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package jalview.datamodel; |
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import java.util.ArrayList; |
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import java.util.BitSet; |
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import java.util.List; |
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@author |
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| 86.9% |
Uncovered Elements: 13 (99) |
Complexity: 29 |
Complexity Density: 0.47 |
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public class SearchResults implements SearchResultsI |
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{ |
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private List<SearchResultMatchI> matches = new ArrayList<>(); |
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| 89.2% |
Uncovered Elements: 4 (37) |
Complexity: 12 |
Complexity Density: 0.55 |
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public class Match implements SearchResultMatchI |
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{ |
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final SequenceI sequence; |
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final int start; |
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final int end; |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
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public Match(SequenceI seq, int start, int end)... |
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{ |
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sequence = seq; |
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if (start <= end) |
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{ |
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this.start = start; |
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this.end = end; |
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} |
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else |
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{ |
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this.start = end; |
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this.end = start; |
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} |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public SequenceI getSequence() |
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{ |
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return sequence; |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public int getStart() |
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{ |
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return start; |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public int getEnd() |
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{ |
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return end; |
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} |
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| 85.7% |
Uncovered Elements: 1 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
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@Override... |
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public String toString() |
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{ |
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StringBuilder sb = new StringBuilder(); |
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if (sequence != null) |
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{ |
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sb.append(sequence.getName()).append("/"); |
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} |
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sb.append(start).append("-").append(end); |
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return sb.toString(); |
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} |
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| 83.3% |
Uncovered Elements: 1 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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@Override... |
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public int hashCode() |
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{ |
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int hash = sequence == null ? 0 : sequence.hashCode(); |
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hash += 31 * start; |
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hash += 67 * end; |
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return hash; |
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} |
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| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
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@Override... |
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public boolean equals(Object obj) |
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{ |
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if (obj == null || !(obj instanceof SearchResultMatchI)) |
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{ |
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return false; |
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} |
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SearchResultMatchI m = (SearchResultMatchI) obj; |
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return (sequence == m.getSequence() && start == m.getStart() |
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&& end == m.getEnd()); |
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} |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
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@Override... |
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public SearchResultMatchI addResult(SequenceI seq, int start, int end) |
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{ |
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Match m = new Match(seq, start, end); |
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matches.add(m); |
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return m; |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 4 |
Complexity Density: 0.67 |
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@Override... |
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public boolean involvesSequence(SequenceI sequence) |
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{ |
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SequenceI ds = sequence.getDatasetSequence(); |
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for (SearchResultMatchI _m : matches) |
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{ |
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SequenceI matched = _m.getSequence(); |
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if (matched != null && (matched == sequence || matched == ds)) |
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{ |
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return true; |
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} |
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} |
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return false; |
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} |
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@see |
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| 77.8% |
Uncovered Elements: 10 (45) |
Complexity: 11 |
Complexity Density: 0.38 |
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@Override... |
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public int[] getResults(SequenceI sequence, int start, int end) |
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{ |
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if (matches.isEmpty()) |
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{ |
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return null; |
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} |
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int[] result = null; |
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int[] tmp = null; |
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int resultLength, matchStart = 0, matchEnd = 0; |
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boolean mfound; |
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Match m; |
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for (SearchResultMatchI _m : matches) |
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{ |
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m = (Match) _m; |
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mfound = false; |
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if (m.sequence == sequence |
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|| m.sequence == sequence.getDatasetSequence()) |
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{ |
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mfound = true; |
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matchStart = sequence.findIndex(m.start) - 1; |
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matchEnd = m.start == m.end ? matchStart : sequence |
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.findIndex(m.end) - 1; |
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} |
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if (mfound) |
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{ |
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if (matchStart <= end && matchEnd >= start) |
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{ |
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if (matchStart < start) |
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{ |
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matchStart = start; |
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} |
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if (matchEnd > end) |
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{ |
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matchEnd = end; |
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} |
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if (result == null) |
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{ |
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result = new int[] { matchStart, matchEnd }; |
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} |
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else |
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{ |
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resultLength = result.length; |
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tmp = new int[resultLength + 2]; |
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System.arraycopy(result, 0, tmp, 0, resultLength); |
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result = tmp; |
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result[resultLength] = matchStart; |
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result[resultLength + 1] = matchEnd; |
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} |
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} |
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else |
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{ |
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} |
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} |
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} |
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return result; |
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} |
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| 100% |
Uncovered Elements: 0 (18) |
Complexity: 3 |
Complexity Density: 0.21 |
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@Override... |
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public int markColumns(SequenceCollectionI sqcol, BitSet bs) |
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{ |
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int count = 0; |
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BitSet mask = new BitSet(); |
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int startRes = sqcol.getStartRes(); |
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int endRes = sqcol.getEndRes(); |
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for (SequenceI s : sqcol.getSequences()) |
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{ |
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int[] cols = getResults(s, startRes, endRes); |
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if (cols != null) |
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{ |
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for (int pair = 0; pair < cols.length; pair += 2) |
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{ |
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mask.set(cols[pair], cols[pair + 1] + 1); |
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} |
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} |
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} |
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BitSet original = (BitSet) bs.clone(); |
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original.and(mask); |
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count = mask.cardinality() - original.cardinality(); |
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bs.or(mask); |
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return count; |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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8 |
@Override... |
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public int getSize() |
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{ |
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return matches.size(); |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public boolean isEmpty() |
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{ |
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return matches.isEmpty(); |
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} |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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public List<SearchResultMatchI> getResults() |
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{ |
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return matches; |
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} |
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@return |
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| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
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3 |
@Override... |
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public String toString() |
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{ |
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return matches == null ? "" : matches.toString(); |
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} |
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@see |
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@see |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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6 |
@Override... |
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public int hashCode() |
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{ |
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6 |
return matches.hashCode(); |
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} |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
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36 |
@Override... |
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public boolean equals(Object obj) |
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{ |
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36 |
if (obj == null || !(obj instanceof SearchResultsI)) |
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{ |
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return false; |
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} |
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29 |
SearchResultsI sr = (SearchResultsI) obj; |
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return matches.equals(sr.getResults()); |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
@Override... |
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public void addSearchResults(SearchResultsI toAdd) |
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{ |
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matches.addAll(toAdd.getResults()); |
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} |
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} |