| 1 |
|
|
| 2 |
|
|
| 3 |
|
|
| 4 |
|
|
| 5 |
|
|
| 6 |
|
|
| 7 |
|
|
| 8 |
|
|
| 9 |
|
|
| 10 |
|
|
| 11 |
|
|
| 12 |
|
|
| 13 |
|
|
| 14 |
|
|
| 15 |
|
|
| 16 |
|
|
| 17 |
|
|
| 18 |
|
|
| 19 |
|
|
| 20 |
|
|
| 21 |
|
package jalview.bin.argparser; |
| 22 |
|
|
| 23 |
|
import java.io.File; |
| 24 |
|
import java.util.ArrayList; |
| 25 |
|
import java.util.Arrays; |
| 26 |
|
import java.util.Collections; |
| 27 |
|
import java.util.HashMap; |
| 28 |
|
import java.util.HashSet; |
| 29 |
|
import java.util.List; |
| 30 |
|
import java.util.Locale; |
| 31 |
|
import java.util.Map; |
| 32 |
|
import java.util.Set; |
| 33 |
|
|
| 34 |
|
import jalview.bin.Cache; |
| 35 |
|
import jalview.bin.Console; |
| 36 |
|
import jalview.bin.argparser.Arg.Opt; |
| 37 |
|
import jalview.bin.argparser.Arg.Type; |
| 38 |
|
import jalview.util.FileUtils; |
| 39 |
|
|
| 40 |
|
|
| 41 |
|
|
| 42 |
|
|
| 43 |
|
|
| |
|
| 69.5% |
Uncovered Elements: 130 (426) |
Complexity: 159 |
Complexity Density: 0.69 |
|
| 44 |
|
public class ArgValuesMap |
| 45 |
|
{ |
| 46 |
|
private List<ArgInfo> argInfoList = new ArrayList<>(); |
| 47 |
|
|
| 48 |
|
protected Map<Arg, ArgValues> m; |
| 49 |
|
|
| 50 |
|
private String linkedId; |
| 51 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
| 52 |
766 |
protected ArgValuesMap(String linkedId)... |
| 53 |
|
{ |
| 54 |
766 |
this.linkedId = linkedId; |
| 55 |
766 |
this.newMap(); |
| 56 |
|
} |
| 57 |
|
|
| |
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
| 58 |
0 |
protected ArgValuesMap(String linkedId, Map<Arg, ArgValues> map)... |
| 59 |
|
{ |
| 60 |
0 |
this.linkedId = linkedId; |
| 61 |
0 |
this.m = map; |
| 62 |
|
} |
| 63 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 64 |
700 |
public String getLinkedId()... |
| 65 |
|
{ |
| 66 |
700 |
return linkedId; |
| 67 |
|
} |
| 68 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 69 |
0 |
private Map<Arg, ArgValues> getMap()... |
| 70 |
|
{ |
| 71 |
0 |
return m; |
| 72 |
|
} |
| 73 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 74 |
766 |
private void newMap()... |
| 75 |
|
{ |
| 76 |
766 |
m = new HashMap<Arg, ArgValues>(); |
| 77 |
|
} |
| 78 |
|
|
| |
|
| 62.5% |
Uncovered Elements: 3 (8) |
Complexity: 3 |
Complexity Density: 0.75 |
|
| 79 |
1248 |
private void newArg(Arg a)... |
| 80 |
|
{ |
| 81 |
1248 |
if (m == null) |
| 82 |
|
{ |
| 83 |
0 |
newMap(); |
| 84 |
|
} |
| 85 |
1248 |
if (!containsArg(a)) |
| 86 |
|
{ |
| 87 |
1248 |
m.put(a, new ArgValues(a, this)); |
| 88 |
|
} |
| 89 |
|
} |
| 90 |
|
|
| |
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
| 91 |
4919 |
public ArgValues getArgValues(Arg a)... |
| 92 |
|
{ |
| 93 |
4919 |
return m == null ? null : m.get(a); |
| 94 |
|
} |
| 95 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
| 96 |
1394 |
public ArgValues getOrCreateArgValues(Arg a)... |
| 97 |
|
{ |
| 98 |
1394 |
ArgValues avs = m.get(a); |
| 99 |
1394 |
if (avs == null) |
| 100 |
1248 |
newArg(a); |
| 101 |
1394 |
return getArgValues(a); |
| 102 |
|
} |
| 103 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
| 104 |
2500 |
public List<ArgValue> getArgValueList(Arg a)... |
| 105 |
|
{ |
| 106 |
2500 |
ArgValues avs = getArgValues(a); |
| 107 |
2500 |
return avs == null ? new ArrayList<>() : avs.getArgValueList(); |
| 108 |
|
} |
| 109 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 110 |
15 |
public List<ArgValue> getArgValueListFromSubValOrArg(ArgValue av, Arg a,... |
| 111 |
|
SubVals sv) |
| 112 |
|
{ |
| 113 |
15 |
return getArgValueListFromSubValArgOrPrefWithSubstitutionsWithinTypes( |
| 114 |
|
null, a, Position.AFTER, av, sv, null, null, null, true, null); |
| 115 |
|
} |
| 116 |
|
|
| |
|
| 68.7% |
Uncovered Elements: 21 (67) |
Complexity: 24 |
Complexity Density: 0.62 |
|
| 117 |
15 |
public List<ArgValue> getArgValueListFromSubValArgOrPrefWithSubstitutionsWithinTypes(... |
| 118 |
|
ArgParser ap, Arg a, ArgValuesMap.Position pos, ArgValue av, |
| 119 |
|
SubVals sv, String key, String pref, String def, |
| 120 |
|
boolean withinTypes, Type type) |
| 121 |
|
{ |
| 122 |
15 |
if (key == null) |
| 123 |
|
{ |
| 124 |
15 |
key = a.getName(); |
| 125 |
|
} |
| 126 |
15 |
Set<Type> types = new HashSet<>(); |
| 127 |
15 |
if (type == null) |
| 128 |
|
{ |
| 129 |
15 |
types.addAll(Arrays.asList(av.getArg().getTypes())); |
| 130 |
|
} |
| 131 |
|
else |
| 132 |
|
{ |
| 133 |
0 |
types.add(type); |
| 134 |
|
} |
| 135 |
15 |
List<ArgValue> avList = new ArrayList<>(); |
| 136 |
15 |
if (sv != null && sv.has(key) && sv.get(key) != null) |
| 137 |
|
{ |
| 138 |
0 |
String value = ap == null ? sv.get(key) |
| 139 |
|
: sv.getWithSubstitutions(ap, getLinkedId(), key); |
| 140 |
|
|
| 141 |
|
|
| 142 |
|
|
| 143 |
0 |
ArgValue svav = new ArgValue(a, null, null, value, av.getArgIndex(), |
| 144 |
|
false, null, this.getLinkedId()); |
| 145 |
0 |
avList.add(svav); |
| 146 |
|
} |
| 147 |
15 |
else if (containsArg(a)) |
| 148 |
|
{ |
| 149 |
15 |
if (pos == ArgValuesMap.Position.FIRST && getValue(a) != null) |
| 150 |
0 |
avList.add(getArgValue(a)); |
| 151 |
15 |
else if (pos == ArgValuesMap.Position.BEFORE |
| 152 |
|
&& getClosestPreviousArgValueOfArg(av, a) != null) |
| 153 |
|
{ |
| 154 |
0 |
for (ArgValue tmpAv : getArgValues(a).getArgValueList()) |
| 155 |
|
{ |
| 156 |
0 |
if (tmpAv.getArgIndex() >= av.getArgIndex()) |
| 157 |
|
{ |
| 158 |
0 |
continue; |
| 159 |
|
} |
| 160 |
0 |
avList.add(tmpAv); |
| 161 |
|
} |
| 162 |
|
} |
| 163 |
15 |
else if (pos == ArgValuesMap.Position.AFTER |
| 164 |
|
&& getClosestNextArgValueOfArg(av, a, withinTypes) != null) |
| 165 |
|
{ |
| 166 |
15 |
for (ArgValue tmpAv : getArgValues(a).getArgValueList()) |
| 167 |
|
{ |
| 168 |
49 |
if (tmpAv.getArgIndex() <= av.getArgIndex()) |
| 169 |
|
{ |
| 170 |
15 |
continue; |
| 171 |
|
} |
| 172 |
34 |
avList.add(tmpAv); |
| 173 |
|
} |
| 174 |
|
} |
| 175 |
|
} |
| 176 |
|
|
| 177 |
|
|
| 178 |
|
|
| 179 |
15 |
if (withinTypes && !avList.isEmpty()) |
| 180 |
|
{ |
| 181 |
15 |
int nextPrimaryArgOfSameTypeIndex = Integer.MAX_VALUE; |
| 182 |
|
|
| 183 |
15 |
for (Arg tmpA : this.getArgKeys()) |
| 184 |
|
{ |
| 185 |
|
|
| 186 |
|
|
| 187 |
90 |
if (tmpA.hasType(types) && tmpA.hasOption(Opt.PRIMARY)) |
| 188 |
|
{ |
| 189 |
15 |
for (ArgValue tmpAv : getArgValueList(tmpA)) |
| 190 |
|
{ |
| 191 |
27 |
int tmpArgIndex = tmpAv.getArgIndex(); |
| 192 |
27 |
if (tmpArgIndex > av.getArgIndex() |
| 193 |
|
&& tmpArgIndex < nextPrimaryArgOfSameTypeIndex) |
| 194 |
|
{ |
| 195 |
5 |
nextPrimaryArgOfSameTypeIndex = tmpArgIndex; |
| 196 |
|
} |
| 197 |
|
} |
| 198 |
|
} |
| 199 |
|
} |
| 200 |
15 |
List<ArgValue> tmpList = new ArrayList<>(); |
| 201 |
15 |
for (ArgValue tmpAv : avList) |
| 202 |
|
{ |
| 203 |
34 |
int tmpAvIndex = tmpAv.getArgIndex(); |
| 204 |
34 |
if (av.getArgIndex() < tmpAvIndex |
| 205 |
|
&& tmpAvIndex < nextPrimaryArgOfSameTypeIndex) |
| 206 |
|
{ |
| 207 |
23 |
tmpList.add(tmpAv); |
| 208 |
|
} |
| 209 |
|
} |
| 210 |
15 |
avList = tmpList; |
| 211 |
|
} |
| 212 |
|
|
| 213 |
15 |
return avList; |
| 214 |
|
} |
| 215 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 3 |
Complexity Density: 1.5 |
|
| 216 |
1332 |
public ArgValue getArgValue(Arg a)... |
| 217 |
|
{ |
| 218 |
1332 |
List<ArgValue> vals = getArgValueList(a); |
| 219 |
1332 |
return (vals == null || vals.size() == 0) ? null : vals.get(0); |
| 220 |
|
} |
| 221 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
| 222 |
357 |
public String getValue(Arg a)... |
| 223 |
|
{ |
| 224 |
357 |
ArgValue av = getArgValue(a); |
| 225 |
357 |
return av == null ? null : av.getValue(); |
| 226 |
|
} |
| 227 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 228 |
330 |
public List<String> getValues(Arg a)... |
| 229 |
|
{ |
| 230 |
330 |
return toValues(getArgValueList(a)); |
| 231 |
|
} |
| 232 |
|
|
| |
|
| 75% |
Uncovered Elements: 2 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
| 233 |
347 |
public static List<String> toValues(List<ArgValue> avl)... |
| 234 |
|
{ |
| 235 |
347 |
if (avl == null) |
| 236 |
|
{ |
| 237 |
0 |
return null; |
| 238 |
|
} |
| 239 |
347 |
List<String> vl = new ArrayList<>(); |
| 240 |
347 |
for (ArgValue av : avl) |
| 241 |
|
{ |
| 242 |
37 |
vl.add(av.getValue()); |
| 243 |
|
} |
| 244 |
347 |
return vl; |
| 245 |
|
} |
| 246 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 4 |
Complexity Density: 1.33 |
|
| 247 |
5471 |
public boolean containsArg(Arg a)... |
| 248 |
|
{ |
| 249 |
5471 |
if (m == null || !m.containsKey(a)) |
| 250 |
4450 |
return false; |
| 251 |
1021 |
return a.hasOption(Opt.STRING) ? getArgValue(a) != null : true; |
| 252 |
|
} |
| 253 |
|
|
| |
|
| 0% |
Uncovered Elements: 11 (11) |
Complexity: 7 |
Complexity Density: 1 |
|
| 254 |
0 |
public boolean hasValue(Arg a, String val)... |
| 255 |
|
{ |
| 256 |
0 |
if (m == null || !m.containsKey(a)) |
| 257 |
0 |
return false; |
| 258 |
0 |
for (ArgValue av : getArgValueList(a)) |
| 259 |
|
{ |
| 260 |
0 |
String avVal = av.getValue(); |
| 261 |
0 |
if ((val == null && avVal == null) |
| 262 |
|
|| (val != null && val.equals(avVal))) |
| 263 |
|
{ |
| 264 |
0 |
return true; |
| 265 |
|
} |
| 266 |
|
} |
| 267 |
0 |
return false; |
| 268 |
|
} |
| 269 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
| 270 |
566 |
public boolean getBoolean(Arg a)... |
| 271 |
|
{ |
| 272 |
566 |
ArgValues av = getArgValues(a); |
| 273 |
566 |
return av == null ? false : av.getBoolean(); |
| 274 |
|
} |
| 275 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 276 |
422 |
public Set<Arg> getArgKeys()... |
| 277 |
|
{ |
| 278 |
422 |
return m.keySet(); |
| 279 |
|
} |
| 280 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 281 |
7 |
public ArgValue getArgValueOfArgWithSubValKey(Arg a, String svKey)... |
| 282 |
|
{ |
| 283 |
7 |
return getArgValueOfArgWithSubValKey(a, svKey, false); |
| 284 |
|
} |
| 285 |
|
|
| |
|
| 84.2% |
Uncovered Elements: 3 (19) |
Complexity: 6 |
Complexity Density: 0.55 |
|
| 286 |
7 |
public ArgValue getArgValueOfArgWithSubValKey(Arg a, String svKey,... |
| 287 |
|
boolean last) |
| 288 |
|
{ |
| 289 |
7 |
ArgValues avs = this.getArgValues(a); |
| 290 |
7 |
if (avs == null) |
| 291 |
|
{ |
| 292 |
0 |
return null; |
| 293 |
|
} |
| 294 |
7 |
List<ArgValue> compareAvs = avs.getArgValueList(); |
| 295 |
15 |
for (int i = 0; i < compareAvs.size(); i++) |
| 296 |
|
{ |
| 297 |
10 |
int index = last ? compareAvs.size() - 1 - i : i; |
| 298 |
10 |
ArgValue av = compareAvs.get(index); |
| 299 |
10 |
SubVals sv = av.getSubVals(); |
| 300 |
10 |
if (sv.has(svKey) && !sv.get(svKey).equals("false")) |
| 301 |
|
{ |
| 302 |
2 |
return av; |
| 303 |
|
} |
| 304 |
|
} |
| 305 |
5 |
return null; |
| 306 |
|
} |
| 307 |
|
|
| |
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.3 |
|
| 308 |
0 |
public ArgValue getClosestPreviousArgValueOfArg(ArgValue thisAv, Arg a)... |
| 309 |
|
{ |
| 310 |
0 |
ArgValue closestAv = null; |
| 311 |
0 |
int thisArgIndex = thisAv.getArgIndex(); |
| 312 |
0 |
ArgValues compareAvs = this.getArgValues(a); |
| 313 |
0 |
int closestPreviousIndex = -1; |
| 314 |
0 |
for (ArgValue av : compareAvs.getArgValueList()) |
| 315 |
|
{ |
| 316 |
0 |
int argIndex = av.getArgIndex(); |
| 317 |
0 |
if (argIndex < thisArgIndex && argIndex > closestPreviousIndex) |
| 318 |
|
{ |
| 319 |
0 |
closestPreviousIndex = argIndex; |
| 320 |
0 |
closestAv = av; |
| 321 |
|
} |
| 322 |
|
} |
| 323 |
0 |
return closestAv; |
| 324 |
|
} |
| 325 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (34) |
Complexity: 11 |
Complexity Density: 0.5 |
|
| 326 |
343 |
public ArgValue getClosestNextArgValueOfArg(ArgValue thisAv, Arg a,... |
| 327 |
|
boolean withinTypes) |
| 328 |
|
{ |
| 329 |
|
|
| 330 |
|
|
| 331 |
|
|
| 332 |
343 |
ArgValue closestAv = null; |
| 333 |
343 |
int thisArgIndex = thisAv.getArgIndex(); |
| 334 |
343 |
if (!containsArg(a)) |
| 335 |
33 |
return null; |
| 336 |
310 |
ArgValues compareAvs = this.getArgValues(a); |
| 337 |
310 |
int closestNextIndex = Integer.MAX_VALUE; |
| 338 |
310 |
for (ArgValue av : compareAvs.getArgValueList()) |
| 339 |
|
{ |
| 340 |
782 |
int argIndex = av.getArgIndex(); |
| 341 |
782 |
if (argIndex > thisArgIndex && argIndex < closestNextIndex) |
| 342 |
|
{ |
| 343 |
303 |
closestNextIndex = argIndex; |
| 344 |
303 |
closestAv = av; |
| 345 |
|
} |
| 346 |
|
} |
| 347 |
|
|
| 348 |
|
|
| 349 |
|
|
| 350 |
310 |
if (withinTypes && closestAv != null) |
| 351 |
|
{ |
| 352 |
303 |
int nextPrimaryArgOfSameTypeIndex = Integer.MAX_VALUE; |
| 353 |
303 |
for (Arg tmpA : this.getArgKeys()) |
| 354 |
|
{ |
| 355 |
|
|
| 356 |
2208 |
if (tmpA.sharesType(a) && tmpA.hasOption(Opt.PRIMARY)) |
| 357 |
|
{ |
| 358 |
310 |
for (ArgValue tmpAv : getArgValueList(tmpA)) |
| 359 |
|
{ |
| 360 |
1016 |
int tmpArgIndex = tmpAv.getArgIndex(); |
| 361 |
1016 |
if (tmpArgIndex > thisArgIndex |
| 362 |
|
&& tmpArgIndex < nextPrimaryArgOfSameTypeIndex) |
| 363 |
|
{ |
| 364 |
147 |
nextPrimaryArgOfSameTypeIndex = tmpArgIndex; |
| 365 |
|
} |
| 366 |
|
} |
| 367 |
|
} |
| 368 |
|
} |
| 369 |
303 |
if (nextPrimaryArgOfSameTypeIndex < closestAv.getArgIndex()) |
| 370 |
|
{ |
| 371 |
|
|
| 372 |
22 |
return null; |
| 373 |
|
} |
| 374 |
|
} |
| 375 |
|
|
| 376 |
288 |
return closestAv; |
| 377 |
|
} |
| 378 |
|
|
| 379 |
|
|
| |
|
| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
| 380 |
0 |
public ArgValue[] getArgValuesReferringTo(String key, String value, Arg a)... |
| 381 |
|
{ |
| 382 |
|
|
| 383 |
|
|
| 384 |
|
|
| 385 |
0 |
List<ArgValue> avList = new ArrayList<>(); |
| 386 |
0 |
Arg[] args = a == null ? (Arg[]) this.getMap().keySet().toArray() |
| 387 |
|
: new Arg[] |
| 388 |
|
{ a }; |
| 389 |
0 |
for (Arg keyArg : args) |
| 390 |
|
{ |
| 391 |
0 |
for (ArgValue av : this.getArgValueList(keyArg)) |
| 392 |
|
{ |
| 393 |
|
|
| 394 |
|
} |
| 395 |
|
} |
| 396 |
0 |
return (ArgValue[]) avList.toArray(); |
| 397 |
|
} |
| 398 |
|
|
| |
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
| 399 |
0 |
public boolean hasId(Arg a, String id)... |
| 400 |
|
{ |
| 401 |
0 |
ArgValues avs = this.getArgValues(a); |
| 402 |
0 |
return avs == null ? false : avs.hasId(id); |
| 403 |
|
} |
| 404 |
|
|
| |
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 1 |
|
| 405 |
0 |
public ArgValue getId(Arg a, String id)... |
| 406 |
|
{ |
| 407 |
0 |
ArgValues avs = this.getArgValues(a); |
| 408 |
0 |
return avs == null ? null : avs.getId(id); |
| 409 |
|
} |
| 410 |
|
|
| 411 |
|
|
| 412 |
|
|
| 413 |
|
|
| 414 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 415 |
74 |
public String getBasename()... |
| 416 |
|
{ |
| 417 |
74 |
return getDirBasenameOrExtension(false, false, false); |
| 418 |
|
} |
| 419 |
|
|
| 420 |
|
|
| 421 |
|
|
| 422 |
|
|
| 423 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 424 |
0 |
public String getExtension()... |
| 425 |
|
{ |
| 426 |
0 |
return getDirBasenameOrExtension(false, true, false); |
| 427 |
|
} |
| 428 |
|
|
| 429 |
|
|
| 430 |
|
|
| 431 |
|
|
| 432 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 433 |
86 |
public String getDirname()... |
| 434 |
|
{ |
| 435 |
86 |
return getDirBasenameOrExtension(true, false, false); |
| 436 |
|
} |
| 437 |
|
|
| |
|
| 87% |
Uncovered Elements: 3 (23) |
Complexity: 7 |
Complexity Density: 0.54 |
|
| 438 |
160 |
public String getDirBasenameOrExtension(boolean dirname,... |
| 439 |
|
boolean extension, boolean absoluteDirname) |
| 440 |
|
{ |
| 441 |
160 |
String filename = null; |
| 442 |
160 |
String appendVal = getValue(Arg.APPEND); |
| 443 |
160 |
String openVal = getValue(Arg.OPEN); |
| 444 |
160 |
if (appendVal != null) |
| 445 |
28 |
filename = appendVal; |
| 446 |
160 |
if (filename == null && openVal != null) |
| 447 |
132 |
filename = openVal; |
| 448 |
160 |
if (filename == null) |
| 449 |
0 |
return null; |
| 450 |
|
|
| 451 |
160 |
File file = new File(filename); |
| 452 |
160 |
if (dirname) |
| 453 |
|
{ |
| 454 |
86 |
return FileUtils.getDirname(file); |
| 455 |
|
} |
| 456 |
74 |
return extension ? FileUtils.getExtension(file) |
| 457 |
|
: FileUtils.getBasename(file); |
| 458 |
|
} |
| 459 |
|
|
| 460 |
|
|
| 461 |
|
|
| 462 |
|
|
| |
|
| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
| 463 |
104 |
public boolean hasArgWithOption(Opt o)... |
| 464 |
|
{ |
| 465 |
104 |
for (Arg a : getArgKeys()) |
| 466 |
|
{ |
| 467 |
130 |
if (a.hasOption(o)) |
| 468 |
104 |
return true; |
| 469 |
|
} |
| 470 |
0 |
return false; |
| 471 |
|
} |
| 472 |
|
|
| 473 |
|
|
| 474 |
|
|
| 475 |
|
|
| 476 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 477 |
0 |
public void addArgInfo(Arg arg, String value, SubVals subVals,... |
| 478 |
|
int argIndex) |
| 479 |
|
{ |
| 480 |
0 |
argInfoList.add(new ArgInfo(arg, value, subVals, argIndex)); |
| 481 |
|
} |
| 482 |
|
|
| |
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
| 483 |
0 |
public List<ArgInfo> getArgInfoList()... |
| 484 |
|
{ |
| 485 |
0 |
Collections.sort(argInfoList); |
| 486 |
0 |
return argInfoList; |
| 487 |
|
} |
| 488 |
|
|
| 489 |
|
|
| 490 |
|
|
| 491 |
|
|
| |
|
| 42.9% |
Uncovered Elements: 8 (14) |
Complexity: 6 |
Complexity Density: 0.75 |
|
| 492 |
330 |
public List<String> getValuesFromSubValOrArgs(ArgParser ap, Arg a,... |
| 493 |
|
SubVals sv) |
| 494 |
|
{ |
| 495 |
330 |
List<String> vals = new ArrayList<>(); |
| 496 |
330 |
String key = a.getName(); |
| 497 |
330 |
if (sv != null && sv.has(key) && sv.get(key) != null) |
| 498 |
|
{ |
| 499 |
0 |
String value = ap == null ? sv.get(key) |
| 500 |
|
: sv.getWithSubstitutions(ap, getLinkedId(), key); |
| 501 |
0 |
if (value != null) |
| 502 |
|
{ |
| 503 |
0 |
vals.add(value); |
| 504 |
|
} |
| 505 |
|
} |
| 506 |
330 |
vals.addAll(getValues(a)); |
| 507 |
330 |
return vals; |
| 508 |
|
} |
| 509 |
|
|
| 510 |
|
|
| 511 |
|
|
| 512 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 513 |
524 |
public String getValueFromSubValOrArg(ArgValue av, Arg a, SubVals sv)... |
| 514 |
|
{ |
| 515 |
524 |
return getFromSubValArgOrPref(av, a, sv, null, null, null); |
| 516 |
|
} |
| 517 |
|
|
| 518 |
|
|
| 519 |
|
|
| 520 |
|
|
| 521 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 522 |
854 |
public String getFromSubValArgOrPref(ArgValue av, Arg a, SubVals sv,... |
| 523 |
|
String key, String pref, String def) |
| 524 |
|
{ |
| 525 |
854 |
return getFromSubValArgOrPref(a, Position.AFTER, av, sv, key, pref, |
| 526 |
|
def); |
| 527 |
|
} |
| 528 |
|
|
| 529 |
|
|
| 530 |
|
|
| 531 |
|
|
| 532 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 533 |
923 |
public String getFromSubValArgOrPref(Arg a, Position pos, ArgValue av,... |
| 534 |
|
SubVals sv, String key, String pref, String def) |
| 535 |
|
{ |
| 536 |
923 |
return getFromSubValArgOrPrefWithSubstitutions(null, a, pos, av, sv, |
| 537 |
|
key, pref, def); |
| 538 |
|
} |
| 539 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 540 |
1100 |
public String getFromSubValArgOrPrefWithSubstitutions(ArgParser ap, Arg a,... |
| 541 |
|
Position pos, ArgValue av, SubVals sv, String key, String pref, |
| 542 |
|
String def) |
| 543 |
|
{ |
| 544 |
1100 |
return getFromSubValArgOrPrefWithSubstitutionsWithinTypes(ap, a, pos, |
| 545 |
|
av, sv, key, pref, def, true); |
| 546 |
|
} |
| 547 |
|
|
| |
|
| 90% |
Uncovered Elements: 5 (50) |
Complexity: 23 |
Complexity Density: 0.96 |
|
| 548 |
1100 |
public String getFromSubValArgOrPrefWithSubstitutionsWithinTypes(... |
| 549 |
|
ArgParser ap, Arg a, Position pos, ArgValue av, SubVals sv, |
| 550 |
|
String key, String pref, String def, boolean withinTypes) |
| 551 |
|
{ |
| 552 |
1100 |
if (key == null) |
| 553 |
1100 |
key = a.getName(); |
| 554 |
1100 |
String value = null; |
| 555 |
1100 |
if (sv != null && sv.has(key) && sv.get(key) != null) |
| 556 |
|
{ |
| 557 |
12 |
value = ap == null ? sv.get(key) |
| 558 |
|
: sv.getWithSubstitutions(ap, getLinkedId(), key); |
| 559 |
|
} |
| 560 |
1088 |
else if (containsArg(a)) |
| 561 |
|
{ |
| 562 |
149 |
if (pos == ArgValuesMap.Position.FIRST && getValue(a) != null) |
| 563 |
0 |
value = getValue(a); |
| 564 |
149 |
else if (pos == ArgValuesMap.Position.BEFORE |
| 565 |
|
&& getClosestPreviousArgValueOfArg(av, a) != null) |
| 566 |
0 |
value = getClosestPreviousArgValueOfArg(av, a).getValue(); |
| 567 |
149 |
else if (pos == ArgValuesMap.Position.AFTER |
| 568 |
|
&& getClosestNextArgValueOfArg(av, a, withinTypes) != null) |
| 569 |
120 |
value = getClosestNextArgValueOfArg(av, a, withinTypes).getValue(); |
| 570 |
|
|
| 571 |
|
|
| 572 |
149 |
Arg arg = av.getArg(); |
| 573 |
149 |
if (value == null && arg.hasOption(Opt.PRIMARY) |
| 574 |
|
&& arg.hasType(Type.STRUCTURE) && !a.hasOption(Opt.PRIMARY) |
| 575 |
|
&& (a.getFirstType() == Type.STRUCTURE |
| 576 |
|
|
| 577 |
|
)) |
| 578 |
|
{ |
| 579 |
7 |
ArgValue av2 = getArgValueOfArgWithSubValKey(a, |
| 580 |
|
Arg.ALLSTRUCTURES.getName()); |
| 581 |
7 |
if (av2 != null) |
| 582 |
|
{ |
| 583 |
2 |
value = av2.getValue(); |
| 584 |
|
} |
| 585 |
|
} |
| 586 |
|
|
| 587 |
149 |
if (value == null) |
| 588 |
|
{ |
| 589 |
|
|
| 590 |
27 |
for (ArgValue tmpAv : this.getArgValueList(a)) |
| 591 |
|
{ |
| 592 |
91 |
if (tmpAv.setByWildcardLinkedId()) |
| 593 |
|
{ |
| 594 |
13 |
value = tmpAv.getValue(); |
| 595 |
|
} |
| 596 |
|
} |
| 597 |
|
} |
| 598 |
|
} |
| 599 |
1100 |
if (value == null) |
| 600 |
|
{ |
| 601 |
953 |
value = pref != null ? Cache.getDefault(pref, def) : def; |
| 602 |
|
} |
| 603 |
1100 |
return value; |
| 604 |
|
} |
| 605 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 606 |
45 |
public boolean getBoolFromSubVal(Arg a, SubVals sv, boolean def)... |
| 607 |
|
{ |
| 608 |
45 |
return getFromSubValArgOrPref(a, sv, null, null, def); |
| 609 |
|
} |
| 610 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 611 |
165 |
public boolean getBoolFromSubValOrArg(Arg a, SubVals sv)... |
| 612 |
|
{ |
| 613 |
165 |
return getFromSubValArgOrPref(a, sv, null, null, false); |
| 614 |
|
} |
| 615 |
|
|
| |
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 616 |
1140 |
public boolean getFromSubValArgOrPref(Arg a, SubVals sv, String key,... |
| 617 |
|
String pref, boolean def) |
| 618 |
|
{ |
| 619 |
1140 |
return getFromSubValArgOrPref(a, sv, key, pref, def, false); |
| 620 |
|
} |
| 621 |
|
|
| |
|
| 64% |
Uncovered Elements: 18 (50) |
Complexity: 20 |
Complexity Density: 0.83 |
|
| 622 |
1199 |
public boolean getFromSubValArgOrPref(Arg a, SubVals sv, String key,... |
| 623 |
|
String pref, boolean def, boolean invertPref) |
| 624 |
|
{ |
| 625 |
1199 |
if ((key == null && a == null) || (sv == null && a == null)) |
| 626 |
0 |
return false; |
| 627 |
|
|
| 628 |
1199 |
boolean usingArgKey = false; |
| 629 |
1199 |
if (key == null) |
| 630 |
|
{ |
| 631 |
1199 |
key = a.getName(); |
| 632 |
1199 |
usingArgKey = true; |
| 633 |
|
} |
| 634 |
|
|
| 635 |
1199 |
String nokey = ArgParser.NEGATESTRING + key; |
| 636 |
|
|
| 637 |
|
|
| 638 |
1199 |
if (sv != null) |
| 639 |
|
{ |
| 640 |
|
|
| 641 |
1199 |
if (sv.has(key) && sv.get(key) != null) |
| 642 |
|
{ |
| 643 |
2 |
if (usingArgKey) |
| 644 |
|
{ |
| 645 |
2 |
if (!(a.hasOption(Opt.BOOLEAN) || a.hasOption(Opt.UNARY))) |
| 646 |
|
{ |
| 647 |
0 |
Console.debug( |
| 648 |
|
"Looking for boolean in subval from non-boolean/non-unary Arg " |
| 649 |
|
+ a.getName()); |
| 650 |
0 |
return false; |
| 651 |
|
} |
| 652 |
|
} |
| 653 |
2 |
return sv.get(key).toLowerCase(Locale.ROOT).equals("true"); |
| 654 |
|
} |
| 655 |
|
|
| 656 |
|
|
| 657 |
1197 |
if (sv.has(nokey) && sv.get(nokey) != null) |
| 658 |
|
{ |
| 659 |
0 |
if (usingArgKey) |
| 660 |
|
{ |
| 661 |
0 |
if (!(a.hasOption(Opt.BOOLEAN))) |
| 662 |
|
{ |
| 663 |
0 |
Console.debug( |
| 664 |
|
"Looking for negative boolean in subval from non-boolean Arg " |
| 665 |
|
+ a.getName()); |
| 666 |
0 |
return false; |
| 667 |
|
} |
| 668 |
|
} |
| 669 |
0 |
return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true"); |
| 670 |
|
} |
| 671 |
|
} |
| 672 |
|
|
| 673 |
|
|
| 674 |
1197 |
if (containsArg(a)) |
| 675 |
67 |
return getBoolean(a); |
| 676 |
|
|
| 677 |
|
|
| 678 |
1130 |
boolean prefVal = pref != null ? Cache.getDefault(pref, def) : false; |
| 679 |
881 |
return pref != null ? (invertPref ? !prefVal : prefVal) : def; |
| 680 |
|
} |
| 681 |
|
|
| |
|
| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
|
| 682 |
0 |
@Override... |
| 683 |
|
public String toString() |
| 684 |
|
{ |
| 685 |
0 |
StringBuilder sb = new StringBuilder(); |
| 686 |
0 |
for (Arg a : this.getArgKeys()) |
| 687 |
|
{ |
| 688 |
0 |
sb.append(a.argString()); |
| 689 |
0 |
sb.append(":\n"); |
| 690 |
0 |
for (ArgValue av : this.getArgValueList(a)) |
| 691 |
|
{ |
| 692 |
0 |
sb.append(" "); |
| 693 |
0 |
sb.append(av.getValue()); |
| 694 |
0 |
sb.append("\n"); |
| 695 |
|
} |
| 696 |
|
} |
| 697 |
0 |
return sb.toString(); |
| 698 |
|
} |
| 699 |
|
|
| |
|
| 0% |
Uncovered Elements: 15 (15) |
Complexity: 6 |
Complexity Density: 0.67 |
|
| 700 |
|
public class ArgInfo implements Comparable<ArgInfo> |
| 701 |
|
{ |
| 702 |
|
private Arg arg; |
| 703 |
|
|
| 704 |
|
private String value; |
| 705 |
|
|
| 706 |
|
private SubVals subVals; |
| 707 |
|
|
| 708 |
|
private int argIndex; |
| 709 |
|
|
| |
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
| 710 |
0 |
public ArgInfo(Arg arg, String value, SubVals subVals, int argIndex)... |
| 711 |
|
{ |
| 712 |
0 |
this.arg = arg; |
| 713 |
0 |
this.value = value; |
| 714 |
0 |
this.subVals = subVals; |
| 715 |
0 |
this.argIndex = argIndex; |
| 716 |
|
} |
| 717 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 718 |
0 |
public Arg arg()... |
| 719 |
|
{ |
| 720 |
0 |
return arg; |
| 721 |
|
} |
| 722 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 723 |
0 |
public String value()... |
| 724 |
|
{ |
| 725 |
0 |
return value; |
| 726 |
|
} |
| 727 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 728 |
0 |
public SubVals subVals()... |
| 729 |
|
{ |
| 730 |
0 |
return subVals; |
| 731 |
|
} |
| 732 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 733 |
0 |
public int argIndex()... |
| 734 |
|
{ |
| 735 |
0 |
return argIndex; |
| 736 |
|
} |
| 737 |
|
|
| |
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
| 738 |
0 |
@Override... |
| 739 |
|
public int compareTo(ArgInfo ai2) |
| 740 |
|
{ |
| 741 |
0 |
return Integer.compare(this.argIndex(), ai2.argIndex()); |
| 742 |
|
} |
| 743 |
|
} |
| 744 |
|
|
| |
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 0 |
Complexity Density: - |
|
| 745 |
|
public static enum Position |
| 746 |
|
{ |
| 747 |
|
FIRST, BEFORE, AFTER |
| 748 |
|
} |
| 749 |
|
} |