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package jalview.datamodel; |
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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.Iterator; |
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import java.util.List; |
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import java.util.Locale; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import jalview.analysis.Rna; |
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import jalview.analysis.SecStrConsensus.SimpleBP; |
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import jalview.analysis.WUSSParseException; |
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import jalview.structure.StructureImportSettings; |
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@author |
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@version |
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| 78.2% |
Uncovered Elements: 175 (804) |
Complexity: 299 |
Complexity Density: 0.65 |
|
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public class AlignmentAnnotation |
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{ |
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private static final String ANNOTATION_ID_PREFIX = "ann"; |
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public static final int SEQUENCE_PROFILE = 0; |
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public static final int STRUCTURE_PROFILE = 1; |
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public static final int CDNA_PROFILE = 2; |
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private static long counter = 0; |
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private long noOfSequencesIncluded = -1; |
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public boolean autoCalculated = false; |
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public String annotationId; |
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public SequenceI sequenceRef; |
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public String label; |
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public String description; |
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public Annotation[] annotations; |
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public List<SimpleBP> bps = null; |
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public SequenceFeature[] _rnasecstr = null; |
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private long invalidrnastruc = -2; |
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private StructureImportSettings.TFType tfType = StructureImportSettings.TFType.DEFAULT; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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219 |
public void setTFType(StructureImportSettings.TFType t)... |
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{ |
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tfType = t; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public StructureImportSettings.TFType getTFType()... |
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{ |
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return tfType; |
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} |
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@param |
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| 93.3% |
Uncovered Elements: 1 (15) |
Complexity: 5 |
Complexity Density: 0.45 |
|
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1386 |
private void _updateRnaSecStr(CharSequence rnaAnnotation)... |
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{ |
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1386 |
try |
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{ |
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1386 |
_rnasecstr = Rna.getHelixMap(rnaAnnotation); |
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974 |
invalidrnastruc = -1; |
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} catch (WUSSParseException px) |
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{ |
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invalidrnastruc = px.getProblemPos(); |
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} |
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1386 |
if (invalidrnastruc > -1) |
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{ |
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return; |
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} |
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if (_rnasecstr != null && _rnasecstr.length > 0) |
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{ |
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974 |
isrna = true; |
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showAllColLabels = true; |
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974 |
scaleColLabel = true; |
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974 |
_markRnaHelices(); |
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} |
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} |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 4 |
Complexity Density: 0.36 |
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974 |
private void _markRnaHelices()... |
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{ |
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974 |
int mxval = 0; |
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19791 |
for (int x = 0; x < _rnasecstr.length; x++) |
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{ |
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18817 |
int val = 0; |
167 |
18817 |
try |
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{ |
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18817 |
val = Integer.valueOf(_rnasecstr[x].getFeatureGroup()); |
170 |
18817 |
if (mxval < val) |
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{ |
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311 |
mxval = val; |
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} |
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} catch (NumberFormatException q) |
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{ |
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} |
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18817 |
; |
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18817 |
annotations[_rnasecstr[x].getBegin()].value = val; |
180 |
18817 |
annotations[_rnasecstr[x].getEnd()].value = val; |
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} |
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974 |
setScore(mxval); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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12 |
public SequenceFeature[] getRnaSecondaryStructure()... |
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{ |
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return this._rnasecstr; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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4 |
public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that)... |
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{ |
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return rnaSecondaryStructureEquivalent(that, true); |
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} |
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| 70.3% |
Uncovered Elements: 11 (37) |
Complexity: 13 |
Complexity Density: 0.62 |
|
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4 |
public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that,... |
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boolean compareType) |
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{ |
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4 |
SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure(); |
209 |
4 |
SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure(); |
210 |
4 |
if (thisSfArray == null || thatSfArray == null) |
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{ |
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0 |
return thisSfArray == null && thatSfArray == null; |
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} |
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4 |
if (thisSfArray.length != thatSfArray.length) |
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{ |
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1 |
return false; |
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} |
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3 |
Arrays.sort(thisSfArray, new SFSortByEnd()); |
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3 |
Arrays.sort(thatSfArray, new SFSortByEnd()); |
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15 |
for (int i = 0; i < thisSfArray.length; i++) |
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{ |
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13 |
SequenceFeature thisSf = thisSfArray[i]; |
225 |
13 |
SequenceFeature thatSf = thatSfArray[i]; |
226 |
13 |
if (compareType) |
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{ |
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13 |
if (thisSf.getType() == null || thatSf.getType() == null) |
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{ |
230 |
0 |
if (thisSf.getType() == null && thatSf.getType() == null) |
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{ |
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0 |
continue; |
233 |
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} |
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else |
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{ |
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0 |
return false; |
237 |
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} |
238 |
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} |
239 |
13 |
if (!thisSf.getType().equals(thatSf.getType())) |
240 |
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{ |
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0 |
return false; |
242 |
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} |
243 |
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} |
244 |
13 |
if (!(thisSf.getBegin() == thatSf.getBegin() |
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&& thisSf.getEnd() == thatSf.getEnd())) |
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{ |
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1 |
return false; |
248 |
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} |
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} |
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2 |
return true; |
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} |
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private Map<Integer, Annotation> sequenceMapping; |
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public float graphMin; |
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public float graphMax; |
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public double score = Double.NaN; |
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274 |
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275 |
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276 |
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public boolean hasScore = false; |
278 |
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public GraphLine threshold; |
280 |
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281 |
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282 |
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283 |
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public boolean editable = false; |
285 |
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286 |
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public boolean hasIcons; |
288 |
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289 |
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290 |
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public boolean hasText; |
291 |
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292 |
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293 |
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public boolean visible = true; |
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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public boolean hasData=true; |
300 |
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301 |
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302 |
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303 |
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public int graphGroup = -1; |
304 |
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305 |
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306 |
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public int height = 0; |
307 |
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308 |
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public int graph = 0; |
309 |
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310 |
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public int graphHeight = 40; |
311 |
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312 |
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public boolean padGaps = false; |
313 |
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314 |
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public static final int NO_GRAPH = 0; |
315 |
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316 |
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public static final int BAR_GRAPH = 1; |
317 |
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318 |
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public static final int LINE_GRAPH = 2; |
319 |
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320 |
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public static final int CONTACT_MAP = 4; |
321 |
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322 |
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323 |
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324 |
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325 |
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326 |
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public static final String CONTACT_MAP_NOGROUPS = "CMNOGRPS"; |
327 |
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328 |
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public boolean belowAlignment = true; |
329 |
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330 |
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public SequenceGroup groupRef = null; |
331 |
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332 |
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333 |
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334 |
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335 |
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public boolean showAllColLabels = false; |
336 |
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337 |
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338 |
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339 |
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340 |
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public boolean scaleColLabel = false; |
341 |
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342 |
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343 |
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344 |
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345 |
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public boolean centreColLabels = false; |
346 |
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347 |
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private boolean isrna; |
348 |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
349 |
213 |
public static int getGraphValueFromString(String string)... |
350 |
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{ |
351 |
213 |
if (string.equalsIgnoreCase("BAR_GRAPH")) |
352 |
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{ |
353 |
23 |
return BAR_GRAPH; |
354 |
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} |
355 |
190 |
else if (string.equalsIgnoreCase("LINE_GRAPH")) |
356 |
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{ |
357 |
162 |
return LINE_GRAPH; |
358 |
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} |
359 |
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else |
360 |
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{ |
361 |
28 |
return NO_GRAPH; |
362 |
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} |
363 |
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} |
364 |
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365 |
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366 |
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367 |
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368 |
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@param |
369 |
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370 |
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@param |
371 |
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372 |
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@param |
373 |
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|
374 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
375 |
34577 |
public AlignmentAnnotation(String label, String description,... |
376 |
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Annotation[] annotations) |
377 |
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{ |
378 |
34577 |
setAnnotationId(); |
379 |
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|
380 |
34577 |
editable = true; |
381 |
34577 |
this.label = label; |
382 |
34577 |
this.description = description; |
383 |
34577 |
this.annotations = annotations; |
384 |
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|
385 |
34577 |
validateRangeAndDisplay(); |
386 |
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} |
387 |
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388 |
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|
389 |
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|
390 |
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|
391 |
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| 96.5% |
Uncovered Elements: 2 (57) |
Complexity: 73 |
Complexity Density: 2.35 |
|
392 |
5788 |
void areLabelsSecondaryStructure()... |
393 |
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{ |
394 |
5788 |
boolean nonSSLabel = false; |
395 |
5788 |
isrna = false; |
396 |
5788 |
StringBuffer rnastring = new StringBuffer(); |
397 |
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|
398 |
5788 |
char firstChar = 0; |
399 |
614201 |
for (int i = 0; i < annotations.length; i++) |
400 |
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{ |
401 |
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|
402 |
608413 |
if (annotations[i] == null) |
403 |
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{ |
404 |
116875 |
continue; |
405 |
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} |
406 |
491538 |
if (annotations[i].secondaryStructure == 'H' |
407 |
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|| annotations[i].secondaryStructure == 'E') |
408 |
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{ |
409 |
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|
410 |
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|
411 |
50925 |
hasIcons |= true; |
412 |
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} |
413 |
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else |
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 |
440613 |
if (annotations[i].secondaryStructure == '(' |
424 |
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|| annotations[i].secondaryStructure == '[' |
425 |
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|| annotations[i].secondaryStructure == '<' |
426 |
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|| annotations[i].secondaryStructure == '{' |
427 |
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|| annotations[i].secondaryStructure == 'A' |
428 |
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429 |
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430 |
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|| annotations[i].secondaryStructure == 'D' |
431 |
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432 |
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433 |
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|| annotations[i].secondaryStructure == 'F' |
434 |
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435 |
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436 |
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437 |
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438 |
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|| annotations[i].secondaryStructure == 'J' |
439 |
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|| annotations[i].secondaryStructure == 'K' |
440 |
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|| annotations[i].secondaryStructure == 'L' |
441 |
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|| annotations[i].secondaryStructure == 'M' |
442 |
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|| annotations[i].secondaryStructure == 'N' |
443 |
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|| annotations[i].secondaryStructure == 'O' |
444 |
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|| annotations[i].secondaryStructure == 'P' |
445 |
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|| annotations[i].secondaryStructure == 'Q' |
446 |
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|| annotations[i].secondaryStructure == 'R' |
447 |
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|
448 |
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449 |
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|| annotations[i].secondaryStructure == 'U' |
450 |
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|| annotations[i].secondaryStructure == 'V' |
451 |
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|| annotations[i].secondaryStructure == 'W' |
452 |
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|
453 |
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|| annotations[i].secondaryStructure == 'Y' |
454 |
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|| annotations[i].secondaryStructure == 'Z') |
455 |
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{ |
456 |
14602 |
hasIcons |= true; |
457 |
14602 |
isrna |= true; |
458 |
|
} |
459 |
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} |
460 |
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|
461 |
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|
462 |
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|
463 |
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|
464 |
491539 |
if (annotations[i].displayCharacter == null |
465 |
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|| annotations[i].displayCharacter.length() == 0) |
466 |
|
{ |
467 |
165729 |
rnastring.append('.'); |
468 |
165729 |
continue; |
469 |
|
} |
470 |
325810 |
if (annotations[i].displayCharacter.length() == 1) |
471 |
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{ |
472 |
272186 |
firstChar = annotations[i].displayCharacter.charAt(0); |
473 |
|
|
474 |
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|
475 |
272186 |
if (annotations[i].secondaryStructure != ' ' && !hasIcons && |
476 |
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|
477 |
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|
478 |
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|
479 |
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|
480 |
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|
481 |
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|
482 |
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|
483 |
|
firstChar != ' ' && firstChar != '$' && firstChar != 0xCE |
484 |
|
&& firstChar != '(' && firstChar != '[' && firstChar != '<' |
485 |
|
&& firstChar != '{' && firstChar != 'A' && firstChar != 'B' |
486 |
|
&& firstChar != 'C' && firstChar != 'D' && firstChar != 'E' |
487 |
|
&& firstChar != 'F' && firstChar != 'G' && firstChar != 'H' |
488 |
|
&& firstChar != 'I' && firstChar != 'J' && firstChar != 'K' |
489 |
|
&& firstChar != 'L' && firstChar != 'M' && firstChar != 'N' |
490 |
|
&& firstChar != 'O' && firstChar != 'P' && firstChar != 'Q' |
491 |
|
&& firstChar != 'R' && firstChar != 'S' && firstChar != 'T' |
492 |
|
&& firstChar != 'U' && firstChar != 'V' && firstChar != 'W' |
493 |
|
&& firstChar != 'X' && firstChar != 'Y' && firstChar != 'Z' |
494 |
|
&& firstChar != '-' |
495 |
|
&& firstChar < jalview.schemes.ResidueProperties.aaIndex.length) |
496 |
|
{ |
497 |
174 |
if (jalview.schemes.ResidueProperties.aaIndex[firstChar] < 23) |
498 |
|
|
499 |
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|
500 |
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|
501 |
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|
502 |
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|
503 |
|
{ |
504 |
11 |
nonSSLabel = true; |
505 |
|
} |
506 |
|
} |
507 |
|
} |
508 |
|
else |
509 |
|
{ |
510 |
53624 |
rnastring.append(annotations[i].displayCharacter.charAt(1)); |
511 |
|
} |
512 |
|
|
513 |
325810 |
if (annotations[i].displayCharacter.length() > 0) |
514 |
|
{ |
515 |
325810 |
hasText = true; |
516 |
|
} |
517 |
|
} |
518 |
|
|
519 |
5788 |
if (nonSSLabel) |
520 |
|
{ |
521 |
1 |
hasIcons = false; |
522 |
12 |
for (int j = 0; j < annotations.length; j++) |
523 |
|
{ |
524 |
11 |
if (annotations[j] != null |
525 |
|
&& annotations[j].secondaryStructure != ' ') |
526 |
|
{ |
527 |
11 |
annotations[j].displayCharacter = String |
528 |
|
.valueOf(annotations[j].secondaryStructure); |
529 |
11 |
annotations[j].secondaryStructure = ' '; |
530 |
|
} |
531 |
|
|
532 |
|
} |
533 |
|
} |
534 |
|
else |
535 |
|
{ |
536 |
5787 |
if (isrna) |
537 |
|
{ |
538 |
958 |
_updateRnaSecStr(new AnnotCharSequence()); |
539 |
|
} |
540 |
|
} |
541 |
|
} |
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
@author |
548 |
|
|
549 |
|
|
|
|
| 92.6% |
Uncovered Elements: 2 (27) |
Complexity: 17 |
Complexity Density: 1.55 |
|
550 |
|
private class AnnotCharSequence implements CharSequence |
551 |
|
{ |
552 |
|
int offset = 0; |
553 |
|
|
554 |
|
int max = 0; |
555 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
556 |
1394 |
public AnnotCharSequence()... |
557 |
|
{ |
558 |
1394 |
this(0, annotations.length); |
559 |
|
} |
560 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
561 |
1394 |
AnnotCharSequence(int start, int end)... |
562 |
|
{ |
563 |
1394 |
offset = start; |
564 |
1394 |
max = end; |
565 |
|
} |
566 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
567 |
0 |
@Override... |
568 |
|
public CharSequence subSequence(int start, int end) |
569 |
|
{ |
570 |
0 |
return new AnnotCharSequence(offset + start, offset + end); |
571 |
|
} |
572 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
573 |
66378 |
@Override... |
574 |
|
public int length() |
575 |
|
{ |
576 |
66378 |
return max - offset; |
577 |
|
} |
578 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 7 |
Complexity Density: 7 |
|
579 |
65420 |
@Override... |
580 |
|
public char charAt(int index) |
581 |
|
{ |
582 |
65420 |
return ((index + offset < 0) || (index + offset) >= max |
583 |
|
|| annotations[index + offset] == null |
584 |
|
|| (annotations[index + offset].secondaryStructure <= ' ') |
585 |
|
? ' ' |
586 |
27210 |
: annotations[index + offset].displayCharacter == null |
587 |
|
|| annotations[index |
588 |
|
+ offset].displayCharacter |
589 |
|
.length() == 0 |
590 |
|
? annotations[index |
591 |
|
+ offset].secondaryStructure |
592 |
|
: annotations[index |
593 |
|
+ offset].displayCharacter |
594 |
|
.charAt(0)); |
595 |
|
} |
596 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 6 |
Complexity Density: 1.2 |
|
597 |
436 |
@Override... |
598 |
|
public String toString() |
599 |
|
{ |
600 |
436 |
char[] string = new char[max - offset]; |
601 |
436 |
int mx = annotations.length; |
602 |
|
|
603 |
31968 |
for (int i = offset; i < mx; i++) |
604 |
|
{ |
605 |
31532 |
string[i] = (annotations[i] == null |
606 |
|
|| (annotations[i].secondaryStructure <= 32)) |
607 |
|
? ' ' |
608 |
13402 |
: (annotations[i].displayCharacter == null |
609 |
|
|| annotations[i].displayCharacter |
610 |
|
.length() == 0 |
611 |
|
? annotations[i].secondaryStructure |
612 |
|
: annotations[i].displayCharacter |
613 |
|
.charAt(0)); |
614 |
|
} |
615 |
436 |
return new String(string); |
616 |
|
} |
617 |
|
}; |
618 |
|
|
619 |
|
private long _lastrnaannot = -1; |
620 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 3 |
Complexity Density: 0.43 |
|
621 |
3393 |
public String getRNAStruc()... |
622 |
|
{ |
623 |
3393 |
if (isrna) |
624 |
|
{ |
625 |
436 |
String rnastruc = new AnnotCharSequence().toString(); |
626 |
436 |
if (_lastrnaannot != rnastruc.hashCode()) |
627 |
|
{ |
628 |
|
|
629 |
428 |
_lastrnaannot = rnastruc.hashCode(); |
630 |
428 |
_updateRnaSecStr(rnastruc); |
631 |
|
} |
632 |
436 |
return rnastruc; |
633 |
|
} |
634 |
2957 |
return null; |
635 |
|
} |
636 |
|
|
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
@param |
641 |
|
|
642 |
|
@param |
643 |
|
|
644 |
|
@param |
645 |
|
|
646 |
|
@param |
647 |
|
|
648 |
|
@param |
649 |
|
|
650 |
|
@param |
651 |
|
|
652 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
653 |
3143 |
public AlignmentAnnotation(String label, String description,... |
654 |
|
Annotation[] annotations, float min, float max, int graphType) |
655 |
|
{ |
656 |
3143 |
setAnnotationId(); |
657 |
|
|
658 |
3143 |
editable = graphType == 0; |
659 |
|
|
660 |
3143 |
this.label = label; |
661 |
3143 |
this.description = description; |
662 |
3143 |
this.annotations = annotations; |
663 |
3143 |
graph = graphType; |
664 |
3143 |
graphMin = min; |
665 |
3143 |
graphMax = max; |
666 |
3143 |
validateRangeAndDisplay(); |
667 |
|
} |
668 |
|
|
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
|
|
|
| 96.6% |
Uncovered Elements: 2 (59) |
Complexity: 18 |
Complexity Density: 0.55 |
|
673 |
39276 |
public void validateRangeAndDisplay()... |
674 |
|
{ |
675 |
|
|
676 |
39276 |
if (annotations == null) |
677 |
|
{ |
678 |
33488 |
visible = false; |
679 |
33488 |
invalidrnastruc = -1; |
680 |
33488 |
return; |
681 |
|
} |
682 |
|
|
683 |
5788 |
int graphType = graph; |
684 |
5788 |
float min = graphMin; |
685 |
5788 |
float max = graphMax; |
686 |
5788 |
boolean drawValues = true; |
687 |
5788 |
_linecolour = null; |
688 |
5788 |
if (min == max) |
689 |
|
{ |
690 |
2774 |
min = 999999999; |
691 |
506178 |
for (int i = 0; i < annotations.length; i++) |
692 |
|
{ |
693 |
503404 |
if (annotations[i] == null) |
694 |
|
{ |
695 |
107868 |
continue; |
696 |
|
} |
697 |
|
|
698 |
395536 |
if (drawValues && annotations[i].displayCharacter != null |
699 |
|
&& annotations[i].displayCharacter.length() > 1) |
700 |
|
{ |
701 |
1245 |
drawValues = false; |
702 |
|
} |
703 |
|
|
704 |
395536 |
if (annotations[i].value > max) |
705 |
|
{ |
706 |
2435 |
max = annotations[i].value; |
707 |
|
} |
708 |
|
|
709 |
395536 |
if (annotations[i].value < min) |
710 |
|
{ |
711 |
4942 |
min = annotations[i].value; |
712 |
|
} |
713 |
395536 |
if (_linecolour == null && annotations[i].colour != null) |
714 |
|
{ |
715 |
750 |
_linecolour = annotations[i].colour; |
716 |
|
} |
717 |
|
} |
718 |
|
|
719 |
2774 |
if (min > 0) |
720 |
|
{ |
721 |
1320 |
min = 0; |
722 |
|
} |
723 |
|
else |
724 |
|
{ |
725 |
1454 |
if (max < 0) |
726 |
|
{ |
727 |
0 |
max = 0; |
728 |
|
} |
729 |
|
} |
730 |
|
} |
731 |
|
|
732 |
5788 |
graphMin = min; |
733 |
5788 |
graphMax = max; |
734 |
|
|
735 |
5788 |
areLabelsSecondaryStructure(); |
736 |
|
|
737 |
5788 |
if (!drawValues && graphType != NO_GRAPH) |
738 |
|
{ |
739 |
27176 |
for (int i = 0; i < annotations.length; i++) |
740 |
|
{ |
741 |
27004 |
if (annotations[i] != null) |
742 |
|
{ |
743 |
21912 |
annotations[i].displayCharacter = ""; |
744 |
|
} |
745 |
|
} |
746 |
|
} |
747 |
|
} |
748 |
|
|
749 |
|
|
750 |
|
|
751 |
|
|
752 |
|
|
753 |
|
@param |
754 |
|
|
|
|
| 88.4% |
Uncovered Elements: 10 (86) |
Complexity: 16 |
Complexity Density: 0.29 |
|
755 |
835 |
public AlignmentAnnotation(AlignmentAnnotation annotation)... |
756 |
|
{ |
757 |
835 |
setAnnotationId(); |
758 |
835 |
this.label = new String(annotation.label); |
759 |
835 |
if (annotation.description != null) |
760 |
|
{ |
761 |
811 |
this.description = new String(annotation.description); |
762 |
|
} |
763 |
835 |
this.graphMin = annotation.graphMin; |
764 |
835 |
this.graphMax = annotation.graphMax; |
765 |
835 |
this.graph = annotation.graph; |
766 |
835 |
this.graphHeight = annotation.graphHeight; |
767 |
835 |
this.graphGroup = annotation.graphGroup; |
768 |
835 |
this.groupRef = annotation.groupRef; |
769 |
835 |
this.editable = annotation.editable; |
770 |
835 |
this.autoCalculated = annotation.autoCalculated; |
771 |
835 |
this.hasIcons = annotation.hasIcons; |
772 |
835 |
this.hasText = annotation.hasText; |
773 |
835 |
this.height = annotation.height; |
774 |
835 |
this.label = annotation.label; |
775 |
835 |
this.padGaps = annotation.padGaps; |
776 |
835 |
this.visible = annotation.visible; |
777 |
835 |
this.hasData = annotation.hasData; |
778 |
835 |
this.centreColLabels = annotation.centreColLabels; |
779 |
835 |
this.scaleColLabel = annotation.scaleColLabel; |
780 |
835 |
this.showAllColLabels = annotation.showAllColLabels; |
781 |
835 |
this.calcId = annotation.calcId; |
782 |
835 |
if (annotation.properties != null) |
783 |
|
{ |
784 |
835 |
properties = new HashMap<>(); |
785 |
835 |
for (Map.Entry<String, String> val : annotation.properties.entrySet()) |
786 |
|
{ |
787 |
16 |
properties.put(val.getKey(), val.getValue()); |
788 |
|
} |
789 |
|
} |
790 |
? |
if (this.hasScore = annotation.hasScore) |
791 |
|
{ |
792 |
129 |
this.score = annotation.score; |
793 |
|
} |
794 |
835 |
if (annotation.threshold != null) |
795 |
|
{ |
796 |
0 |
threshold = new GraphLine(annotation.threshold); |
797 |
|
} |
798 |
835 |
Annotation[] ann = annotation.annotations; |
799 |
835 |
if (annotation.annotations != null) |
800 |
|
{ |
801 |
832 |
this.annotations = new Annotation[ann.length]; |
802 |
96754 |
for (int i = 0; i < ann.length; i++) |
803 |
|
{ |
804 |
95922 |
if (ann[i] != null) |
805 |
|
{ |
806 |
70050 |
annotations[i] = new Annotation(ann[i]); |
807 |
70050 |
if (_linecolour != null) |
808 |
|
{ |
809 |
0 |
_linecolour = annotations[i].colour; |
810 |
|
} |
811 |
|
} |
812 |
|
} |
813 |
|
} |
814 |
835 |
if (annotation.sequenceRef != null) |
815 |
|
{ |
816 |
649 |
this.sequenceRef = annotation.sequenceRef; |
817 |
649 |
if (annotation.sequenceMapping != null) |
818 |
|
{ |
819 |
647 |
Integer p = null; |
820 |
647 |
sequenceMapping = new HashMap<>(); |
821 |
647 |
Iterator<Integer> pos = annotation.sequenceMapping.keySet() |
822 |
|
.iterator(); |
823 |
49575 |
while (pos.hasNext()) |
824 |
|
{ |
825 |
|
|
826 |
48928 |
p = pos.next(); |
827 |
48928 |
Annotation a = annotation.sequenceMapping.get(p); |
828 |
48928 |
if (a == null) |
829 |
|
{ |
830 |
0 |
continue; |
831 |
|
} |
832 |
48928 |
if (ann != null) |
833 |
|
{ |
834 |
8326407 |
for (int i = 0; i < ann.length; i++) |
835 |
|
{ |
836 |
8277479 |
if (ann[i] == a) |
837 |
|
{ |
838 |
48886 |
sequenceMapping.put(p, annotations[i]); |
839 |
|
} |
840 |
|
} |
841 |
|
} |
842 |
|
} |
843 |
|
} |
844 |
|
else |
845 |
|
{ |
846 |
2 |
this.sequenceMapping = null; |
847 |
|
} |
848 |
|
|
849 |
|
} |
850 |
|
|
851 |
|
|
852 |
|
{ |
853 |
|
|
854 |
|
} |
855 |
835 |
validateRangeAndDisplay(); |
856 |
|
} |
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
|
861 |
|
|
862 |
|
@param |
863 |
|
@param |
864 |
|
|
|
|
| 78.3% |
Uncovered Elements: 10 (46) |
Complexity: 12 |
Complexity Density: 0.46 |
|
865 |
108 |
public void restrict(int startRes, int endRes)... |
866 |
|
{ |
867 |
108 |
if (annotations == null) |
868 |
|
{ |
869 |
|
|
870 |
0 |
return; |
871 |
|
} |
872 |
108 |
if (startRes < 0) |
873 |
|
{ |
874 |
0 |
startRes = 0; |
875 |
|
} |
876 |
108 |
if (startRes >= annotations.length) |
877 |
|
{ |
878 |
0 |
startRes = annotations.length - 1; |
879 |
|
} |
880 |
108 |
if (endRes >= annotations.length) |
881 |
|
{ |
882 |
100 |
endRes = annotations.length - 1; |
883 |
|
} |
884 |
108 |
if (annotations == null) |
885 |
|
{ |
886 |
0 |
return; |
887 |
|
} |
888 |
108 |
Annotation[] temp = new Annotation[endRes - startRes + 1]; |
889 |
108 |
if (startRes < annotations.length) |
890 |
|
{ |
891 |
108 |
System.arraycopy(annotations, startRes, temp, 0, |
892 |
|
endRes - startRes + 1); |
893 |
|
} |
894 |
108 |
if (sequenceRef != null) |
895 |
|
{ |
896 |
|
|
897 |
102 |
int spos = sequenceRef.findPosition(startRes); |
898 |
102 |
int epos = sequenceRef.findPosition(endRes); |
899 |
102 |
if (sequenceMapping != null) |
900 |
|
{ |
901 |
102 |
Map<Integer, Annotation> newmapping = new HashMap<>(); |
902 |
102 |
Iterator<Integer> e = sequenceMapping.keySet().iterator(); |
903 |
7896 |
while (e.hasNext()) |
904 |
|
{ |
905 |
7794 |
Integer pos = e.next(); |
906 |
7794 |
if (pos.intValue() >= spos && pos.intValue() <= epos) |
907 |
|
{ |
908 |
7750 |
newmapping.put(pos, sequenceMapping.get(pos)); |
909 |
|
} |
910 |
|
} |
911 |
102 |
sequenceMapping.clear(); |
912 |
102 |
sequenceMapping = newmapping; |
913 |
|
} |
914 |
|
} |
915 |
108 |
annotations = temp; |
916 |
|
} |
917 |
|
|
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
@param |
922 |
|
|
923 |
|
@return |
924 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
925 |
0 |
public boolean padAnnotation(int length)... |
926 |
|
{ |
927 |
0 |
if (annotations == null) |
928 |
|
{ |
929 |
0 |
return true; |
930 |
|
|
931 |
|
} |
932 |
0 |
if (annotations.length < length) |
933 |
|
{ |
934 |
0 |
Annotation[] na = new Annotation[length]; |
935 |
0 |
System.arraycopy(annotations, 0, na, 0, annotations.length); |
936 |
0 |
annotations = na; |
937 |
0 |
return true; |
938 |
|
} |
939 |
0 |
return annotations.length > length; |
940 |
|
|
941 |
|
} |
942 |
|
|
943 |
|
|
944 |
|
|
945 |
|
|
946 |
|
@return |
947 |
|
|
|
|
| 88.2% |
Uncovered Elements: 4 (34) |
Complexity: 9 |
Complexity Density: 0.5 |
|
948 |
209 |
@Override... |
949 |
|
public String toString() |
950 |
|
{ |
951 |
209 |
if (annotations == null) |
952 |
|
{ |
953 |
126 |
return ""; |
954 |
|
} |
955 |
83 |
StringBuilder buffer = new StringBuilder(256); |
956 |
|
|
957 |
192 |
for (int i = 0; i < annotations.length; i++) |
958 |
|
{ |
959 |
109 |
if (annotations[i] != null) |
960 |
|
{ |
961 |
109 |
if (graph != 0) |
962 |
|
{ |
963 |
25 |
buffer.append(annotations[i].value); |
964 |
|
} |
965 |
84 |
else if (hasIcons) |
966 |
|
{ |
967 |
84 |
buffer.append(annotations[i].secondaryStructure); |
968 |
|
} |
969 |
|
else |
970 |
|
{ |
971 |
0 |
buffer.append(annotations[i].displayCharacter); |
972 |
|
} |
973 |
|
} |
974 |
|
|
975 |
109 |
buffer.append(", "); |
976 |
|
} |
977 |
|
|
978 |
83 |
if (label.indexOf("Consensus") == 0) |
979 |
|
{ |
980 |
1 |
buffer.append("\n"); |
981 |
|
|
982 |
6 |
for (int i = 0; i < annotations.length; i++) |
983 |
|
{ |
984 |
5 |
if (annotations[i] != null) |
985 |
|
{ |
986 |
5 |
buffer.append(annotations[i].description); |
987 |
|
} |
988 |
|
|
989 |
5 |
buffer.append(", "); |
990 |
|
} |
991 |
|
} |
992 |
|
|
993 |
83 |
return buffer.toString(); |
994 |
|
} |
995 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
996 |
185 |
public void setThreshold(GraphLine line)... |
997 |
|
{ |
998 |
185 |
threshold = line; |
999 |
|
} |
1000 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1001 |
624 |
public GraphLine getThreshold()... |
1002 |
|
{ |
1003 |
624 |
return threshold; |
1004 |
|
} |
1005 |
|
|
1006 |
|
|
1007 |
|
|
1008 |
|
|
1009 |
|
|
1010 |
|
|
1011 |
|
@param |
1012 |
|
@param |
1013 |
|
@param |
1014 |
|
|
|
|
| 91.3% |
Uncovered Elements: 2 (23) |
Complexity: 6 |
Complexity Density: 0.46 |
|
1015 |
1618 |
public void createSequenceMapping(SequenceI seqRef, int startRes,... |
1016 |
|
boolean alreadyMapped) |
1017 |
|
{ |
1018 |
|
|
1019 |
1618 |
if (seqRef == null) |
1020 |
|
{ |
1021 |
0 |
return; |
1022 |
|
} |
1023 |
1618 |
sequenceRef = seqRef; |
1024 |
1618 |
if (annotations == null) |
1025 |
|
{ |
1026 |
103 |
return; |
1027 |
|
} |
1028 |
1515 |
sequenceMapping = new HashMap<>(); |
1029 |
|
|
1030 |
1515 |
int seqPos; |
1031 |
|
|
1032 |
273408 |
for (int i = 0; i < annotations.length; i++) |
1033 |
|
{ |
1034 |
271893 |
if (annotations[i] != null) |
1035 |
|
{ |
1036 |
233212 |
if (alreadyMapped) |
1037 |
|
{ |
1038 |
150949 |
seqPos = seqRef.findPosition(i); |
1039 |
|
} |
1040 |
|
else |
1041 |
|
{ |
1042 |
82263 |
seqPos = i + startRes; |
1043 |
|
} |
1044 |
|
|
1045 |
233212 |
sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]); |
1046 |
|
} |
1047 |
|
} |
1048 |
|
|
1049 |
|
} |
1050 |
|
|
1051 |
|
|
1052 |
|
|
1053 |
|
|
1054 |
|
|
1055 |
|
|
1056 |
|
|
|
|
| 96.7% |
Uncovered Elements: 1 (30) |
Complexity: 7 |
Complexity Density: 0.39 |
|
1057 |
2147 |
public void adjustForAlignment()... |
1058 |
|
{ |
1059 |
2147 |
if (sequenceRef == null) |
1060 |
|
{ |
1061 |
212 |
return; |
1062 |
|
} |
1063 |
|
|
1064 |
1935 |
if (annotations == null) |
1065 |
|
{ |
1066 |
103 |
return; |
1067 |
|
} |
1068 |
|
|
1069 |
1832 |
int a = 0, aSize = sequenceRef.getLength(); |
1070 |
|
|
1071 |
1832 |
if (aSize == 0) |
1072 |
|
{ |
1073 |
|
|
1074 |
1 |
return; |
1075 |
|
} |
1076 |
|
|
1077 |
1831 |
int position; |
1078 |
1831 |
Annotation[] temp = new Annotation[aSize]; |
1079 |
1831 |
Integer index; |
1080 |
1831 |
if (sequenceMapping != null) |
1081 |
|
{ |
1082 |
251958 |
for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++) |
1083 |
|
{ |
1084 |
250127 |
index = Integer.valueOf(a); |
1085 |
250127 |
Annotation annot = sequenceMapping.get(index); |
1086 |
250127 |
if (annot != null) |
1087 |
|
{ |
1088 |
194728 |
position = sequenceRef.findIndex(a) - 1; |
1089 |
|
|
1090 |
194728 |
temp[position] = annot; |
1091 |
|
} |
1092 |
|
} |
1093 |
|
} |
1094 |
1831 |
annotations = temp; |
1095 |
|
} |
1096 |
|
|
1097 |
|
|
1098 |
|
|
1099 |
|
|
1100 |
|
|
1101 |
|
@return |
1102 |
|
|
|
|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 4 |
Complexity Density: 0.33 |
|
1103 |
0 |
public int compactAnnotationArray()... |
1104 |
|
{ |
1105 |
0 |
int i = 0, iSize = annotations.length; |
1106 |
0 |
while (i < iSize) |
1107 |
|
{ |
1108 |
0 |
if (annotations[i] == null) |
1109 |
|
{ |
1110 |
0 |
if (i + 1 < iSize) |
1111 |
|
{ |
1112 |
0 |
System.arraycopy(annotations, i + 1, annotations, i, |
1113 |
|
iSize - i - 1); |
1114 |
|
} |
1115 |
0 |
iSize--; |
1116 |
|
} |
1117 |
|
else |
1118 |
|
{ |
1119 |
0 |
i++; |
1120 |
|
} |
1121 |
|
} |
1122 |
0 |
Annotation[] ann = annotations; |
1123 |
0 |
annotations = new Annotation[i]; |
1124 |
0 |
System.arraycopy(ann, 0, annotations, 0, i); |
1125 |
0 |
ann = null; |
1126 |
0 |
return iSize; |
1127 |
|
} |
1128 |
|
|
1129 |
|
|
1130 |
|
|
1131 |
|
|
1132 |
|
|
1133 |
|
|
1134 |
|
|
1135 |
|
|
1136 |
|
|
1137 |
|
@param |
1138 |
|
|
|
|
| 63.6% |
Uncovered Elements: 8 (22) |
Complexity: 15 |
Complexity Density: 1.07 |
|
1139 |
2690 |
public void setSequenceRef(SequenceI sequenceI)... |
1140 |
|
{ |
1141 |
2690 |
if (sequenceI != null) |
1142 |
|
{ |
1143 |
2627 |
if (sequenceRef != null) |
1144 |
|
{ |
1145 |
1533 |
boolean rIsDs = sequenceRef.getDatasetSequence() == null, |
1146 |
|
tIsDs = sequenceI.getDatasetSequence() == null; |
1147 |
1533 |
if (sequenceRef != sequenceI |
1148 |
|
&& (rIsDs && !tIsDs |
1149 |
|
&& sequenceRef != sequenceI.getDatasetSequence()) |
1150 |
|
&& (!rIsDs && tIsDs |
1151 |
|
&& sequenceRef.getDatasetSequence() != sequenceI) |
1152 |
|
&& (!rIsDs && !tIsDs |
1153 |
|
&& sequenceRef.getDatasetSequence() != sequenceI |
1154 |
|
.getDatasetSequence()) |
1155 |
|
&& !sequenceRef.equals(sequenceI)) |
1156 |
|
{ |
1157 |
|
|
1158 |
|
|
1159 |
0 |
sequenceRef = null; |
1160 |
0 |
if (sequenceMapping != null) |
1161 |
|
{ |
1162 |
0 |
sequenceMapping = null; |
1163 |
|
|
1164 |
|
} |
1165 |
0 |
createSequenceMapping(sequenceI, 1, true); |
1166 |
0 |
adjustForAlignment(); |
1167 |
|
} |
1168 |
|
else |
1169 |
|
{ |
1170 |
|
|
1171 |
1533 |
sequenceRef = sequenceI; |
1172 |
|
} |
1173 |
|
} |
1174 |
|
else |
1175 |
|
{ |
1176 |
|
|
1177 |
1094 |
createSequenceMapping(sequenceI, 1, true); |
1178 |
1094 |
adjustForAlignment(); |
1179 |
|
} |
1180 |
|
} |
1181 |
|
else |
1182 |
|
{ |
1183 |
|
|
1184 |
63 |
sequenceMapping = null; |
1185 |
63 |
sequenceRef = null; |
1186 |
|
} |
1187 |
|
} |
1188 |
|
|
1189 |
|
|
1190 |
|
@return |
1191 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1192 |
156 |
public double getScore()... |
1193 |
|
{ |
1194 |
156 |
return score; |
1195 |
|
} |
1196 |
|
|
1197 |
|
|
1198 |
|
@param |
1199 |
|
|
1200 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1201 |
34591 |
public void setScore(double score)... |
1202 |
|
{ |
1203 |
34591 |
hasScore = true; |
1204 |
34591 |
this.score = score; |
1205 |
|
} |
1206 |
|
|
1207 |
|
|
1208 |
|
|
1209 |
|
@return |
1210 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1211 |
833 |
public boolean hasScore()... |
1212 |
|
{ |
1213 |
833 |
return hasScore || !Double.isNaN(score); |
1214 |
|
} |
1215 |
|
|
1216 |
|
|
1217 |
|
|
1218 |
|
|
1219 |
|
@param |
1220 |
|
@param |
1221 |
|
@param |
1222 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1223 |
33442 |
public AlignmentAnnotation(String label, String description, double score)... |
1224 |
|
{ |
1225 |
33442 |
this(label, description, null); |
1226 |
33442 |
setScore(score); |
1227 |
|
} |
1228 |
|
|
1229 |
|
|
1230 |
|
|
1231 |
|
|
1232 |
|
@param |
1233 |
|
@param |
1234 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
1235 |
0 |
public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,... |
1236 |
|
HiddenColumns hidden) |
1237 |
|
{ |
1238 |
0 |
this(alignmentAnnotation); |
1239 |
0 |
if (annotations == null) |
1240 |
|
{ |
1241 |
0 |
return; |
1242 |
|
} |
1243 |
0 |
makeVisibleAnnotation(hidden); |
1244 |
|
} |
1245 |
|
|
|
|
| 0% |
Uncovered Elements: 16 (16) |
Complexity: 6 |
Complexity Density: 0.75 |
|
1246 |
0 |
public void setPadGaps(boolean padgaps, char gapchar)... |
1247 |
|
{ |
1248 |
0 |
this.padGaps = padgaps; |
1249 |
0 |
if (padgaps) |
1250 |
|
{ |
1251 |
0 |
hasText = true; |
1252 |
0 |
for (int i = 0; i < annotations.length; i++) |
1253 |
|
{ |
1254 |
0 |
if (annotations[i] == null) |
1255 |
|
{ |
1256 |
0 |
annotations[i] = new Annotation(String.valueOf(gapchar), null, |
1257 |
|
' ', 0f, null); |
1258 |
|
} |
1259 |
0 |
else if (annotations[i].displayCharacter == null |
1260 |
|
|| annotations[i].displayCharacter.equals(" ")) |
1261 |
|
{ |
1262 |
0 |
annotations[i].displayCharacter = String.valueOf(gapchar); |
1263 |
|
} |
1264 |
|
} |
1265 |
|
} |
1266 |
|
} |
1267 |
|
|
1268 |
|
|
1269 |
|
|
1270 |
|
|
1271 |
|
@param |
1272 |
|
@return |
1273 |
|
|
1274 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (10) |
Complexity: 4 |
Complexity Density: 0.67 |
|
1275 |
10 |
public String getDescription(boolean seqname)... |
1276 |
|
{ |
1277 |
10 |
if (seqname && this.sequenceRef != null) |
1278 |
|
{ |
1279 |
3 |
int i = description.toLowerCase(Locale.ROOT).indexOf("<html>"); |
1280 |
3 |
if (i > -1) |
1281 |
|
{ |
1282 |
|
|
1283 |
1 |
return "<html>" + sequenceRef.getName() + " : " |
1284 |
|
+ description.substring(i + 6); |
1285 |
|
} |
1286 |
2 |
return sequenceRef.getName() + " : " + description; |
1287 |
|
} |
1288 |
7 |
return description; |
1289 |
|
} |
1290 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1291 |
234 |
public boolean isValidStruc()... |
1292 |
|
{ |
1293 |
234 |
return invalidrnastruc == -1; |
1294 |
|
} |
1295 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1296 |
1162138 |
public long getInvalidStrucPos()... |
1297 |
|
{ |
1298 |
1162138 |
return invalidrnastruc; |
1299 |
|
} |
1300 |
|
|
1301 |
|
|
1302 |
|
|
1303 |
|
|
1304 |
|
protected String calcId = ""; |
1305 |
|
|
1306 |
|
|
1307 |
|
|
1308 |
|
|
1309 |
|
protected Map<String, String> properties = new HashMap<>(); |
1310 |
|
|
1311 |
|
|
1312 |
|
|
1313 |
|
|
1314 |
|
|
1315 |
|
public java.awt.Color _linecolour; |
1316 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1317 |
12755 |
public String getCalcId()... |
1318 |
|
{ |
1319 |
12755 |
return calcId; |
1320 |
|
} |
1321 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1322 |
1308 |
public void setCalcId(String calcId)... |
1323 |
|
{ |
1324 |
1308 |
this.calcId = calcId; |
1325 |
|
} |
1326 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1327 |
13711 |
public boolean isRNA()... |
1328 |
|
{ |
1329 |
13711 |
return isrna; |
1330 |
|
} |
1331 |
|
|
1332 |
|
|
1333 |
|
|
1334 |
|
|
1335 |
|
|
1336 |
|
@param |
1337 |
|
@param |
1338 |
|
|
1339 |
|
|
|
|
| 80% |
Uncovered Elements: 5 (25) |
Complexity: 8 |
Complexity Density: 0.62 |
|
1340 |
200 |
public void liftOver(SequenceI sq, Mapping sp2sq)... |
1341 |
|
{ |
1342 |
200 |
if (sp2sq.getMappedWidth() != sp2sq.getWidth()) |
1343 |
|
{ |
1344 |
|
|
1345 |
|
|
1346 |
0 |
throw new Error( |
1347 |
|
"liftOver currently not implemented for transfer of annotation between different types of seqeunce"); |
1348 |
|
} |
1349 |
200 |
boolean mapIsTo = (sp2sq != null) |
1350 |
|
? (sp2sq.getTo() == sq |
1351 |
|
|| sp2sq.getTo() == sq.getDatasetSequence()) |
1352 |
|
: false; |
1353 |
|
|
1354 |
|
|
1355 |
200 |
Map<Integer, Annotation> mapForsq = new HashMap<>(); |
1356 |
200 |
if (sequenceMapping != null) |
1357 |
|
{ |
1358 |
200 |
if (sp2sq != null) |
1359 |
|
{ |
1360 |
200 |
for (Entry<Integer, Annotation> ie : sequenceMapping.entrySet()) |
1361 |
|
{ |
1362 |
16514 |
Integer mpos = Integer |
1363 |
16514 |
.valueOf(mapIsTo ? sp2sq.getMappedPosition(ie.getKey()) |
1364 |
|
: sp2sq.getPosition(ie.getKey())); |
1365 |
16514 |
if (mpos >= sq.getStart() && mpos <= sq.getEnd()) |
1366 |
|
{ |
1367 |
16506 |
mapForsq.put(mpos, ie.getValue()); |
1368 |
|
} |
1369 |
|
} |
1370 |
200 |
sequenceMapping = mapForsq; |
1371 |
200 |
sequenceRef = sq; |
1372 |
200 |
adjustForAlignment(); |
1373 |
|
} |
1374 |
|
else |
1375 |
|
{ |
1376 |
|
|
1377 |
|
} |
1378 |
|
} |
1379 |
|
} |
1380 |
|
|
1381 |
|
|
1382 |
|
|
1383 |
|
|
1384 |
|
|
1385 |
|
|
1386 |
|
|
1387 |
|
@param |
1388 |
|
|
1389 |
|
|
1390 |
|
@param |
1391 |
|
|
1392 |
|
@param |
1393 |
|
|
1394 |
|
@param |
1395 |
|
|
1396 |
|
@param |
1397 |
|
|
1398 |
|
|
1399 |
|
|
1400 |
|
|
1401 |
|
|
|
|
| 0% |
Uncovered Elements: 38 (38) |
Complexity: 11 |
Complexity Density: 0.5 |
|
1402 |
0 |
public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,... |
1403 |
|
int from, int to, int idxoffset) |
1404 |
|
{ |
1405 |
0 |
if (mapping != null) |
1406 |
|
{ |
1407 |
0 |
Map<Integer, Annotation> old = sequenceMapping; |
1408 |
0 |
Map<Integer, Annotation> remap = new HashMap<>(); |
1409 |
0 |
int index = -1; |
1410 |
0 |
for (int mp[] : mapping.values()) |
1411 |
|
{ |
1412 |
0 |
if (index++ < 0) |
1413 |
|
{ |
1414 |
0 |
continue; |
1415 |
|
} |
1416 |
0 |
Annotation ann = null; |
1417 |
0 |
if (from == -1) |
1418 |
|
{ |
1419 |
0 |
ann = sequenceMapping.get(Integer.valueOf(idxoffset + index)); |
1420 |
|
} |
1421 |
|
else |
1422 |
|
{ |
1423 |
0 |
if (mp != null && mp.length > from) |
1424 |
|
{ |
1425 |
0 |
ann = sequenceMapping.get(Integer.valueOf(mp[from])); |
1426 |
|
} |
1427 |
|
} |
1428 |
0 |
if (ann != null) |
1429 |
|
{ |
1430 |
0 |
if (to == -1) |
1431 |
|
{ |
1432 |
0 |
remap.put(Integer.valueOf(idxoffset + index), ann); |
1433 |
|
} |
1434 |
|
else |
1435 |
|
{ |
1436 |
0 |
if (to > -1 && to < mp.length) |
1437 |
|
{ |
1438 |
0 |
remap.put(Integer.valueOf(mp[to]), ann); |
1439 |
|
} |
1440 |
|
} |
1441 |
|
} |
1442 |
|
} |
1443 |
0 |
sequenceMapping = remap; |
1444 |
0 |
old.clear(); |
1445 |
0 |
if (newref != null) |
1446 |
|
{ |
1447 |
0 |
sequenceRef = newref; |
1448 |
|
} |
1449 |
0 |
adjustForAlignment(); |
1450 |
|
} |
1451 |
|
} |
1452 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1453 |
57035 |
public String getProperty(String property)... |
1454 |
|
{ |
1455 |
57035 |
if (properties == null) |
1456 |
|
{ |
1457 |
0 |
return null; |
1458 |
|
} |
1459 |
57035 |
return properties.get(property); |
1460 |
|
} |
1461 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1462 |
49 |
public void setProperty(String property, String value)... |
1463 |
|
{ |
1464 |
49 |
if (properties == null) |
1465 |
|
{ |
1466 |
0 |
properties = new HashMap<>(); |
1467 |
|
} |
1468 |
49 |
properties.put(property, value); |
1469 |
|
} |
1470 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1471 |
437 |
public boolean hasProperties()... |
1472 |
|
{ |
1473 |
437 |
return properties != null && properties.size() > 0; |
1474 |
|
} |
1475 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1476 |
1 |
public Collection<String> getProperties()... |
1477 |
|
{ |
1478 |
1 |
if (properties == null) |
1479 |
|
{ |
1480 |
0 |
return Collections.emptyList(); |
1481 |
|
} |
1482 |
1 |
return properties.keySet(); |
1483 |
|
} |
1484 |
|
|
1485 |
|
|
1486 |
|
|
1487 |
|
|
1488 |
|
|
1489 |
|
@param |
1490 |
|
@return |
1491 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1492 |
112641 |
public Annotation getAnnotationForPosition(int position)... |
1493 |
|
{ |
1494 |
112641 |
return sequenceMapping == null ? null : sequenceMapping.get(position); |
1495 |
|
|
1496 |
|
} |
1497 |
|
|
1498 |
|
|
1499 |
|
|
1500 |
|
|
1501 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1502 |
38555 |
protected final void setAnnotationId()... |
1503 |
|
{ |
1504 |
38555 |
this.annotationId = ANNOTATION_ID_PREFIX + Long.toString(nextId()); |
1505 |
|
} |
1506 |
|
|
1507 |
|
|
1508 |
|
|
1509 |
|
|
1510 |
|
|
1511 |
|
@param |
1512 |
|
@return |
1513 |
|
|
|
|
| 91.3% |
Uncovered Elements: 4 (46) |
Complexity: 12 |
Complexity Density: 0.46 |
|
1514 |
43 |
public String getDefaultRnaHelixSymbol(int column)... |
1515 |
|
{ |
1516 |
43 |
String result = "("; |
1517 |
43 |
if (annotations == null) |
1518 |
|
{ |
1519 |
1 |
return result; |
1520 |
|
} |
1521 |
|
|
1522 |
|
|
1523 |
|
|
1524 |
|
|
1525 |
|
|
1526 |
|
|
1527 |
150 |
for (int col = column - 1; col >= 0; col--) |
1528 |
|
{ |
1529 |
142 |
Annotation annotation = annotations[col]; |
1530 |
142 |
if (annotation == null) |
1531 |
|
{ |
1532 |
66 |
continue; |
1533 |
|
} |
1534 |
76 |
String displayed = annotation.displayCharacter; |
1535 |
76 |
if (displayed == null || displayed.length() != 1) |
1536 |
|
{ |
1537 |
0 |
continue; |
1538 |
|
} |
1539 |
76 |
char symbol = displayed.charAt(0); |
1540 |
76 |
if (!Rna.isOpeningParenthesis(symbol)) |
1541 |
|
{ |
1542 |
24 |
continue; |
1543 |
|
} |
1544 |
|
|
1545 |
|
|
1546 |
|
|
1547 |
|
|
1548 |
|
|
1549 |
|
|
1550 |
|
|
1551 |
52 |
String closer = String |
1552 |
|
.valueOf(Rna.getMatchingClosingParenthesis(symbol)); |
1553 |
52 |
String opener = String.valueOf(symbol); |
1554 |
52 |
int count = 0; |
1555 |
256 |
for (int j = col + 1; j < column; j++) |
1556 |
|
{ |
1557 |
204 |
if (annotations[j] != null) |
1558 |
|
{ |
1559 |
90 |
String s = annotations[j].displayCharacter; |
1560 |
90 |
if (closer.equals(s)) |
1561 |
|
{ |
1562 |
18 |
count++; |
1563 |
|
} |
1564 |
72 |
else if (opener.equals(s)) |
1565 |
|
{ |
1566 |
0 |
count--; |
1567 |
|
} |
1568 |
|
} |
1569 |
|
} |
1570 |
52 |
if (count < 1) |
1571 |
|
{ |
1572 |
34 |
return closer; |
1573 |
|
} |
1574 |
|
} |
1575 |
8 |
return result; |
1576 |
|
} |
1577 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1578 |
38555 |
protected static synchronized long nextId()... |
1579 |
|
{ |
1580 |
38555 |
return counter++; |
1581 |
|
} |
1582 |
|
|
1583 |
|
|
1584 |
|
|
1585 |
|
@return |
1586 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1587 |
5 |
public boolean isQuantitative()... |
1588 |
|
{ |
1589 |
5 |
return graphMin < graphMax; |
1590 |
|
} |
1591 |
|
|
1592 |
|
|
1593 |
|
@return |
1594 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1595 |
92099 |
public boolean isForDisplay()... |
1596 |
|
{ |
1597 |
92099 |
return hasData && visible; |
1598 |
|
} |
1599 |
|
|
1600 |
|
|
1601 |
|
|
1602 |
|
|
1603 |
|
|
1604 |
|
@param |
1605 |
|
|
1606 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
1607 |
2 |
public void makeVisibleAnnotation(HiddenColumns hiddenColumns)... |
1608 |
|
{ |
1609 |
2 |
if (annotations != null) |
1610 |
|
{ |
1611 |
1 |
makeVisibleAnnotation(0, annotations.length, hiddenColumns); |
1612 |
|
} |
1613 |
|
} |
1614 |
|
|
1615 |
|
|
1616 |
|
|
1617 |
|
|
1618 |
|
|
1619 |
|
@param |
1620 |
|
|
1621 |
|
@param |
1622 |
|
|
1623 |
|
@param |
1624 |
|
|
1625 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
1626 |
10 |
public void makeVisibleAnnotation(int start, int end,... |
1627 |
|
HiddenColumns hiddenColumns) |
1628 |
|
{ |
1629 |
10 |
if (annotations != null) |
1630 |
|
{ |
1631 |
9 |
if (hiddenColumns.hasHiddenColumns()) |
1632 |
|
{ |
1633 |
3 |
removeHiddenAnnotation(start, end, hiddenColumns); |
1634 |
|
} |
1635 |
|
else |
1636 |
|
{ |
1637 |
6 |
restrict(start, end); |
1638 |
|
} |
1639 |
|
} |
1640 |
|
} |
1641 |
|
|
1642 |
|
|
1643 |
|
|
1644 |
|
|
1645 |
|
@param |
1646 |
|
|
1647 |
|
@param |
1648 |
|
|
1649 |
|
@param |
1650 |
|
|
1651 |
|
|
|
|
| 96.9% |
Uncovered Elements: 1 (32) |
Complexity: 5 |
Complexity Density: 0.21 |
|
1652 |
3 |
private void removeHiddenAnnotation(int start, int end,... |
1653 |
|
HiddenColumns hiddenColumns) |
1654 |
|
{ |
1655 |
|
|
1656 |
3 |
ArrayList<Annotation[]> annels = new ArrayList<>(); |
1657 |
3 |
Annotation[] els = null; |
1658 |
|
|
1659 |
3 |
int w = 0; |
1660 |
|
|
1661 |
3 |
Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start, |
1662 |
|
end + 1, false); |
1663 |
|
|
1664 |
3 |
int copylength; |
1665 |
3 |
int annotationLength; |
1666 |
9 |
while (blocks.hasNext()) |
1667 |
|
{ |
1668 |
6 |
int[] block = blocks.next(); |
1669 |
6 |
annotationLength = block[1] - block[0] + 1; |
1670 |
|
|
1671 |
6 |
if (blocks.hasNext()) |
1672 |
|
{ |
1673 |
|
|
1674 |
3 |
copylength = annotationLength; |
1675 |
|
} |
1676 |
|
else |
1677 |
|
{ |
1678 |
3 |
if (annotationLength + block[0] <= annotations.length) |
1679 |
|
{ |
1680 |
|
|
1681 |
2 |
copylength = annotationLength; |
1682 |
|
} |
1683 |
|
else |
1684 |
|
{ |
1685 |
|
|
1686 |
1 |
copylength = annotations.length - block[0]; |
1687 |
|
} |
1688 |
|
} |
1689 |
|
|
1690 |
6 |
els = new Annotation[annotationLength]; |
1691 |
6 |
annels.add(els); |
1692 |
6 |
System.arraycopy(annotations, block[0], els, 0, copylength); |
1693 |
6 |
w += annotationLength; |
1694 |
|
} |
1695 |
|
|
1696 |
3 |
if (w != 0) |
1697 |
|
{ |
1698 |
3 |
annotations = new Annotation[w]; |
1699 |
|
|
1700 |
3 |
w = 0; |
1701 |
3 |
for (Annotation[] chnk : annels) |
1702 |
|
{ |
1703 |
6 |
System.arraycopy(chnk, 0, annotations, w, chnk.length); |
1704 |
6 |
w += chnk.length; |
1705 |
|
} |
1706 |
|
} |
1707 |
|
} |
1708 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 10 |
Complexity Density: 2 |
|
1709 |
163 |
public static Iterable<AlignmentAnnotation> findAnnotations(... |
1710 |
|
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId, |
1711 |
|
String label) |
1712 |
|
{ |
1713 |
|
|
1714 |
163 |
ArrayList<AlignmentAnnotation> aa = new ArrayList<>(); |
1715 |
163 |
for (AlignmentAnnotation ann : list) |
1716 |
|
{ |
1717 |
1129 |
if ((calcId == null || (ann.getCalcId() != null |
1718 |
|
&& ann.getCalcId().equals(calcId))) |
1719 |
|
&& (seq == null || (ann.sequenceRef != null |
1720 |
|
&& ann.sequenceRef == seq)) |
1721 |
|
&& (label == null |
1722 |
|
|| (ann.label != null && ann.label.equals(label)))) |
1723 |
|
{ |
1724 |
182 |
aa.add(ann); |
1725 |
|
} |
1726 |
|
} |
1727 |
163 |
return aa; |
1728 |
|
} |
1729 |
|
|
1730 |
|
|
1731 |
|
|
1732 |
|
|
1733 |
|
@param |
1734 |
|
|
1735 |
|
@param |
1736 |
|
@return |
1737 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 4 |
Complexity Density: 0.8 |
|
1738 |
0 |
public static boolean hasAnnotation(List<AlignmentAnnotation> list,... |
1739 |
|
String calcId) |
1740 |
|
{ |
1741 |
|
|
1742 |
0 |
if (calcId != null && !"".equals(calcId)) |
1743 |
|
{ |
1744 |
0 |
for (AlignmentAnnotation a : list) |
1745 |
|
{ |
1746 |
0 |
if (a.getCalcId() == calcId) |
1747 |
|
{ |
1748 |
0 |
return true; |
1749 |
|
} |
1750 |
|
} |
1751 |
|
} |
1752 |
0 |
return false; |
1753 |
|
} |
1754 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 6 |
Complexity Density: 0.86 |
|
1755 |
486 |
public static Iterable<AlignmentAnnotation> findAnnotation(... |
1756 |
|
List<AlignmentAnnotation> list, String calcId) |
1757 |
|
{ |
1758 |
|
|
1759 |
486 |
List<AlignmentAnnotation> aa = new ArrayList<>(); |
1760 |
486 |
if (calcId == null) |
1761 |
|
{ |
1762 |
1 |
return aa; |
1763 |
|
} |
1764 |
485 |
for (AlignmentAnnotation a : list) |
1765 |
|
{ |
1766 |
|
|
1767 |
2551 |
if (a.getCalcId() == calcId || (a.getCalcId() != null |
1768 |
|
&& calcId != null && a.getCalcId().equals(calcId))) |
1769 |
|
{ |
1770 |
509 |
aa.add(a); |
1771 |
|
} |
1772 |
|
} |
1773 |
485 |
return aa; |
1774 |
|
} |
1775 |
|
|
1776 |
|
|
1777 |
|
|
1778 |
|
|
1779 |
|
|
1780 |
|
@return |
1781 |
|
|
1782 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1783 |
144 |
public boolean isShowGroupsForContactMatrix()... |
1784 |
|
{ |
1785 |
144 |
return getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS) == null |
1786 |
|
|| "".equals( |
1787 |
|
getProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS)); |
1788 |
|
} |
1789 |
|
|
1790 |
|
|
1791 |
|
|
1792 |
|
|
1793 |
|
@see |
1794 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
1795 |
2 |
public void setShowGroupsForContactMatrix(boolean showGroups)... |
1796 |
|
{ |
1797 |
2 |
setProperty(AlignmentAnnotation.CONTACT_MAP_NOGROUPS, |
1798 |
2 |
showGroups ? "" : "nogroups"); |
1799 |
|
} |
1800 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1801 |
521204 |
public long getNoOfSequencesIncluded()... |
1802 |
|
{ |
1803 |
521204 |
return noOfSequencesIncluded; |
1804 |
|
} |
1805 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1806 |
905 |
public void setNoOfSequencesIncluded(long noOfSequencesIncluded)... |
1807 |
|
{ |
1808 |
905 |
this.noOfSequencesIncluded = noOfSequencesIncluded; |
1809 |
|
} |
1810 |
|
|
1811 |
|
} |