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package jalview.analysis; |
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import java.util.Locale; |
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import jalview.analysis.scoremodels.ScoreMatrix; |
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import jalview.analysis.scoremodels.ScoreModels; |
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import jalview.api.analysis.ScoreModelI; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.ResidueCount; |
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import jalview.datamodel.ResidueCount.SymbolCounts; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.schemes.ResidueProperties; |
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import jalview.util.Comparison; |
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import jalview.util.Format; |
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import java.awt.Color; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Map.Entry; |
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import java.util.SortedMap; |
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import java.util.TreeMap; |
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import java.util.Vector; |
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| 95.5% |
Uncovered Elements: 19 (419) |
Complexity: 105 |
Complexity Density: 0.41 |
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public class Conservation |
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{ |
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private static final int THRESHOLD_PERCENT = 3; |
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private static final int TOUPPERCASE = 'a' - 'A'; |
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private static final int GAP_INDEX = -1; |
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private static final Format FORMAT_3DP = new Format("%2.5f"); |
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SequenceI[] sequences; |
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int start; |
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int end; |
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Vector<int[]> seqNums; |
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int maxLength = 0; |
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boolean seqNumsChanged = false; |
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Map<String, Integer>[] total; |
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boolean canonicaliseAa = true; |
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private Vector<Double> quality; |
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private double qualityMinimum; |
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private double qualityMaximum; |
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private Sequence consSequence; |
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private int threshold; |
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private String name = ""; |
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private int[][] cons2; |
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private int[] cons2GapCounts; |
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private String[] consSymbs; |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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976 |
public Conservation(String name, List<SequenceI> sequences, int start,... |
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int end) |
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{ |
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this(name, THRESHOLD_PERCENT, sequences, start, end); |
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} |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 89.5% |
Uncovered Elements: 2 (19) |
Complexity: 4 |
Complexity Density: 0.27 |
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public Conservation(String name, int threshold, List<SequenceI> sequences,... |
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int start, int end) |
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{ |
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this.name = name; |
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this.threshold = threshold; |
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this.start = start; |
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this.end = end; |
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maxLength = end - start + 1; |
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int s, sSize = sequences.size(); |
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SequenceI[] sarray = new SequenceI[sSize]; |
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this.sequences = sarray; |
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try |
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{ |
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11852 |
for (s = 0; s < sSize; s++) |
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{ |
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10872 |
sarray[s] = sequences.get(s); |
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10871 |
if (sarray[s].getLength() > maxLength) |
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{ |
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maxLength = sarray[s].getLength(); |
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} |
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} |
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} catch (ArrayIndexOutOfBoundsException ex) |
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{ |
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this.sequences = new SequenceI[0]; |
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maxLength = 0; |
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} |
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} |
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@param |
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@param |
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| 81.6% |
Uncovered Elements: 7 (38) |
Complexity: 9 |
Complexity Density: 0.38 |
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10798 |
private void calcSeqNum(int i, ScoreMatrix sm)... |
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{ |
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int sSize = sequences.length; |
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10798 |
if ((i > -1) && (i < sSize)) |
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{ |
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10798 |
String sq = sequences[i].getSequenceAsString(); |
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10797 |
if (seqNums.size() <= i) |
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{ |
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10797 |
seqNums.addElement(new int[sq.length() + 1]); |
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} |
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if (sq.hashCode() != seqNums.elementAt(i)[0]) |
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{ |
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int j; |
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int len; |
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seqNumsChanged = true; |
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len = sq.length(); |
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10798 |
if (maxLength < len) |
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{ |
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maxLength = len; |
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} |
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10798 |
int[] sqnum = new int[len + 1]; |
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10798 |
sqnum[0] = sq.hashCode(); |
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1796677 |
for (j = 1; j <= len; j++) |
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{ |
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1786275 |
char residue = sq.charAt(j - 1); |
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1786575 |
if (Comparison.isGap(residue)) |
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{ |
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403096 |
sqnum[j] = GAP_INDEX; |
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} |
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else |
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{ |
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1383958 |
sqnum[j] = sm.getMatrixIndex(residue); |
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1383601 |
if (sqnum[j] == -1) |
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{ |
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sqnum[j] = GAP_INDEX; |
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} |
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} |
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} |
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10798 |
seqNums.setElementAt(sqnum, i); |
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} |
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else |
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{ |
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jalview.bin.Console.outPrintln("SEQUENCE HAS BEEN DELETED!!!"); |
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} |
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} |
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else |
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{ |
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jalview.bin.Console.errPrintln( |
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"ERROR: calcSeqNum called with out of range sequence index for Alignment\n"); |
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} |
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} |
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| 96.3% |
Uncovered Elements: 1 (27) |
Complexity: 6 |
Complexity Density: 0.35 |
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976 |
public void calculate()... |
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{ |
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int height = sequences.length; |
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total = new Map[maxLength]; |
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267 |
137241 |
for (int column = start; column <= end; column++) |
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{ |
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136266 |
ResidueCount values = countResidues(column); |
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int thresh = (threshold * height) / 100; |
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136273 |
SortedMap<String, Integer> resultHash = new TreeMap<>(); |
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136273 |
SymbolCounts symbolCounts = values.getSymbolCounts(); |
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136272 |
char[] symbols = symbolCounts.symbols; |
285 |
136274 |
int[] counts = symbolCounts.values; |
286 |
439649 |
for (int j = 0; j < symbols.length; j++) |
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{ |
288 |
303395 |
char c = symbols[j]; |
289 |
303383 |
if (counts[j] > thresh) |
290 |
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{ |
291 |
303376 |
recordConservation(resultHash, String.valueOf(c)); |
292 |
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} |
293 |
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} |
294 |
136273 |
if (values.getGapCount() > thresh) |
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{ |
296 |
79488 |
recordConservation(resultHash, "-"); |
297 |
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} |
298 |
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299 |
136265 |
if (total.length > 0) |
300 |
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{ |
301 |
136267 |
total[column - start] = resultHash; |
302 |
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} |
303 |
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} |
304 |
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} |
305 |
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307 |
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308 |
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309 |
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@param |
310 |
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311 |
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312 |
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313 |
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@param |
314 |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 5 |
Complexity Density: 0.45 |
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315 |
382821 |
protected static void recordConservation(Map<String, Integer> resultMap,... |
316 |
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String res) |
317 |
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{ |
318 |
382827 |
res = res.toUpperCase(Locale.ROOT); |
319 |
382858 |
for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash |
320 |
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.entrySet()) |
321 |
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{ |
322 |
3820477 |
String propertyName = property.getKey(); |
323 |
3821724 |
Integer residuePropertyValue = property.getValue().get(res); |
324 |
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325 |
3827267 |
if (!resultMap.containsKey(propertyName)) |
326 |
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{ |
327 |
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329 |
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330 |
1362156 |
if (residuePropertyValue != null) |
331 |
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{ |
332 |
1361929 |
resultMap.put(propertyName, residuePropertyValue); |
333 |
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} |
334 |
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else |
335 |
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{ |
336 |
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337 |
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338 |
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339 |
140 |
resultMap.put(propertyName, property.getValue().get("-")); |
340 |
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} |
341 |
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} |
342 |
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else |
343 |
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{ |
344 |
2464635 |
Integer currentResult = resultMap.get(propertyName); |
345 |
2465455 |
if (currentResult.intValue() != -1 |
346 |
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&& !currentResult.equals(residuePropertyValue)) |
347 |
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{ |
348 |
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349 |
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350 |
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351 |
715722 |
resultMap.put(propertyName, Integer.valueOf(-1)); |
352 |
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} |
353 |
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} |
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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@param |
361 |
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@return |
362 |
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| 91.3% |
Uncovered Elements: 2 (23) |
Complexity: 6 |
Complexity Density: 0.46 |
|
363 |
136266 |
protected ResidueCount countResidues(int column)... |
364 |
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{ |
365 |
136266 |
ResidueCount values = new ResidueCount(false); |
366 |
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|
367 |
1944976 |
for (int row = 0; row < sequences.length; row++) |
368 |
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{ |
369 |
1808732 |
if (sequences[row].getLength() > column) |
370 |
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{ |
371 |
1794485 |
char c = sequences[row].getCharAt(column); |
372 |
1794489 |
if (canonicaliseAa) |
373 |
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{ |
374 |
1794460 |
int index = ResidueProperties.aaIndex[c]; |
375 |
1794796 |
c = index > 20 ? '-' : ResidueProperties.aa[index].charAt(0); |
376 |
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} |
377 |
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else |
378 |
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{ |
379 |
0 |
c = toUpperCase(c); |
380 |
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} |
381 |
1794729 |
if (Comparison.isGap(c)) |
382 |
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{ |
383 |
404346 |
values.addGap(); |
384 |
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} |
385 |
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else |
386 |
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{ |
387 |
1390445 |
values.add(c); |
388 |
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} |
389 |
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} |
390 |
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else |
391 |
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{ |
392 |
14327 |
values.addGap(); |
393 |
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} |
394 |
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} |
395 |
136272 |
return values; |
396 |
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} |
397 |
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398 |
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399 |
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400 |
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|
401 |
|
@return |
402 |
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| 94.1% |
Uncovered Elements: 2 (34) |
Complexity: 8 |
Complexity Density: 0.4 |
|
403 |
136257 |
public int[] countConservationAndGaps(int column)... |
404 |
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{ |
405 |
136257 |
int gapCount = 0; |
406 |
136259 |
boolean fullyConserved = true; |
407 |
136260 |
int iSize = sequences.length; |
408 |
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|
409 |
136261 |
if (iSize == 0) |
410 |
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{ |
411 |
0 |
return new int[] { 0, 0 }; |
412 |
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} |
413 |
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|
414 |
136261 |
char lastRes = '0'; |
415 |
1943615 |
for (int i = 0; i < iSize; i++) |
416 |
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{ |
417 |
1807547 |
if (column >= sequences[i].getLength()) |
418 |
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{ |
419 |
14327 |
gapCount++; |
420 |
14327 |
continue; |
421 |
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} |
422 |
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|
423 |
1793308 |
char c = sequences[i].getCharAt(column); |
424 |
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|
425 |
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|
426 |
1793865 |
if (Comparison.isGap((c))) |
427 |
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{ |
428 |
404255 |
gapCount++; |
429 |
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} |
430 |
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else |
431 |
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{ |
432 |
1389656 |
c = toUpperCase(c); |
433 |
1389820 |
if (lastRes == '0') |
434 |
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{ |
435 |
128840 |
lastRes = c; |
436 |
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} |
437 |
1390351 |
if (c != lastRes) |
438 |
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{ |
439 |
436297 |
fullyConserved = false; |
440 |
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} |
441 |
|
} |
442 |
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} |
443 |
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|
444 |
136260 |
int[] r = new int[] { fullyConserved ? 1 : 0, gapCount }; |
445 |
136256 |
return r; |
446 |
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} |
447 |
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448 |
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449 |
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450 |
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451 |
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|
452 |
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@param |
453 |
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@return |
454 |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
455 |
1389695 |
char toUpperCase(char c)... |
456 |
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{ |
457 |
1389687 |
if ('a' <= c && c <= 'z') |
458 |
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{ |
459 |
6813 |
c -= TOUPPERCASE; |
460 |
|
} |
461 |
1389751 |
return c; |
462 |
|
} |
463 |
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464 |
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465 |
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466 |
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467 |
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@param |
468 |
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|
469 |
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|
470 |
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@param |
471 |
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472 |
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|
473 |
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| 100% |
Uncovered Elements: 0 (55) |
Complexity: 13 |
Complexity Density: 0.39 |
|
474 |
974 |
public void verdict(boolean positiveOnly, float maxPercentageGaps)... |
475 |
|
{ |
476 |
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477 |
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|
478 |
974 |
StringBuilder consString = new StringBuilder(end); |
479 |
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|
480 |
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|
481 |
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482 |
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|
483 |
1064 |
for (int i = 0; i < start; i++) |
484 |
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{ |
485 |
90 |
consString.append('-'); |
486 |
|
} |
487 |
974 |
consSymbs = new String[end - start + 1]; |
488 |
137224 |
for (int i = start; i <= end; i++) |
489 |
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{ |
490 |
136252 |
int[] gapcons = countConservationAndGaps(i); |
491 |
136255 |
boolean fullyConserved = gapcons[0] == 1; |
492 |
136259 |
int totGaps = gapcons[1]; |
493 |
136260 |
float pgaps = (totGaps * 100f) / sequences.length; |
494 |
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|
495 |
136265 |
if (maxPercentageGaps > pgaps) |
496 |
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{ |
497 |
96075 |
Map<String, Integer> resultHash = total[i - start]; |
498 |
96075 |
int count = 0; |
499 |
96074 |
StringBuilder positives = new StringBuilder(64); |
500 |
96073 |
StringBuilder negatives = new StringBuilder(32); |
501 |
96071 |
for (String type : resultHash.keySet()) |
502 |
|
{ |
503 |
960221 |
int result = resultHash.get(type).intValue(); |
504 |
960651 |
if (result == -1) |
505 |
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{ |
506 |
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|
507 |
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|
508 |
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|
509 |
443341 |
continue; |
510 |
|
} |
511 |
517222 |
count++; |
512 |
517321 |
if (result == 1) |
513 |
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{ |
514 |
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|
515 |
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|
516 |
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|
517 |
162415 |
positives.append(positives.length() == 0 ? "" : " "); |
518 |
162418 |
positives.append(type); |
519 |
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} |
520 |
517294 |
if (result == 0 && !positiveOnly) |
521 |
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{ |
522 |
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|
523 |
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|
524 |
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|
525 |
354906 |
negatives.append(negatives.length() == 0 ? "" : " "); |
526 |
354888 |
negatives.append("!").append(type); |
527 |
|
} |
528 |
|
} |
529 |
96076 |
if (negatives.length() > 0) |
530 |
|
{ |
531 |
56601 |
positives.append(" ").append(negatives); |
532 |
|
} |
533 |
96067 |
consSymbs[i - start] = positives.toString(); |
534 |
|
|
535 |
96071 |
if (count < 10) |
536 |
|
{ |
537 |
65273 |
consString.append(count); |
538 |
|
} |
539 |
|
else |
540 |
|
{ |
541 |
30801 |
consString.append(fullyConserved ? "*" : "+"); |
542 |
|
} |
543 |
|
} |
544 |
|
else |
545 |
|
{ |
546 |
40189 |
consString.append('-'); |
547 |
|
} |
548 |
|
} |
549 |
|
|
550 |
974 |
consSequence = new Sequence(name, consString.toString(), start, end); |
551 |
|
} |
552 |
|
|
553 |
|
|
554 |
|
|
555 |
|
|
556 |
|
@return |
557 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
558 |
993 |
public SequenceI getConsSequence()... |
559 |
|
{ |
560 |
993 |
return consSequence; |
561 |
|
} |
562 |
|
|
563 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
564 |
962 |
public void findQuality()... |
565 |
|
{ |
566 |
962 |
findQuality(0, maxLength - 1, getQualitySubstMat()); |
567 |
|
} |
568 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
569 |
962 |
public ScoreMatrix getQualitySubstMat()... |
570 |
|
{ |
571 |
962 |
return sm; |
572 |
|
} |
573 |
|
|
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
private ScoreMatrix sm = ScoreModels.getInstance().getBlosum62(); |
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
|
582 |
|
@param |
583 |
|
|
584 |
|
|
585 |
|
|
|
|
| 75% |
Uncovered Elements: 1 (4) |
Complexity: 3 |
Complexity Density: 1.5 |
|
586 |
962 |
public void setQualitySubstMat(ScoreMatrix scoreMatrix)... |
587 |
|
{ |
588 |
962 |
if (scoreMatrix != null && scoreMatrix.isProtein()) |
589 |
|
{ |
590 |
962 |
sm = scoreMatrix; |
591 |
|
} |
592 |
|
} |
593 |
|
|
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
@param |
598 |
|
|
|
|
| 96.7% |
Uncovered Elements: 1 (30) |
Complexity: 8 |
Complexity Density: 0.44 |
|
599 |
962 |
private void percentIdentity(ScoreMatrix sm)... |
600 |
|
{ |
601 |
962 |
seqNums = new Vector<>(); |
602 |
962 |
int i = 0, iSize = sequences.length; |
603 |
|
|
604 |
11760 |
for (i = 0; i < iSize; i++) |
605 |
|
{ |
606 |
10798 |
calcSeqNum(i, sm); |
607 |
|
} |
608 |
|
|
609 |
962 |
if ((cons2 == null) || seqNumsChanged) |
610 |
|
{ |
611 |
|
|
612 |
|
|
613 |
962 |
cons2 = new int[maxLength][24]; |
614 |
962 |
cons2GapCounts = new int[maxLength]; |
615 |
|
|
616 |
962 |
int j = 0; |
617 |
|
|
618 |
11760 |
while (j < sequences.length) |
619 |
|
{ |
620 |
10798 |
int[] sqnum = seqNums.elementAt(j); |
621 |
|
|
622 |
1797480 |
for (i = 1; i < sqnum.length; i++) |
623 |
|
{ |
624 |
1786726 |
int index = sqnum[i]; |
625 |
1787197 |
if (index == GAP_INDEX) |
626 |
|
{ |
627 |
403132 |
cons2GapCounts[i - 1]++; |
628 |
|
} |
629 |
|
else |
630 |
|
{ |
631 |
1383998 |
cons2[i - 1][index]++; |
632 |
|
} |
633 |
|
} |
634 |
|
|
635 |
|
|
636 |
25080 |
for (i = sqnum.length - 1; i < maxLength; i++) |
637 |
|
{ |
638 |
14282 |
cons2GapCounts[i]++; |
639 |
|
} |
640 |
10798 |
j++; |
641 |
|
} |
642 |
|
} |
643 |
|
} |
644 |
|
|
645 |
|
|
646 |
|
|
647 |
|
|
648 |
|
|
649 |
|
@param |
650 |
|
@param |
651 |
|
@param |
652 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (61) |
Complexity: 11 |
Complexity Density: 0.27 |
|
653 |
962 |
protected void findQuality(int startCol, int endCol,... |
654 |
|
ScoreMatrix scoreMatrix) |
655 |
|
{ |
656 |
962 |
quality = new Vector<>(); |
657 |
|
|
658 |
962 |
double max = -Double.MAX_VALUE; |
659 |
962 |
float[][] scores = scoreMatrix.getMatrix(); |
660 |
|
|
661 |
962 |
percentIdentity(scoreMatrix); |
662 |
|
|
663 |
962 |
int size = seqNums.size(); |
664 |
962 |
int[] lengths = new int[size]; |
665 |
|
|
666 |
11760 |
for (int l = 0; l < size; l++) |
667 |
|
{ |
668 |
10798 |
lengths[l] = seqNums.elementAt(l).length - 1; |
669 |
|
} |
670 |
|
|
671 |
962 |
final int symbolCount = scoreMatrix.getSize(); |
672 |
|
|
673 |
136350 |
for (int j = startCol; j <= endCol; j++) |
674 |
|
{ |
675 |
135393 |
double bigtot = 0; |
676 |
|
|
677 |
|
|
678 |
135394 |
double[] x = new double[symbolCount]; |
679 |
|
|
680 |
3379993 |
for (int ii = 0; ii < symbolCount; ii++) |
681 |
|
{ |
682 |
3244852 |
x[ii] = 0; |
683 |
|
|
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
|
688 |
|
|
689 |
76810284 |
for (int i2 = 0; i2 < symbolCount - 1; i2++) |
690 |
|
{ |
691 |
73608151 |
x[ii] += (((double) cons2[j][i2] * scores[ii][i2]) + 4D); |
692 |
|
} |
693 |
3245788 |
x[ii] += 4D + cons2GapCounts[j] * scoreMatrix.getMinimumScore(); |
694 |
|
|
695 |
3245865 |
x[ii] /= size; |
696 |
|
} |
697 |
|
|
698 |
|
|
699 |
1935026 |
for (int k = 0; k < size; k++) |
700 |
|
{ |
701 |
1799850 |
double tot = 0; |
702 |
1800141 |
double[] xx = new double[symbolCount]; |
703 |
|
|
704 |
1800533 |
int seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] |
705 |
|
: GAP_INDEX; |
706 |
|
|
707 |
42541338 |
for (int i = 0; i < symbolCount - 1; i++) |
708 |
|
{ |
709 |
40843747 |
double sr = 4D; |
710 |
40999475 |
if (seqNum == GAP_INDEX) |
711 |
|
{ |
712 |
9583184 |
sr += scoreMatrix.getMinimumScore(); |
713 |
|
} |
714 |
|
else |
715 |
|
{ |
716 |
31460246 |
sr += scores[i][seqNum]; |
717 |
|
} |
718 |
|
|
719 |
40995854 |
xx[i] = x[i] - sr; |
720 |
|
|
721 |
40991333 |
tot += (xx[i] * xx[i]); |
722 |
|
} |
723 |
|
|
724 |
1799817 |
bigtot += Math.sqrt(tot); |
725 |
|
} |
726 |
|
|
727 |
135385 |
max = Math.max(max, bigtot); |
728 |
|
|
729 |
135385 |
quality.addElement(Double.valueOf(bigtot)); |
730 |
|
} |
731 |
|
|
732 |
962 |
double newmax = -Double.MAX_VALUE; |
733 |
|
|
734 |
136360 |
for (int j = startCol; j <= endCol; j++) |
735 |
|
{ |
736 |
135398 |
double tmp = quality.elementAt(j).doubleValue(); |
737 |
|
|
738 |
135398 |
tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size; |
739 |
|
|
740 |
|
|
741 |
135398 |
quality.setElementAt(Double.valueOf(tmp), j); |
742 |
|
|
743 |
135398 |
if (tmp > newmax) |
744 |
|
{ |
745 |
2610 |
newmax = tmp; |
746 |
|
} |
747 |
|
} |
748 |
|
|
749 |
962 |
qualityMinimum = 0D; |
750 |
962 |
qualityMaximum = newmax; |
751 |
|
} |
752 |
|
|
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
@param |
759 |
|
|
760 |
|
@param |
761 |
|
|
762 |
|
@param |
763 |
|
|
764 |
|
@param |
765 |
|
|
766 |
|
|
|
|
| 96.7% |
Uncovered Elements: 2 (60) |
Complexity: 16 |
Complexity Density: 0.4 |
|
767 |
962 |
public void completeAnnotations(AlignmentAnnotation conservation,... |
768 |
|
AlignmentAnnotation quality2, int istart, int alWidth) |
769 |
|
{ |
770 |
962 |
SequenceI cons = getConsSequence(); |
771 |
|
|
772 |
|
|
773 |
|
|
774 |
|
|
775 |
962 |
float minR = 0.3f; |
776 |
962 |
float minG = 0.0f; |
777 |
962 |
float minB = 0f; |
778 |
962 |
float maxR = 1.0f - minR; |
779 |
962 |
float maxG = 0.9f - minG; |
780 |
962 |
float maxB = 0f - minB; |
781 |
|
|
782 |
962 |
float min = 0f; |
783 |
962 |
float max = 11f; |
784 |
962 |
float qmin = 0f; |
785 |
962 |
float qmax = 0f; |
786 |
|
|
787 |
962 |
if (conservation != null && conservation.annotations != null |
788 |
|
&& conservation.annotations.length != alWidth) |
789 |
|
{ |
790 |
365 |
conservation.annotations = new Annotation[alWidth]; |
791 |
|
} |
792 |
|
|
793 |
962 |
if (quality2 != null) |
794 |
|
{ |
795 |
962 |
quality2.graphMax = (float) qualityMaximum; |
796 |
962 |
if (quality2.annotations != null |
797 |
|
&& quality2.annotations.length != alWidth) |
798 |
|
{ |
799 |
366 |
quality2.annotations = new Annotation[alWidth]; |
800 |
|
} |
801 |
962 |
qmin = (float) qualityMinimum; |
802 |
962 |
qmax = (float) qualityMaximum; |
803 |
|
} |
804 |
|
|
805 |
136356 |
for (int i = istart; i < alWidth; i++) |
806 |
|
{ |
807 |
135395 |
float value = 0; |
808 |
|
|
809 |
135398 |
char c = cons.getCharAt(i); |
810 |
|
|
811 |
135397 |
if (Character.isDigit(c)) |
812 |
|
{ |
813 |
64983 |
value = c - '0'; |
814 |
|
} |
815 |
70414 |
else if (c == '*') |
816 |
|
{ |
817 |
30413 |
value = 11; |
818 |
|
} |
819 |
40001 |
else if (c == '+') |
820 |
|
{ |
821 |
90 |
value = 10; |
822 |
|
} |
823 |
|
|
824 |
135392 |
if (conservation != null) |
825 |
|
{ |
826 |
135235 |
float vprop = value - min; |
827 |
135236 |
vprop /= max; |
828 |
135236 |
int consp = i - start; |
829 |
135240 |
String conssym = (value > 0 && consp > -1 |
830 |
|
&& consp < consSymbs.length) ? consSymbs[consp] : ""; |
831 |
135235 |
conservation.annotations[i] = new Annotation(String.valueOf(c), |
832 |
|
conssym, ' ', value, new Color(minR + (maxR * vprop), |
833 |
|
minG + (maxG * vprop), minB + (maxB * vprop))); |
834 |
|
} |
835 |
|
|
836 |
|
|
837 |
135398 |
if (quality2 != null) |
838 |
|
{ |
839 |
135397 |
value = quality.elementAt(i).floatValue(); |
840 |
135398 |
float vprop = value - qmin; |
841 |
135398 |
vprop /= qmax; |
842 |
135398 |
String description = FORMAT_3DP.form(value); |
843 |
135398 |
quality2.annotations[i] = new Annotation(" ", description, ' ', |
844 |
|
value, new Color(minR + (maxR * vprop), |
845 |
|
minG + (maxG * vprop), minB + (maxB * vprop))); |
846 |
|
} |
847 |
|
} |
848 |
|
} |
849 |
|
|
850 |
|
|
851 |
|
|
852 |
|
|
853 |
|
@param |
854 |
|
|
855 |
|
@param |
856 |
|
@param |
857 |
|
|
858 |
|
@param |
859 |
|
|
860 |
|
@param |
861 |
|
|
862 |
|
|
863 |
|
@param |
864 |
|
|
865 |
|
@param |
866 |
|
|
867 |
|
@return |
868 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
869 |
3 |
public static Conservation calculateConservation(String name,... |
870 |
|
List<SequenceI> seqs, int start, int end, boolean positiveOnly, |
871 |
|
int maxPercentGaps, boolean calcQuality) |
872 |
|
{ |
873 |
3 |
return calculateConservation(name, seqs, start, end, positiveOnly, |
874 |
|
maxPercentGaps, calcQuality, null); |
875 |
|
} |
876 |
|
|
877 |
|
|
878 |
|
|
879 |
|
|
880 |
|
@param |
881 |
|
|
882 |
|
@param |
883 |
|
@param |
884 |
|
|
885 |
|
@param |
886 |
|
|
887 |
|
@param |
888 |
|
|
889 |
|
|
890 |
|
@param |
891 |
|
|
892 |
|
@param |
893 |
|
|
894 |
|
@param |
895 |
|
|
896 |
|
@return |
897 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
898 |
965 |
public static Conservation calculateConservation(String name,... |
899 |
|
List<SequenceI> seqs, int start, int end, boolean positiveOnly, |
900 |
|
int maxPercentGaps, boolean calcQuality, ScoreMatrix scoreMatrix) |
901 |
|
{ |
902 |
965 |
Conservation cons = new Conservation(name, seqs, start, end); |
903 |
965 |
if (scoreMatrix != null) |
904 |
|
{ |
905 |
962 |
cons.setQualitySubstMat(scoreMatrix); |
906 |
|
} |
907 |
965 |
cons.calculate(); |
908 |
965 |
cons.verdict(positiveOnly, maxPercentGaps); |
909 |
|
|
910 |
965 |
if (calcQuality) |
911 |
|
{ |
912 |
962 |
cons.findQuality(); |
913 |
|
} |
914 |
|
|
915 |
965 |
return cons; |
916 |
|
} |
917 |
|
|
918 |
|
|
919 |
|
|
920 |
|
|
921 |
|
|
922 |
|
|
923 |
|
|
924 |
|
@param |
925 |
|
@return |
926 |
|
|
|
|
| 90% |
Uncovered Elements: 1 (10) |
Complexity: 5 |
Complexity Density: 0.83 |
|
927 |
7 |
String getTooltip(int column)... |
928 |
|
{ |
929 |
7 |
SequenceI cons = getConsSequence(); |
930 |
7 |
char val = column < cons.getLength() ? cons.getCharAt(column) : '-'; |
931 |
7 |
boolean hasConservation = val != '-' && val != '0'; |
932 |
7 |
int consp = column - start; |
933 |
7 |
String tip = (hasConservation && consp > -1 && consp < consSymbs.length) |
934 |
|
? consSymbs[consp] |
935 |
|
: ""; |
936 |
7 |
return tip; |
937 |
|
} |
938 |
|
} |