/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.awt.Color;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.ResidueCount.SymbolCounts;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+import java.util.Vector;
/**
* Calculates conservation values for a given set of sequences
- *
- * @author $author$
- * @version $Revision$
*/
public class Conservation
{
+ /*
+ * need to have a minimum of 3% of sequences with a residue
+ * for it to be included in the conservation calculation
+ */
+ private static final int THRESHOLD_PERCENT = 3;
+
+ private static final int TOUPPERCASE = 'a' - 'A';
+
SequenceI[] sequences;
int start;
int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
+ Vector<int[]> seqNums; // vector of int vectors where first is sequence
+ // checksum
int maxLength = 0; // used by quality calcs
boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
- Hashtable[] total;
+ /*
+ * a map per column with {property, conservation} where conservation value is
+ * 1 (property is conserved), 0 (absence of property is conserved) or -1
+ * (property is not conserved i.e. column has residues with and without it)
+ */
+ Map<String, Integer>[] total;
boolean canonicaliseAa = true; // if true then conservation calculation will
// symbol
/** Stores calculated quality values */
- public Vector quality;
+ private Vector<Double> quality;
/** Stores maximum and minimum values of quality values */
- public Double[] qualityRange = new Double[2];
+ private double[] qualityRange = new double[2];
- String consString = "";
+ private Sequence consSequence;
- Sequence consSequence;
+ /*
+ * percentage of residues in a column to qualify for counting conservation
+ */
+ private int threshold;
- Hashtable propHash;
+ private String name = "";
- int threshold;
+ private int[][] cons2;
- String name = "";
+ private String[] consSymbs;
- int[][] cons2;
+ /**
+ * Constructor using default threshold of 3%
+ *
+ * @param name
+ * Name of conservation
+ * @param sequences
+ * sequences to be used in calculation
+ * @param start
+ * start residue position
+ * @param end
+ * end residue position
+ */
+ public Conservation(String name, List<SequenceI> sequences, int start,
+ int end)
+ {
+ this(name, THRESHOLD_PERCENT, sequences, start, end);
+ }
/**
- * Creates a new Conservation object.
+ * Constructor
*
* @param name
- * Name of conservation
- * @param propHash
- * hash of properties for each symbol
+ * Name of conservation
* @param threshold
- * to count the residues in residueHash(). commonly used value
- * is 3
+ * percentage of sequences at or below which property conservation is
+ * ignored
* @param sequences
- * sequences to be used in calculation
+ * sequences to be used in calculation
* @param start
- * start residue position
+ * start column position
* @param end
- * end residue position
+ * end column position
*/
- public Conservation(String name, Hashtable propHash, int threshold,
- Vector sequences, int start, int end)
+ public Conservation(String name, int threshold,
+ List<SequenceI> sequences, int start, int end)
{
-
this.name = name;
- this.propHash = propHash;
this.threshold = threshold;
this.start = start;
this.end = end;
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
this.sequences = sarray;
-
- for (s = 0; s < sSize; s++)
+ try
{
- sarray[s] = (SequenceI) sequences.elementAt(s);
- if (sarray[s].getLength() > maxLength)
+ for (s = 0; s < sSize; s++)
{
- maxLength = sarray[s].getLength();
+ sarray[s] = sequences.get(s);
+ if (sarray[s].getLength() > maxLength)
+ {
+ maxLength = sarray[s].getLength();
+ }
}
+ } catch (ArrayIndexOutOfBoundsException ex)
+ {
+ // bail - another thread has modified the sequence array, so the current
+ // calculation is probably invalid.
+ this.sequences = new SequenceI[0];
+ maxLength = 0;
}
}
seqNums.addElement(new int[sq.length() + 1]);
}
- if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+ if (sq.hashCode() != seqNums.elementAt(i)[0])
{
int j;
int len;
*/
public void calculate()
{
- Hashtable resultHash, ht;
- int thresh, j, jSize = sequences.length;
- int[] values; // Replaces residueHash
- String type, res = null;
- char c;
- Enumeration enumeration2;
+ int height = sequences.length;
- total = new Hashtable[maxLength];
+ total = new Map[maxLength];
- for (int i = start; i <= end; i++)
+ for (int column = start; column <= end; column++)
{
- values = new int[255];
+ ResidueCount values = countResidues(column);
- for (j = 0; j < jSize; j++)
+ /*
+ * percentage count at or below which we ignore residues
+ */
+ int thresh = (threshold * height) / 100;
+
+ /*
+ * check observed residues in column and record whether each
+ * physico-chemical property is conserved (+1), absence conserved (0),
+ * or not conserved (-1)
+ * Using TreeMap means properties are displayed in alphabetical order
+ */
+ Map<String, Integer> resultHash = new TreeMap<String, Integer>();
+ SymbolCounts symbolCounts = values.getSymbolCounts();
+ char[] symbols = symbolCounts.symbols;
+ int[] counts = symbolCounts.values;
+ for (int j = 0; j < symbols.length; j++)
{
- if (sequences[j].getLength() > i)
+ char c = symbols[j];
+ if (counts[j] > thresh)
{
- c = sequences[j].getCharAt(i);
-
- if (canonicaliseAa)
- { // lookup the base aa code symbol
- c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
- .getCharAt(i)];
- if (c > 20)
- {
- c = '-';
- }
- else
- {
- // recover canonical aa symbol
- c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
- }
- }
- else
- {
- // original behaviour - operate on ascii symbols directly
- // No need to check if its a '-'
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
- }
- values[c]++;
+ recordConservation(resultHash, String.valueOf(c));
+ }
+ }
+ if (values.getGapCount() > thresh)
+ {
+ recordConservation(resultHash, "-");
+ }
+
+ if (total.length > 0)
+ {
+ total[column - start] = resultHash;
+ }
+ }
+ }
+
+ /**
+ * Updates the conservation results for an observed residue
+ *
+ * @param resultMap
+ * a map of {property, conservation} where conservation value is +1
+ * (all residues have the property), 0 (no residue has the property)
+ * or -1 (some do, some don't)
+ * @param res
+ */
+ protected static void recordConservation(Map<String, Integer> resultMap,
+ String res)
+ {
+ res = res.toUpperCase();
+ for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
+ .entrySet())
+ {
+ String propertyName = property.getKey();
+ Integer residuePropertyValue = property.getValue().get(res);
+
+ if (!resultMap.containsKey(propertyName))
+ {
+ /*
+ * first time we've seen this residue - note whether it has this property
+ */
+ if (residuePropertyValue != null)
+ {
+ resultMap.put(propertyName, residuePropertyValue);
}
else
{
- values['-']++;
+ /*
+ * unrecognised residue - use default value for property
+ */
+ resultMap.put(propertyName, property.getValue().get("-"));
}
}
-
- // What is the count threshold to count the residues in residueHash()
- thresh = (threshold * (jSize)) / 100;
-
- // loop over all the found residues
- resultHash = new Hashtable();
- for (char v = '-'; v < 'Z'; v++)
+ else
{
-
- if (values[v] > thresh)
+ Integer currentResult = resultMap.get(propertyName);
+ if (currentResult.intValue() != -1
+ && !currentResult.equals(residuePropertyValue))
{
- res = String.valueOf(v);
+ /*
+ * property is unconserved - residues seen both with and without it
+ */
+ resultMap.put(propertyName, Integer.valueOf(-1));
+ }
+ }
+ }
+ }
- // Now loop over the properties
- enumeration2 = propHash.keys();
+ /**
+ * Counts residues (upper-cased) and gaps in the given column
+ *
+ * @param column
+ * @return
+ */
+ protected ResidueCount countResidues(int column)
+ {
+ ResidueCount values = new ResidueCount(false);
- while (enumeration2.hasMoreElements())
- {
- type = (String) enumeration2.nextElement();
- ht = (Hashtable) propHash.get(type);
-
- // Have we ticked this before?
- if (!resultHash.containsKey(type))
- {
- if (ht.containsKey(res))
- {
- resultHash.put(type, ht.get(res));
- }
- else
- {
- resultHash.put(type, ht.get("-"));
- }
- }
- else if (((Integer) resultHash.get(type)).equals((Integer) ht
- .get(res)) == false)
- {
- resultHash.put(type, new Integer(-1));
- }
- }
+ for (int row = 0; row < sequences.length; row++)
+ {
+ if (sequences[row].getLength() > column)
+ {
+ char c = sequences[row].getCharAt(column);
+ if (canonicaliseAa)
+ {
+ int index = ResidueProperties.aaIndex[c];
+ c = index > 20 ? '-' : ResidueProperties.aa[index].charAt(0);
+ }
+ else
+ {
+ c = toUpperCase(c);
+ }
+ if (Comparison.isGap(c))
+ {
+ values.addGap();
+ }
+ else
+ {
+ values.add(c);
}
}
-
- total[i - start] = resultHash;
+ else
+ {
+ values.addGap();
+ }
}
+ return values;
}
- /*****************************************************************************
- * count conservation for the j'th column of the alignment
+ /**
+ * Counts conservation and gaps for a column of the alignment
*
- * @return { gap count, conserved residue count}
+ * @return { 1 if fully conserved, else 0, gap count }
*/
- public int[] countConsNGaps(int j)
+ public int[] countConservationAndGaps(int column)
{
- int count = 0;
- int cons = 0;
- int nres = 0;
- int[] r = new int[2];
- char f = '$';
- int i, iSize = sequences.length;
- char c;
+ int gapCount = 0;
+ boolean fullyConserved = true;
+ int iSize = sequences.length;
- for (i = 0; i < iSize; i++)
+ if (iSize == 0)
{
- if (j >= sequences[i].getLength())
+ return new int[] { 0, 0 };
+ }
+
+ char lastRes = '0';
+ for (int i = 0; i < iSize; i++)
+ {
+ if (column >= sequences[i].getLength())
{
- count++;
+ gapCount++;
continue;
}
- c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
+ char c = sequences[i].getCharAt(column); // gaps do not have upper/lower case
- if (jalview.util.Comparison.isGap((c)))
+ if (Comparison.isGap((c)))
{
- count++;
+ gapCount++;
}
else
{
- nres++;
-
- if (nres == 1)
+ c = toUpperCase(c);
+ if (lastRes == '0')
{
- f = c;
- cons++;
+ lastRes = c;
}
- else if (f == c)
+ if (c != lastRes)
{
- cons++;
+ fullyConserved = false;
}
}
}
- r[0] = (nres == cons) ? 1 : 0;
- r[1] = count;
-
+ int[] r = new int[] { fullyConserved ? 1 : 0, gapCount };
return r;
}
/**
+ * Returns the upper-cased character if between 'a' and 'z', else the
+ * unchanged value
+ *
+ * @param c
+ * @return
+ */
+ char toUpperCase(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= TOUPPERCASE;
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
- * @param consflag
- * if true, poitiveve conservation; false calculates negative
- * conservation
- * @param percentageGaps
- * commonly used value is 25
+ * @param positiveOnly
+ * if true, calculate positive conservation; else calculate both
+ * positive and negative conservation
+ * @param maxPercentageGaps
+ * the percentage of gaps in a column, at or above which no
+ * conservation is asserted
*/
- public void verdict(boolean consflag, float percentageGaps)
+ public void verdict(boolean positiveOnly, float maxPercentageGaps)
{
- StringBuffer consString = new StringBuffer();
- String type;
- Integer result;
- int[] gapcons;
- int totGaps, count;
- float pgaps;
- Hashtable resultHash;
- Enumeration enumeration;
+ // TODO call this at the end of calculate(), should not be a public method
+
+ StringBuilder consString = new StringBuilder(end);
// NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
// EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
{
consString.append('-');
}
-
+ consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
- gapcons = countConsNGaps(i);
- totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.length;
+ int[] gapcons = countConservationAndGaps(i);
+ boolean fullyConserved = gapcons[0] == 1;
+ int totGaps = gapcons[1];
+ float pgaps = (totGaps * 100f) / sequences.length;
- if (percentageGaps > pgaps)
+ if (maxPercentageGaps > pgaps)
{
- resultHash = total[i - start];
-
- // Now find the verdict
- count = 0;
- enumeration = resultHash.keys();
-
- while (enumeration.hasMoreElements())
+ Map<String, Integer> resultHash = total[i - start];
+ int count = 0;
+ StringBuilder positives = new StringBuilder(64);
+ StringBuilder negatives = new StringBuilder(32);
+ for (String type : resultHash.keySet())
{
- type = (String) enumeration.nextElement();
- result = (Integer) resultHash.get(type);
-
- // Do we want to count +ve conservation or +ve and -ve cons.?
- if (consflag)
+ int result = resultHash.get(type).intValue();
+ if (result == -1)
+ {
+ /*
+ * not conserved (present or absent)
+ */
+ continue;
+ }
+ count++;
+ if (result == 1)
{
- if (result.intValue() == 1)
- {
- count++;
- }
+ /*
+ * positively conserved property (all residues have it)
+ */
+ positives.append(positives.length() == 0 ? "" : " ");
+ positives.append(type);
}
- else
+ if (result == 0 && !positiveOnly)
{
- if (result.intValue() != -1)
- {
- count++;
- }
+ /*
+ * absense of property is conserved (all residues lack it)
+ */
+ negatives.append(negatives.length() == 0 ? "" : " ");
+ negatives.append("!").append(type);
}
}
+ if (negatives.length() > 0)
+ {
+ positives.append(" ").append(negatives);
+ }
+ consSymbs[i - start] = positives.toString();
if (count < 10)
{
}
else
{
- consString.append((gapcons[0] == 1) ? "*" : "+");
+ consString.append(fullyConserved ? "*" : "+");
}
}
else
*/
private void percentIdentity2()
{
- seqNums = new Vector();
+ seqNums = new Vector<int[]>();
// calcSeqNum(s);
int i = 0, iSize = sequences.length;
// Do we need to calculate this again?
while (j < sequences.length)
{
- sqnum = (int[]) seqNums.elementAt(j);
+ sqnum = seqNums.elementAt(j);
for (i = 1; i < sqnum.length; i++)
{
/**
* Calculates the quality of the set of sequences
*
- * @param start
- * Start residue
- * @param end
- * End residue
+ * @param startRes
+ * Start residue
+ * @param endRes
+ * End residue
*/
- public void findQuality(int start, int end)
+ public void findQuality(int startRes, int endRes)
{
- quality = new Vector();
+ quality = new Vector<Double>();
double max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+ int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
// Loop over columns // JBPNote Profiling info
// long ts = System.currentTimeMillis();
for (l = 0; l < size; l++)
{
- lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
+ lengths[l] = seqNums.elementAt(l).length - 1;
}
- for (j = start; j <= end; j++)
+ for (j = startRes; j <= endRes; j++)
{
bigtot = 0;
{
tot = 0;
xx = new double[24];
- seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
- : 23; // Sequence, or gap at the end
+ seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : 23; // Sequence,
+ // or gap
+ // at the
+ // end
// This is a loop over r
for (i = 0; i < 23; i++)
double newmax = -10000;
- for (j = start; j <= end; j++)
+ for (j = startRes; j <= endRes; j++)
{
- tmp = ((Double) quality.elementAt(j)).doubleValue();
+ tmp = quality.elementAt(j).doubleValue();
tmp = ((max - tmp) * (size - cons2[j][23])) / size;
// System.out.println(tmp+ " " + j);
}
// System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
+ qualityRange[0] = 0D;
+ qualityRange[1] = newmax;
}
/**
- * complete the given consensus and quuality annotation rows.
- * Note: currently this method will enlarge the given annotation row if it is too small, otherwise will leave its length unchanged.
- * @param conservation conservation annotation row
- * @param quality2 (optional - may be null)
- * @param istart first column for conservation
- * @param alWidth extent of conservation
+ * Complete the given consensus and quuality annotation rows. Note: currently
+ * this method will enlarge the given annotation row if it is too small,
+ * otherwise will leave its length unchanged.
+ *
+ * @param conservation
+ * conservation annotation row
+ * @param quality2
+ * (optional - may be null)
+ * @param istart
+ * first column for conservation
+ * @param alWidth
+ * extent of conservation
*/
public void completeAnnotations(AlignmentAnnotation conservation,
AlignmentAnnotation quality2, int istart, int alWidth)
maxR = 1.0f - minR;
maxG = 0.9f - minG;
maxB = 0f - minB; // scalable range for colouring both Conservation and
- // Quality
+ // Quality
float min = 0f;
float max = 11f;
char c;
- if (conservation.annotations !=null && conservation.annotations.length<alWidth)
- { conservation.annotations = new Annotation[alWidth]; }
-
+ if (conservation != null && conservation.annotations != null
+ && conservation.annotations.length < alWidth)
+ {
+ conservation.annotations = new Annotation[alWidth];
+ }
if (quality2 != null)
{
- quality2.graphMax = qualityRange[1].floatValue();
- if (quality2.annotations!=null && quality2.annotations.length<alWidth) {
+ quality2.graphMax = (float) qualityRange[1];
+ if (quality2.annotations != null
+ && quality2.annotations.length < alWidth)
+ {
quality2.annotations = new Annotation[alWidth];
}
- qmin = qualityRange[0].floatValue();
- qmax = qualityRange[1].floatValue();
+ qmin = (float) qualityRange[0];
+ qmax = (float) qualityRange[1];
}
- for (int i = 0; i < alWidth; i++)
+ for (int i = istart; i < alWidth; i++)
{
float value = 0;
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
value = 10;
}
- float vprop = value - min;
- vprop /= max;
- conservation.annotations[i] = new Annotation(String.valueOf(c),
- String.valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ if (conservation != null)
+ {
+ float vprop = value - min;
+ vprop /= max;
+ int consp = i - start;
+ String conssym = (value > 0 && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
+ conservation.annotations[i] = new Annotation(String.valueOf(c),
+ conssym, ' ', value, new Color(minR + (maxR * vprop), minG
+ + (maxG * vprop), minB + (maxB * vprop)));
+ }
// Quality calc
if (quality2 != null)
{
- value = ((Double) quality.get(i)).floatValue();
- vprop = value - qmin;
+ value = quality.elementAt(i).floatValue();
+ float vprop = value - qmin;
vprop /= qmax;
- quality2.annotations[i] = new Annotation(" ", String
- .valueOf(value), ' ', value, new Color(minR
- + (maxR * vprop), minG + (maxG * vprop), minB
- + (maxB * vprop)));
+ quality2.annotations[i] = new Annotation(" ",
+ String.valueOf(value), ' ', value, new Color(minR
+ + (maxR * vprop), minG + (maxG * vprop), minB
+ + (maxB * vprop)));
}
}
}
+
+ /**
+ * construct and call the calculation methods on a new Conservation object
+ *
+ * @param name
+ * - name of conservation
+ * @param seqs
+ * @param start
+ * first column in calculation window
+ * @param end
+ * last column in calculation window
+ * @param positiveOnly
+ * calculate positive (true) or positive and negative (false)
+ * conservation
+ * @param maxPercentGaps
+ * percentage of gaps tolerated in column
+ * @param calcQuality
+ * flag indicating if alignment quality should be calculated
+ * @return Conservation object ready for use in visualization
+ */
+ public static Conservation calculateConservation(String name,
+ List<SequenceI> seqs, int start, int end, boolean positiveOnly,
+ int maxPercentGaps, boolean calcQuality)
+ {
+ Conservation cons = new Conservation(name, seqs, start, end);
+ cons.calculate();
+ cons.verdict(positiveOnly, maxPercentGaps);
+
+ if (calcQuality)
+ {
+ cons.findQuality();
+ }
+
+ return cons;
+ }
+
+ /**
+ * Returns the computed tooltip (annotation description) for a given column.
+ * The tip is empty if the conservation score is zero, otherwise holds the
+ * conserved properties (and, optionally, properties whose absence is
+ * conserved).
+ *
+ * @param column
+ * @return
+ */
+ String getTooltip(int column)
+ {
+ char[] sequence = getConsSequence().getSequence();
+ char val = column < sequence.length ? sequence[column] : '-';
+ boolean hasConservation = val != '-' && val != '0';
+ int consp = column - start;
+ String tip = (hasConservation && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
+ return tip;
+ }
}