X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=6cc9dd344addced46f9e8f5a06f7184ce47a86a7;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=c216471835ecaec274cb40a6cb2bdb948c6e2122;hpb=7652d1d5889b737d52dbd15f3919d8b0dbdbc48b;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index c216471..6cc9dd3 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,139 +1,211 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
- *
- * 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 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
+import java.util.Locale;
+
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+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.util.Format;
+
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.SortedMap;
+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';
+
+ private static final int GAP_INDEX = -1;
+
+ private static final Format FORMAT_3DP = new Format("%2.5f");
+
SequenceI[] sequences;
int start;
int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
+ /*
+ * a list whose i'th element is an array whose first entry is the checksum
+ * of the i'th sequence, followed by residues encoded to score matrix index
+ */
+ Vector seqNums;
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[] total;
+
+ /*
+ * if true then conservation calculation will map all symbols to canonical aa
+ * numbering rather than consider conservation of that symbol
+ */
+ boolean canonicaliseAa = true;
+
+ private Vector quality;
- boolean canonicaliseAa = true; // if true then conservation calculation will
- // map all symbols to canonical aa numbering
- // rather than consider conservation of that
- // symbol
+ private double qualityMinimum;
- /** Stores calculated quality values */
- public Vector quality;
+ private double qualityMaximum;
- /** Stores maximum and minimum values of quality values */
- public Double[] qualityRange = new Double[2];
+ private Sequence consSequence;
- String consString = "";
+ /*
+ * percentage of residues in a column to qualify for counting conservation
+ */
+ private int threshold;
- Sequence consSequence;
+ private String name = "";
- Hashtable propHash;
+ /*
+ * an array, for each column, of counts of symbols (by score matrix index)
+ */
+ private int[][] cons2;
- int threshold;
+ /*
+ * gap counts for each column
+ */
+ private int[] cons2GapCounts;
- 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 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 sequences,
+ int start, int end)
{
-
this.name = name;
- this.propHash = propHash;
this.threshold = threshold;
this.start = start;
this.end = end;
maxLength = end - start + 1; // default width includes bounds of
- // calculation
+ // calculation
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;
}
}
/**
- * Translate sequence i into a numerical
- * representation and store it in the i'th position of the seqNums array.
+ * Translate sequence i into score matrix indices and store it in the i'th
+ * position of the seqNums array.
*
* @param i
+ * @param sm
*/
- private void calcSeqNum(int i)
+ private void calcSeqNum(int i, ScoreMatrix sm)
{
- String sq = null; // for dumb jbuilder not-inited exception warning
- int[] sqnum = null;
-
int sSize = sequences.length;
if ((i > -1) && (i < sSize))
{
- sq = sequences[i].getSequenceAsString();
+ String sq = sequences[i].getSequenceAsString();
if (seqNums.size() <= i)
{
seqNums.addElement(new int[sq.length() + 1]);
}
- if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
+ /*
+ * the first entry in the array is the sequence's hashcode,
+ * following entries are matrix indices of sequence characters
+ */
+ if (sq.hashCode() != seqNums.elementAt(i)[0])
{
int j;
int len;
@@ -145,14 +217,26 @@ public class Conservation
maxLength = len;
}
- sqnum = new int[len + 1]; // better to always make a new array -
- // sequence can change its length
+ int[] sqnum = new int[len + 1]; // better to always make a new array -
+ // sequence can change its length
sqnum[0] = sq.hashCode();
for (j = 1; j <= len; j++)
{
- sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq
- .charAt(j - 1)];
+ // sqnum[j] = ResidueProperties.aaIndex[sq.charAt(j - 1)];
+ char residue = sq.charAt(j - 1);
+ if (Comparison.isGap(residue))
+ {
+ sqnum[j] = GAP_INDEX;
+ }
+ else
+ {
+ sqnum[j] = sm.getMatrixIndex(residue);
+ if (sqnum[j] == -1)
+ {
+ sqnum[j] = GAP_INDEX;
+ }
+ }
}
seqNums.setElementAt(sqnum, i);
@@ -165,8 +249,8 @@ public class Conservation
else
{
// JBPNote INFO level debug
- System.err
- .println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+ System.err.println(
+ "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
}
}
@@ -175,175 +259,222 @@ public class Conservation
*/
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);
+
+ /*
+ * percentage count at or below which we ignore residues
+ */
+ int thresh = (threshold * height) / 100;
- for (j = 0; j < jSize; j++)
+ /*
+ * 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
+ */
+ SortedMap resultHash = new TreeMap<>();
+ 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);
+ recordConservation(resultHash, String.valueOf(c));
+ }
+ }
+ if (values.getGapCount() > thresh)
+ {
+ recordConservation(resultHash, "-");
+ }
- 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 (total.length > 0)
+ {
+ total[column - start] = resultHash;
+ }
+ }
+ }
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
- }
- values[c]++;
+ /**
+ * 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 resultMap,
+ String res)
+ {
+ res = res.toUpperCase(Locale.ROOT);
+ for (Entry> 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);
-
- // Now loop over the properties
- enumeration2 = propHash.keys();
+ /*
+ * property is unconserved - residues seen both with and without it
+ */
+ resultMap.put(propertyName, Integer.valueOf(-1));
+ }
+ }
+ }
+ }
- while (enumeration2.hasMoreElements())
- {
- type = (String) enumeration2.nextElement();
- ht = (Hashtable) propHash.get(type);
+ /**
+ * Counts residues (upper-cased) and gaps in the given column
+ *
+ * @param column
+ * @return
+ */
+ protected ResidueCount countResidues(int column)
+ {
+ ResidueCount values = new ResidueCount(false);
- // 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
- * @return { gap count, conserved residue count}
+ /**
+ * Counts conservation and gaps for a column of the alignment
+ *
+ * @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)
+ {
+ return new int[] { 0, 0 };
+ }
+
+ char lastRes = '0';
+ for (int i = 0; i < iSize; i++)
{
- if (j >= sequences[i].getLength())
+ 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
@@ -352,42 +483,53 @@ public class Conservation
{
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 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)
{
- if (result.intValue() == 1)
- {
- count++;
- }
+ /*
+ * not conserved (present or absent)
+ */
+ continue;
}
- else
+ count++;
+ if (result == 1)
{
- if (result.intValue() != -1)
- {
- count++;
- }
+ /*
+ * positively conserved property (all residues have it)
+ */
+ positives.append(positives.length() == 0 ? "" : " ");
+ positives.append(type);
}
+ if (result == 0 && !positiveOnly)
+ {
+ /*
+ * 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)
{
@@ -395,7 +537,7 @@ public class Conservation
}
else
{
- consString.append((gapcons[0] == 1) ? "*" : "+");
+ consString.append(fullyConserved ? "*" : "+");
}
}
else
@@ -412,7 +554,7 @@ public class Conservation
*
* @return Conservation sequence
*/
- public Sequence getConsSequence()
+ public SequenceI getConsSequence()
{
return consSequence;
}
@@ -420,136 +562,134 @@ public class Conservation
// From Alignment.java in jalview118
public void findQuality()
{
- findQuality(0, maxLength - 1);
+ findQuality(0, maxLength - 1, ScoreModels.getInstance().getBlosum62());
}
/**
* DOCUMENT ME!
+ *
+ * @param sm
*/
- private void percentIdentity2()
+ private void percentIdentity(ScoreMatrix sm)
{
- seqNums = new Vector();
- // calcSeqNum(s);
+ seqNums = new Vector<>();
int i = 0, iSize = sequences.length;
// Do we need to calculate this again?
for (i = 0; i < iSize; i++)
{
- calcSeqNum(i);
+ calcSeqNum(i, sm);
}
if ((cons2 == null) || seqNumsChanged)
{
+ // FIXME remove magic number 24 without changing calc
+ // sm.getSize() returns 25 so doesn't quite do it...
cons2 = new int[maxLength][24];
+ cons2GapCounts = new int[maxLength];
- // Initialize the array
- for (int j = 0; j < 24; j++)
- {
- for (i = 0; i < maxLength; i++)
- {
- cons2[i][j] = 0;
- }
- }
-
- int[] sqnum;
int j = 0;
while (j < sequences.length)
{
- sqnum = (int[]) seqNums.elementAt(j);
+ int[] sqnum = seqNums.elementAt(j);
for (i = 1; i < sqnum.length; i++)
{
- cons2[i - 1][sqnum[i]]++;
+ int index = sqnum[i];
+ if (index == GAP_INDEX)
+ {
+ cons2GapCounts[i - 1]++;
+ }
+ else
+ {
+ cons2[i - 1][index]++;
+ }
}
+ // TODO should this start from sqnum.length?
for (i = sqnum.length - 1; i < maxLength; i++)
{
- cons2[i][23]++; // gap count
+ cons2GapCounts[i]++;
}
-
j++;
}
-
- // unnecessary ?
-
- /*
- * for (int i=start; i <= end; i++) { int max = -1000; int maxi = -1; int
- * maxj = -1;
- *
- * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
- * maxi = i; maxj = j; }
- * } }
- */
}
}
/**
- * Calculates the quality of the set of sequences
+ * Calculates the quality of the set of sequences over the given inclusive
+ * column range, using the specified substitution score matrix
*
- * @param start
- * Start residue
- * @param end
- * End residue
+ * @param startCol
+ * @param endCol
+ * @param scoreMatrix
*/
- public void findQuality(int start, int end)
+ protected void findQuality(int startCol, int endCol,
+ ScoreMatrix scoreMatrix)
{
- quality = new Vector();
+ quality = new Vector<>();
- double max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+ double max = -Double.MAX_VALUE;
+ float[][] scores = scoreMatrix.getMatrix();
- // Loop over columns // JBPNote Profiling info
- // long ts = System.currentTimeMillis();
- // long te = System.currentTimeMillis();
- percentIdentity2();
+ percentIdentity(scoreMatrix);
int size = seqNums.size();
int[] lengths = new int[size];
- double tot, bigtot, sr, tmp;
- double[] x, xx;
- int l, j, i, ii, i2, k, seqNum;
- for (l = 0; l < size; l++)
+ for (int 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++)
+ final int symbolCount = scoreMatrix.getSize();
+
+ for (int j = startCol; j <= endCol; j++)
{
- bigtot = 0;
+ double bigtot = 0;
// First Xr = depends on column only
- x = new double[24];
+ double[] x = new double[symbolCount];
- for (ii = 0; ii < 24; ii++)
+ for (int ii = 0; ii < symbolCount; ii++)
{
x[ii] = 0;
- for (i2 = 0; i2 < 24; i2++)
+ /*
+ * todo JAL-728 currently assuming last symbol in matrix is * for gap
+ * (which we ignore as counted separately); true for BLOSUM62 but may
+ * not be once alternative matrices are supported
+ */
+ for (int i2 = 0; i2 < symbolCount - 1; i2++)
{
- x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4);
+ x[ii] += (((double) cons2[j][i2] * scores[ii][i2]) + 4D);
}
+ x[ii] += 4D + cons2GapCounts[j] * scoreMatrix.getMinimumScore();
x[ii] /= size;
}
// Now calculate D for each position and sum
- for (k = 0; k < size; k++)
+ for (int k = 0; k < size; k++)
{
- tot = 0;
- xx = new double[24];
- seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
- : 23; // Sequence, or gap at the end
+ double tot = 0;
+ double[] xx = new double[symbolCount];
+ // sequence character index, or implied gap if sequence too short
+ int seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1]
+ : GAP_INDEX;
- // This is a loop over r
- for (i = 0; i < 23; i++)
+ for (int i = 0; i < symbolCount - 1; i++)
{
- sr = 0;
-
- sr = (double) BLOSUM62[i][seqNum] + 4;
+ double sr = 4D;
+ if (seqNum == GAP_INDEX)
+ {
+ sr += scoreMatrix.getMinimumScore();
+ }
+ else
+ {
+ sr += scores[i][seqNum];
+ }
- // Calculate X with another loop over residues
- // System.out.println("Xi " + i + " " + x[i] + " " + sr);
xx[i] = x[i] - sr;
tot += (xx[i] * xx[i]);
@@ -558,27 +698,21 @@ public class Conservation
bigtot += Math.sqrt(tot);
}
- // This is the quality for one column
- if (max < bigtot)
- {
- max = bigtot;
- }
+ max = Math.max(max, bigtot);
- // bigtot = bigtot * (size-cons2[j][23])/size;
- quality.addElement(new Double(bigtot));
-
- // Need to normalize by gaps
+ quality.addElement(Double.valueOf(bigtot));
}
- double newmax = -10000;
+ double newmax = -Double.MAX_VALUE;
- for (j = start; j <= end; j++)
+ for (int j = startCol; j <= endCol; j++)
{
- tmp = ((Double) quality.elementAt(j)).doubleValue();
- tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+ double tmp = quality.elementAt(j).doubleValue();
+ // tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+ tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
// System.out.println(tmp+ " " + j);
- quality.setElementAt(new Double(tmp), j);
+ quality.setElementAt(Double.valueOf(tmp), j);
if (tmp > newmax)
{
@@ -586,8 +720,160 @@ public class Conservation
}
}
- // System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
+ qualityMinimum = 0D;
+ qualityMaximum = newmax;
+ }
+
+ /**
+ * Complete the given consensus and quuality annotation rows. Note: currently
+ * this method will reallocate the given annotation row if it is different to
+ * the calculated width, 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)
+ {
+ SequenceI cons = getConsSequence();
+
+ /*
+ * colour scale for Conservation and Quality;
+ */
+ float minR = 0.3f;
+ float minG = 0.0f;
+ float minB = 0f;
+ float maxR = 1.0f - minR;
+ float maxG = 0.9f - minG;
+ float maxB = 0f - minB;
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ if (conservation != null && conservation.annotations != null
+ && conservation.annotations.length != alWidth)
+ {
+ conservation.annotations = new Annotation[alWidth];
+ }
+
+ if (quality2 != null)
+ {
+ quality2.graphMax = (float) qualityMaximum;
+ if (quality2.annotations != null
+ && quality2.annotations.length != alWidth)
+ {
+ quality2.annotations = new Annotation[alWidth];
+ }
+ qmin = (float) qualityMinimum;
+ qmax = (float) qualityMaximum;
+ }
+
+ for (int i = istart; i < alWidth; i++)
+ {
+ float value = 0;
+
+ char c = cons.getCharAt(i);
+
+ if (Character.isDigit(c))
+ {
+ value = c - '0';
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ 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 = quality.elementAt(i).floatValue();
+ float vprop = value - qmin;
+ vprop /= qmax;
+ String description = FORMAT_3DP.form(value);
+ quality2.annotations[i] = new Annotation(" ", description,
+ ' ', 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 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)
+ {
+ SequenceI cons = getConsSequence();
+ char val = column < cons.getLength() ? cons.getCharAt(column) : '-';
+ boolean hasConservation = val != '-' && val != '0';
+ int consp = column - start;
+ String tip = (hasConservation && consp > -1 && consp < consSymbs.length)
+ ? consSymbs[consp]
+ : "";
+ return tip;
}
}