sequences,
int start, int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
@@ -61,297 +83,637 @@ public class AAFrequency
for (int i = 0; i < sequences.size(); i++)
{
seqs[i] = sequences.get(i);
- if (seqs[i].getLength() > width)
+ int length = seqs[i].getLength();
+ if (length > width)
{
- width = seqs[i].getLength();
+ width = length;
}
}
- Hashtable[] reply = new Hashtable[width];
-
if (end >= width)
{
end = width;
}
- calculate(seqs, start, end, reply, profile);
+ ProfilesI reply = calculate(seqs, width, start, end, profile);
return reply;
}
}
- public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result)
- {
- calculate(sequences, start, end, result, false);
- }
-
- public static final void calculate(SequenceI[] sequences, int start,
- int end, Hashtable[] result, boolean profile)
+ /**
+ * Calculate the consensus symbol(s) for each column in the given range.
+ *
+ * @param sequences
+ * @param width
+ * the full width of the alignment
+ * @param start
+ * start column (inclusive, base zero)
+ * @param end
+ * end column (exclusive)
+ * @param saveFullProfile
+ * if true, store all symbol counts
+ */
+ public static final ProfilesI calculate(final SequenceI[] sequences,
+ int width, int start, int end, boolean saveFullProfile)
{
- Hashtable residueHash;
- int maxCount, nongap, i, j, v, jSize = sequences.length;
- String maxResidue;
- char c;
- float percentage;
+ // long now = System.currentTimeMillis();
+ int seqCount = sequences.length;
+ boolean nucleotide = false;
+ int nucleotideCount = 0;
+ int peptideCount = 0;
- int[] values = new int[255];
+ ProfileI[] result = new ProfileI[width];
- char[] seq;
-
- for (i = start; i < end; i++)
+ for (int column = start; column < end; column++)
{
- residueHash = new Hashtable();
- maxCount = 0;
- maxResidue = "";
- nongap = 0;
- values = new int[255];
+ /*
+ * Apply a heuristic to detect nucleotide data (which can
+ * be counted in more compact arrays); here we test for
+ * more than 90% nucleotide; recheck every 10 columns in case
+ * of misleading data e.g. highly conserved Alanine in peptide!
+ * Mistakenly guessing nucleotide has a small performance cost,
+ * as it will result in counting in sparse arrays.
+ * Mistakenly guessing peptide has a small space cost,
+ * as it will use a larger than necessary array to hold counts.
+ */
+ if (nucleotideCount > 100 && column % 10 == 0)
+ {
+ nucleotide = (9 * peptideCount < nucleotideCount);
+ }
+ ResidueCount residueCounts = new ResidueCount(nucleotide);
- for (j = 0; j < jSize; j++)
+ for (int row = 0; row < seqCount; row++)
{
- if (sequences[j] == null)
+ if (sequences[row] == null)
{
System.err
.println("WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- seq = sequences[j].getSequence();
- if (seq.length > i)
+ char[] seq = sequences[row].getSequence();
+ if (seq.length > column)
{
- c = seq[i];
-
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (c == '-')
+ char c = seq[column];
+ residueCounts.add(c);
+ if (Comparison.isNucleotide(c))
{
- values['-']++;
- continue;
+ nucleotideCount++;
}
- else if ('a' <= c && c <= 'z')
+ else if (!Comparison.isGap(c))
{
- c -= 32; // ('a' - 'A');
+ peptideCount++;
}
-
- nongap++;
- values[c]++;
-
}
else
{
- values['-']++;
+ /*
+ * count a gap if the sequence doesn't reach this column
+ */
+ residueCounts.addGap();
}
}
- for (v = 'A'; v < 'Z'; v++)
- {
- if (values[v] < 2 || values[v] < maxCount)
- {
- continue;
- }
+ int maxCount = residueCounts.getModalCount();
+ String maxResidue = residueCounts.getResiduesForCount(maxCount);
+ int gapCount = residueCounts.getGapCount();
+ ProfileI profile = new Profile(seqCount, gapCount, maxCount,
+ maxResidue);
- if (values[v] > maxCount)
- {
- maxResidue = String.valueOf((char) v);
- }
- else if (values[v] == maxCount)
- {
- maxResidue += String.valueOf((char) v);
- }
- maxCount = values[v];
- }
-
- if (maxResidue.length() == 0)
- {
- maxResidue = "-";
- }
- if (profile)
+ if (saveFullProfile)
{
- residueHash.put(PROFILE, new int[][]
- { values, new int[]
- { jSize, nongap } });
+ profile.setCounts(residueCounts);
}
- residueHash.put(MAXCOUNT, new Integer(maxCount));
- residueHash.put(MAXRESIDUE, maxResidue);
-
- percentage = ((float) maxCount * 100) / jSize;
- residueHash.put(PID_GAPS, new Float(percentage));
- percentage = ((float) maxCount * 100) / nongap;
- residueHash.put(PID_NOGAPS, new Float(percentage));
- result[i] = residueHash;
+ result[column] = profile;
}
+ return new Profiles(result);
+ // long elapsed = System.currentTimeMillis() - now;
+ // System.out.println(elapsed);
}
/**
- * Compute all or part of the annotation row from the given consensus
- * hashtable
+ * Make an estimate of the profile size we are going to compute i.e. how many
+ * different characters may be present in it. Overestimating has a cost of
+ * using more memory than necessary. Underestimating has a cost of needing to
+ * extend the SparseIntArray holding the profile counts.
*
- * @param consensus
- * - pre-allocated annotation row
- * @param hconsensus
- * @param iStart
- * @param width
- * @param ignoreGapsInConsensusCalculation
- * @param includeAllConsSymbols
- * @param nseq
+ * @param profileSizes
+ * counts of sizes of profiles so far encountered
+ * @return
*/
- public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
- boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, long nseq)
+ static int estimateProfileSize(SparseIntArray profileSizes)
{
- completeConsensus(consensus, hconsensus, iStart, width,
- ignoreGapsInConsensusCalculation, includeAllConsSymbols, null, nseq); // new
- // char[]
- // { 'A', 'C', 'G', 'T', 'U' });
+ if (profileSizes.size() == 0)
+ {
+ return 4;
+ }
+
+ /*
+ * could do a statistical heuristic here e.g. 75%ile
+ * for now just return the largest value
+ */
+ return profileSizes.keyAt(profileSizes.size() - 1);
}
+ /**
+ * Derive the consensus annotations to be added to the alignment for display.
+ * This does not recompute the raw data, but may be called on a change in
+ * display options, such as 'ignore gaps', which may in turn result in a
+ * change in the derived values.
+ *
+ * @param consensus
+ * the annotation row to add annotations to
+ * @param profiles
+ * the source consensus data
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
+ * @param ignoreGaps
+ * if true, normalise residue percentages ignoring gaps
+ * @param showSequenceLogo
+ * if true include all consensus symbols, else just show modal
+ * residue
+ * @param nseq
+ * number of sequences
+ */
public static void completeConsensus(AlignmentAnnotation consensus,
- Hashtable[] hconsensus, int iStart, int width,
- boolean ignoreGapsInConsensusCalculation,
- boolean includeAllConsSymbols, char[] alphabet, long nseq)
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
+ boolean showSequenceLogo, long nseq)
{
- float tval, value;
+ // long now = System.currentTimeMillis();
if (consensus == null || consensus.annotations == null
- || consensus.annotations.length < width)
+ || consensus.annotations.length < endCol)
{
- // called with a bad alignment annotation row - wait for it to be
- // initialised properly
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
return;
}
- String fmtstr="%3.1f";
- int precision=2;
- while (nseq>100) {
- precision++;
- nseq/=10;
+
+ for (int i = startCol; i < endCol; i++)
+ {
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
+ {
+ /*
+ * happens if sequences calculated over were
+ * shorter than alignment width
+ */
+ consensus.annotations[i] = null;
+ return;
+ }
+
+ final int dp = getPercentageDp(nseq);
+
+ float value = profile.getPercentageIdentity(ignoreGaps);
+
+ String description = getTooltip(profile, value, showSequenceLogo,
+ ignoreGaps, dp);
+
+ String modalResidue = profile.getModalResidue();
+ if ("".equals(modalResidue))
+ {
+ modalResidue = "-";
+ }
+ else if (modalResidue.length() > 1)
+ {
+ modalResidue = "+";
+ }
+ consensus.annotations[i] = new Annotation(modalResidue, description,
+ ' ', value);
}
- if (precision>2)
+ // long elapsed = System.currentTimeMillis() - now;
+ // System.out.println(-elapsed);
+ }
+
+ /**
+ * Derive the gap count annotation row.
+ *
+ * @param consensus
+ * the annotation row to add annotations to
+ * @param profiles
+ * the source consensus data
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
+ */
+ public static void completeGapAnnot(AlignmentAnnotation consensus,
+ ProfilesI profiles, int startCol, int endCol, long nseq)
+ {
+ if (consensus == null || consensus.annotations == null
+ || consensus.annotations.length < endCol)
{
- fmtstr = "%"+(2+precision)+"."+precision+"f";
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
+ return;
}
- Format fmt = new Format(fmtstr);
- for (int i = iStart; i < width; i++)
+ // always set ranges again
+ consensus.graphMax = nseq;
+ consensus.graphMin = 0;
+ for (int i = startCol; i < endCol; i++)
{
- Hashtable hci;
- if (i >= hconsensus.length || ((hci = hconsensus[i]) == null))
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
{
- // happens if sequences calculated over were shorter than alignment
- // width
+ /*
+ * happens if sequences calculated over were
+ * shorter than alignment width
+ */
consensus.annotations[i] = null;
- continue;
+ return;
}
- value = 0;
- Float fv;
- if (ignoreGapsInConsensusCalculation)
+
+ final int gapped = profile.getNonGapped();
+
+ String description = String.valueOf(gapped);
+
+ consensus.annotations[i] = new Annotation(description, description,
+ '\0',
+ gapped);
+ }
+ }
+
+ /**
+ * Returns a tooltip showing either
+ *
+ * - the full profile (percentages of all residues present), if
+ * showSequenceLogo is true, or
+ * - just the modal (most common) residue(s), if showSequenceLogo is false
+ *
+ * Percentages are as a fraction of all sequence, or only ungapped sequences
+ * if ignoreGaps is true.
+ *
+ * @param profile
+ * @param pid
+ * @param showSequenceLogo
+ * @param ignoreGaps
+ * @param dp
+ * the number of decimal places to format percentages to
+ * @return
+ */
+ static String getTooltip(ProfileI profile, float pid,
+ boolean showSequenceLogo, boolean ignoreGaps, int dp)
+ {
+ ResidueCount counts = profile.getCounts();
+
+ String description = null;
+ if (counts != null && showSequenceLogo)
+ {
+ int normaliseBy = ignoreGaps ? profile.getNonGapped() : profile
+ .getHeight();
+ description = counts.getTooltip(normaliseBy, dp);
+ }
+ else
+ {
+ StringBuilder sb = new StringBuilder(64);
+ String maxRes = profile.getModalResidue();
+ if (maxRes.length() > 1)
{
- fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
+ sb.append("[").append(maxRes).append("]");
}
else
{
- fv = (Float) hci.get(AAFrequency.PID_GAPS);
+ sb.append(maxRes);
}
- if (fv == null)
+ if (maxRes.length() > 0)
{
- consensus.annotations[i] = null;
- // data has changed below us .. give up and
+ sb.append(" ");
+ Format.appendPercentage(sb, pid, dp);
+ sb.append("%");
+ }
+ description = sb.toString();
+ }
+ return description;
+ }
+
+ /**
+ * Returns the sorted profile for the given consensus data. The returned array
+ * contains
+ *
+ *
+ * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value
+ *
+ *
+ * @param profile
+ * the data object from which to extract and sort values
+ * @param ignoreGaps
+ * if true, only non-gapped values are included in percentage
+ * calculations
+ * @return
+ */
+ public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
+ {
+ int[] rtnval = new int[64];
+ ResidueCount counts = profile.getCounts();
+ if (counts == null)
+ {
+ return null;
+ }
+
+ SymbolCounts symbolCounts = counts.getSymbolCounts();
+ char[] symbols = symbolCounts.symbols;
+ int[] values = symbolCounts.values;
+ QuickSort.sort(values, symbols);
+ int nextArrayPos = 2;
+ int totalPercentage = 0;
+ final int divisor = ignoreGaps ? profile.getNonGapped() : profile
+ .getHeight();
+
+ /*
+ * traverse the arrays in reverse order (highest counts first)
+ */
+ for (int i = symbols.length - 1; i >= 0; i--)
+ {
+ int theChar = symbols[i];
+ int charCount = values[i];
+
+ rtnval[nextArrayPos++] = theChar;
+ final int percentage = (charCount * 100) / divisor;
+ rtnval[nextArrayPos++] = percentage;
+ totalPercentage += percentage;
+ }
+ rtnval[0] = symbols.length;
+ rtnval[1] = totalPercentage;
+ int[] result = new int[rtnval.length + 1];
+ result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+ System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+
+ return result;
+ }
+
+ /**
+ * Extract a sorted extract of cDNA codon profile data. The returned array
+ * contains
+ *
+ *
+ * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value, where the character values encode codon triplets
+ *
+ *
+ * @param hashtable
+ * @return
+ */
+ public static int[] extractCdnaProfile(Hashtable hashtable,
+ boolean ignoreGaps)
+ {
+ // this holds #seqs, #ungapped, and then codon count, indexed by encoded
+ // codon triplet
+ int[] codonCounts = (int[]) hashtable.get(PROFILE);
+ int[] sortedCounts = new int[codonCounts.length - 2];
+ System.arraycopy(codonCounts, 2, sortedCounts, 0,
+ codonCounts.length - 2);
+
+ int[] result = new int[3 + 2 * sortedCounts.length];
+ // first value is just the type of profile data
+ result[0] = AlignmentAnnotation.CDNA_PROFILE;
+
+ char[] codons = new char[sortedCounts.length];
+ for (int i = 0; i < codons.length; i++)
+ {
+ codons[i] = (char) i;
+ }
+ QuickSort.sort(sortedCounts, codons);
+ int totalPercentage = 0;
+ int distinctValuesCount = 0;
+ int j = 3;
+ int divisor = ignoreGaps ? codonCounts[1] : codonCounts[0];
+ for (int i = codons.length - 1; i >= 0; i--)
+ {
+ final int codonCount = sortedCounts[i];
+ if (codonCount == 0)
+ {
+ break; // nothing else of interest here
+ }
+ distinctValuesCount++;
+ result[j++] = codons[i];
+ final int percentage = codonCount * 100 / divisor;
+ result[j++] = percentage;
+ totalPercentage += percentage;
+ }
+ result[2] = totalPercentage;
+
+ /*
+ * Just return the non-zero values
+ */
+ // todo next value is redundant if we limit the array to non-zero counts
+ result[1] = distinctValuesCount;
+ return Arrays.copyOfRange(result, 0, j);
+ }
+
+ /**
+ * Compute a consensus for the cDNA coding for a protein alignment.
+ *
+ * @param alignment
+ * the protein alignment (which should hold mappings to cDNA
+ * sequences)
+ * @param hconsensus
+ * the consensus data stores to be populated (one per column)
+ */
+ public static void calculateCdna(AlignmentI alignment,
+ Hashtable[] hconsensus)
+ {
+ final char gapCharacter = alignment.getGapCharacter();
+ List mappings = alignment.getCodonFrames();
+ if (mappings == null || mappings.isEmpty())
+ {
+ return;
+ }
+
+ int cols = alignment.getWidth();
+ for (int col = 0; col < cols; col++)
+ {
+ // todo would prefer a Java bean for consensus data
+ Hashtable columnHash = new Hashtable();
+ // #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
+ int[] codonCounts = new int[66];
+ codonCounts[0] = alignment.getSequences().size();
+ int ungappedCount = 0;
+ for (SequenceI seq : alignment.getSequences())
+ {
+ if (seq.getCharAt(col) == gapCharacter)
+ {
+ continue;
+ }
+ List codons = MappingUtils
+ .findCodonsFor(seq, col, mappings);
+ for (char[] codon : codons)
+ {
+ int codonEncoded = CodingUtils.encodeCodon(codon);
+ if (codonEncoded >= 0)
+ {
+ codonCounts[codonEncoded + 2]++;
+ ungappedCount++;
+ }
+ }
+ }
+ codonCounts[1] = ungappedCount;
+ // todo: sort values here, save counts and codons?
+ columnHash.put(PROFILE, codonCounts);
+ hconsensus[col] = columnHash;
+ }
+ }
+
+ /**
+ * Derive displayable cDNA consensus annotation from computed consensus data.
+ *
+ * @param consensusAnnotation
+ * the annotation row to be populated for display
+ * @param consensusData
+ * the computed consensus data
+ * @param showProfileLogo
+ * if true show all symbols present at each position, else only the
+ * modal value
+ * @param nseqs
+ * the number of sequences in the alignment
+ */
+ public static void completeCdnaConsensus(
+ AlignmentAnnotation consensusAnnotation,
+ Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
+ {
+ if (consensusAnnotation == null
+ || consensusAnnotation.annotations == null
+ || consensusAnnotation.annotations.length < consensusData.length)
+ {
+ // called with a bad alignment annotation row - wait for it to be
+ // initialised properly
+ return;
+ }
+
+ // ensure codon triplet scales with font size
+ consensusAnnotation.scaleColLabel = true;
+ for (int col = 0; col < consensusData.length; col++)
+ {
+ Hashtable hci = consensusData[col];
+ if (hci == null)
+ {
+ // gapped protein column?
continue;
}
- value = fv.floatValue();
- String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
- String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
- if (maxRes.length() > 1)
+ // array holds #seqs, #ungapped, then codon counts indexed by codon
+ final int[] codonCounts = (int[]) hci.get(PROFILE);
+ int totalCount = 0;
+
+ /*
+ * First pass - get total count and find the highest
+ */
+ final char[] codons = new char[codonCounts.length - 2];
+ for (int j = 2; j < codonCounts.length; j++)
{
- mouseOver = "[" + maxRes + "] ";
- maxRes = "+";
+ final int codonCount = codonCounts[j];
+ codons[j - 2] = (char) (j - 2);
+ totalCount += codonCount;
}
- int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
- if (profile != null && includeAllConsSymbols)
+
+ /*
+ * Sort array of encoded codons by count ascending - so the modal value
+ * goes to the end; start by copying the count (dropping the first value)
+ */
+ int[] sortedCodonCounts = new int[codonCounts.length - 2];
+ System.arraycopy(codonCounts, 2, sortedCodonCounts, 0,
+ codonCounts.length - 2);
+ QuickSort.sort(sortedCodonCounts, codons);
+
+ int modalCodonEncoded = codons[codons.length - 1];
+ int modalCodonCount = sortedCodonCounts[codons.length - 1];
+ String modalCodon = String.valueOf(CodingUtils
+ .decodeCodon(modalCodonEncoded));
+ if (sortedCodonCounts.length > 1
+ && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
{
- mouseOver = "";
- if (alphabet != null)
+ /*
+ * two or more codons share the modal count
+ */
+ modalCodon = "+";
+ }
+ float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100
+ / (float) totalCount;
+
+ /*
+ * todo ? Replace consensus hashtable with sorted arrays of codons and
+ * counts (non-zero only). Include total count in count array [0].
+ */
+
+ /*
+ * Scan sorted array backwards for most frequent values first. Show
+ * repeated values compactly.
+ */
+ StringBuilder mouseOver = new StringBuilder(32);
+ StringBuilder samePercent = new StringBuilder();
+ String percent = null;
+ String lastPercent = null;
+ int percentDecPl = getPercentageDp(nseqs);
+
+ for (int j = codons.length - 1; j >= 0; j--)
+ {
+ int codonCount = sortedCodonCounts[j];
+ if (codonCount == 0)
{
- for (int c = 0; c < alphabet.length; c++)
+ /*
+ * remaining codons are 0% - ignore, but finish off the last one if
+ * necessary
+ */
+ if (samePercent.length() > 0)
{
- tval = profile[0][alphabet[c]] * 100f
- / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
- mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
- + fmt.form(tval) + "%";
+ mouseOver.append(samePercent).append(": ").append(percent)
+ .append("% ");
}
+ break;
}
- else
+ int codonEncoded = codons[j];
+ final int pct = codonCount * 100 / totalCount;
+ String codon = String
+ .valueOf(CodingUtils.decodeCodon(codonEncoded));
+ StringBuilder sb = new StringBuilder();
+ Format.appendPercentage(sb, pct, percentDecPl);
+ percent = sb.toString();
+ if (showProfileLogo || codonCount == modalCodonCount)
{
- Object[] ca = new Object[profile[0].length];
- float[] vl = new float[profile[0].length];
- for (int c = 0; c < ca.length; c++)
+ if (percent.equals(lastPercent) && j > 0)
{
- ca[c] = new char[]
- { (char) c };
- vl[c] = profile[0][c];
+ samePercent.append(samePercent.length() == 0 ? "" : ", ");
+ samePercent.append(codon);
}
- ;
- jalview.util.QuickSort.sort(vl, ca);
- for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ else
{
- if (((char[]) ca[c])[0] != '-')
+ if (samePercent.length() > 0)
{
- tval = profile[0][((char[]) ca[c])[0]]
- * 100f
- / profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
- mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
- + " " + fmt.form(tval) + "%";
- p++;
-
+ mouseOver.append(samePercent).append(": ")
+ .append(lastPercent).append("% ");
}
+ samePercent.setLength(0);
+ samePercent.append(codon);
}
-
+ lastPercent = percent;
}
}
- else
- {
- mouseOver += (fmt.form(value) + "%");
- }
- consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
- value);
+
+ consensusAnnotation.annotations[col] = new Annotation(modalCodon,
+ mouseOver.toString(), ' ', pid);
}
}
/**
- * get the sorted profile for the given position of the consensus
+ * Returns the number of decimal places to show for profile percentages. For
+ * less than 100 sequences, returns zero (the integer percentage value will be
+ * displayed). For 100-999 sequences, returns 1, for 1000-9999 returns 2, etc.
*
- * @param hconsensus
+ * @param nseq
* @return
*/
- public static int[] extractProfile(Hashtable hconsensus,
- boolean ignoreGapsInConsensusCalculation)
+ protected static int getPercentageDp(long nseq)
{
- int[] rtnval = new int[64];
- int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
- if (profile == null)
- return null;
- Object[] ca = new Object[profile[0].length];
- float[] vl = new float[profile[0].length];
- for (int c = 0; c < ca.length; c++)
- {
- ca[c] = new char[]
- { (char) c };
- vl[c] = profile[0][c];
- }
- ;
- jalview.util.QuickSort.sort(vl, ca);
- rtnval[0] = 2;
- rtnval[1] = 0;
- for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+ int scale = 0;
+ while (nseq >= 100)
{
- if (((char[]) ca[c])[0] != '-')
- {
- rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
- rtnval[rtnval[0]] = (int) (profile[0][((char[]) ca[c])[0]] * 100f / profile[1][ignoreGapsInConsensusCalculation ? 1
- : 0]);
- rtnval[1] += rtnval[rtnval[0]++];
- }
+ scale++;
+ nseq /= 10;
}
- return rtnval;
+ return scale;
}
}