2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import jalview.datamodel.AlignedCodonFrame;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.Annotation;
27 import jalview.datamodel.HiddenMarkovModel;
28 import jalview.datamodel.Profile;
29 import jalview.datamodel.ProfileI;
30 import jalview.datamodel.Profiles;
31 import jalview.datamodel.ProfilesI;
32 import jalview.datamodel.ResidueCount;
33 import jalview.datamodel.ResidueCount.SymbolCounts;
34 import jalview.datamodel.SequenceI;
35 import jalview.ext.android.SparseIntArray;
36 import jalview.schemes.ResidueProperties;
37 import jalview.util.Comparison;
38 import jalview.util.Format;
39 import jalview.util.MappingUtils;
40 import jalview.util.QuickSort;
42 import java.awt.Color;
43 import java.util.Arrays;
44 import java.util.Hashtable;
45 import java.util.List;
48 * Takes in a vector or array of sequences and column start and column end and
49 * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
50 * This class is used extensively in calculating alignment colourschemes that
51 * depend on the amount of conservation in each alignment column.
56 public class AAFrequency
58 public static final String PROFILE = "P";
60 private static final String AMINO = "amino";
62 private static final String DNA = "DNA";
64 private static final String RNA = "RNA";
67 * Quick look-up of String value of char 'A' to 'Z'
69 private static final String[] CHARS = new String['Z' - 'A' + 1];
73 for (char c = 'A'; c <= 'Z'; c++)
75 CHARS[c - 'A'] = String.valueOf(c);
79 public static final ProfilesI calculate(List<SequenceI> list, int start,
82 return calculate(list, start, end, false);
85 public static final ProfilesI calculate(List<SequenceI> sequences,
86 int start, int end, boolean profile)
88 SequenceI[] seqs = new SequenceI[sequences.size()];
90 synchronized (sequences)
92 for (int i = 0; i < sequences.size(); i++)
94 seqs[i] = sequences.get(i);
95 int length = seqs[i].getLength();
107 ProfilesI reply = calculate(seqs, width, start, end, profile);
115 * Calculate the consensus symbol(s) for each column in the given range.
119 * the full width of the alignment
121 * start column (inclusive, base zero)
123 * end column (exclusive)
124 * @param saveFullProfile
125 * if true, store all symbol counts
127 public static final ProfilesI calculate(final SequenceI[] sequences,
128 int width, int start, int end, boolean saveFullProfile)
130 // long now = System.currentTimeMillis();
131 int seqCount = sequences.length;
132 boolean nucleotide = false;
133 int nucleotideCount = 0;
134 int peptideCount = 0;
136 ProfileI[] result = new ProfileI[width];
138 for (int column = start; column < end; column++)
141 * Apply a heuristic to detect nucleotide data (which can
142 * be counted in more compact arrays); here we test for
143 * more than 90% nucleotide; recheck every 10 columns in case
144 * of misleading data e.g. highly conserved Alanine in peptide!
145 * Mistakenly guessing nucleotide has a small performance cost,
146 * as it will result in counting in sparse arrays.
147 * Mistakenly guessing peptide has a small space cost,
148 * as it will use a larger than necessary array to hold counts.
150 if (nucleotideCount > 100 && column % 10 == 0)
152 nucleotide = (9 * peptideCount < nucleotideCount);
154 ResidueCount residueCounts = new ResidueCount(nucleotide);
156 for (int row = 0; row < seqCount; row++)
158 if (sequences[row] == null)
161 .println("WARNING: Consensus skipping null sequence - possible race condition.");
164 char[] seq = sequences[row].getSequence();
165 if (seq.length > column)
167 char c = seq[column];
168 residueCounts.add(c);
169 if (Comparison.isNucleotide(c))
173 else if (!Comparison.isGap(c))
181 * count a gap if the sequence doesn't reach this column
183 residueCounts.addGap();
187 int maxCount = residueCounts.getModalCount();
188 String maxResidue = residueCounts.getResiduesForCount(maxCount);
189 int gapCount = residueCounts.getGapCount();
190 ProfileI profile = new Profile(seqCount, gapCount, maxCount,
195 profile.setCounts(residueCounts);
198 result[column] = profile;
200 return new Profiles(result);
201 // long elapsed = System.currentTimeMillis() - now;
202 // System.out.println(elapsed);
206 * Returns the full set of profiles for a hidden Markov model. The underlying
207 * data is the raw probabilities of a residue being emitted at each node,
208 * however the profiles returned by this function contain the percentage
209 * chance of a residue emission.
213 * The width of the Profile array (Profiles) to be returned.
215 * The alignment column on which the first profile is based.
217 * The alignment column on which the last profile is based.
218 * @param saveFullProfile
219 * Flag for saving the counts for each profile
220 * @param removeBelowBackground
221 * Flag for removing any characters with a match emission probability
222 * less than its background frequency
225 public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
226 int width, int start, int end, boolean saveFullProfile,
227 boolean removeBelowBackground)
229 ProfileI[] result = new ProfileI[width];
230 int symbolCount = hmm.getNumberOfSymbols();
231 String alph = hmm.getAlphabetType();
232 for (int column = start; column < end; column++)
234 ResidueCount counts = new ResidueCount();
235 for (char symbol : hmm.getSymbols())
237 int value = getAnalogueCount(hmm, column, removeBelowBackground,
239 counts.put(symbol, value);
241 int maxCount = counts.getModalCount();
242 String maxResidue = counts.getResiduesForCount(maxCount);
243 int gapCount = counts.getGapCount();
244 ProfileI profile = new Profile(symbolCount, gapCount, maxCount,
249 profile.setCounts(counts);
252 result[column] = profile;
254 return new Profiles(result);
258 * Make an estimate of the profile size we are going to compute i.e. how many
259 * different characters may be present in it. Overestimating has a cost of
260 * using more memory than necessary. Underestimating has a cost of needing to
261 * extend the SparseIntArray holding the profile counts.
263 * @param profileSizes
264 * counts of sizes of profiles so far encountered
267 static int estimateProfileSize(SparseIntArray profileSizes)
269 if (profileSizes.size() == 0)
275 * could do a statistical heuristic here e.g. 75%ile
276 * for now just return the largest value
278 return profileSizes.keyAt(profileSizes.size() - 1);
282 * Derive the consensus annotations to be added to the alignment for display.
283 * This does not recompute the raw data, but may be called on a change in
284 * display options, such as 'ignore gaps', which may in turn result in a
285 * change in the derived values.
288 * the annotation row to add annotations to
290 * the source consensus data
292 * start column (inclusive)
294 * end column (exclusive)
296 * if true, normalise residue percentages ignoring gaps
297 * @param showSequenceLogo
298 * if true include all consensus symbols, else just show modal
301 * number of sequences
303 public static void completeConsensus(AlignmentAnnotation consensus,
304 ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
305 boolean showSequenceLogo, long nseq)
307 // long now = System.currentTimeMillis();
308 if (consensus == null || consensus.annotations == null
309 || consensus.annotations.length < endCol)
312 * called with a bad alignment annotation row
313 * wait for it to be initialised properly
318 for (int i = startCol; i < endCol; i++)
320 ProfileI profile = profiles.get(i);
324 * happens if sequences calculated over were
325 * shorter than alignment width
327 consensus.annotations[i] = null;
331 final int dp = getPercentageDp(nseq);
333 float value = profile.getPercentageIdentity(ignoreGaps);
335 String description = getTooltip(profile, value, showSequenceLogo,
338 String modalResidue = profile.getModalResidue();
339 if ("".equals(modalResidue))
343 else if (modalResidue.length() > 1)
347 consensus.annotations[i] = new Annotation(modalResidue, description,
350 // long elapsed = System.currentTimeMillis() - now;
351 // System.out.println(-elapsed);
355 * Derive the information annotations to be added to the alignment for
356 * display. This does not recompute the raw data, but may be called on a
357 * change in display options, such as 'ignore below background frequency',
358 * which may in turn result in a change in the derived values.
361 * the annotation row to add annotations to
363 * the source information data
365 * start column (inclusive)
367 * end column (exclusive)
369 * if true, normalise residue percentages
370 * @param showSequenceLogo
371 * if true include all information symbols, else just show modal
374 * number of sequences
376 public static void completeInformation(AlignmentAnnotation information,
377 ProfilesI profiles, int startCol, int endCol,
378 boolean ignoreBelowBackground,
379 boolean showSequenceLogo, long nseq)
381 // long now = System.currentTimeMillis();
382 if (information == null || information.annotations == null
383 || information.annotations.length < endCol)
386 * called with a bad alignment annotation row
387 * wait for it to be initialised properly
394 for (int i = startCol; i < endCol; i++)
396 ProfileI profile = profiles.get(i);
400 * happens if sequences calculated over were
401 * shorter than alignment width
403 information.annotations[i] = null;
407 HiddenMarkovModel hmm;
409 SequenceI hmmSeq = information.sequenceRef;
411 hmm = hmmSeq.getHMM();
413 Float value = getInformationContent(i, hmm);
420 String description = value + " bits";
421 information.annotations[i] = new Annotation(
422 Character.toString(hmm.getConsensusAtAlignColumn(i)),
423 description, ' ', value);
425 information.graphMax = max;
426 // long elapsed = System.currentTimeMillis() - now;
427 // System.out.println(-elapsed);
431 * Derive the gap count annotation row.
434 * the annotation row to add annotations to
436 * the source consensus data
438 * start column (inclusive)
440 * end column (exclusive)
442 public static void completeGapAnnot(AlignmentAnnotation gaprow,
443 ProfilesI profiles, int startCol, int endCol, long nseq)
445 if (gaprow == null || gaprow.annotations == null
446 || gaprow.annotations.length < endCol)
449 * called with a bad alignment annotation row
450 * wait for it to be initialised properly
454 // always set ranges again
455 gaprow.graphMax = nseq;
457 double scale = 0.8/nseq;
458 for (int i = startCol; i < endCol; i++)
460 ProfileI profile = profiles.get(i);
464 * happens if sequences calculated over were
465 * shorter than alignment width
467 gaprow.annotations[i] = null;
471 final int gapped = profile.getNonGapped();
473 String description = "" + gapped;
475 gaprow.annotations[i] = new Annotation("", description,
476 '\0', gapped, jalview.util.ColorUtils.bleachColour(
477 Color.DARK_GRAY, (float) scale * gapped));
482 * Returns a tooltip showing either
484 * <li>the full profile (percentages of all residues present), if
485 * showSequenceLogo is true, or</li>
486 * <li>just the modal (most common) residue(s), if showSequenceLogo is false</li>
488 * Percentages are as a fraction of all sequence, or only ungapped sequences
489 * if ignoreGaps is true.
493 * @param showSequenceLogo
496 * the number of decimal places to format percentages to
499 static String getTooltip(ProfileI profile, float pid,
500 boolean showSequenceLogo, boolean ignoreGaps, int dp)
502 ResidueCount counts = profile.getCounts();
504 String description = null;
505 if (counts != null && showSequenceLogo)
507 int normaliseBy = ignoreGaps ? profile.getNonGapped() : profile
509 description = counts.getTooltip(normaliseBy, dp);
513 StringBuilder sb = new StringBuilder(64);
514 String maxRes = profile.getModalResidue();
515 if (maxRes.length() > 1)
517 sb.append("[").append(maxRes).append("]");
523 if (maxRes.length() > 0)
526 Format.appendPercentage(sb, pid, dp);
529 description = sb.toString();
535 * Returns the sorted profile for the given consensus data. The returned array
539 * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
540 * in descending order of percentage value
544 * the data object from which to extract and sort values
546 * if true, only non-gapped values are included in percentage
550 public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
552 int[] rtnval = new int[64];
553 ResidueCount counts = profile.getCounts();
559 SymbolCounts symbolCounts = counts.getSymbolCounts();
560 char[] symbols = symbolCounts.symbols;
561 int[] values = symbolCounts.values;
562 QuickSort.sort(values, symbols);
563 int nextArrayPos = 2;
564 int totalPercentage = 0;
565 final int divisor = ignoreGaps ? profile.getNonGapped() : profile
569 * traverse the arrays in reverse order (highest counts first)
571 for (int i = symbols.length - 1; i >= 0; i--)
573 int theChar = symbols[i];
574 int charCount = values[i];
576 rtnval[nextArrayPos++] = theChar;
577 final int percentage = (charCount * 100) / divisor;
578 rtnval[nextArrayPos++] = percentage;
579 totalPercentage += percentage;
581 rtnval[0] = symbols.length;
582 rtnval[1] = totalPercentage;
583 int[] result = new int[rtnval.length + 1];
584 result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
585 System.arraycopy(rtnval, 0, result, 1, rtnval.length);
592 * Extract a sorted extract of cDNA codon profile data. The returned array
596 * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
597 * in descending order of percentage value, where the character values encode codon triplets
603 public static int[] extractCdnaProfile(Hashtable hashtable,
606 // this holds #seqs, #ungapped, and then codon count, indexed by encoded
608 int[] codonCounts = (int[]) hashtable.get(PROFILE);
609 int[] sortedCounts = new int[codonCounts.length - 2];
610 System.arraycopy(codonCounts, 2, sortedCounts, 0,
611 codonCounts.length - 2);
613 int[] result = new int[3 + 2 * sortedCounts.length];
614 // first value is just the type of profile data
615 result[0] = AlignmentAnnotation.CDNA_PROFILE;
617 char[] codons = new char[sortedCounts.length];
618 for (int i = 0; i < codons.length; i++)
620 codons[i] = (char) i;
622 QuickSort.sort(sortedCounts, codons);
623 int totalPercentage = 0;
624 int distinctValuesCount = 0;
626 int divisor = ignoreGaps ? codonCounts[1] : codonCounts[0];
627 for (int i = codons.length - 1; i >= 0; i--)
629 final int codonCount = sortedCounts[i];
632 break; // nothing else of interest here
634 distinctValuesCount++;
635 result[j++] = codons[i];
636 final int percentage = codonCount * 100 / divisor;
637 result[j++] = percentage;
638 totalPercentage += percentage;
640 result[2] = totalPercentage;
643 * Just return the non-zero values
645 // todo next value is redundant if we limit the array to non-zero counts
646 result[1] = distinctValuesCount;
647 return Arrays.copyOfRange(result, 0, j);
651 * Compute a consensus for the cDNA coding for a protein alignment.
654 * the protein alignment (which should hold mappings to cDNA
657 * the consensus data stores to be populated (one per column)
659 public static void calculateCdna(AlignmentI alignment,
660 Hashtable[] hconsensus)
662 final char gapCharacter = alignment.getGapCharacter();
663 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
664 if (mappings == null || mappings.isEmpty())
669 int cols = alignment.getWidth();
670 for (int col = 0; col < cols; col++)
672 // todo would prefer a Java bean for consensus data
673 Hashtable<String, int[]> columnHash = new Hashtable<>();
674 // #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
675 int[] codonCounts = new int[66];
676 codonCounts[0] = alignment.getSequences().size();
677 int ungappedCount = 0;
678 for (SequenceI seq : alignment.getSequences())
680 if (seq.getCharAt(col) == gapCharacter)
684 List<char[]> codons = MappingUtils
685 .findCodonsFor(seq, col, mappings);
686 for (char[] codon : codons)
688 int codonEncoded = CodingUtils.encodeCodon(codon);
689 if (codonEncoded >= 0)
691 codonCounts[codonEncoded + 2]++;
696 codonCounts[1] = ungappedCount;
697 // todo: sort values here, save counts and codons?
698 columnHash.put(PROFILE, codonCounts);
699 hconsensus[col] = columnHash;
704 * Derive displayable cDNA consensus annotation from computed consensus data.
706 * @param consensusAnnotation
707 * the annotation row to be populated for display
708 * @param consensusData
709 * the computed consensus data
710 * @param showProfileLogo
711 * if true show all symbols present at each position, else only the
714 * the number of sequences in the alignment
716 public static void completeCdnaConsensus(
717 AlignmentAnnotation consensusAnnotation,
718 Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
720 if (consensusAnnotation == null
721 || consensusAnnotation.annotations == null
722 || consensusAnnotation.annotations.length < consensusData.length)
724 // called with a bad alignment annotation row - wait for it to be
725 // initialised properly
729 // ensure codon triplet scales with font size
730 consensusAnnotation.scaleColLabel = true;
731 for (int col = 0; col < consensusData.length; col++)
733 Hashtable hci = consensusData[col];
736 // gapped protein column?
739 // array holds #seqs, #ungapped, then codon counts indexed by codon
740 final int[] codonCounts = (int[]) hci.get(PROFILE);
744 * First pass - get total count and find the highest
746 final char[] codons = new char[codonCounts.length - 2];
747 for (int j = 2; j < codonCounts.length; j++)
749 final int codonCount = codonCounts[j];
750 codons[j - 2] = (char) (j - 2);
751 totalCount += codonCount;
755 * Sort array of encoded codons by count ascending - so the modal value
756 * goes to the end; start by copying the count (dropping the first value)
758 int[] sortedCodonCounts = new int[codonCounts.length - 2];
759 System.arraycopy(codonCounts, 2, sortedCodonCounts, 0,
760 codonCounts.length - 2);
761 QuickSort.sort(sortedCodonCounts, codons);
763 int modalCodonEncoded = codons[codons.length - 1];
764 int modalCodonCount = sortedCodonCounts[codons.length - 1];
765 String modalCodon = String.valueOf(CodingUtils
766 .decodeCodon(modalCodonEncoded));
767 if (sortedCodonCounts.length > 1
768 && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
771 * two or more codons share the modal count
775 float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100
776 / (float) totalCount;
779 * todo ? Replace consensus hashtable with sorted arrays of codons and
780 * counts (non-zero only). Include total count in count array [0].
784 * Scan sorted array backwards for most frequent values first. Show
785 * repeated values compactly.
787 StringBuilder mouseOver = new StringBuilder(32);
788 StringBuilder samePercent = new StringBuilder();
789 String percent = null;
790 String lastPercent = null;
791 int percentDecPl = getPercentageDp(nseqs);
793 for (int j = codons.length - 1; j >= 0; j--)
795 int codonCount = sortedCodonCounts[j];
799 * remaining codons are 0% - ignore, but finish off the last one if
802 if (samePercent.length() > 0)
804 mouseOver.append(samePercent).append(": ").append(percent)
809 int codonEncoded = codons[j];
810 final int pct = codonCount * 100 / totalCount;
811 String codon = String
812 .valueOf(CodingUtils.decodeCodon(codonEncoded));
813 StringBuilder sb = new StringBuilder();
814 Format.appendPercentage(sb, pct, percentDecPl);
815 percent = sb.toString();
816 if (showProfileLogo || codonCount == modalCodonCount)
818 if (percent.equals(lastPercent) && j > 0)
820 samePercent.append(samePercent.length() == 0 ? "" : ", ");
821 samePercent.append(codon);
825 if (samePercent.length() > 0)
827 mouseOver.append(samePercent).append(": ")
828 .append(lastPercent).append("% ");
830 samePercent.setLength(0);
831 samePercent.append(codon);
833 lastPercent = percent;
837 consensusAnnotation.annotations[col] = new Annotation(modalCodon,
838 mouseOver.toString(), ' ', pid);
843 * Returns the number of decimal places to show for profile percentages. For
844 * less than 100 sequences, returns zero (the integer percentage value will be
845 * displayed). For 100-999 sequences, returns 1, for 1000-9999 returns 2, etc.
850 protected static int getPercentageDp(long nseq)
862 * Returns the information content at a specified column.
865 * Index of the column, starting from 0.
868 public static float getInformationContent(int column,
869 HiddenMarkovModel hmm)
871 float informationContent = 0f;
873 for (char symbol : hmm.getSymbols())
876 freq = ResidueProperties.backgroundFrequencies
877 .get(hmm.getAlphabetType()).get(symbol);
878 Double hmmProb = hmm.getMatchEmissionProbability(column, symbol);
879 float prob = hmmProb.floatValue();
880 informationContent += prob * (Math.log(prob / freq) / Math.log(2));
884 return informationContent;
888 * Produces a HMM profile for a column in an alignment
891 * Alignment annotation for which the profile is being calculated.
893 * Column in the alignment the profile is being made for.
894 * @param removeBelowBackground
895 * Boolean indicating whether to ignore residues with probabilities
896 * less than their background frequencies.
899 public static int[] extractHMMProfile(HiddenMarkovModel hmm, int column,
900 boolean removeBelowBackground)
905 String alph = hmm.getAlphabetType();
906 int size = hmm.getNumberOfSymbols();
907 char symbols[] = new char[size];
908 int values[] = new int[size];
909 List<Character> charList = hmm.getSymbols();
910 Integer totalCount = 0;
912 for (int i = 0; i < size; i++)
914 char symbol = charList.get(i);
916 int value = getAnalogueCount(hmm, column, removeBelowBackground,
922 QuickSort.sort(values, symbols);
924 int[] profile = new int[3 + size * 2];
926 profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
933 for (int k = size - 1; k >= 0; k--)
936 Integer value = values[k];
937 if (removeBelowBackground)
939 percentage = (value.floatValue() / totalCount.floatValue())
944 percentage = value.floatValue() / 100f;
946 int intPercent = Math.round(percentage);
947 profile[arrayPos] = symbols[k];
948 profile[arrayPos + 1] = intPercent;
958 * Converts the emission probability of a residue at a column in the alignment
959 * to a 'count' to allow for processing by the annotation renderer.
963 * @param removeBelowBackground
965 * The alphabet the HMM is based on
969 private static int getAnalogueCount(HiddenMarkovModel hmm, int column,
970 boolean removeBelowBackground, String alph, char symbol)
974 value = hmm.getMatchEmissionProbability(column, symbol);
977 freq = ResidueProperties.backgroundFrequencies.get(alph).get(symbol);
978 if (value < freq && removeBelowBackground)
983 value = value * 10000;
984 return Math.round(value.floatValue());