X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=e77a67af4b504b45b17a761910f0e656bc88856a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=4eb1218bb8257acbb45bd87c440b690bc0077947;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 4eb1218..e77a67a 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,95 +1,139 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* Calculates conservation values for a given set of sequences
- *
+ *
* @author $author$
* @version $Revision$
*/
public class Conservation
{
SequenceI[] sequences;
+
int start;
+
int end;
+
Vector seqNums; // vector of int vectors where first is sequence checksum
- int maxLength = 0; // used by quality calcs
+
+ int maxLength = 0; // used by quality calcs
+
boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
+
Hashtable[] total;
+ boolean canonicaliseAa = true; // if true then conservation calculation will
+
+ // map all symbols to canonical aa numbering
+ // rather than consider conservation of that
+ // symbol
+
/** Stores calculated quality values */
public Vector quality;
- /** Stores maximum and minimum values of quality values */
+ /** Stores maximum and minimum values of quality values */
public Double[] qualityRange = new Double[2];
+
String consString = "";
+
Sequence consSequence;
+
Hashtable propHash;
+
int threshold;
+
String name = "";
+
int[][] cons2;
+ private String[] consSymbs;
+
/**
* Creates a new Conservation object.
- *
- * @param name Name of conservation
- * @param propHash DOCUMENT ME!
- * @param threshold to count the residues in residueHash(). commonly used value is 3
- * @param sequences sequences to be used in calculation
- * @param start start residue position
- * @param end end residue position
+ *
+ * @param name
+ * Name of conservation
+ * @param propHash
+ * hash of properties for each symbol
+ * @param threshold
+ * to count the residues in residueHash(). commonly used value is 3
+ * @param sequences
+ * sequences to be used in calculation
+ * @param start
+ * start residue position
+ * @param end
+ * end residue position
*/
public Conservation(String name, Hashtable propHash, int threshold,
- Vector sequences, int start, int end)
+ 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
+ maxLength = end - start + 1; // default width includes bounds of
+ // 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;
}
}
/**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
+ * Translate sequence i into a numerical representation and store it in the
+ * i'th position of the seqNums array.
+ *
+ * @param i
*/
private void calcSeqNum(int i)
{
@@ -98,7 +142,7 @@ public class Conservation
int sSize = sequences.length;
- if ( (i > -1) && (i < sSize))
+ if ((i > -1) && (i < sSize))
{
sq = sequences[i].getSequenceAsString();
@@ -107,7 +151,7 @@ public class Conservation
seqNums.addElement(new int[sq.length() + 1]);
}
- if (sq.hashCode() != ( (int[]) seqNums.elementAt(i))[0])
+ if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
{
int j;
int len;
@@ -119,12 +163,14 @@ public class Conservation
maxLength = len;
}
- sqnum = new int[len + 1]; // better to always make a new array - sequence can change its length
+ 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] = jalview.schemes.ResidueProperties.aaIndex[sq
+ .charAt(j - 1)];
}
seqNums.setElementAt(sqnum, i);
@@ -137,8 +183,8 @@ 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");
}
}
@@ -166,17 +212,34 @@ public class Conservation
{
c = sequences[j].getCharAt(i);
- // No need to check if its a '-'
- if (c == '.' || c == ' ')
- {
- c = '-';
+ 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);
+ }
}
-
- if ('a' <= c && c <= 'z')
+ else
{
- c -= (32); // 32 = 'a' - 'A'
- }
+ // 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]++;
}
else
@@ -185,10 +248,10 @@ public class Conservation
}
}
- //What is the count threshold to count the residues in residueHash()
+ // What is the count threshold to count the residues in residueHash()
thresh = (threshold * (jSize)) / 100;
- //loop over all the found residues
+ // loop over all the found residues
resultHash = new Hashtable();
for (char v = '-'; v < 'Z'; v++)
{
@@ -197,7 +260,7 @@ public class Conservation
{
res = String.valueOf(v);
- //Now loop over the properties
+ // Now loop over the properties
enumeration2 = propHash.keys();
while (enumeration2.hasMoreElements())
@@ -205,7 +268,7 @@ public class Conservation
type = (String) enumeration2.nextElement();
ht = (Hashtable) propHash.get(type);
- //Have we ticked this before?
+ // Have we ticked this before?
if (!resultHash.containsKey(type))
{
if (ht.containsKey(res))
@@ -217,22 +280,25 @@ public class Conservation
resultHash.put(type, ht.get("-"));
}
}
- else if ( ( (Integer) resultHash.get(type)).equals(
- (Integer) ht.get(res)) == false)
+ else if (((Integer) resultHash.get(type)).equals(ht.get(res)) == false)
{
- resultHash.put(type, new Integer( -1));
+ resultHash.put(type, new Integer(-1));
}
}
}
}
- total[i - start] = resultHash;
+ if (total.length > 0)
+ {
+ total[i - start] = resultHash;
+ }
}
}
- /***
- * countConsNGaps
- * returns gap count in int[0], and conserved residue count in int[1]
+ /*****************************************************************************
+ * count conservation for the j'th column of the alignment
+ *
+ * @return { gap count, conserved residue count}
*/
public int[] countConsNGaps(int j)
{
@@ -254,7 +320,7 @@ public class Conservation
c = sequences[i].getCharAt(j); // gaps do not have upper/lower case
- if (jalview.util.Comparison.isGap( (c)))
+ if (jalview.util.Comparison.isGap((c)))
{
count++;
}
@@ -282,9 +348,12 @@ public class Conservation
/**
* Calculates the conservation sequence
- *
- * @param consflag if true, poitiveve conservation; false calculates negative conservation
- * @param percentageGaps commonly used value is 25
+ *
+ * @param consflag
+ * if true, poitiveve conservation; false calculates negative
+ * conservation
+ * @param percentageGaps
+ * commonly used value is 25
*/
public void verdict(boolean consflag, float percentageGaps)
{
@@ -297,25 +366,25 @@ public class Conservation
Hashtable resultHash;
Enumeration enumeration;
- //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
- //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
- //DOES NOT EXIST IN JALVIEW 2.1.2
+ // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
+ // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
+ // DOES NOT EXIST IN JALVIEW 2.1.2
for (int i = 0; i < start; i++)
{
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;
+ pgaps = ((float) totGaps * 100) / sequences.length;
+ consSymbs[i - start] = new String();
if (percentageGaps > pgaps)
{
resultHash = total[i - start];
-
- //Now find the verdict
+ // Now find the verdict
count = 0;
enumeration = resultHash.keys();
@@ -323,12 +392,12 @@ public class Conservation
{
type = (String) enumeration.nextElement();
result = (Integer) resultHash.get(type);
-
- //Do we want to count +ve conservation or +ve and -ve cons.?
+ // Do we want to count +ve conservation or +ve and -ve cons.?
if (consflag)
{
if (result.intValue() == 1)
{
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
}
@@ -336,6 +405,17 @@ public class Conservation
{
if (result.intValue() != -1)
{
+ {
+ if (result.intValue() == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
+ }
+
count++;
}
}
@@ -347,7 +427,7 @@ public class Conservation
}
else
{
- consString.append( (gapcons[0] == 1) ? "*" : "+");
+ consString.append((gapcons[0] == 1) ? "*" : "+");
}
}
else
@@ -360,8 +440,8 @@ public class Conservation
}
/**
- *
- *
+ *
+ *
* @return Conservation sequence
*/
public Sequence getConsSequence()
@@ -383,13 +463,13 @@ public class Conservation
seqNums = new Vector();
// calcSeqNum(s);
int i = 0, iSize = sequences.length;
- //Do we need to calculate this again?
+ // Do we need to calculate this again?
for (i = 0; i < iSize; i++)
{
calcSeqNum(i);
}
- if ( (cons2 == null) || seqNumsChanged)
+ if ((cons2 == null) || seqNumsChanged)
{
cons2 = new int[maxLength][24];
@@ -424,28 +504,23 @@ public class Conservation
// 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;
- }
-
- }
- } */
+ /*
+ * 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
- *
- * @param start Start residue
- * @param end End residue
+ *
+ * @param start
+ * Start residue
+ * @param end
+ * End residue
*/
public void findQuality(int start, int end)
{
@@ -454,9 +529,9 @@ public class Conservation
double max = -10000;
int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
- //Loop over columns // JBPNote Profiling info
- //long ts = System.currentTimeMillis();
- //long te = System.currentTimeMillis();
+ // Loop over columns // JBPNote Profiling info
+ // long ts = System.currentTimeMillis();
+ // long te = System.currentTimeMillis();
percentIdentity2();
int size = seqNums.size();
@@ -467,7 +542,7 @@ public class Conservation
for (l = 0; l < size; l++)
{
- lengths[l] = ( (int[]) seqNums.elementAt(l)).length - 1;
+ lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
}
for (j = start; j <= end; j++)
@@ -483,8 +558,7 @@ public class Conservation
for (i2 = 0; i2 < 24; i2++)
{
- x[ii] += ( ( (double) cons2[j][i2] * BLOSUM62[ii][i2]) +
- 4);
+ x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4);
}
x[ii] /= size;
@@ -495,8 +569,8 @@ public class Conservation
{
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]) ? ((int[]) seqNums.elementAt(k))[j + 1]
+ : 23; // Sequence, or gap at the end
// This is a loop over r
for (i = 0; i < 23; i++)
@@ -505,8 +579,8 @@ public class Conservation
sr = (double) BLOSUM62[i][seqNum] + 4;
- //Calculate X with another loop over residues
- // System.out.println("Xi " + i + " " + x[i] + " " + sr);
+ // 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]);
@@ -521,7 +595,7 @@ public class Conservation
max = bigtot;
}
- // bigtot = bigtot * (size-cons2[j][23])/size;
+ // bigtot = bigtot * (size-cons2[j][23])/size;
quality.addElement(new Double(bigtot));
// Need to normalize by gaps
@@ -531,10 +605,10 @@ public class Conservation
for (j = start; j <= end; j++)
{
- tmp = ( (Double) quality.elementAt(j)).doubleValue();
- tmp = ( (max - tmp) * (size - cons2[j][23])) / size;
+ tmp = ((Double) quality.elementAt(j)).doubleValue();
+ tmp = ((max - tmp) * (size - cons2[j][23])) / size;
- // System.out.println(tmp+ " " + j);
+ // System.out.println(tmp+ " " + j);
quality.setElementAt(new Double(tmp), j);
if (tmp > newmax)
@@ -543,8 +617,164 @@ public class Conservation
}
}
- // System.out.println("Quality " + s);
+ // System.out.println("Quality " + s);
qualityRange[0] = new Double(0);
qualityRange[1] = new Double(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
+ */
+ public void completeAnnotations(AlignmentAnnotation conservation,
+ AlignmentAnnotation quality2, int istart, int alWidth)
+ {
+ char[] sequence = getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and
+ // Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ if (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.annotations = new Annotation[alWidth];
+ }
+ qmin = qualityRange[0].floatValue();
+ qmax = qualityRange[1].floatValue();
+ }
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
+
+ if (Character.isDigit(c))
+ {
+ value = c - '0';
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ 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.elementAt(i)).floatValue();
+ 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)));
+ }
+ }
+ }
+
+ /**
+ * construct and call the calculation methods on a new Conservation object
+ *
+ * @param name
+ * - name of conservation
+ * @param consHash
+ * - hash table of properties for each amino acid (normally
+ * ResidueProperties.propHash)
+ * @param threshold
+ * - minimum number of conserved residues needed to indicate
+ * conservation (typically 3)
+ * @param seqs
+ * @param start
+ * first column in calculation window
+ * @param end
+ * last column in calculation window
+ * @param posOrNeg
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * 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,
+ Hashtable consHash, int threshold, List seqs,
+ int start, int end, boolean posOrNeg, int consPercGaps,
+ boolean calcQuality)
+ {
+ Conservation cons = new Conservation(name, consHash, threshold, seqs,
+ start, end);
+ return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
+ }
+
+ /**
+ * @param b
+ * positive (true) or negative (false) conservation
+ * @param consPercGaps
+ * 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(Conservation cons,
+ boolean b, int consPercGaps, boolean calcQuality)
+ {
+ cons.calculate();
+ cons.verdict(b, consPercGaps);
+
+ if (calcQuality)
+ {
+ cons.findQuality();
+ }
+
+ return cons;
+ }
}