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package jalview.util; |
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import static jalview.util.UrlConstants.DB_ACCESSION; |
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import static jalview.util.UrlConstants.DELIM; |
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import static jalview.util.UrlConstants.SEP; |
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import static jalview.util.UrlConstants.SEQUENCE_ID; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.SequenceI; |
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import java.util.Arrays; |
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import java.util.Collections; |
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import java.util.Comparator; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Vector; |
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| 86.4% |
Uncovered Elements: 36 (264) |
Complexity: 85 |
Complexity Density: 0.57 |
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public class UrlLink |
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{ |
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private static final String SEQUENCEID_PLACEHOLDER = DELIM + SEQUENCE_ID |
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+ DELIM; |
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private static final String ACCESSION_PLACEHOLDER = DELIM + DB_ACCESSION |
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+ DELIM; |
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public static final Comparator<String> LINK_COMPARATOR = new Comparator<String>() |
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{ |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 7 |
Complexity Density: 1 |
|
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118 |
@Override... |
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public int compare(String link1, String link2) |
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{ |
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if (link1 == null || link2 == null) |
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{ |
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return 0; |
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} |
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if (link1.contains(SEQUENCEID_PLACEHOLDER) |
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&& link2.contains(ACCESSION_PLACEHOLDER)) |
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{ |
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return -1; |
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} |
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if (link2.contains(SEQUENCEID_PLACEHOLDER) |
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&& link1.contains(ACCESSION_PLACEHOLDER)) |
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{ |
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return 1; |
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} |
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return String.CASE_INSENSITIVE_ORDER.compare(link1, link2); |
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} |
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}; |
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private static final String EQUALS = "="; |
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private static final String SPACE = " "; |
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private String urlSuffix; |
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private String urlPrefix; |
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private String target; |
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private String label; |
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private String dbname; |
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private String regexReplace; |
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private boolean dynamic = false; |
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private boolean usesDBaccession = false; |
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private String invalidMessage = null; |
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@param |
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| 100% |
Uncovered Elements: 0 (31) |
Complexity: 4 |
Complexity Density: 0.16 |
|
113 |
15399 |
public UrlLink(String link)... |
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{ |
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15399 |
int sep = link.indexOf(SEP); |
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int psqid = link.indexOf(DELIM + DB_ACCESSION); |
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15399 |
int nsqid = link.indexOf(DELIM + SEQUENCE_ID); |
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15399 |
if (psqid > -1) |
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{ |
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15216 |
dynamic = true; |
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15216 |
usesDBaccession = true; |
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15216 |
sep = parseLabel(sep, psqid, link); |
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15216 |
int endOfRegex = parseUrl(link, DB_ACCESSION, psqid, sep); |
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15216 |
parseTarget(link, sep, endOfRegex); |
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} |
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else if (nsqid > -1) |
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{ |
130 |
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dynamic = true; |
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sep = parseLabel(sep, nsqid, link); |
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int endOfRegex = parseUrl(link, SEQUENCE_ID, nsqid, sep); |
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parseTarget(link, sep, endOfRegex); |
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} |
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else |
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{ |
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label = link.substring(0, sep).trim(); |
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143 |
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int lastsep = link.lastIndexOf(SEP); |
144 |
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if (lastsep != sep) |
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{ |
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urlPrefix = link.substring(sep + 1, lastsep).trim(); |
147 |
8 |
target = link.substring(lastsep + 1).trim(); |
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} |
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else |
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{ |
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urlPrefix = link.substring(sep + 1).trim(); |
152 |
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target = label; |
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} |
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155 |
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regexReplace = null; |
156 |
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urlSuffix = null; |
157 |
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} |
158 |
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15399 |
label = label.trim(); |
160 |
15399 |
target = target.trim(); |
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} |
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@param |
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@param |
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170 |
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@param |
171 |
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172 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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15252 |
public UrlLink(String name, String url, String desc)... |
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{ |
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15252 |
this(name + SEP + url + SEP + desc); |
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} |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public String getUrlSuffix()... |
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{ |
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return urlSuffix; |
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} |
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186 |
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187 |
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@return |
188 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public String getUrlPrefix()... |
190 |
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{ |
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return urlPrefix; |
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} |
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194 |
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195 |
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@return |
196 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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32 |
public String getTarget()... |
198 |
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{ |
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return target; |
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} |
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203 |
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@return |
204 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
205 |
135 |
public String getLabel()... |
206 |
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{ |
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return label; |
208 |
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} |
209 |
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| 90% |
Uncovered Elements: 1 (10) |
Complexity: 5 |
Complexity Density: 2.5 |
|
210 |
372 |
public String getUrlWithToken()... |
211 |
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{ |
212 |
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String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID); |
213 |
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214 |
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return urlPrefix |
215 |
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+ (dynamic |
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? (DELIM + var |
217 |
361 |
+ ((regexReplace != null) |
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? EQUALS + regexReplace + EQUALS + DELIM |
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: DELIM)) |
220 |
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: "") |
221 |
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+ ((urlSuffix == null) ? "" : urlSuffix); |
222 |
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} |
223 |
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224 |
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225 |
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@return |
226 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
227 |
80 |
public String getRegexReplace()... |
228 |
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{ |
229 |
80 |
return regexReplace; |
230 |
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} |
231 |
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232 |
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|
233 |
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@return |
234 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
235 |
13 |
public String getInvalidMessage()... |
236 |
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{ |
237 |
13 |
return invalidMessage; |
238 |
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} |
239 |
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240 |
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241 |
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242 |
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243 |
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@return |
244 |
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|
245 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
246 |
104 |
public boolean isValid()... |
247 |
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{ |
248 |
104 |
return invalidMessage == null; |
249 |
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} |
250 |
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251 |
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252 |
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253 |
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@return |
254 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
255 |
6 |
public boolean isDynamic()... |
256 |
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{ |
257 |
6 |
return dynamic; |
258 |
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} |
259 |
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260 |
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261 |
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262 |
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@return |
263 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
264 |
136 |
public boolean usesDBAccession()... |
265 |
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{ |
266 |
136 |
return usesDBaccession; |
267 |
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} |
268 |
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269 |
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270 |
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271 |
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272 |
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@param |
273 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
274 |
44 |
public void setLabel(String newlabel)... |
275 |
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{ |
276 |
44 |
this.label = newlabel; |
277 |
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} |
278 |
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279 |
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280 |
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281 |
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282 |
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@param |
283 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
284 |
6 |
public void setTarget(String desc)... |
285 |
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{ |
286 |
6 |
target = desc; |
287 |
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} |
288 |
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289 |
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290 |
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291 |
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292 |
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@param |
293 |
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@param |
294 |
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295 |
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296 |
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@return |
297 |
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|
298 |
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| 65.2% |
Uncovered Elements: 23 (66) |
Complexity: 19 |
Complexity Density: 0.5 |
|
299 |
55 |
public String[] makeUrls(String idstring, boolean onlyIfMatches)... |
300 |
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{ |
301 |
55 |
if (dynamic) |
302 |
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{ |
303 |
55 |
if (regexReplace != null) |
304 |
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{ |
305 |
8 |
com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex |
306 |
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.perlCode("/" + regexReplace + "/"); |
307 |
8 |
if (rg.search(idstring)) |
308 |
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{ |
309 |
6 |
int ns = rg.numSubs(); |
310 |
6 |
if (ns == 0) |
311 |
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{ |
312 |
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|
313 |
0 |
return new String[] { rg.stringMatched(), |
314 |
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urlPrefix + rg.stringMatched() + urlSuffix }; |
315 |
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} |
316 |
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317 |
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318 |
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319 |
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320 |
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else |
321 |
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{ |
322 |
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323 |
24 |
for (int s = 0; s <= rg.numSubs(); s++) |
324 |
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{ |
325 |
18 |
jalview.bin.Console.errPrintln("Sub " + s + " : " |
326 |
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+ rg.matchedFrom(s) + " : " + rg.matchedTo(s) + " : '" |
327 |
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+ rg.stringMatched(s) + "'"); |
328 |
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} |
329 |
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|
330 |
6 |
Vector<String> subs = new Vector<>(); |
331 |
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|
332 |
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|
333 |
6 |
int s = 0; |
334 |
24 |
while (s <= ns) |
335 |
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{ |
336 |
18 |
if (s + 1 <= ns && rg.matchedTo(s) > -1 |
337 |
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&& rg.matchedTo(s + 1) > -1 |
338 |
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&& rg.matchedTo(s + 1) < rg.matchedTo(s)) |
339 |
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{ |
340 |
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|
341 |
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|
342 |
0 |
int r = s + 1; |
343 |
0 |
String mtch = ""; |
344 |
0 |
while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s)) |
345 |
|
{ |
346 |
0 |
if (rg.matchedFrom(r) > -1) |
347 |
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{ |
348 |
0 |
mtch += rg.stringMatched(r); |
349 |
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} |
350 |
0 |
r++; |
351 |
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} |
352 |
0 |
if (mtch.length() > 0) |
353 |
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{ |
354 |
0 |
subs.addElement(mtch); |
355 |
0 |
subs.addElement(urlPrefix + mtch + urlSuffix); |
356 |
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} |
357 |
0 |
s = r; |
358 |
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} |
359 |
|
else |
360 |
|
{ |
361 |
18 |
if (rg.matchedFrom(s) > -1) |
362 |
|
{ |
363 |
6 |
subs.addElement(rg.stringMatched(s)); |
364 |
6 |
subs.addElement( |
365 |
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urlPrefix + rg.stringMatched(s) + urlSuffix); |
366 |
|
} |
367 |
18 |
s++; |
368 |
|
} |
369 |
|
} |
370 |
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|
371 |
6 |
String[] res = new String[subs.size()]; |
372 |
18 |
for (int r = 0, rs = subs.size(); r < rs; r++) |
373 |
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{ |
374 |
12 |
res[r] = subs.elementAt(r); |
375 |
|
} |
376 |
6 |
subs.removeAllElements(); |
377 |
6 |
return res; |
378 |
|
} |
379 |
|
} |
380 |
2 |
if (onlyIfMatches) |
381 |
|
{ |
382 |
1 |
return null; |
383 |
|
} |
384 |
|
} |
385 |
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|
386 |
48 |
if (idstring.indexOf(SEP) > -1) |
387 |
|
{ |
388 |
0 |
idstring = idstring.substring(idstring.lastIndexOf(SEP) + 1); |
389 |
|
} |
390 |
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|
391 |
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|
392 |
48 |
return new String[] { idstring, urlPrefix + idstring + urlSuffix }; |
393 |
|
} |
394 |
|
else |
395 |
|
{ |
396 |
0 |
return new String[] { "", urlPrefix }; |
397 |
|
} |
398 |
|
} |
399 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
400 |
286 |
@Override... |
401 |
|
public String toString() |
402 |
|
{ |
403 |
286 |
return label + SEP + getUrlWithToken(); |
404 |
|
} |
405 |
|
|
406 |
|
|
407 |
|
@return |
408 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
409 |
17 |
public String toStringWithTarget()... |
410 |
|
{ |
411 |
17 |
return label + SEP + getUrlWithToken() + SEP + target; |
412 |
|
} |
413 |
|
|
414 |
|
|
415 |
|
|
416 |
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|
417 |
|
@param |
418 |
|
|
419 |
|
@param |
420 |
|
|
421 |
|
@param |
422 |
|
|
423 |
|
@return |
424 |
|
|
|
|
| 88.9% |
Uncovered Elements: 1 (9) |
Complexity: 3 |
Complexity Density: 0.43 |
|
425 |
15388 |
protected int parseLabel(int firstSep, int psqid, String link)... |
426 |
|
{ |
427 |
15388 |
int p = firstSep; |
428 |
15388 |
int sep = firstSep; |
429 |
15388 |
do |
430 |
|
{ |
431 |
15388 |
sep = p; |
432 |
15388 |
p = link.indexOf(SEP, sep + 1); |
433 |
15388 |
} while (p > sep && p < psqid); |
434 |
|
|
435 |
|
|
436 |
15388 |
label = link.substring(0, sep); |
437 |
|
|
438 |
15388 |
return sep; |
439 |
|
} |
440 |
|
|
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
@param |
445 |
|
|
446 |
|
@param |
447 |
|
|
448 |
|
@param |
449 |
|
|
450 |
|
|
|
|
| 85.7% |
Uncovered Elements: 2 (14) |
Complexity: 5 |
Complexity Density: 0.62 |
|
451 |
15388 |
protected void parseTarget(String link, int sep, int endOfRegex)... |
452 |
|
{ |
453 |
15388 |
int lastsep = link.lastIndexOf(SEP); |
454 |
|
|
455 |
15388 |
if ((lastsep != sep) && (lastsep > endOfRegex)) |
456 |
|
{ |
457 |
|
|
458 |
15245 |
target = link.substring(lastsep + 1).trim(); |
459 |
|
} |
460 |
|
else |
461 |
|
{ |
462 |
143 |
target = label; |
463 |
|
} |
464 |
|
|
465 |
15388 |
if (target.indexOf(SEP) > -1) |
466 |
|
{ |
467 |
|
|
468 |
0 |
target = target.substring(0, target.indexOf(SEP)); |
469 |
|
} |
470 |
15388 |
else if (target.indexOf(SPACE) > 2) |
471 |
|
{ |
472 |
|
|
473 |
94 |
target = target.substring(0, target.indexOf(SPACE)); |
474 |
|
} |
475 |
|
} |
476 |
|
|
477 |
|
|
478 |
|
|
479 |
|
|
480 |
|
@param |
481 |
|
|
482 |
|
@param |
483 |
|
|
484 |
|
@param |
485 |
|
|
486 |
|
@param |
487 |
|
|
488 |
|
@return |
489 |
|
|
|
|
| 96.7% |
Uncovered Elements: 1 (30) |
Complexity: 7 |
Complexity Density: 0.32 |
|
490 |
15388 |
protected int parseUrl(String link, String varName, int sqidPos, int sep)... |
491 |
|
{ |
492 |
15388 |
urlPrefix = link.substring(sep + 1, sqidPos).trim(); |
493 |
|
|
494 |
|
|
495 |
15388 |
String startDelimiter = DELIM + varName + "=/"; |
496 |
|
|
497 |
|
|
498 |
15388 |
String endDelimiter = "/=" + DELIM; |
499 |
|
|
500 |
15388 |
int startLength = startDelimiter.length(); |
501 |
|
|
502 |
|
|
503 |
15388 |
int p = link.indexOf(endDelimiter, sqidPos + startLength); |
504 |
|
|
505 |
15388 |
if (link.indexOf(startDelimiter) == sqidPos |
506 |
|
&& (p > sqidPos + startLength)) |
507 |
|
{ |
508 |
|
|
509 |
4 |
urlSuffix = link.substring(p + endDelimiter.length()); |
510 |
4 |
regexReplace = link.substring(sqidPos + startLength, p); |
511 |
4 |
try |
512 |
|
{ |
513 |
4 |
com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex |
514 |
|
.perlCode("/" + regexReplace + "/"); |
515 |
4 |
if (rg == null) |
516 |
|
{ |
517 |
1 |
invalidMessage = "Invalid Regular Expression : '" + regexReplace |
518 |
|
+ "'\n"; |
519 |
|
} |
520 |
|
} catch (Exception e) |
521 |
|
{ |
522 |
0 |
invalidMessage = "Invalid Regular Expression : '" + regexReplace |
523 |
|
+ "'\n"; |
524 |
|
} |
525 |
|
} |
526 |
|
else |
527 |
|
{ |
528 |
|
|
529 |
15384 |
regexReplace = null; |
530 |
|
|
531 |
15384 |
if (link.indexOf(DELIM + varName + DELIM) == sqidPos) |
532 |
|
{ |
533 |
15381 |
int lastsep = link.lastIndexOf(SEP); |
534 |
15381 |
if (lastsep < sqidPos + startLength - 1) |
535 |
|
{ |
536 |
|
|
537 |
139 |
lastsep = link.length(); |
538 |
|
} |
539 |
15381 |
urlSuffix = link.substring(sqidPos + startLength - 1, lastsep) |
540 |
|
.trim(); |
541 |
15381 |
regexReplace = null; |
542 |
|
} |
543 |
|
else |
544 |
|
{ |
545 |
3 |
invalidMessage = "Warning: invalid regex structure for URL link : " |
546 |
|
+ link; |
547 |
|
} |
548 |
|
} |
549 |
|
|
550 |
15388 |
return p; |
551 |
|
} |
552 |
|
|
553 |
|
|
554 |
|
|
555 |
|
|
556 |
|
@param |
557 |
|
|
558 |
|
@param |
559 |
|
|
560 |
|
|
561 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
562 |
97 |
public void createLinksFromSeq(final SequenceI seq,... |
563 |
|
Map<String, List<String>> linkset) |
564 |
|
{ |
565 |
97 |
if (seq != null && dynamic) |
566 |
|
{ |
567 |
94 |
createDynamicLinks(seq, linkset); |
568 |
|
} |
569 |
|
else |
570 |
|
{ |
571 |
3 |
createStaticLink(linkset); |
572 |
|
} |
573 |
|
} |
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
@param |
579 |
|
|
580 |
|
|
581 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
582 |
3 |
protected void createStaticLink(Map<String, List<String>> linkset)... |
583 |
|
{ |
584 |
3 |
if (!linkset.containsKey(label + SEP + getUrlPrefix())) |
585 |
|
{ |
586 |
|
|
587 |
3 |
linkset.put(label + SEP + getUrlPrefix(), |
588 |
|
Arrays.asList(target, label, null, getUrlPrefix())); |
589 |
|
} |
590 |
|
} |
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
595 |
|
@param |
596 |
|
|
597 |
|
@param |
598 |
|
|
599 |
|
|
600 |
|
|
|
|
| 80% |
Uncovered Elements: 5 (25) |
Complexity: 10 |
Complexity Density: 0.77 |
|
601 |
94 |
protected void createDynamicLinks(final SequenceI seq,... |
602 |
|
Map<String, List<String>> linkset) |
603 |
|
{ |
604 |
|
|
605 |
94 |
String id = seq.getName(); |
606 |
94 |
String descr = seq.getDescription(); |
607 |
94 |
if (descr != null && descr.length() < 1) |
608 |
|
{ |
609 |
0 |
descr = null; |
610 |
|
} |
611 |
|
|
612 |
94 |
if (usesDBAccession()) |
613 |
|
{ |
614 |
|
|
615 |
70 |
List<DBRefEntry> dbr = DBRefUtils.selectRefs(seq.getDBRefs(), |
616 |
|
new String[] |
617 |
|
{ target }); |
618 |
|
|
619 |
|
|
620 |
70 |
if (dbr != null) |
621 |
|
{ |
622 |
16 |
for (int r = 0, nd = dbr.size(); r < nd; r++) |
623 |
|
{ |
624 |
|
|
625 |
10 |
createBareURLLink(dbr.get(r).getAccessionId(), true, linkset); |
626 |
|
} |
627 |
|
} |
628 |
|
} |
629 |
24 |
else if (!usesDBAccession() && id != null) |
630 |
|
{ |
631 |
|
|
632 |
24 |
createBareURLLink(id, false, linkset); |
633 |
|
} |
634 |
|
|
635 |
|
|
636 |
|
|
637 |
94 |
if (descr != null && getRegexReplace() != null) |
638 |
|
{ |
639 |
|
|
640 |
0 |
createBareURLLink(descr, false, linkset); |
641 |
|
} |
642 |
|
} |
643 |
|
|
644 |
|
|
645 |
|
|
646 |
|
|
647 |
|
|
|
|
| 87.5% |
Uncovered Elements: 2 (16) |
Complexity: 5 |
Complexity Density: 0.62 |
|
648 |
34 |
protected void createBareURLLink(String id, Boolean combineLabel,... |
649 |
|
Map<String, List<String>> linkset) |
650 |
|
{ |
651 |
34 |
String[] urls = makeUrls(id, true); |
652 |
34 |
if (urls != null) |
653 |
|
{ |
654 |
68 |
for (int u = 0; u < urls.length; u += 2) |
655 |
|
{ |
656 |
34 |
if (!linkset.containsKey(urls[u] + SEP + urls[u + 1])) |
657 |
|
{ |
658 |
34 |
String thisLabel = label; |
659 |
34 |
if (combineLabel) |
660 |
|
{ |
661 |
|
|
662 |
10 |
thisLabel = label + SEP + urls[u]; |
663 |
|
} |
664 |
|
|
665 |
34 |
linkset.put(urls[u] + SEP + urls[u + 1], |
666 |
|
Arrays.asList(target, thisLabel, urls[u], urls[u + 1])); |
667 |
|
} |
668 |
|
} |
669 |
|
} |
670 |
|
} |
671 |
|
|
672 |
|
|
673 |
|
|
674 |
|
|
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
|
679 |
|
|
680 |
|
|
681 |
|
@param |
682 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
683 |
23 |
public static void sort(List<String> nlinks)... |
684 |
|
{ |
685 |
23 |
Collections.sort(nlinks, LINK_COMPARATOR); |
686 |
|
} |
687 |
|
} |