*/
package jalview.analysis;
-import jalview.analysis.ResidueCount.SymbolCounts;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.ResidueCount.SymbolCounts;
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;
*/
public class AAFrequency
{
- public static final String MAXCOUNT = "C";
-
- public static final String MAXRESIDUE = "R";
-
- public static final String PID_GAPS = "G";
-
- public static final String PID_NOGAPS = "N";
-
public static final String PROFILE = "P";
- public static final String ENCODED_CHARS = "E";
-
/*
* Quick look-up of String value of char 'A' to 'Z'
*/
}
}
- public static final Profile[] calculate(List<SequenceI> list,
- int start, int end)
+ public static final ProfilesI calculate(List<SequenceI> list, int start,
+ int end)
{
return calculate(list, start, end, false);
}
- public static final Profile[] calculate(List<SequenceI> sequences,
+ public static final ProfilesI calculate(List<SequenceI> sequences,
int start, int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
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;
}
}
- Profile[] reply = new Profile[width];
-
if (end >= width)
{
end = width;
}
- calculate(seqs, start, end, reply, profile);
+ ProfilesI reply = calculate(seqs, width, start, end, profile);
return reply;
}
}
* 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
- * @param result
- * array in which to store profile per column
+ * end column (exclusive)
* @param saveFullProfile
* if true, store all symbol counts
*/
- public static final void calculate(final SequenceI[] sequences,
- int start, int end, Profile[] result, boolean saveFullProfile)
+ public static final ProfilesI calculate(final SequenceI[] sequences,
+ int width, int start, int end, boolean saveFullProfile)
{
// long now = System.currentTimeMillis();
int seqCount = sequences.length;
int nucleotideCount = 0;
int peptideCount = 0;
+ ProfileI[] result = new ProfileI[width];
+
for (int column = start; column < end; column++)
{
/*
{
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))
{
else
{
/*
- * here we count a gap if the sequence doesn't
- * reach this column (is that correct?)
+ * count a gap if the sequence doesn't reach this column
*/
residueCounts.addGap();
}
int maxCount = residueCounts.getModalCount();
String maxResidue = residueCounts.getResiduesForCount(maxCount);
int gapCount = residueCounts.getGapCount();
- Profile profile = new Profile(seqCount, gapCount, maxCount,
+ ProfileI profile = new Profile(seqCount, gapCount, maxCount,
maxResidue);
if (saveFullProfile)
result[column] = profile;
}
+ return new Profiles(result);
// long elapsed = System.currentTimeMillis() - now;
- // System.out.println(elapsed);
+ // jalview.bin.Console.outPrintln(elapsed);
}
/**
/**
* 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 'show logo', which may in turn result in a change
- * in the derived values.
+ * 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 iStart
- * start column
- * @param width
- * end column
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
* @param ignoreGaps
* if true, normalise residue percentages ignoring gaps
* @param showSequenceLogo
* number of sequences
*/
public static void completeConsensus(AlignmentAnnotation consensus,
- Profile[] profiles, int iStart, int width, boolean ignoreGaps,
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
boolean showSequenceLogo, long nseq)
{
// 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
return;
}
- final int dp = getPercentageDp(nseq);
-
- for (int i = iStart; i < width; i++)
+ for (int i = startCol; i < endCol; i++)
{
- Profile profile;
- if (i >= profiles.length || ((profile = profiles[i]) == null))
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
{
/*
* happens if sequences calculated over were
* shorter than alignment width
*/
consensus.annotations[i] = null;
- continue;
+ return;
}
+ final int dp = getPercentageDp(nseq);
+
float value = profile.getPercentageIdentity(ignoreGaps);
String description = getTooltip(profile, value, showSequenceLogo,
ignoreGaps, dp);
- consensus.annotations[i] = new Annotation(profile.getModalResidue(),
- description, ' ', value);
+ String modalResidue = profile.getModalResidue();
+ if ("".equals(modalResidue))
+ {
+ modalResidue = "-";
+ }
+ else if (modalResidue.length() > 1)
+ {
+ modalResidue = "+";
+ }
+ consensus.annotations[i] = new Annotation(modalResidue, description,
+ ' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
- // System.out.println(-elapsed);
+ // jalview.bin.Console.outPrintln(-elapsed);
+ }
+
+ /**
+ * Derive the gap count annotation row.
+ *
+ * @param gaprow
+ * 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 gaprow,
+ ProfilesI profiles, int startCol, int endCol, long nseq)
+ {
+ if (gaprow == null || gaprow.annotations == null
+ || gaprow.annotations.length < endCol)
+ {
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
+ return;
+ }
+ // 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);
+ if (profile == null)
+ {
+ /*
+ * happens if sequences calculated over were
+ * shorter than alignment width
+ */
+ gaprow.annotations[i] = null;
+ return;
+ }
+
+ final int gapped = profile.getNonGapped();
+
+ String description = "" + 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.
* the number of decimal places to format percentages to
* @return
*/
- static String getTooltip(Profile profile, float pid,
+ 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();
+ int normaliseBy = ignoreGaps ? profile.getNonGapped()
+ : profile.getHeight();
description = counts.getTooltip(normaliseBy, dp);
}
else
String maxRes = profile.getModalResidue();
if (maxRes.length() > 1)
{
- sb.append("[").append(maxRes).append("] ");
- maxRes = "+";
+ sb.append("[").append(maxRes).append("]");
}
else
{
- sb.append(maxRes).append(" ");
+ sb.append(maxRes);
+ }
+ if (maxRes.length() > 0)
+ {
+ sb.append(" ");
+ Format.appendPercentage(sb, pid, dp);
+ sb.append("%");
}
- Format.appendPercentage(sb, pid, dp);
- sb.append("%");
description = sb.toString();
}
return description;
* contains
*
* <pre>
- * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercent, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value
* </pre>
*
* calculations
* @return
*/
- public static int[] extractProfile(Profile profile,
- boolean ignoreGaps)
+ public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
{
- int[] rtnval = new int[64];
ResidueCount counts = profile.getCounts();
if (counts == null)
{
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