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package jalview.io; |
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import java.util.Collection; |
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import java.util.Comparator; |
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import java.util.LinkedHashMap; |
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import java.util.List; |
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import java.util.Map; |
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import jalview.api.FeatureColourI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.GeneLociI; |
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import jalview.datamodel.MappedFeatures; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.util.MessageManager; |
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import jalview.util.StringUtils; |
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import jalview.util.UrlLink; |
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import jalview.viewmodel.seqfeatures.FeatureRendererModel; |
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@author |
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| 81.1% |
Uncovered Elements: 58 (307) |
Complexity: 85 |
Complexity Density: 0.46 |
|
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public class SequenceAnnotationReport |
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{ |
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private static final int MAX_DESCRIPTION_LENGTH = 40; |
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private static final String COMMA = ","; |
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private static final String ELLIPSIS = "..."; |
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private static final int MAX_REFS_PER_SOURCE = 4; |
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private static final int MAX_SOURCES = 40; |
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private static String linkImageURL; |
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private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>() |
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{ |
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| 77.8% |
Uncovered Elements: 8 (36) |
Complexity: 12 |
Complexity Density: 0.67 |
|
69 |
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@Override... |
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public int compare(DBRefEntry ref1, DBRefEntry ref2) |
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{ |
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if (ref1 instanceof GeneLociI) |
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{ |
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0 |
return -1; |
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} |
76 |
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if (ref2 instanceof GeneLociI) |
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{ |
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0 |
return 1; |
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} |
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String s1 = ref1.getSource(); |
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String s2 = ref2.getSource(); |
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boolean s1Primary = DBRefSource.isPrimarySource(s1); |
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boolean s2Primary = DBRefSource.isPrimarySource(s2); |
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if (s1Primary && !s2Primary) |
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{ |
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return -1; |
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} |
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if (!s1Primary && s2Primary) |
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{ |
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return 1; |
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} |
92 |
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int comp = s1 == null ? -1 : (s2 == null ? 1 : s1 |
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.compareToIgnoreCase(s2)); |
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if (comp == 0) |
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{ |
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String a1 = ref1.getAccessionId(); |
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String a2 = ref2.getAccessionId(); |
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comp = a1 == null ? -1 : (a2 == null ? 1 : a1 |
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.compareToIgnoreCase(a2)); |
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} |
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return comp; |
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} |
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}; |
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private boolean forTooltip; |
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@param |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
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public SequenceAnnotationReport(boolean isForTooltip)... |
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{ |
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this.forTooltip = isForTooltip; |
135 |
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if (linkImageURL == null) |
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{ |
137 |
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linkImageURL = getClass().getResource("/images/link.gif").toString(); |
138 |
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} |
139 |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 77.8% |
Uncovered Elements: 2 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
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1 |
public int appendFeatures(final StringBuilder sb,... |
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int residuePos, List<SequenceFeature> features, |
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FeatureRendererModel fr, int maxlength) |
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{ |
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for (int i = 0; i < features.size(); i++) |
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{ |
157 |
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SequenceFeature feature = features.get(i); |
158 |
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if (appendFeature(sb, residuePos, fr, feature, null, maxlength)) |
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{ |
160 |
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return features.size() - i; |
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} |
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} |
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return 0; |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
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public int appendFeatures(StringBuilder sb, int residuePos,... |
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MappedFeatures mf, FeatureRendererModel fr, int maxlength) |
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{ |
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for (int i = 0; i < mf.features.size(); i++) |
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{ |
182 |
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SequenceFeature feature = mf.features.get(i); |
183 |
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if (appendFeature(sb, residuePos, fr, feature, mf, maxlength)) |
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{ |
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return mf.features.size() - i; |
186 |
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} |
187 |
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} |
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return 0; |
189 |
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} |
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192 |
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@param |
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@param |
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@param |
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@param |
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| 96.7% |
Uncovered Elements: 3 (90) |
Complexity: 25 |
Complexity Density: 0.46 |
|
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41 |
boolean appendFeature(final StringBuilder sb0, int rpos,... |
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FeatureRendererModel fr, SequenceFeature feature, |
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MappedFeatures mf, int maxlength) |
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{ |
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int begin = feature.getBegin(); |
204 |
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int end = feature.getEnd(); |
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206 |
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207 |
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208 |
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209 |
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210 |
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int[] beginRange = null; |
211 |
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int[] endRange = null; |
212 |
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if (mf != null) |
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{ |
214 |
3 |
beginRange = mf.getMappedPositions(begin, begin); |
215 |
3 |
endRange = mf.getMappedPositions(end, end); |
216 |
3 |
if (beginRange == null || endRange == null) |
217 |
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{ |
218 |
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219 |
0 |
return false; |
220 |
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} |
221 |
3 |
begin = beginRange[0]; |
222 |
3 |
end = endRange[endRange.length - 1]; |
223 |
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} |
224 |
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225 |
41 |
StringBuilder sb = new StringBuilder(); |
226 |
41 |
if (feature.isContactFeature()) |
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{ |
228 |
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229 |
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230 |
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3 |
boolean showContact = (mf == null) && (rpos == begin || rpos == end); |
232 |
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boolean showMappedContact = (mf != null) && ((rpos >= beginRange[0] |
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&& rpos <= beginRange[beginRange.length - 1]) |
234 |
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|| (rpos >= endRange[0] |
235 |
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&& rpos <= endRange[endRange.length - 1])); |
236 |
3 |
if (showContact || showMappedContact) |
237 |
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{ |
238 |
2 |
if (sb0.length() > 6) |
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{ |
240 |
1 |
sb.append("<br/>"); |
241 |
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} |
242 |
2 |
sb.append(feature.getType()).append(" ").append(begin).append(":") |
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.append(end); |
244 |
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} |
245 |
3 |
return appendText(sb0, sb, maxlength); |
246 |
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} |
247 |
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248 |
38 |
if (sb0.length() > 6) |
249 |
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{ |
250 |
21 |
sb.append("<br/>"); |
251 |
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} |
252 |
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253 |
38 |
boolean linkOnly = feature.getValue("linkonly") != null; |
254 |
38 |
if (!linkOnly) |
255 |
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{ |
256 |
38 |
sb.append(feature.getType()).append(" "); |
257 |
38 |
if (rpos != 0) |
258 |
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{ |
259 |
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260 |
21 |
sb.append(begin); |
261 |
21 |
if (begin != end) |
262 |
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{ |
263 |
19 |
sb.append(" ").append(end); |
264 |
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} |
265 |
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} |
266 |
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267 |
38 |
String description = feature.getDescription(); |
268 |
38 |
if (description != null && !description.equals(feature.getType())) |
269 |
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{ |
270 |
37 |
description = StringUtils.stripHtmlTags(description); |
271 |
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272 |
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273 |
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274 |
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275 |
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276 |
37 |
int linkindex = description.toLowerCase().indexOf("<a "); |
277 |
37 |
boolean hasLink = linkindex > -1 |
278 |
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&& linkindex < MAX_DESCRIPTION_LENGTH; |
279 |
37 |
if (description.length() > MAX_DESCRIPTION_LENGTH && !hasLink) |
280 |
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{ |
281 |
6 |
description = description.substring(0, MAX_DESCRIPTION_LENGTH) |
282 |
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+ ELLIPSIS; |
283 |
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} |
284 |
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|
285 |
37 |
sb.append("; ").append(description); |
286 |
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} |
287 |
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|
288 |
38 |
if (showScore(feature, fr)) |
289 |
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{ |
290 |
5 |
sb.append(" Score=").append(String.valueOf(feature.getScore())); |
291 |
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} |
292 |
38 |
String status = (String) feature.getValue("status"); |
293 |
38 |
if (status != null && status.length() > 0) |
294 |
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{ |
295 |
2 |
sb.append("; (").append(status).append(")"); |
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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301 |
38 |
if (fr != null) |
302 |
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{ |
303 |
27 |
FeatureColourI fc = fr.getFeatureColours().get(feature.getType()); |
304 |
27 |
if (fc != null && fc.isColourByAttribute()) |
305 |
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{ |
306 |
5 |
String[] attName = fc.getAttributeName(); |
307 |
5 |
String attVal = feature.getValueAsString(attName); |
308 |
5 |
if (attVal != null) |
309 |
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{ |
310 |
4 |
sb.append("; ").append(String.join(":", attName)).append("=") |
311 |
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.append(attVal); |
312 |
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} |
313 |
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} |
314 |
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} |
315 |
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|
316 |
38 |
if (mf != null) |
317 |
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{ |
318 |
3 |
String variants = mf.findProteinVariants(feature); |
319 |
3 |
if (!variants.isEmpty()) |
320 |
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{ |
321 |
1 |
sb.append(" ").append(variants); |
322 |
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} |
323 |
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} |
324 |
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} |
325 |
38 |
return appendText(sb0, sb, maxlength); |
326 |
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} |
327 |
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328 |
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329 |
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330 |
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331 |
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332 |
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333 |
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@param |
334 |
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@param |
335 |
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@param |
336 |
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@return |
337 |
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|
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
|
338 |
41 |
private static boolean appendText(StringBuilder sb0, StringBuilder sb,... |
339 |
|
int maxlength) |
340 |
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{ |
341 |
41 |
if (maxlength == 0 || sb0.length() + sb.length() < maxlength) |
342 |
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{ |
343 |
40 |
sb0.append(sb); |
344 |
40 |
return false; |
345 |
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} |
346 |
1 |
return true; |
347 |
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} |
348 |
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349 |
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350 |
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351 |
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|
352 |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 6 |
Complexity Density: 0.75 |
|
353 |
38 |
boolean showScore(SequenceFeature feature, FeatureRendererModel fr)... |
354 |
|
{ |
355 |
38 |
if (Float.isNaN(feature.getScore())) |
356 |
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{ |
357 |
11 |
return false; |
358 |
|
} |
359 |
27 |
if (fr == null) |
360 |
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{ |
361 |
3 |
return true; |
362 |
|
} |
363 |
24 |
float[][] minMax = fr.getMinMax().get(feature.getType()); |
364 |
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|
365 |
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|
366 |
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|
367 |
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|
368 |
24 |
if (minMax == null || minMax[0] == null || minMax[0][0] == minMax[0][1]) |
369 |
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{ |
370 |
22 |
return false; |
371 |
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} |
372 |
2 |
return true; |
373 |
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} |
374 |
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375 |
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376 |
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377 |
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|
378 |
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|
379 |
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@param |
380 |
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@param |
381 |
|
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| 0% |
Uncovered Elements: 15 (15) |
Complexity: 5 |
Complexity Density: 0.56 |
|
382 |
0 |
void appendLinks(final StringBuffer sb, SequenceFeature feature)... |
383 |
|
{ |
384 |
0 |
if (feature.links != null) |
385 |
|
{ |
386 |
0 |
if (linkImageURL != null) |
387 |
|
{ |
388 |
0 |
sb.append(" <img src=\"" + linkImageURL + "\">"); |
389 |
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} |
390 |
|
else |
391 |
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{ |
392 |
0 |
for (String urlstring : feature.links) |
393 |
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{ |
394 |
0 |
try |
395 |
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{ |
396 |
0 |
for (List<String> urllink : createLinksFrom(null, urlstring)) |
397 |
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{ |
398 |
0 |
sb.append("<br/> <a href=\"" |
399 |
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+ urllink.get(3) |
400 |
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+ "\" target=\"" |
401 |
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+ urllink.get(0) |
402 |
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+ "\">" |
403 |
0 |
+ (urllink.get(0).toLowerCase() |
404 |
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.equals(urllink.get(1).toLowerCase()) ? urllink |
405 |
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.get(0) : (urllink.get(0) + ":" + urllink |
406 |
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.get(1))) |
407 |
|
+ "</a><br/>"); |
408 |
|
} |
409 |
|
} catch (Exception x) |
410 |
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{ |
411 |
0 |
System.err.println("problem when creating links from " |
412 |
|
+ urlstring); |
413 |
0 |
x.printStackTrace(); |
414 |
|
} |
415 |
|
} |
416 |
|
} |
417 |
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|
418 |
|
} |
419 |
|
} |
420 |
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|
421 |
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|
422 |
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|
423 |
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@param |
424 |
|
@param |
425 |
|
@return |
426 |
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|
427 |
|
|
|
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
428 |
0 |
Collection<List<String>> createLinksFrom(SequenceI seq, String link)... |
429 |
|
{ |
430 |
0 |
Map<String, List<String>> urlSets = new LinkedHashMap<>(); |
431 |
0 |
UrlLink urlLink = new UrlLink(link); |
432 |
0 |
if (!urlLink.isValid()) |
433 |
|
{ |
434 |
0 |
System.err.println(urlLink.getInvalidMessage()); |
435 |
0 |
return null; |
436 |
|
} |
437 |
|
|
438 |
0 |
urlLink.createLinksFromSeq(seq, urlSets); |
439 |
|
|
440 |
0 |
return urlSets.values(); |
441 |
|
} |
442 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
443 |
10 |
public void createSequenceAnnotationReport(final StringBuilder tip,... |
444 |
|
SequenceI sequence, boolean showDbRefs, boolean showNpFeats, |
445 |
|
FeatureRendererModel fr) |
446 |
|
{ |
447 |
10 |
createSequenceAnnotationReport(tip, sequence, showDbRefs, showNpFeats, |
448 |
|
fr, false); |
449 |
|
} |
450 |
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|
451 |
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|
452 |
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|
453 |
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|
454 |
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|
455 |
|
@param |
456 |
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|
457 |
|
@param |
458 |
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|
459 |
|
@param |
460 |
|
|
461 |
|
@param |
462 |
|
|
463 |
|
@param |
464 |
|
@param |
465 |
|
@return |
466 |
|
|
|
|
| 92.9% |
Uncovered Elements: 2 (28) |
Complexity: 5 |
Complexity Density: 0.25 |
|
467 |
11 |
int createSequenceAnnotationReport(final StringBuilder sb,... |
468 |
|
SequenceI sequence, boolean showDbRefs, boolean showNpFeats, |
469 |
|
FeatureRendererModel fr, boolean summary) |
470 |
|
{ |
471 |
11 |
String tmp; |
472 |
11 |
sb.append("<i>"); |
473 |
|
|
474 |
11 |
int maxWidth = 0; |
475 |
11 |
if (sequence.getDescription() != null) |
476 |
|
{ |
477 |
10 |
tmp = sequence.getDescription(); |
478 |
10 |
sb.append(tmp); |
479 |
10 |
maxWidth = Math.max(maxWidth, tmp.length()); |
480 |
|
} |
481 |
11 |
SequenceI ds = sequence; |
482 |
11 |
while (ds.getDatasetSequence() != null) |
483 |
|
{ |
484 |
0 |
ds = ds.getDatasetSequence(); |
485 |
|
} |
486 |
|
|
487 |
11 |
if (showDbRefs) |
488 |
|
{ |
489 |
9 |
maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary)); |
490 |
|
} |
491 |
|
|
492 |
|
|
493 |
|
|
494 |
|
|
495 |
11 |
if (showNpFeats) |
496 |
|
{ |
497 |
9 |
for (SequenceFeature sf : sequence.getFeatures() |
498 |
|
.getNonPositionalFeatures()) |
499 |
|
{ |
500 |
17 |
int sz = -sb.length(); |
501 |
17 |
appendFeature(sb, 0, fr, sf, null, 0); |
502 |
17 |
sz += sb.length(); |
503 |
17 |
maxWidth = Math.max(maxWidth, sz); |
504 |
|
} |
505 |
|
} |
506 |
11 |
sb.append("</i>"); |
507 |
11 |
return maxWidth; |
508 |
|
} |
509 |
|
|
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
|
@param |
515 |
|
@param |
516 |
|
@param |
517 |
|
@return |
518 |
|
|
|
|
| 97.1% |
Uncovered Elements: 2 (68) |
Complexity: 16 |
Complexity Density: 0.33 |
|
519 |
9 |
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,... |
520 |
|
boolean summary) |
521 |
|
{ |
522 |
9 |
List<DBRefEntry> dbrefs = ds.getDBRefs(); |
523 |
9 |
if (dbrefs == null) |
524 |
|
{ |
525 |
6 |
return 0; |
526 |
|
} |
527 |
|
|
528 |
|
|
529 |
3 |
dbrefs.sort(comparator); |
530 |
3 |
boolean ellipsis = false; |
531 |
3 |
String source = null; |
532 |
3 |
String lastSource = null; |
533 |
3 |
int countForSource = 0; |
534 |
3 |
int sourceCount = 0; |
535 |
3 |
boolean moreSources = false; |
536 |
3 |
int maxLineLength = 0; |
537 |
3 |
int lineLength = 0; |
538 |
|
|
539 |
3 |
for (DBRefEntry ref : dbrefs) |
540 |
|
{ |
541 |
49 |
source = ref.getSource(); |
542 |
49 |
if (source == null) |
543 |
|
{ |
544 |
|
|
545 |
0 |
continue; |
546 |
|
} |
547 |
49 |
boolean sourceChanged = !source.equals(lastSource); |
548 |
49 |
if (sourceChanged) |
549 |
|
{ |
550 |
45 |
lineLength = 0; |
551 |
45 |
countForSource = 0; |
552 |
45 |
sourceCount++; |
553 |
|
} |
554 |
49 |
if (sourceCount > MAX_SOURCES && summary) |
555 |
|
{ |
556 |
1 |
ellipsis = true; |
557 |
1 |
moreSources = true; |
558 |
1 |
break; |
559 |
|
} |
560 |
48 |
lastSource = source; |
561 |
48 |
countForSource++; |
562 |
48 |
if (countForSource == 1 || !summary) |
563 |
|
{ |
564 |
44 |
sb.append("<br/>"); |
565 |
|
} |
566 |
48 |
if (countForSource <= MAX_REFS_PER_SOURCE || !summary) |
567 |
|
{ |
568 |
47 |
String accessionId = ref.getAccessionId(); |
569 |
47 |
lineLength += accessionId.length() + 1; |
570 |
47 |
if (countForSource > 1 && summary) |
571 |
|
{ |
572 |
3 |
sb.append(", ").append(accessionId); |
573 |
3 |
lineLength++; |
574 |
|
} |
575 |
|
else |
576 |
|
{ |
577 |
44 |
sb.append(source).append(" ").append(accessionId); |
578 |
44 |
lineLength += source.length(); |
579 |
|
} |
580 |
47 |
maxLineLength = Math.max(maxLineLength, lineLength); |
581 |
|
} |
582 |
48 |
if (countForSource == MAX_REFS_PER_SOURCE && summary) |
583 |
|
{ |
584 |
1 |
sb.append(COMMA).append(ELLIPSIS); |
585 |
1 |
ellipsis = true; |
586 |
|
} |
587 |
|
} |
588 |
3 |
if (moreSources) |
589 |
|
{ |
590 |
1 |
sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS); |
591 |
|
} |
592 |
3 |
if (ellipsis) |
593 |
|
{ |
594 |
1 |
sb.append("<br/>("); |
595 |
1 |
sb.append(MessageManager.getString("label.output_seq_details")); |
596 |
1 |
sb.append(")"); |
597 |
|
} |
598 |
|
|
599 |
3 |
return maxLineLength; |
600 |
|
} |
601 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
602 |
0 |
public void createTooltipAnnotationReport(final StringBuilder tip,... |
603 |
|
SequenceI sequence, boolean showDbRefs, boolean showNpFeats, |
604 |
|
FeatureRendererModel fr) |
605 |
|
{ |
606 |
0 |
int maxWidth = createSequenceAnnotationReport(tip, sequence, |
607 |
|
showDbRefs, showNpFeats, fr, true); |
608 |
|
|
609 |
0 |
if (maxWidth > 60) |
610 |
|
{ |
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
} |
615 |
|
} |
616 |
|
} |