|
List<SequenceI> proteinSeqs, GeneticCodeI codeTable) |
441 |
|
{ |
442 |
217 |
List<int[]> skip = new ArrayList<>(); |
443 |
217 |
int[] skipint = null; |
444 |
|
|
445 |
217 |
int npos = 0; |
446 |
217 |
int vc = 0; |
447 |
|
|
448 |
217 |
int[] scontigs = new int[startcontigs.length]; |
449 |
217 |
System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length); |
450 |
|
|
451 |
|
|
452 |
217 |
StringBuilder protein = new StringBuilder(seqstring.length() / 2); |
453 |
217 |
String seq = seqstring.replace('U', 'T').replace('u', 'T'); |
454 |
217 |
char codon[] = new char[3]; |
455 |
217 |
int cdp[] = new int[3]; |
456 |
217 |
int rf = 0; |
457 |
217 |
int lastnpos = 0; |
458 |
217 |
int nend; |
459 |
217 |
int aspos = 0; |
460 |
217 |
int resSize = 0; |
461 |
6275 |
for (npos = 0, nend = seq.length(); npos < nend; npos++) |
462 |
|
{ |
463 |
6058 |
if (!Comparison.isGap(seq.charAt(npos))) |
464 |
|
{ |
465 |
6028 |
cdp[rf] = npos; |
466 |
6028 |
codon[rf++] = seq.charAt(npos); |
467 |
|
} |
468 |
6058 |
if (rf == 3) |
469 |
|
{ |
470 |
|
|
471 |
|
|
472 |
|
|
473 |
1888 |
AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], |
474 |
|
cdp[2]); |
475 |
1888 |
String aa = codeTable.translate(new String(codon)); |
476 |
1888 |
rf = 0; |
477 |
1888 |
final String gapString = String.valueOf(gapChar); |
478 |
1888 |
if (aa == null) |
479 |
|
{ |
480 |
1 |
aa = gapString; |
481 |
1 |
if (skipint == null) |
482 |
|
{ |
483 |
1 |
skipint = new int[] { alignedCodon.pos1, |
484 |
|
alignedCodon.pos3 |
485 |
|
|
486 |
|
|
487 |
|
}; |
488 |
|
} |
489 |
1 |
skipint[1] = alignedCodon.pos3; |
490 |
|
} |
491 |
|
else |
492 |
|
{ |
493 |
1887 |
if (skipint != null) |
494 |
|
{ |
495 |
|
|
496 |
1 |
skipint[0] = vismapping.shift(skipint[0]); |
497 |
1 |
skipint[1] = vismapping.shift(skipint[1]); |
498 |
2 |
for (vc = 0; vc < scontigs.length;) |
499 |
|
{ |
500 |
1 |
if (scontigs[vc + 1] < skipint[0]) |
501 |
|
{ |
502 |
|
|
503 |
0 |
vc += 2; |
504 |
0 |
continue; |
505 |
|
} |
506 |
1 |
if (scontigs[vc] > skipint[1]) |
507 |
|
{ |
508 |
|
|
509 |
0 |
break; |
510 |
|
} |
511 |
|
|
512 |
|
|
513 |
1 |
int[] t; |
514 |
|
|
515 |
|
|
516 |
|
|
517 |
|
|
518 |
|
|
519 |
1 |
if (scontigs[vc] <= skipint[0]) |
520 |
|
{ |
521 |
1 |
if (skipint[0] == scontigs[vc]) |
522 |
|
{ |
523 |
|
|
524 |
|
|
525 |
0 |
if (scontigs[vc + 1] > skipint[1]) |
526 |
|
{ |
527 |
0 |
scontigs[vc] = skipint[1]; |
528 |
0 |
vc += 2; |
529 |
|
} |
530 |
|
else |
531 |
|
{ |
532 |
0 |
if (scontigs[vc + 1] == skipint[1]) |
533 |
|
{ |
534 |
|
|
535 |
0 |
t = new int[scontigs.length - 2]; |
536 |
0 |
if (vc > 0) |
537 |
|
{ |
538 |
0 |
System.arraycopy(scontigs, 0, t, 0, vc - 1); |
539 |
|
} |
540 |
0 |
if (vc + 2 < t.length) |
541 |
|
{ |
542 |
0 |
System.arraycopy(scontigs, vc + 2, t, vc, |
543 |
|
t.length - vc + 2); |
544 |
|
} |
545 |
0 |
scontigs = t; |
546 |
|
} |
547 |
|
else |
548 |
|
{ |
549 |
|
|
550 |
0 |
scontigs[vc + 1] = skipint[0] - 1; |
551 |
0 |
vc += 2; |
552 |
|
} |
553 |
|
} |
554 |
|
} |
555 |
|
else |
556 |
|
{ |
557 |
|
|
558 |
1 |
if (scontigs[vc + 1] < skipint[1]) |
559 |
|
{ |
560 |
|
|
561 |
0 |
scontigs[vc + 1] = skipint[0] - 1; |
562 |
0 |
vc += 2; |
563 |
|
} |
564 |
|
else |
565 |
|
{ |
566 |
|
|
567 |
1 |
t = new int[scontigs.length + 2]; |
568 |
1 |
System.arraycopy(scontigs, 0, t, 0, vc + 1); |
569 |
1 |
t[vc + 1] = skipint[0]; |
570 |
1 |
t[vc + 2] = skipint[1]; |
571 |
1 |
System.arraycopy(scontigs, vc + 1, t, vc + 3, |
572 |
|
scontigs.length - (vc + 1)); |
573 |
1 |
scontigs = t; |
574 |
1 |
vc += 4; |
575 |
|
} |
576 |
|
} |
577 |
|
} |
578 |
|
} |
579 |
1 |
skip.add(skipint); |
580 |
1 |
skipint = null; |
581 |
|
} |
582 |
1887 |
if (aa.equals(ResidueProperties.STOP)) |
583 |
|
{ |
584 |
0 |
aa = STOP_ASTERIX; |
585 |
|
} |
586 |
1887 |
resSize++; |
587 |
|
} |
588 |
1888 |
boolean findpos = true; |
589 |
5150 |
while (findpos) |
590 |
|
{ |
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
595 |
3262 |
final int compareCodonPos = compareCodonPos(alignedCodon, |
596 |
|
alignedCodons[aspos]); |
597 |
3262 |
switch (compareCodonPos) |
598 |
|
{ |
599 |
178 |
case -1: |
600 |
|
|
601 |
|
|
602 |
|
|
603 |
|
|
604 |
|
|
605 |
178 |
insertAAGap(aspos, proteinSeqs); |
606 |
178 |
findpos = false; |
607 |
178 |
break; |
608 |
|
|
609 |
1374 |
case +1: |
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
1374 |
aa = gapString + aa; |
616 |
1374 |
aspos++; |
617 |
1374 |
break; |
618 |
|
|
619 |
1710 |
case 0: |
620 |
|
|
621 |
|
|
622 |
|
|
623 |
|
|
624 |
1710 |
findpos = false; |
625 |
|
} |
626 |
|
} |
627 |
1888 |
protein.append(aa); |
628 |
1888 |
lastnpos = npos; |
629 |
1888 |
if (alignedCodons[aspos] == null) |
630 |
|
{ |
631 |
|
|
632 |
466 |
alignedCodons[aspos] = alignedCodon; |
633 |
|
} |
634 |
1422 |
else if (!alignedCodons[aspos].equals(alignedCodon)) |
635 |
|
{ |
636 |
0 |
throw new IllegalStateException( |
637 |
|
"Tried to coalign " + alignedCodons[aspos].toString() |
638 |
|
+ " with " + alignedCodon.toString()); |
639 |
|
} |
640 |
1888 |
if (aspos >= aaWidth) |
641 |
|
{ |
642 |
|
|
643 |
449 |
aaWidth = aspos; |
644 |
|
} |
645 |
|
|
646 |
1888 |
aspos++; |
647 |
|
} |
648 |
|
} |
649 |
217 |
if (resSize > 0) |
650 |
|
{ |
651 |
217 |
SequenceI newseq = new Sequence(selection.getName(), |
652 |
|
protein.toString()); |
653 |
217 |
if (rf != 0) |
654 |
|
{ |
655 |
188 |
final String errMsg = "trimming contigs for incomplete terminal codon."; |
656 |
188 |
jalview.bin.Console.errPrintln(errMsg); |
657 |
|
|
658 |
188 |
vc = scontigs.length - 1; |
659 |
188 |
lastnpos = vismapping.shift(lastnpos); |
660 |
|
|
661 |
|
|
662 |
|
|
663 |
|
|
664 |
376 |
while (vc >= 0 && scontigs[vc] > lastnpos) |
665 |
|
{ |
666 |
188 |
if (vc > 0 && scontigs[vc - 1] > lastnpos) |
667 |
|
{ |
668 |
0 |
vc -= 2; |
669 |
|
} |
670 |
|
else |
671 |
|
{ |
672 |
|
|
673 |
188 |
scontigs[vc] = lastnpos; |
674 |
|
} |
675 |
|
} |
676 |
|
|
677 |
188 |
if (vc > 0 && (vc + 1) < scontigs.length) |
678 |
|
{ |
679 |
|
|
680 |
0 |
int t[] = new int[vc + 1]; |
681 |
0 |
System.arraycopy(scontigs, 0, t, 0, vc + 1); |
682 |
0 |
scontigs = t; |
683 |
|
} |
684 |
188 |
if (vc <= 0) |
685 |
|
{ |
686 |
0 |
scontigs = null; |
687 |
|
} |
688 |
|
} |
689 |
217 |
if (scontigs != null) |
690 |
|
{ |
691 |
217 |
npos = 0; |
692 |
|
|
693 |
412 |
for (vc = 0; vc < scontigs.length; vc += 2) |
694 |
|
{ |
695 |
220 |
scontigs[vc] = selection.findPosition(scontigs[vc]); |
696 |
220 |
scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); |
697 |
220 |
if (scontigs[vc + 1] == selection.getEnd()) |
698 |
|
{ |
699 |
25 |
break; |
700 |
|
} |
701 |
|
} |
702 |
|
|
703 |
217 |
if ((vc + 2) < scontigs.length) |
704 |
|
{ |
705 |
0 |
int t[] = new int[vc + 2]; |
706 |
0 |
System.arraycopy(scontigs, 0, t, 0, vc + 2); |
707 |
0 |
scontigs = t; |
708 |
|
} |
709 |
|
|
710 |
|
|
711 |
|
|
712 |
|
|
713 |
|
|
714 |
|
|
715 |
|
|
716 |
|
|
717 |
|
|
718 |
|
|
719 |
|
|
720 |
|
|
721 |
|
|
722 |
|
|
723 |
217 |
MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1); |
724 |
|
|
725 |
217 |
transferCodedFeatures(selection, newseq, map); |
726 |
|
|
727 |
|
|
728 |
|
|
729 |
|
|
730 |
217 |
SequenceI rseq = newseq.deriveSequence(); |
731 |
|
|
732 |
|
|
733 |
|
|
734 |
|
|
735 |
|
|
736 |
|
|
737 |
217 |
acf.addMap(selection, rseq, map); |
738 |
217 |
return rseq; |
739 |
|
} |
740 |
|
} |
741 |
|
|
742 |
|
|
743 |
0 |
return null; |
744 |
|
} |
745 |
|
|
746 |
|
|
747 |
|
|
748 |
|
|
749 |
|
@param |
750 |
|
@param |
751 |
|
@return |
752 |
|
|
|
|
| 90% |
Uncovered Elements: 1 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
753 |
178 |
protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)... |
754 |
|
{ |
755 |
178 |
aaWidth++; |
756 |
178 |
for (SequenceI seq : proteinSeqs) |
757 |
|
{ |
758 |
598 |
seq.insertCharAt(pos, gapChar); |
759 |
|
} |
760 |
|
|
761 |
178 |
checkCodonFrameWidth(); |
762 |
178 |
if (pos < aaWidth) |
763 |
|
{ |
764 |
178 |
aaWidth++; |
765 |
|
|
766 |
|
|
767 |
|
|
768 |
|
|
769 |
178 |
System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1, |
770 |
|
alignedCodons.length - pos - 1); |
771 |
178 |
alignedCodons[pos] = null; |
772 |
|
} |
773 |
|
} |
774 |
|
|
775 |
|
|
776 |
|
|
777 |
|
|
778 |
|
|
|
|
| 33.3% |
Uncovered Elements: 4 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
779 |
178 |
protected void checkCodonFrameWidth()... |
780 |
|
{ |
781 |
178 |
if (alignedCodons[alignedCodons.length - 1] != null) |
782 |
|
{ |
783 |
|
|
784 |
|
|
785 |
|
|
786 |
0 |
AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10]; |
787 |
0 |
System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length); |
788 |
0 |
alignedCodons = c; |
789 |
|
} |
790 |
|
} |
791 |
|
|
792 |
|
|
793 |
|
|
794 |
|
|
795 |
|
|
796 |
|
@param |
797 |
|
@param |
798 |
|
@param |
799 |
|
|
|
|
| 25% |
Uncovered Elements: 3 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
800 |
217 |
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,... |
801 |
|
MapList map) |
802 |
|
{ |
803 |
|
|
804 |
|
|
805 |
|
|
806 |
|
|
807 |
|
|
808 |
|
|
809 |
|
|
810 |
|
|
811 |
|
|
812 |
|
|
813 |
|
|
814 |
|
|
815 |
|
|
816 |
|
|
817 |
217 |
for (SequenceFeature sf : dna.getFeatures().getAllFeatures()) |
818 |
|
{ |
819 |
0 |
if (FeatureProperties.isCodingFeature(null, sf.getType())) |
820 |
|
{ |
821 |
|
|
822 |
|
{ |
823 |
|
|
824 |
|
} |
825 |
|
} |
826 |
|
} |
827 |
|
} |
828 |
|
|
829 |
|
|
830 |
|
|
831 |
|
|
832 |
|
|
833 |
|
@param |
834 |
|
@return |
835 |
|
|
|
|
| 92.9% |
Uncovered Elements: 1 (14) |
Complexity: 3 |
Complexity Density: 0.3 |
|
836 |
1 |
public AlignmentI reverseCdna(boolean complement)... |
837 |
|
{ |
838 |
1 |
int sSize = selection.size(); |
839 |
1 |
List<SequenceI> reversed = new ArrayList<>(); |
840 |
2 |
for (int s = 0; s < sSize; s++) |
841 |
|
{ |
842 |
1 |
SequenceI newseq = reverseSequence(selection.get(s).getName(), |
843 |
|
seqstring[s], complement); |
844 |
|
|
845 |
1 |
if (newseq != null) |
846 |
|
{ |
847 |
1 |
reversed.add(newseq); |
848 |
|
} |
849 |
|
} |
850 |
|
|
851 |
1 |
SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]); |
852 |
1 |
AlignmentI al = new Alignment(newseqs); |
853 |
1 |
((Alignment) al).createDatasetAlignment(); |
854 |
1 |
return al; |
855 |
|
} |
856 |
|
|
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
|
861 |
|
|
862 |
|
|
863 |
|
@param |
864 |
|
@param |
865 |
|
@return |
866 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (20) |
Complexity: 5 |
Complexity Density: 0.42 |
|
867 |
3 |
public static SequenceI reverseSequence(String seqName, String sequence,... |
868 |
|
boolean complement) |
869 |
|
{ |
870 |
3 |
String newName = seqName + "|rev" + (complement ? "comp" : ""); |
871 |
3 |
char[] originalSequence = sequence.toCharArray(); |
872 |
3 |
int length = originalSequence.length; |
873 |
3 |
char[] reversedSequence = new char[length]; |
874 |
3 |
int bases = 0; |
875 |
63 |
for (int i = 0; i < length; i++) |
876 |
|
{ |
877 |
60 |
char c = complement ? getComplement(originalSequence[i]) |
878 |
|
: originalSequence[i]; |
879 |
60 |
reversedSequence[length - i - 1] = c; |
880 |
60 |
if (!Comparison.isGap(c)) |
881 |
|
{ |
882 |
45 |
bases++; |
883 |
|
} |
884 |
|
} |
885 |
3 |
SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases); |
886 |
3 |
return reversed; |
887 |
|
} |
888 |
|
|
889 |
|
|
890 |
|
|
891 |
|
|
892 |
|
@see |
893 |
|
@param |
894 |
|
@return |
895 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
896 |
0 |
public static String reverseComplement(String s)... |
897 |
|
{ |
898 |
0 |
StringBuilder sb = new StringBuilder(s.length()); |
899 |
0 |
for (int i = s.length() - 1; i >= 0; i--) |
900 |
|
{ |
901 |
0 |
sb.append(Dna.getComplement(s.charAt(i))); |
902 |
|
} |
903 |
0 |
return sb.toString(); |
904 |
|
} |
905 |
|
|
906 |
|
|
907 |
|
|
908 |
|
|
909 |
|
|
910 |
|
|
911 |
|
@param |
912 |
|
@return |
913 |
|
|
|
|
| 97.6% |
Uncovered Elements: 2 (85) |
Complexity: 30 |
Complexity Density: 0.35 |
|
914 |
66 |
public static char getComplement(char c)... |
915 |
|
{ |
916 |
66 |
char result = c; |
917 |
66 |
switch (c) |
918 |
|
{ |
919 |
7 |
case '-': |
920 |
0 |
case '.': |
921 |
0 |
case ' ': |
922 |
7 |
break; |
923 |
2 |
case 'a': |
924 |
2 |
result = 't'; |
925 |
2 |
break; |
926 |
5 |
case 'A': |
927 |
5 |
result = 'T'; |
928 |
5 |
break; |
929 |
3 |
case 'c': |
930 |
3 |
result = 'g'; |
931 |
3 |
break; |
932 |
4 |
case 'C': |
933 |
4 |
result = 'G'; |
934 |
4 |
break; |
935 |
3 |
case 'g': |
936 |
3 |
result = 'c'; |
937 |
3 |
break; |
938 |
5 |
case 'G': |
939 |
5 |
result = 'C'; |
940 |
5 |
break; |
941 |
3 |
case 't': |
942 |
3 |
result = 'a'; |
943 |
3 |
break; |
944 |
4 |
case 'T': |
945 |
4 |
result = 'A'; |
946 |
4 |
break; |
947 |
1 |
case 'u': |
948 |
1 |
result = 'a'; |
949 |
1 |
break; |
950 |
2 |
case 'U': |
951 |
2 |
result = 'A'; |
952 |
2 |
break; |
953 |
2 |
case 'r': |
954 |
2 |
result = 'y'; |
955 |
2 |
break; |
956 |
1 |
case 'R': |
957 |
1 |
result = 'Y'; |
958 |
1 |
break; |
959 |
1 |
case 'y': |
960 |
1 |
result = 'r'; |
961 |
1 |
break; |
962 |
2 |
case 'Y': |
963 |
2 |
result = 'R'; |
964 |
2 |
break; |
965 |
2 |
case 'k': |
966 |
2 |
result = 'm'; |
967 |
2 |
break; |
968 |
1 |
case 'K': |
969 |
1 |
result = 'M'; |
970 |
1 |
break; |
971 |
1 |
case 'm': |
972 |
1 |
result = 'k'; |
973 |
1 |
break; |
974 |
2 |
case 'M': |
975 |
2 |
result = 'K'; |
976 |
2 |
break; |
977 |
2 |
case 'b': |
978 |
2 |
result = 'v'; |
979 |
2 |
break; |
980 |
1 |
case 'B': |
981 |
1 |
result = 'V'; |
982 |
1 |
break; |
983 |
1 |
case 'v': |
984 |
1 |
result = 'b'; |
985 |
1 |
break; |
986 |
2 |
case 'V': |
987 |
2 |
result = 'B'; |
988 |
2 |
break; |
989 |
2 |
case 'd': |
990 |
2 |
result = 'h'; |
991 |
2 |
break; |
992 |
1 |
case 'D': |
993 |
1 |
result = 'H'; |
994 |
1 |
break; |
995 |
1 |
case 'h': |
996 |
1 |
result = 'd'; |
997 |
1 |
break; |
998 |
2 |
case 'H': |
999 |
2 |
result = 'D'; |
1000 |
2 |
break; |
1001 |
|
} |
1002 |
|
|
1003 |
66 |
return result; |
1004 |
|
} |
1005 |
|
} |