X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=75dec63ac63c6930428fba667e573786f5c38a36;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=2a065f6cb37fd8adff3d8ad6cccec467af3463a8;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 2a065f6..75dec63 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,26 +1,36 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* Calculates conservation values for a given set of sequences
@@ -36,13 +46,14 @@ public class Conservation
int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
+ Vector 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;
+ Map[] total;
boolean canonicaliseAa = true; // if true then conservation calculation will
@@ -51,30 +62,26 @@ public class Conservation
// symbol
/** Stores calculated quality values */
- public Vector quality;
+ private Vector 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;
+ private int threshold;
- Hashtable propHash;
+ private String name = "";
- int threshold;
+ private int[][] cons2;
- String name = "";
-
- int[][] cons2;
+ private String[] consSymbs;
/**
* Creates a new Conservation object.
*
* @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
@@ -84,12 +91,10 @@ public class Conservation
* @param end
* end residue 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;
@@ -100,20 +105,22 @@ public class Conservation
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
this.sequences = sarray;
- try {
- 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;
+ // bail - another thread has modified the sequence array, so the current
+ // calculation is probably invalid.
+ this.sequences = new SequenceI[0];
+ maxLength = 0;
}
}
@@ -139,7 +146,7 @@ public class Conservation
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;
@@ -181,12 +188,9 @@ 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;
total = new Hashtable[maxLength];
@@ -202,8 +206,7 @@ public class Conservation
if (canonicaliseAa)
{ // lookup the base aa code symbol
- c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
- .getCharAt(i)];
+ c = (char) ResidueProperties.aaIndex[sequences[j].getCharAt(i)];
if (c > 20)
{
c = '-';
@@ -211,7 +214,7 @@ public class Conservation
else
{
// recover canonical aa symbol
- c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
+ c = ResidueProperties.aa[c].charAt(0);
}
}
else
@@ -223,10 +226,7 @@ public class Conservation
c = '-';
}
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
+ c = toUpperCase(c);
}
values[c]++;
}
@@ -240,21 +240,18 @@ public class Conservation
thresh = (threshold * (jSize)) / 100;
// loop over all the found residues
- resultHash = new Hashtable();
+ Hashtable resultHash = new Hashtable();
for (char v = '-'; v < 'Z'; v++)
{
if (values[v] > thresh)
{
- res = String.valueOf(v);
+ String res = String.valueOf(v);
// Now loop over the properties
- enumeration2 = propHash.keys();
-
- while (enumeration2.hasMoreElements())
+ for (String type : ResidueProperties.propHash.keySet())
{
- type = (String) enumeration2.nextElement();
- ht = (Hashtable) propHash.get(type);
+ Map ht = ResidueProperties.propHash.get(type);
// Have we ticked this before?
if (!resultHash.containsKey(type))
@@ -268,8 +265,7 @@ public class Conservation
resultHash.put(type, ht.get("-"));
}
}
- else if (((Integer) resultHash.get(type)).equals((Integer) ht
- .get(res)) == false)
+ else if (!resultHash.get(type).equals(ht.get(res)))
{
resultHash.put(type, new Integer(-1));
}
@@ -277,7 +273,8 @@ public class Conservation
}
}
- if (total.length>0) {
+ if (total.length > 0)
+ {
total[i - start] = resultHash;
}
}
@@ -314,6 +311,7 @@ public class Conservation
}
else
{
+ c = toUpperCase(c);
nres++;
if (nres == 1)
@@ -335,10 +333,26 @@ public class Conservation
}
/**
+ * 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 -= (32); // 32 = 'a' - 'A'
+ }
+ return c;
+ }
+
+ /**
* Calculates the conservation sequence
*
* @param consflag
- * if true, poitiveve conservation; false calculates negative
+ * if true, positive conservation; false calculates negative
* conservation
* @param percentageGaps
* commonly used value is 25
@@ -346,13 +360,6 @@ public class Conservation
public void verdict(boolean consflag, float percentageGaps)
{
StringBuffer consString = new StringBuffer();
- String type;
- Integer result;
- int[] gapcons;
- int totGaps, count;
- float pgaps;
- Hashtable resultHash;
- Enumeration enumeration;
// NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
// EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
@@ -361,38 +368,43 @@ 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 = countConsNGaps(i);
+ int totGaps = gapcons[1];
+ float pgaps = ((float) totGaps * 100) / sequences.length;
+ consSymbs[i - start] = new String();
if (percentageGaps > pgaps)
{
- resultHash = total[i - start];
-
+ Map resultHash = total[i - start];
// Now find the verdict
- count = 0;
- enumeration = resultHash.keys();
-
- while (enumeration.hasMoreElements())
+ int count = 0;
+ for (String type : resultHash.keySet())
{
- type = (String) enumeration.nextElement();
- result = (Integer) resultHash.get(type);
-
+ int result = resultHash.get(type).intValue();
// Do we want to count +ve conservation or +ve and -ve cons.?
if (consflag)
{
- if (result.intValue() == 1)
+ if (result == 1)
{
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
count++;
}
}
else
{
- if (result.intValue() != -1)
+ if (result != -1)
{
+ if (result == 0)
+ {
+ consSymbs[i - start] = consSymbs[i - start] + " !" + type;
+ }
+ else
+ {
+ consSymbs[i - start] = type + " " + consSymbs[i - start];
+ }
count++;
}
}
@@ -437,7 +449,7 @@ public class Conservation
*/
private void percentIdentity2()
{
- seqNums = new Vector();
+ seqNums = new Vector();
// calcSeqNum(s);
int i = 0, iSize = sequences.length;
// Do we need to calculate this again?
@@ -464,7 +476,7 @@ public class Conservation
while (j < sequences.length)
{
- sqnum = (int[]) seqNums.elementAt(j);
+ sqnum = seqNums.elementAt(j);
for (i = 1; i < sqnum.length; i++)
{
@@ -494,17 +506,17 @@ public class Conservation
/**
* Calculates the quality of the set of sequences
*
- * @param start
+ * @param startRes
* Start residue
- * @param end
+ * @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 max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+ int[][] BLOSUM62 = ResidueProperties.getBLOSUM62();
// Loop over columns // JBPNote Profiling info
// long ts = System.currentTimeMillis();
@@ -519,10 +531,10 @@ public class Conservation
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;
@@ -546,8 +558,10 @@ 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]) ? seqNums.elementAt(k)[j + 1] : 23; // Sequence,
+ // or gap
+ // at the
+ // end
// This is a loop over r
for (i = 0; i < 23; i++)
@@ -580,9 +594,9 @@ public class Conservation
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);
@@ -595,12 +609,12 @@ public class Conservation
}
// 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
+ * 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.
*
@@ -638,7 +652,7 @@ public class Conservation
char c;
- if (conservation.annotations != null
+ if (conservation != null && conservation.annotations != null
&& conservation.annotations.length < alWidth)
{
conservation.annotations = new Annotation[alWidth];
@@ -646,17 +660,17 @@ public class Conservation
if (quality2 != null)
{
- quality2.graphMax = qualityRange[1].floatValue();
+ 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;
@@ -664,7 +678,7 @@ public class Conservation
if (Character.isDigit(c))
{
- value = (int) (c - '0');
+ value = c - '0';
}
else if (c == '*')
{
@@ -675,18 +689,23 @@ public class Conservation
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.elementAt(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
@@ -695,4 +714,41 @@ public class Conservation
}
}
}
+
+ /**
+ * construct and call the calculation methods on a new Conservation object
+ *
+ * @param name
+ * - name of conservation
+ * @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,
+ int threshold, List seqs, int start, int end,
+ boolean posOrNeg, int consPercGaps, boolean calcQuality)
+ {
+ Conservation cons = new Conservation(name, threshold, seqs, start, end);
+ cons.calculate();
+ cons.verdict(posOrNeg, consPercGaps);
+
+ if (calcQuality)
+ {
+ cons.findQuality();
+ }
+
+ return cons;
+ }
}