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package jalview.util; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.List; |
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| 86.7% |
Uncovered Elements: 76 (573) |
Complexity: 163 |
Complexity Density: 0.45 |
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public class MapList |
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{ |
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private List<int[]> fromShifts; |
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private List<int[]> toShifts; |
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private int fromRatio; |
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private int toRatio; |
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private int fromLowest; |
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private int fromHighest; |
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private int toLowest; |
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private int toHighest; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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742 |
public MapList()... |
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{ |
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742 |
fromShifts = new ArrayList<>(); |
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742 |
toShifts = new ArrayList<>(); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 8 |
Complexity Density: 1 |
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@Override... |
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public boolean equals(Object o) |
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{ |
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if (o == null || !(o instanceof MapList)) |
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{ |
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return false; |
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} |
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MapList obj = (MapList) o; |
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if (obj == this) |
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{ |
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return true; |
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} |
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if (obj.fromRatio != fromRatio || obj.toRatio != toRatio |
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|| obj.fromShifts == null || obj.toShifts == null) |
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{ |
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return false; |
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} |
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return Arrays.deepEquals(fromShifts.toArray(), obj.fromShifts.toArray()) |
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&& Arrays.deepEquals(toShifts.toArray(), |
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obj.toShifts.toArray()); |
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} |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
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@Override... |
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public int hashCode() |
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{ |
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int hashCode = 31 * fromRatio; |
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hashCode = 31 * hashCode + toRatio; |
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for (int[] shift : fromShifts) |
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{ |
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hashCode = 31 * hashCode + shift[0]; |
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hashCode = 31 * hashCode + shift[1]; |
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} |
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for (int[] shift : toShifts) |
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{ |
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hashCode = 31 * hashCode + shift[0]; |
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hashCode = 31 * hashCode + shift[1]; |
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} |
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return hashCode; |
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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 List<int[]> getFromRanges()... |
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{ |
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return fromShifts; |
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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 List<int[]> getToRanges()... |
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{ |
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return toShifts; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
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protected static int[] getRanges(List<int[]> shifts)... |
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{ |
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int[] rnges = new int[2 * shifts.size()]; |
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int i = 0; |
164 |
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for (int[] r : shifts) |
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{ |
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rnges[i++] = r[0]; |
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rnges[i++] = r[1]; |
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} |
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return rnges; |
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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 int getFromRatio()... |
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{ |
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return fromRatio; |
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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 int getToRatio()... |
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{ |
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return toRatio; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public int getFromLowest()... |
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{ |
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return fromLowest; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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68 |
public int getFromHighest()... |
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{ |
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return fromHighest; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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29 |
public int getToLowest()... |
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{ |
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return toLowest; |
203 |
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} |
204 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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30 |
public int getToHighest()... |
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{ |
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return toHighest; |
208 |
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} |
209 |
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212 |
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213 |
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215 |
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@param |
216 |
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@param |
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219 |
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@param |
220 |
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221 |
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@param |
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| 100% |
Uncovered Elements: 0 (31) |
Complexity: 7 |
Complexity Density: 0.3 |
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653 |
public MapList(int from[], int to[], int fromRatio, int toRatio)... |
225 |
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{ |
226 |
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this(); |
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this.fromRatio = fromRatio; |
228 |
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this.toRatio = toRatio; |
229 |
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fromLowest = Integer.MAX_VALUE; |
230 |
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fromHighest = Integer.MIN_VALUE; |
231 |
653 |
int added = 0; |
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for (int i = 0; i < from.length; i += 2) |
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{ |
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238 |
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239 |
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fromLowest = Math.min(fromLowest, Math.min(from[i], from[i + 1])); |
240 |
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fromHighest = Math.max(fromHighest, Math.max(from[i], from[i + 1])); |
241 |
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if (added > 0 && from[i] == fromShifts.get(added - 1)[1]) |
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{ |
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1 |
fromShifts.get(added - 1)[1] = from[i + 1]; |
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} |
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else |
249 |
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{ |
250 |
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fromShifts.add(new int[] { from[i], from[i + 1] }); |
251 |
885 |
added++; |
252 |
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} |
253 |
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} |
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255 |
652 |
toLowest = Integer.MAX_VALUE; |
256 |
652 |
toHighest = Integer.MIN_VALUE; |
257 |
652 |
added = 0; |
258 |
1413 |
for (int i = 0; i < to.length; i += 2) |
259 |
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{ |
260 |
762 |
toLowest = Math.min(toLowest, Math.min(to[i], to[i + 1])); |
261 |
762 |
toHighest = Math.max(toHighest, Math.max(to[i], to[i + 1])); |
262 |
762 |
if (added > 0 && to[i] == toShifts.get(added - 1)[1]) |
263 |
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{ |
264 |
1 |
toShifts.get(added - 1)[1] = to[i + 1]; |
265 |
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} |
266 |
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else |
267 |
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{ |
268 |
761 |
toShifts.add(new int[] { to[i], to[i + 1] }); |
269 |
761 |
added++; |
270 |
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} |
271 |
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} |
272 |
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} |
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274 |
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275 |
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276 |
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277 |
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@param |
278 |
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| 88.2% |
Uncovered Elements: 2 (17) |
Complexity: 3 |
Complexity Density: 0.23 |
|
279 |
17 |
public MapList(MapList map)... |
280 |
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{ |
281 |
17 |
this(); |
282 |
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283 |
17 |
this.fromLowest = map.fromLowest; |
284 |
17 |
this.fromHighest = map.fromHighest; |
285 |
17 |
this.toLowest = map.toLowest; |
286 |
17 |
this.toHighest = map.toHighest; |
287 |
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|
288 |
17 |
this.fromRatio = map.fromRatio; |
289 |
17 |
this.toRatio = map.toRatio; |
290 |
17 |
if (map.fromShifts != null) |
291 |
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{ |
292 |
17 |
for (int[] r : map.fromShifts) |
293 |
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{ |
294 |
29 |
fromShifts.add(new int[] { r[0], r[1] }); |
295 |
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} |
296 |
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} |
297 |
17 |
if (map.toShifts != null) |
298 |
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{ |
299 |
17 |
for (int[] r : map.toShifts) |
300 |
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{ |
301 |
22 |
toShifts.add(new int[] { r[0], r[1] }); |
302 |
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} |
303 |
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} |
304 |
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} |
305 |
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306 |
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307 |
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308 |
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309 |
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310 |
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@param |
311 |
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@param |
312 |
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@param |
313 |
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@param |
314 |
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| 84% |
Uncovered Elements: 4 (25) |
Complexity: 3 |
Complexity Density: 0.14 |
|
315 |
72 |
public MapList(List<int[]> fromRange, List<int[]> toRange, int fromRatio,... |
316 |
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int toRatio) |
317 |
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{ |
318 |
72 |
this(); |
319 |
72 |
fromRange = coalesceRanges(fromRange); |
320 |
72 |
toRange = coalesceRanges(toRange); |
321 |
72 |
this.fromShifts = fromRange; |
322 |
72 |
this.toShifts = toRange; |
323 |
72 |
this.fromRatio = fromRatio; |
324 |
72 |
this.toRatio = toRatio; |
325 |
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|
326 |
72 |
fromLowest = Integer.MAX_VALUE; |
327 |
72 |
fromHighest = Integer.MIN_VALUE; |
328 |
72 |
for (int[] range : fromRange) |
329 |
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{ |
330 |
97 |
if (range.length != 2) |
331 |
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{ |
332 |
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|
333 |
0 |
System.err.println( |
334 |
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"Invalid format for fromRange " + Arrays.toString(range) |
335 |
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+ " may cause errors"); |
336 |
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} |
337 |
97 |
fromLowest = Math.min(fromLowest, Math.min(range[0], range[1])); |
338 |
97 |
fromHighest = Math.max(fromHighest, Math.max(range[0], range[1])); |
339 |
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} |
340 |
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|
341 |
72 |
toLowest = Integer.MAX_VALUE; |
342 |
72 |
toHighest = Integer.MIN_VALUE; |
343 |
72 |
for (int[] range : toRange) |
344 |
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{ |
345 |
101 |
if (range.length != 2) |
346 |
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{ |
347 |
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|
348 |
0 |
System.err.println("Invalid format for toRange " |
349 |
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+ Arrays.toString(range) |
350 |
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+ " may cause errors"); |
351 |
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} |
352 |
101 |
toLowest = Math.min(toLowest, Math.min(range[0], range[1])); |
353 |
101 |
toHighest = Math.max(toHighest, Math.max(range[0], range[1])); |
354 |
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} |
355 |
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} |
356 |
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357 |
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358 |
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359 |
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|
360 |
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|
361 |
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@param |
362 |
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@return |
363 |
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|
364 |
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| 100% |
Uncovered Elements: 0 (48) |
Complexity: 23 |
Complexity Density: 0.77 |
|
365 |
157 |
public static List<int[]> coalesceRanges(final List<int[]> ranges)... |
366 |
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{ |
367 |
157 |
if (ranges == null || ranges.size() < 2) |
368 |
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{ |
369 |
107 |
return ranges; |
370 |
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} |
371 |
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|
372 |
50 |
boolean changed = false; |
373 |
50 |
List<int[]> merged = new ArrayList<>(); |
374 |
50 |
int[] lastRange = ranges.get(0); |
375 |
50 |
int lastDirection = lastRange[1] >= lastRange[0] ? 1 : -1; |
376 |
50 |
lastRange = new int[] { lastRange[0], lastRange[1] }; |
377 |
50 |
merged.add(lastRange); |
378 |
50 |
boolean first = true; |
379 |
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|
380 |
50 |
for (final int[] range : ranges) |
381 |
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{ |
382 |
128 |
if (first) |
383 |
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{ |
384 |
50 |
first = false; |
385 |
50 |
continue; |
386 |
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} |
387 |
78 |
if (range[0] == lastRange[0] && range[1] == lastRange[1]) |
388 |
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{ |
389 |
|
|
390 |
1 |
changed = true; |
391 |
1 |
continue; |
392 |
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} |
393 |
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|
394 |
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|
395 |
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|
396 |
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|
397 |
77 |
if ((lastDirection == 1 && range[0] >= lastRange[0] |
398 |
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&& range[0] <= lastRange[1] && range[1] >= lastRange[0] |
399 |
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&& range[1] <= lastRange[1]) |
400 |
|
|| (lastDirection == -1 && range[0] <= lastRange[0] |
401 |
|
&& range[0] >= lastRange[1] |
402 |
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&& range[1] <= lastRange[0] |
403 |
|
&& range[1] >= lastRange[1])) |
404 |
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{ |
405 |
5 |
changed = true; |
406 |
5 |
continue; |
407 |
|
} |
408 |
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|
409 |
72 |
int direction = range[1] >= range[0] ? 1 : -1; |
410 |
|
|
411 |
|
|
412 |
|
|
413 |
|
|
414 |
|
|
415 |
72 |
boolean sameDirection = range[1] == range[0] |
416 |
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|| direction == lastDirection; |
417 |
72 |
boolean extending = range[0] == lastRange[1] + lastDirection; |
418 |
72 |
boolean overlapping = (lastDirection == 1 && range[0] >= lastRange[0] |
419 |
|
&& range[0] <= lastRange[1]) |
420 |
|
|| (lastDirection == -1 && range[0] <= lastRange[0] |
421 |
|
&& range[0] >= lastRange[1]); |
422 |
72 |
if (sameDirection && (overlapping || extending)) |
423 |
|
{ |
424 |
14 |
lastRange[1] = range[1]; |
425 |
14 |
changed = true; |
426 |
|
} |
427 |
|
else |
428 |
|
{ |
429 |
58 |
lastRange = new int[] { range[0], range[1] }; |
430 |
58 |
merged.add(lastRange); |
431 |
|
|
432 |
58 |
lastDirection = (range[1] == range[0]) ? lastDirection : direction; |
433 |
|
} |
434 |
|
} |
435 |
|
|
436 |
50 |
return changed ? merged : ranges; |
437 |
|
} |
438 |
|
|
439 |
|
|
440 |
|
|
441 |
|
|
442 |
|
@return |
443 |
|
|
444 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
445 |
2 |
protected int[][] makeFromMap()... |
446 |
|
{ |
447 |
|
|
448 |
2 |
return posMap(fromShifts, fromRatio, toShifts, toRatio); |
449 |
|
} |
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
|
@return |
455 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
456 |
2 |
protected int[][] makeToMap()... |
457 |
|
{ |
458 |
|
|
459 |
2 |
return posMap(toShifts, toRatio, fromShifts, fromRatio); |
460 |
|
} |
461 |
|
|
462 |
|
|
463 |
|
|
464 |
|
|
465 |
|
@param |
466 |
|
@return |
467 |
|
|
468 |
|
|
|
|
| 89.4% |
Uncovered Elements: 7 (66) |
Complexity: 15 |
Complexity Density: 0.39 |
|
469 |
4 |
private int[][] posMap(List<int[]> shiftTo, int ratio,... |
470 |
|
List<int[]> shiftFrom, int toRatio) |
471 |
|
{ |
472 |
|
|
473 |
4 |
int iv = 0, ivSize = shiftTo.size(); |
474 |
4 |
if (iv >= ivSize) |
475 |
|
{ |
476 |
0 |
return null; |
477 |
|
} |
478 |
4 |
int[] intv = shiftTo.get(iv++); |
479 |
4 |
int from = intv[0], to = intv[1]; |
480 |
4 |
if (from > to) |
481 |
|
{ |
482 |
1 |
from = intv[1]; |
483 |
1 |
to = intv[0]; |
484 |
|
} |
485 |
8 |
while (iv < ivSize) |
486 |
|
{ |
487 |
4 |
intv = shiftTo.get(iv++); |
488 |
4 |
if (intv[0] < from) |
489 |
|
{ |
490 |
0 |
from = intv[0]; |
491 |
|
} |
492 |
4 |
if (intv[1] < from) |
493 |
|
{ |
494 |
0 |
from = intv[1]; |
495 |
|
} |
496 |
4 |
if (intv[0] > to) |
497 |
|
{ |
498 |
4 |
to = intv[0]; |
499 |
|
} |
500 |
4 |
if (intv[1] > to) |
501 |
|
{ |
502 |
3 |
to = intv[1]; |
503 |
|
} |
504 |
|
} |
505 |
4 |
int tF = 0, tT = 0; |
506 |
4 |
int mp[][] = new int[to - from + 2][]; |
507 |
102 |
for (int i = 0; i < mp.length; i++) |
508 |
|
{ |
509 |
98 |
int[] m = shift(i + from, shiftTo, ratio, shiftFrom, toRatio); |
510 |
98 |
if (m != null) |
511 |
|
{ |
512 |
80 |
if (i == 0) |
513 |
|
{ |
514 |
4 |
tF = tT = m[0]; |
515 |
|
} |
516 |
|
else |
517 |
|
{ |
518 |
76 |
if (m[0] < tF) |
519 |
|
{ |
520 |
22 |
tF = m[0]; |
521 |
|
} |
522 |
76 |
if (m[0] > tT) |
523 |
|
{ |
524 |
9 |
tT = m[0]; |
525 |
|
} |
526 |
|
} |
527 |
|
} |
528 |
98 |
mp[i] = m; |
529 |
|
} |
530 |
4 |
int[][] map = new int[][] { new int[] { from, to, tF, tT }, |
531 |
|
new int[to - from + 2] }; |
532 |
|
|
533 |
4 |
map[0][2] = tF; |
534 |
4 |
map[0][3] = tT; |
535 |
|
|
536 |
102 |
for (int i = 0; i < mp.length; i++) |
537 |
|
{ |
538 |
98 |
if (mp[i] != null) |
539 |
|
{ |
540 |
80 |
map[1][i] = mp[i][0] - tF; |
541 |
|
} |
542 |
|
else |
543 |
|
{ |
544 |
18 |
map[1][i] = -1; |
545 |
|
} |
546 |
|
} |
547 |
4 |
return map; |
548 |
|
} |
549 |
|
|
550 |
|
|
551 |
|
|
552 |
|
|
553 |
|
@param |
554 |
|
|
555 |
|
@param |
556 |
|
|
557 |
|
|
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
@param |
569 |
|
|
570 |
|
@return |
571 |
|
|
572 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
573 |
677 |
public int[] shiftFrom(int pos)... |
574 |
|
{ |
575 |
677 |
return shift(pos, fromShifts, fromRatio, toShifts, toRatio); |
576 |
|
} |
577 |
|
|
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
@param |
582 |
|
|
583 |
|
@return |
584 |
|
|
585 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
586 |
8453 |
public int[] shiftTo(int pos)... |
587 |
|
{ |
588 |
8453 |
return shift(pos, toShifts, toRatio, fromShifts, fromRatio); |
589 |
|
} |
590 |
|
|
591 |
|
|
592 |
|
|
593 |
|
@param |
594 |
|
@param |
595 |
|
@param |
596 |
|
@param |
597 |
|
@return |
598 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (13) |
Complexity: 3 |
Complexity Density: 0.33 |
|
599 |
9228 |
protected static int[] shift(int pos, List<int[]> shiftTo, int fromRatio,... |
600 |
|
List<int[]> shiftFrom, int toRatio) |
601 |
|
{ |
602 |
|
|
603 |
9228 |
int[] fromCount = countPos(shiftTo, pos); |
604 |
9228 |
if (fromCount == null) |
605 |
|
{ |
606 |
374 |
return null; |
607 |
|
} |
608 |
8854 |
int fromRemainder = (fromCount[0] - 1) % fromRatio; |
609 |
8854 |
int toCount = 1 + (((fromCount[0] - 1) / fromRatio) * toRatio); |
610 |
8854 |
int[] toPos = countToPos(shiftFrom, toCount); |
611 |
8854 |
if (toPos == null) |
612 |
|
{ |
613 |
1 |
return null; |
614 |
|
} |
615 |
|
|
616 |
8853 |
return new int[] { toPos[0], fromRemainder, toPos[1] }; |
617 |
|
} |
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
|
622 |
|
@param |
623 |
|
@param |
624 |
|
@return |
625 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (19) |
Complexity: 7 |
Complexity Density: 0.64 |
|
626 |
9228 |
protected static int[] countPos(List<int[]> shiftTo, int pos)... |
627 |
|
{ |
628 |
9228 |
int count = 0, intv[], iv = 0, ivSize = shiftTo.size(); |
629 |
10152 |
while (iv < ivSize) |
630 |
|
{ |
631 |
9778 |
intv = shiftTo.get(iv++); |
632 |
9778 |
if (intv[0] <= intv[1]) |
633 |
|
{ |
634 |
9348 |
if (pos >= intv[0] && pos <= intv[1]) |
635 |
|
{ |
636 |
8624 |
return new int[] { count + pos - intv[0] + 1, +1 }; |
637 |
|
} |
638 |
|
else |
639 |
|
{ |
640 |
724 |
count += intv[1] - intv[0] + 1; |
641 |
|
} |
642 |
|
} |
643 |
|
else |
644 |
|
{ |
645 |
430 |
if (pos >= intv[1] && pos <= intv[0]) |
646 |
|
{ |
647 |
230 |
return new int[] { count + intv[0] - pos + 1, -1 }; |
648 |
|
} |
649 |
|
else |
650 |
|
{ |
651 |
200 |
count += intv[0] - intv[1] + 1; |
652 |
|
} |
653 |
|
} |
654 |
|
} |
655 |
374 |
return null; |
656 |
|
} |
657 |
|
|
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
@param |
662 |
|
@param |
663 |
|
@return |
664 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (21) |
Complexity: 5 |
Complexity Density: 0.38 |
|
665 |
8854 |
protected static int[] countToPos(List<int[]> shiftFrom, int pos)... |
666 |
|
{ |
667 |
8854 |
int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size(); |
668 |
8854 |
int[] intv = { 0, 0 }; |
669 |
9246 |
while (iv < ivSize) |
670 |
|
{ |
671 |
9245 |
intv = shiftFrom.get(iv++); |
672 |
9245 |
diff = intv[1] - intv[0]; |
673 |
9245 |
if (diff >= 0) |
674 |
|
{ |
675 |
9104 |
if (pos <= count + 1 + diff) |
676 |
|
{ |
677 |
8713 |
return new int[] { pos - count - 1 + intv[0], +1 }; |
678 |
|
} |
679 |
|
else |
680 |
|
{ |
681 |
391 |
count += 1 + diff; |
682 |
|
} |
683 |
|
} |
684 |
|
else |
685 |
|
{ |
686 |
141 |
if (pos <= count + 1 - diff) |
687 |
|
{ |
688 |
140 |
return new int[] { intv[0] - (pos - count - 1), -1 }; |
689 |
|
} |
690 |
|
else |
691 |
|
{ |
692 |
1 |
count += 1 - diff; |
693 |
|
} |
694 |
|
} |
695 |
|
} |
696 |
1 |
return null; |
697 |
|
} |
698 |
|
|
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
@param |
703 |
|
|
704 |
|
@param |
705 |
|
|
706 |
|
@return |
707 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
708 |
1821 |
public int[] locateInFrom(int start, int end)... |
709 |
|
{ |
710 |
|
|
711 |
1821 |
int fromStart[] = shiftTo(start); |
712 |
|
|
713 |
1821 |
int fromEnd[] = shiftTo(end); |
714 |
|
|
715 |
1821 |
return getIntervals(fromShifts, fromStart, fromEnd, fromRatio); |
716 |
|
} |
717 |
|
|
718 |
|
|
719 |
|
|
720 |
|
|
721 |
|
@param |
722 |
|
|
723 |
|
@param |
724 |
|
|
725 |
|
@return |
726 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
727 |
309 |
public int[] locateInTo(int start, int end)... |
728 |
|
{ |
729 |
309 |
int toStart[] = shiftFrom(start); |
730 |
309 |
int toEnd[] = shiftFrom(end); |
731 |
309 |
return getIntervals(toShifts, toStart, toEnd, toRatio); |
732 |
|
} |
733 |
|
|
734 |
|
|
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
@param |
739 |
|
@param |
740 |
|
@param |
741 |
|
@param |
742 |
|
@return |
743 |
|
|
744 |
|
|
|
|
| 75.2% |
Uncovered Elements: 32 (129) |
Complexity: 37 |
Complexity Density: 0.47 |
|
745 |
2130 |
protected static int[] getIntervals(List<int[]> shiftFrom,... |
746 |
|
int[] fromStart, int[] fromEnd, int fromRatio2) |
747 |
|
{ |
748 |
2130 |
if (fromStart == null || fromEnd == null) |
749 |
|
{ |
750 |
168 |
return null; |
751 |
|
} |
752 |
1962 |
int startpos, endpos; |
753 |
1962 |
startpos = fromStart[0]; |
754 |
1962 |
endpos = fromEnd[0]; |
755 |
1962 |
int endindx = (fromRatio2 - 1); |
756 |
|
|
757 |
1962 |
int intv = 0, intvSize = shiftFrom.size(); |
758 |
1962 |
int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; |
759 |
|
|
760 |
|
|
761 |
4098 |
while (intv < intvSize && (fs == -1 || fe == -1)) |
762 |
|
{ |
763 |
2136 |
iv = shiftFrom.get(intv++); |
764 |
2136 |
if (fe_s > -1) |
765 |
|
{ |
766 |
63 |
endpos = iv[0]; |
767 |
63 |
endindx--; |
768 |
|
} |
769 |
2136 |
if (iv[0] <= iv[1]) |
770 |
|
{ |
771 |
2080 |
if (fs == -1 && startpos >= iv[0] && startpos <= iv[1]) |
772 |
|
{ |
773 |
1923 |
fs = i; |
774 |
|
} |
775 |
2080 |
if (endpos >= iv[0] && endpos <= iv[1]) |
776 |
|
{ |
777 |
1970 |
if (fe_s == -1) |
778 |
|
{ |
779 |
1923 |
fe_s = i; |
780 |
|
} |
781 |
1970 |
if (fe_s != -1) |
782 |
|
{ |
783 |
1970 |
if (endpos + endindx <= iv[1]) |
784 |
|
{ |
785 |
1939 |
fe = i; |
786 |
1939 |
endpos = endpos + endindx; |
787 |
|
|
788 |
|
} |
789 |
|
else |
790 |
|
{ |
791 |
31 |
endindx -= iv[1] - endpos; |
792 |
|
} |
793 |
|
} |
794 |
|
} |
795 |
|
} |
796 |
|
else |
797 |
|
{ |
798 |
56 |
if (fs == -1 && startpos <= iv[0] && startpos >= iv[1]) |
799 |
|
{ |
800 |
39 |
fs = i; |
801 |
|
} |
802 |
56 |
if (endpos <= iv[0] && endpos >= iv[1]) |
803 |
|
{ |
804 |
55 |
if (fe_s == -1) |
805 |
|
{ |
806 |
39 |
fe_s = i; |
807 |
|
} |
808 |
55 |
if (fe_s != -1) |
809 |
|
{ |
810 |
55 |
if (endpos - endindx >= iv[1]) |
811 |
|
{ |
812 |
55 |
fe = i; |
813 |
55 |
endpos = endpos - endindx; |
814 |
|
|
815 |
|
} |
816 |
|
else |
817 |
|
{ |
818 |
0 |
endindx -= endpos - iv[1]; |
819 |
|
} |
820 |
|
} |
821 |
|
} |
822 |
|
} |
823 |
2136 |
i++; |
824 |
|
} |
825 |
1962 |
if (fs == fe && fe == -1) |
826 |
|
{ |
827 |
0 |
return null; |
828 |
|
} |
829 |
1962 |
List<int[]> ranges = new ArrayList<>(); |
830 |
1962 |
if (fs <= fe) |
831 |
|
{ |
832 |
1962 |
intv = fs; |
833 |
1962 |
i = fs; |
834 |
|
|
835 |
1962 |
iv = shiftFrom.get(intv++); |
836 |
1962 |
iv = new int[] { iv[0], iv[1] }; |
837 |
1962 |
if (i == fs) |
838 |
|
{ |
839 |
1962 |
iv[0] = startpos; |
840 |
|
} |
841 |
2038 |
while (i != fe) |
842 |
|
{ |
843 |
76 |
ranges.add(iv); |
844 |
76 |
iv = shiftFrom.get(intv++); |
845 |
76 |
iv = new int[] { iv[0], iv[1] }; |
846 |
76 |
i++; |
847 |
|
} |
848 |
1962 |
if (i == fe) |
849 |
|
{ |
850 |
1962 |
iv[1] = endpos; |
851 |
|
} |
852 |
1962 |
ranges.add(iv); |
853 |
|
} |
854 |
|
else |
855 |
|
{ |
856 |
|
|
857 |
0 |
i = shiftFrom.size() - 1; |
858 |
0 |
while (i > fs) |
859 |
|
{ |
860 |
0 |
i--; |
861 |
|
} |
862 |
0 |
iv = shiftFrom.get(i); |
863 |
0 |
iv = new int[] { iv[1], iv[0] }; |
864 |
|
|
865 |
0 |
if (i == fs) |
866 |
|
{ |
867 |
0 |
iv[0] = startpos; |
868 |
|
} |
869 |
0 |
while (--i != fe) |
870 |
|
{ |
871 |
0 |
ranges.add(iv); |
872 |
0 |
iv = shiftFrom.get(i); |
873 |
0 |
iv = new int[] { iv[1], iv[0] }; |
874 |
|
} |
875 |
0 |
if (i == fe) |
876 |
|
{ |
877 |
|
|
878 |
0 |
iv[1] = endpos; |
879 |
|
} |
880 |
0 |
ranges.add(iv); |
881 |
|
} |
882 |
|
|
883 |
1962 |
int[] range = null; |
884 |
1962 |
if (ranges != null && ranges.size() > 0) |
885 |
|
{ |
886 |
1962 |
range = new int[ranges.size() * 2]; |
887 |
1962 |
intv = 0; |
888 |
1962 |
intvSize = ranges.size(); |
889 |
1962 |
i = 0; |
890 |
4000 |
while (intv < intvSize) |
891 |
|
{ |
892 |
2038 |
iv = ranges.get(intv); |
893 |
2038 |
range[i++] = iv[0]; |
894 |
2038 |
range[i++] = iv[1]; |
895 |
2038 |
ranges.set(intv++, null); |
896 |
|
} |
897 |
|
} |
898 |
1962 |
return range; |
899 |
|
} |
900 |
|
|
901 |
|
|
902 |
|
|
903 |
|
|
904 |
|
@param |
905 |
|
|
906 |
|
@return |
907 |
|
|
|
|
| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
908 |
3 |
public int getToPosition(int mpos)... |
909 |
|
{ |
910 |
|
|
911 |
3 |
int[] mp = shiftTo(mpos); |
912 |
3 |
if (mp != null) |
913 |
|
{ |
914 |
3 |
return mp[0]; |
915 |
|
} |
916 |
0 |
return mpos; |
917 |
|
} |
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
|
922 |
|
@param |
923 |
|
|
924 |
|
@return |
925 |
|
|
926 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
927 |
0 |
public int[] getToWord(int mpos)... |
928 |
|
{ |
929 |
0 |
int[] mp = shiftTo(mpos); |
930 |
0 |
if (mp != null) |
931 |
|
{ |
932 |
0 |
return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) }; |
933 |
|
} |
934 |
0 |
return null; |
935 |
|
} |
936 |
|
|
937 |
|
|
938 |
|
|
939 |
|
|
940 |
|
|
941 |
|
@param |
942 |
|
@return |
943 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
944 |
0 |
public int getMappedPosition(int pos)... |
945 |
|
{ |
946 |
|
|
947 |
0 |
int[] mp = shiftFrom(pos); |
948 |
0 |
if (mp != null) |
949 |
|
{ |
950 |
0 |
return mp[0]; |
951 |
|
} |
952 |
0 |
return pos; |
953 |
|
} |
954 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
955 |
0 |
public int[] getMappedWord(int pos)... |
956 |
|
{ |
957 |
|
|
958 |
0 |
int[] mp = shiftFrom(pos); |
959 |
0 |
if (mp != null) |
960 |
|
{ |
961 |
0 |
return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) }; |
962 |
|
} |
963 |
0 |
return null; |
964 |
|
} |
965 |
|
|
966 |
|
|
967 |
|
|
968 |
|
@return |
969 |
|
|
970 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
971 |
32 |
public MapList getInverse()... |
972 |
|
{ |
973 |
32 |
return new MapList(getToRanges(), getFromRanges(), getToRatio(), |
974 |
|
getFromRatio()); |
975 |
|
} |
976 |
|
|
977 |
|
|
978 |
|
|
979 |
|
|
980 |
|
@param |
981 |
|
|
982 |
|
@return |
983 |
|
|
984 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
985 |
0 |
public boolean containsEither(boolean local, MapList map)... |
986 |
|
{ |
987 |
|
|
988 |
0 |
if (local) |
989 |
|
{ |
990 |
0 |
return ((getFromLowest() >= map.getFromLowest() |
991 |
|
&& getFromHighest() <= map.getFromHighest()) |
992 |
|
|| (getFromLowest() <= map.getFromLowest() |
993 |
|
&& getFromHighest() >= map.getFromHighest())); |
994 |
|
} |
995 |
|
else |
996 |
|
{ |
997 |
0 |
return ((getToLowest() >= map.getToLowest() |
998 |
|
&& getToHighest() <= map.getToHighest()) |
999 |
|
|| (getToLowest() <= map.getToLowest() |
1000 |
|
&& getToHighest() >= map.getToHighest())); |
1001 |
|
} |
1002 |
|
} |
1003 |
|
|
1004 |
|
|
1005 |
|
|
1006 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
|
1007 |
11 |
@Override... |
1008 |
|
public String toString() |
1009 |
|
{ |
1010 |
11 |
StringBuilder sb = new StringBuilder(64); |
1011 |
11 |
sb.append("["); |
1012 |
11 |
for (int[] shift : fromShifts) |
1013 |
|
{ |
1014 |
25 |
sb.append(" ").append(Arrays.toString(shift)); |
1015 |
|
} |
1016 |
11 |
sb.append(" ] "); |
1017 |
11 |
sb.append(fromRatio).append(":").append(toRatio); |
1018 |
11 |
sb.append(" to ["); |
1019 |
11 |
for (int[] shift : toShifts) |
1020 |
|
{ |
1021 |
16 |
sb.append(" ").append(Arrays.toString(shift)); |
1022 |
|
} |
1023 |
11 |
sb.append(" ]"); |
1024 |
11 |
return sb.toString(); |
1025 |
|
} |
1026 |
|
|
1027 |
|
|
1028 |
|
|
1029 |
|
|
1030 |
|
|
1031 |
|
|
1032 |
|
@param |
1033 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 2 |
Complexity Density: 0.2 |
|
1034 |
12 |
public void addMapList(MapList map)... |
1035 |
|
{ |
1036 |
12 |
if (this.equals(map)) |
1037 |
|
{ |
1038 |
3 |
return; |
1039 |
|
} |
1040 |
9 |
this.fromLowest = Math.min(fromLowest, map.fromLowest); |
1041 |
9 |
this.toLowest = Math.min(toLowest, map.toLowest); |
1042 |
9 |
this.fromHighest = Math.max(fromHighest, map.fromHighest); |
1043 |
9 |
this.toHighest = Math.max(toHighest, map.toHighest); |
1044 |
|
|
1045 |
9 |
for (int[] range : map.getFromRanges()) |
1046 |
|
{ |
1047 |
10 |
addRange(range, fromShifts); |
1048 |
|
} |
1049 |
9 |
for (int[] range : map.getToRanges()) |
1050 |
|
{ |
1051 |
11 |
addRange(range, toShifts); |
1052 |
|
} |
1053 |
|
} |
1054 |
|
|
1055 |
|
|
1056 |
|
|
1057 |
|
|
1058 |
|
|
1059 |
|
@param |
1060 |
|
@param |
1061 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (24) |
Complexity: 10 |
Complexity Density: 0.62 |
|
1062 |
29 |
static void addRange(int[] range, List<int[]> addTo)... |
1063 |
|
{ |
1064 |
|
|
1065 |
|
|
1066 |
|
|
1067 |
29 |
if (addTo.size() == 0) |
1068 |
|
{ |
1069 |
1 |
addTo.add(range); |
1070 |
1 |
return; |
1071 |
|
} |
1072 |
|
|
1073 |
28 |
int[] last = addTo.get(addTo.size() - 1); |
1074 |
28 |
boolean lastForward = last[1] >= last[0]; |
1075 |
28 |
boolean newForward = range[1] >= range[0]; |
1076 |
|
|
1077 |
|
|
1078 |
|
|
1079 |
|
|
1080 |
28 |
if (lastForward == newForward && last[1] == range[0]) |
1081 |
|
{ |
1082 |
4 |
last[1] = range[1]; |
1083 |
4 |
return; |
1084 |
|
} |
1085 |
|
|
1086 |
|
|
1087 |
|
|
1088 |
|
|
1089 |
24 |
if (lastForward && newForward && range[0] == last[1] + 1) |
1090 |
|
{ |
1091 |
3 |
last[1] = range[1]; |
1092 |
3 |
return; |
1093 |
|
} |
1094 |
|
|
1095 |
|
|
1096 |
|
|
1097 |
|
|
1098 |
21 |
if (!lastForward && !newForward && range[0] == last[1] - 1) |
1099 |
|
{ |
1100 |
4 |
last[1] = range[1]; |
1101 |
4 |
return; |
1102 |
|
} |
1103 |
|
|
1104 |
|
|
1105 |
|
|
1106 |
|
|
1107 |
17 |
addTo.add(range); |
1108 |
|
} |
1109 |
|
|
1110 |
|
|
1111 |
|
|
1112 |
|
|
1113 |
|
|
1114 |
|
|
1115 |
|
|
1116 |
|
@return |
1117 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1118 |
3 |
public boolean isFromForwardStrand()... |
1119 |
|
{ |
1120 |
3 |
return isForwardStrand(getFromRanges()); |
1121 |
|
} |
1122 |
|
|
1123 |
|
|
1124 |
|
|
1125 |
|
|
1126 |
|
|
1127 |
|
|
1128 |
|
|
1129 |
|
@return |
1130 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1131 |
27 |
public boolean isToForwardStrand()... |
1132 |
|
{ |
1133 |
27 |
return isForwardStrand(getToRanges()); |
1134 |
|
} |
1135 |
|
|
1136 |
|
|
1137 |
|
|
1138 |
|
|
1139 |
|
|
1140 |
|
@param |
1141 |
|
@return |
1142 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
1143 |
30 |
private boolean isForwardStrand(List<int[]> ranges)... |
1144 |
|
{ |
1145 |
30 |
boolean forwardStrand = true; |
1146 |
30 |
for (int[] range : ranges) |
1147 |
|
{ |
1148 |
38 |
if (range[1] > range[0]) |
1149 |
|
{ |
1150 |
20 |
break; |
1151 |
|
} |
1152 |
18 |
else if (range[1] < range[0]) |
1153 |
|
{ |
1154 |
8 |
forwardStrand = false; |
1155 |
8 |
break; |
1156 |
|
} |
1157 |
|
} |
1158 |
30 |
return forwardStrand; |
1159 |
|
} |
1160 |
|
|
1161 |
|
|
1162 |
|
|
1163 |
|
@return |
1164 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1165 |
6 |
public boolean isTripletMap()... |
1166 |
|
{ |
1167 |
6 |
return (toRatio == 3 && fromRatio == 1) |
1168 |
|
|| (fromRatio == 3 && toRatio == 1); |
1169 |
|
} |
1170 |
|
|
1171 |
|
|
1172 |
|
|
1173 |
|
|
1174 |
|
|
1175 |
|
|
1176 |
|
|
1177 |
|
|
1178 |
|
|
1179 |
|
|
1180 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
|
1184 |
|
|
1185 |
|
|
1186 |
|
|
1187 |
|
|
1188 |
|
|
1189 |
|
|
1190 |
|
|
1191 |
|
@param |
1192 |
|
@return |
1193 |
|
|
|
|
| 90.9% |
Uncovered Elements: 2 (22) |
Complexity: 5 |
Complexity Density: 0.31 |
|
1194 |
8 |
public MapList traverse(MapList map)... |
1195 |
|
{ |
1196 |
8 |
if (map == null) |
1197 |
|
{ |
1198 |
0 |
return null; |
1199 |
|
} |
1200 |
|
|
1201 |
|
|
1202 |
|
|
1203 |
|
|
1204 |
|
|
1205 |
|
|
1206 |
|
|
1207 |
|
|
1208 |
|
|
1209 |
|
|
1210 |
8 |
int outFromRatio = getFromRatio() * map.getFromRatio(); |
1211 |
8 |
int outToRatio = getToRatio() * map.getToRatio(); |
1212 |
8 |
int gcd = MathUtils.gcd(outFromRatio, outToRatio); |
1213 |
8 |
outFromRatio /= gcd; |
1214 |
8 |
outToRatio /= gcd; |
1215 |
|
|
1216 |
8 |
List<int[]> toRanges = new ArrayList<>(); |
1217 |
8 |
for (int[] range : getToRanges()) |
1218 |
|
{ |
1219 |
9 |
int[] transferred = map.locateInTo(range[0], range[1]); |
1220 |
9 |
if (transferred == null || transferred.length % 2 != 0) |
1221 |
|
{ |
1222 |
1 |
return null; |
1223 |
|
} |
1224 |
|
|
1225 |
|
|
1226 |
|
|
1227 |
|
|
1228 |
|
|
1229 |
24 |
for (int i = 0; i < transferred.length;) |
1230 |
|
{ |
1231 |
16 |
toRanges.add(new int[] { transferred[i], transferred[i + 1] }); |
1232 |
16 |
i += 2; |
1233 |
|
} |
1234 |
|
} |
1235 |
|
|
1236 |
7 |
return new MapList(getFromRanges(), toRanges, outFromRatio, outToRatio); |
1237 |
|
} |
1238 |
|
|
1239 |
|
} |