*/
package jalview.analysis;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.ResidueCount;
import jalview.datamodel.ResidueCount.SymbolCounts;
+import jalview.datamodel.SecondaryStructureCount;
import jalview.datamodel.SequenceI;
import jalview.ext.android.SparseIntArray;
import jalview.util.Comparison;
import jalview.util.MappingUtils;
import jalview.util.QuickSort;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+
/**
* Takes in a vector or array of sequences and column start and column end and
* returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
public class AAFrequency
{
public static final String PROFILE = "P";
+ private static final String SS_ANNOTATION_LABEL = "Secondary Structure";
+ private static final char COIL = 'C';
/*
* Quick look-up of String value of char 'A' to 'Z'
{
if (sequences[row] == null)
{
- System.err
- .println("WARNING: Consensus skipping null sequence - possible race condition.");
+ jalview.bin.Console.errPrintln(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
- char[] seq = sequences[row].getSequence();
- if (seq.length > column)
+ if (sequences[row].getLength() > column)
{
- char c = seq[column];
+ char c = sequences[row].getCharAt(column);
residueCounts.add(c);
if (Comparison.isNucleotide(c))
{
}
return new Profiles(result);
// long elapsed = System.currentTimeMillis() - now;
- // System.out.println(elapsed);
+ // jalview.bin.Console.outPrintln(elapsed);
+ }
+
+
+ public static final ProfilesI calculateSS(List<SequenceI> list, int start,
+ int end)
+ {
+ return calculateSS(list, start, end, false);
+ }
+
+ public static final ProfilesI calculateSS(List<SequenceI> sequences,
+ int start, int end, boolean profile)
+ {
+ SequenceI[] seqs = new SequenceI[sequences.size()];
+ int width = 0;
+ synchronized (sequences)
+ {
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ seqs[i] = sequences.get(i);
+ int length = seqs[i].getLength();
+ if (length > width)
+ {
+ width = length;
+ }
+ }
+
+ if (end >= width)
+ {
+ end = width;
+ }
+
+ ProfilesI reply = calculateSS(seqs, width, start, end, profile);
+ return reply;
+ }
+ }
+
+ public static final ProfilesI calculateSS(final SequenceI[] sequences,
+ int width, int start, int end, boolean saveFullProfile)
+ {
+ // long now = System.currentTimeMillis();
+ int seqCount = sequences.length;
+
+ ProfileI[] result = new ProfileI[width];
+
+ for (int column = start; column < end; column++)
+ {
+ /*
+ * 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.
+ */
+
+ int ssCount = 0;
+
+ SecondaryStructureCount ssCounts = new SecondaryStructureCount();
+
+ for (int row = 0; row < seqCount; row++)
+ {
+ if (sequences[row] == null)
+ {
+ jalview.bin.Console.errPrintln(
+ "WARNING: Consensus skipping null sequence - possible race condition.");
+ continue;
+ }
+
+ char c = sequences[row].getCharAt(column);
+
+ if (sequences[row].getLength() > column && !Comparison.isGap(c))
+ {
+
+ AlignmentAnnotation[] aa = sequences[row].getAnnotation(SS_ANNOTATION_LABEL);
+ if(aa == null) {
+ continue;
+ }
+ int seqPosition = sequences[row].findPosition(column);
+ char ss;
+ if (aa[0].getAnnotationForPosition(seqPosition) != null) {
+ ss = aa[0].getAnnotationForPosition(seqPosition).secondaryStructure;
+
+ //There is no representation for coil and it can be either ' ' or null.
+ if (ss == ' ') {
+ ss = COIL;
+ }
+ }
+ else {
+ ss = COIL;
+ }
+
+ //secondaryStructures[row][column] = ss;
+
+ ssCounts.add(ss);
+ ssCount++;
+
+ }
+ else
+ {
+ /*
+ * count a gap if the sequence doesn't reach this column
+ */
+ ssCounts.addGap();
+ }
+ }
+
+ int maxSSCount = ssCounts.getModalCount();
+ String maxSS = ssCounts.getSSForCount(maxSSCount);
+ int gapCount = ssCounts.getGapCount();
+ ProfileI profile = new Profile(maxSS, ssCount, gapCount,
+ maxSSCount);
+
+ if (saveFullProfile)
+ {
+ profile.setSSCounts(ssCounts);
+ }
+
+ result[column] = profile;
+ }
+ return new Profiles(result);
+ // long elapsed = System.currentTimeMillis() - now;
+ // jalview.bin.Console.outPrintln(elapsed);
}
/**
' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
- // System.out.println(-elapsed);
+ // jalview.bin.Console.outPrintln(-elapsed);
}
+
+
+ public static void completeSSConsensus(AlignmentAnnotation ssConsensus,
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
+ boolean showSequenceLogo, long nseq)
+ {
+ // long now = System.currentTimeMillis();
+ if (ssConsensus == null || ssConsensus.annotations == null
+ || ssConsensus.annotations.length < endCol)
+ {
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
+ return;
+ }
+
+ 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
+ */
+ ssConsensus.annotations[i] = null;
+ return;
+ }
+
+ final int dp = getPercentageDp(nseq);
+
+ float value = profile.getSSPercentageIdentity(ignoreGaps);
+
+ String description = getSSTooltip(profile, value, showSequenceLogo,
+ ignoreGaps, dp);
+
+ String modalSS = profile.getModalSS();
+ if ("".equals(modalSS))
+ {
+ modalSS = "-";
+ }
+ else if (modalSS.length() > 1)
+ {
+ modalSS = "+";
+ }
+ ssConsensus.annotations[i] = new Annotation(modalSS, description,
+ ' ', value);
+ }
+ // long elapsed = System.currentTimeMillis() - now;
+ // jalview.bin.Console.outPrintln(-elapsed);
+ }
/**
* Derive the gap count annotation row.
// always set ranges again
gaprow.graphMax = nseq;
gaprow.graphMin = 0;
+ double scale = 0.8 / nseq;
for (int i = startCol; i < endCol; i++)
{
ProfileI profile = profiles.get(i);
final int gapped = profile.getNonGapped();
- String description = String.valueOf(gapped);
+ String description = "" + gapped;
- gaprow.annotations[i] = new Annotation(description, description,
- '\0',
- gapped);
+ gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+ jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
+ (float) scale * gapped));
}
}
* <ul>
* <li>the full profile (percentages of all residues present), if
* showSequenceLogo is true, or</li>
- * <li>just the modal (most common) residue(s), if showSequenceLogo is false</li>
+ * <li>just the modal (most common) residue(s), if showSequenceLogo is
+ * false</li>
* </ul>
* Percentages are as a fraction of all sequence, or only ungapped sequences
* if ignoreGaps is true.
String description = null;
if (counts != null && showSequenceLogo)
{
- int normaliseBy = ignoreGaps ? profile.getNonGapped() : profile
- .getHeight();
+ int normaliseBy = ignoreGaps ? profile.getNonGapped()
+ : profile.getHeight();
description = counts.getTooltip(normaliseBy, dp);
}
else
}
return description;
}
+
+ static String getSSTooltip(ProfileI profile, float pid,
+ boolean showSequenceLogo, boolean ignoreGaps, int dp)
+ {
+ SecondaryStructureCount counts = profile.getSSCounts();
+
+ 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 maxSS = profile.getModalSS();
+ if (maxSS.length() > 1)
+ {
+ sb.append("[").append(maxSS).append("]");
+ }
+ else
+ {
+ sb.append(maxSS);
+ }
+ if (maxSS.length() > 0)
+ {
+ 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
*
* <pre>
- * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercent, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value
* </pre>
*
*/
public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
{
- int[] rtnval = new int[64];
- ResidueCount counts = profile.getCounts();
- if (counts == null)
+ char[] symbols;
+ int[] values;
+
+ if (profile.getCounts() != null)
{
+ ResidueCount counts = profile.getCounts();
+ SymbolCounts symbolCounts = counts.getSymbolCounts();
+ symbols = symbolCounts.symbols;
+ values = symbolCounts.values;
+
+ }
+ else if(profile.getSSCounts() != null)
+ {
+ SecondaryStructureCount counts = profile.getSSCounts();
+ // to do
+ SecondaryStructureCount.SymbolCounts symbolCounts = counts.getSymbolCounts();
+ symbols = symbolCounts.symbols;
+ values = symbolCounts.values;
+ }
+ else {
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();
+ final int divisor = ignoreGaps ? profile.getNonGapped()
+ : profile.getHeight();
/*
* traverse the arrays in reverse order (highest counts first)
*/
+ int[] result = new int[3 + 2 * symbols.length];
+ int nextArrayPos = 3;
+ int nonZeroCount = 0;
+
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;
+ if (percentage == 0)
+ {
+ /*
+ * this count (and any remaining) round down to 0% - discard
+ */
+ break;
+ }
+ nonZeroCount++;
+ result[nextArrayPos++] = theChar;
+ result[nextArrayPos++] = percentage;
totalPercentage += percentage;
}
- rtnval[0] = symbols.length;
- rtnval[1] = totalPercentage;
- int[] result = new int[rtnval.length + 1];
+
+ /*
+ * truncate array if any zero values were discarded
+ */
+ if (nonZeroCount < symbols.length)
+ {
+ int[] tmp = new int[3 + 2 * nonZeroCount];
+ System.arraycopy(result, 0, tmp, 0, tmp.length);
+ result = tmp;
+ }
+
+ /*
+ * fill in 'header' values
+ */
result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
- System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+ result[1] = nonZeroCount;
+ result[2] = totalPercentage;
return result;
}
* contains
*
* <pre>
- * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercentage, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value, where the character values encode codon triplets
* </pre>
*
* @param hashtable
* @return
*/
- public static int[] extractCdnaProfile(Hashtable hashtable,
- boolean ignoreGaps)
+ public static int[] extractCdnaProfile(
+ Hashtable<String, Object> hashtable, boolean ignoreGaps)
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
// codon triplet
{
break; // nothing else of interest here
}
+ final int percentage = codonCount * 100 / divisor;
+ if (percentage == 0)
+ {
+ /*
+ * this (and any remaining) values rounded down to 0 - discard
+ */
+ break;
+ }
distinctValuesCount++;
result[j++] = codons[i];
- final int percentage = codonCount * 100 / divisor;
result[j++] = percentage;
totalPercentage += percentage;
}
* the consensus data stores to be populated (one per column)
*/
public static void calculateCdna(AlignmentI alignment,
- Hashtable[] hconsensus)
+ Hashtable<String, Object>[] hconsensus)
{
final char gapCharacter = alignment.getGapCharacter();
List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ Hashtable<String, Object> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
{
continue;
}
- List<char[]> codons = MappingUtils
- .findCodonsFor(seq, col, mappings);
+ List<char[]> codons = MappingUtils.findCodonsFor(seq, col,
+ mappings);
for (char[] codon : codons)
{
int codonEncoded = CodingUtils.encodeCodon(codon);
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
+ break;
}
}
}
*/
public static void completeCdnaConsensus(
AlignmentAnnotation consensusAnnotation,
- Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
+ Hashtable<String, Object>[] consensusData,
+ boolean showProfileLogo, int nseqs)
{
if (consensusAnnotation == null
|| consensusAnnotation.annotations == null
consensusAnnotation.scaleColLabel = true;
for (int col = 0; col < consensusData.length; col++)
{
- Hashtable hci = consensusData[col];
+ Hashtable<String, Object> hci = consensusData[col];
if (hci == null)
{
// gapped protein column?
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])
+ String modalCodon = String
+ .valueOf(CodingUtils.decodeCodon(modalCodonEncoded));
+ if (sortedCodonCounts.length > 1 && sortedCodonCounts[codons.length
+ - 2] == sortedCodonCounts[codons.length - 1])
{
/*
* two or more codons share the modal count
{
if (samePercent.length() > 0)
{
- mouseOver.append(samePercent).append(": ")
- .append(lastPercent).append("% ");
+ mouseOver.append(samePercent).append(": ").append(lastPercent)
+ .append("% ");
}
samePercent.setLength(0);
samePercent.append(codon);
git://source.jalview.org / jalview.git / blobdiff