X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=cbc4dcae3130c89b40ccf47d77dfd7e488cd2194;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=b914108dbeb4428eb7eebf2f9d6263feaba02b17;hpb=db8b5a2bbc50c28300729664f5a586b08748bb55;p=jalview.git
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b914108..cbc4dca 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -1,575 +1,879 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* 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.
-*
-* 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
-*/
-package jalview.analysis;
-
-import jalview.datamodel.*;
-
-import java.util.*;
-
-
-/**
- * Calculates conservation values for a given set of sequences
- *
- * @author $author$
- * @version $Revision$
- */
-public class Conservation
-{
- Vector sequences;
- int start;
- int end;
- 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;
- Vector total = new Vector();
-
- /** Stores calculated quality values */
- public Vector quality;
-
- /** 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;
-
- /**
- * 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
- */
- public Conservation(String name, Hashtable propHash, int threshold,
- Vector sequences, int start, int end)
- {
- this.name = name;
- this.propHash = propHash;
- this.threshold = threshold;
- this.sequences = sequences;
- this.start = start;
- this.end = end;
- seqNums = new Vector(sequences.size());
- calcSeqNums();
- }
-
- /**
- * DOCUMENT ME!
- */
- private void calcSeqNums()
- {
- int i=0, iSize=sequences.size();
- for (i=0; i < iSize; i++)
- {
- calcSeqNum(i);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- private void calcSeqNum(int i)
- {
- String sq = null; // for dumb jbuilder not-inited exception warning
- int[] sqnum = null;
-
- if ((i > -1) && (i < sequences.size()))
- {
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();
-
- if (seqNums.size() <= i)
- {
- seqNums.addElement(new int[sq.length() + 1]);
- }
-
- if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
- {
- int j;
- int len;
- seqNumsChanged = true;
- sq = ((SequenceI) sequences.elementAt(i)).getSequence();
- len = sq.length();
-
- if (maxLength < len)
- {
- maxLength = len;
- }
-
- 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] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(String.valueOf(
- sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash
- }
-
- seqNums.setElementAt(sqnum, i);
- }
- }
- else
- {
- // JBPNote INFO level debug
- System.err.println(
- "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
- }
- }
-
- /**
- * Calculates the conservation values for given set of sequences
- */
- public void calculate()
- {
- Hashtable resultHash, residueHash, ht;
- int count, thresh, j, jSize = sequences.size();
- String type, res=null;
- SequenceI sequence;
- char c;
- Enumeration enumeration, enumeration2;
-
- for (int i = start; i <= end; i++)
- {
- resultHash = new Hashtable();
- residueHash = new Hashtable();
-
- for (j = 0; j < jSize; j++)
- {
- // JBPNote - have to make sure elements of the sequences vector
- // are tested like this everywhere...
- sequence = (Sequence) sequences.elementAt(j);
-
- if (sequence.getLength() > i)
- {
- c = sequence.getCharAt(i);
-
- if(jalview.util.Comparison.isGap(c))
- c = '-';
-
- if ('a' <= c && c <= 'z')
- {
- // TO UPPERCASE !!!
- //Faster than toUpperCase
- c -= ('a' - 'A') ;
- }
-
- res = String.valueOf( c );
-
-
- if (residueHash.containsKey(res))
- {
- count = ((Integer) residueHash.get(res)).intValue();
- count++;
- residueHash.put(res, new Integer(count));
- }
- else
- {
- residueHash.put(res, new Integer(1));
- }
- }
- else
- {
- if (residueHash.containsKey("-"))
- {
- count = ((Integer) residueHash.get("-")).intValue();
- count++;
- residueHash.put("-", new Integer(count));
- }
- else
- {
- residueHash.put("-", new Integer(1));
- }
- }
- }
-
- //What is the count threshold to count the residues in residueHash()
- thresh = (threshold * (sequences.size())) / 100;
-
- //loop over all the found residues
- enumeration = residueHash.keys();
-
- while (enumeration.hasMoreElements())
- {
- res = (String) enumeration.nextElement();
-
- if (((Integer) residueHash.get(res)).intValue() > thresh)
- {
- //Now loop over the properties
- enumeration2 = propHash.keys();
-
- 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));
- }
- }
- }
- }
-
- total.addElement(resultHash);
- }
- }
-
-
- /***
- * countConsNGaps
- * returns gap count in int[0], and conserved residue count in int[1]
- */
- public int[] countConsNGaps(int j)
- {
- int count = 0;
- int cons = 0;
- int nres = 0;
- int[] r = new int[2];
- char f = '$';
- int i, iSize = sequences.size();
- char c;
-
- for (i = 0; i < iSize; i++)
- {
- if (j >= ((Sequence) sequences.elementAt(i)).getLength())
- {
- count++;
- continue;
- }
-
- c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case
-
- if (jalview.util.Comparison.isGap((c)))
- {
- count++;
- }
- else
- {
- nres++;
-
- if (nres == 1)
- {
- f = c;
- cons++;
- }
- else if (f == c)
- {
- cons++;
- }
- }
- }
-
- r[0] = (nres == cons) ? 1 : 0;
- r[1] = count;
-
- return r;
- }
-
- /**
- * Calculates the conservation sequence
- *
- * @param consflag if true, poitiveve conservation; false calculates negative conservation
- * @param percentageGaps commonly used value is 25
- */
- 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;
-
-
- for (int i = start; i <= end; i++)
- {
- gapcons = countConsNGaps(i);
- totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / (float) sequences.size();
-
- if (percentageGaps > pgaps)
- {
- resultHash = (Hashtable) total.elementAt(i - start);
-
- //Now find the verdict
- count = 0;
- enumeration = resultHash.keys();
-
- while (enumeration.hasMoreElements())
- {
- type = (String) enumeration.nextElement();
- result = (Integer) resultHash.get(type);
-
- //Do we want to count +ve conservation or +ve and -ve cons.?
- if (consflag)
- {
- if (result.intValue() == 1)
- {
- count++;
- }
- }
- else
- {
- if (result.intValue() != -1)
- {
- count++;
- }
- }
- }
-
- if (count < 10)
- {
- consString.append(count); // Conserved props!=Identity
- }
- else
- {
- consString.append((gapcons[0] == 1) ? "*" : "+");
- }
- }
- else
- {
- consString.append("-");
- }
- }
-
- consSequence = new Sequence(name, consString.toString(), start, end);
- }
-
- /**
- *
- *
- * @return Conservation sequence
- */
- public Sequence getConsSequence()
- {
- return consSequence;
- }
-
- // From Alignment.java in jalview118
- public void findQuality()
- {
- findQuality(0, maxLength - 1);
- }
-
- /**
- * DOCUMENT ME!
- */
- private void percentIdentity2()
- {
- calcSeqNums(); // updates maxLength, too.
-
- if ((cons2 == null) || seqNumsChanged)
- {
- cons2 = new int[maxLength][24];
-
- // Initialize the array
- for (int j = 0; j < 24; j++)
- {
- for (int i = 0; i < maxLength; i++)
- {
- cons2[i][j] = 0;
- }
- }
-
- int[] sqnum;
- int j = 0;
-
- while (j < sequences.size())
- {
- sqnum = (int[]) seqNums.elementAt(j);
-
- for (int i = 1; i < sqnum.length; i++)
- {
- cons2[i - 1][sqnum[i]]++;
- }
-
- for (int i = sqnum.length - 1; i < maxLength; i++)
- {
- cons2[i][23]++; // gap count
- }
-
- 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
- *
- * @param start Start residue
- * @param end End residue
- */
- public void findQuality(int start, int end)
- {
- quality = new Vector();
-
- double max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
-
- //Loop over columns // JBPNote Profiling info
- // long ts = System.currentTimeMillis();
- //long te = System.currentTimeMillis();
- percentIdentity2();
-
- int size = seqNums.size();
- int[] lengths = new int[size];
- double tot, bigtot, sr, tmp;
- double [] x, xx;
- int l, j, i, ii, seqNum;
-
- for (l = 0; l < size; l++)
- lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
-
-
- for (j = start; j <= end; j++)
- {
- bigtot = 0;
-
- // First Xr = depends on column only
- x = new double[24];
-
- for (ii = 0; ii < 24; ii++)
- {
- x[ii] = 0;
-
- try
- {
- for (int i2 = 0; i2 < 24; i2++)
- {
- x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) +
- 4);
- }
- }
- catch (Exception e)
- {
- System.err.println("Exception during quality calculation.");
- e.printStackTrace();
- }
-
- //System.out.println("X " + ii + " " + x[ii]);
- x[ii] /= (size);
-
- //System.out.println("X " + ii + " " + x[ii]);
- }
-
- // Now calculate D for each position and sum
- 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
-
- // This is a loop over r
- for (i = 0; i < 23; i++)
- {
- sr = 0;
-
- try
- {
- sr = (double) BLOSUM62[i][seqNum] + 4;
- }
- catch (Exception e)
- {
- System.out.println("Exception in sr: " + e);
- e.printStackTrace();
- }
-
- //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]);
- }
-
- bigtot += Math.sqrt(tot);
- }
-
- // This is the quality for one column
- if (max < bigtot)
- {
- max = bigtot;
- }
-
- // bigtot = bigtot * (size-cons2[j][23])/size;
- quality.addElement(new Double(bigtot));
-
-
- // Need to normalize by gaps
- }
-
- double newmax = -10000;
-
- for (j = start; j <= end; j++)
- {
- tmp = ((Double) quality.elementAt(j)).doubleValue();
- tmp = ((max - tmp) * (size - cons2[j][23])) / size;
-
- // System.out.println(tmp+ " " + j);
- quality.setElementAt(new Double(tmp), j);
-
- if (tmp > newmax)
- {
- newmax = tmp;
- }
- }
-
- // System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+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
+ */
+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;
+
+ /*
+ * 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;
+
+ /*
+ * 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;
+
+ private double qualityMinimum;
+
+ private double qualityMaximum;
+
+ private Sequence consSequence;
+
+ /*
+ * percentage of residues in a column to qualify for counting conservation
+ */
+ private int threshold;
+
+ private String name = "";
+
+ /*
+ * an array, for each column, of counts of symbols (by score matrix index)
+ */
+ private int[][] cons2;
+
+ /*
+ * gap counts for each column
+ */
+ private int[] cons2GapCounts;
+
+ private String[] consSymbs;
+
+ /**
+ * 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);
+ }
+
+ /**
+ * Constructor
+ *
+ * @param name
+ * Name of conservation
+ * @param threshold
+ * percentage of sequences at or below which property conservation is
+ * ignored
+ * @param sequences
+ * sequences to be used in calculation
+ * @param start
+ * start column position
+ * @param end
+ * end column position
+ */
+ public Conservation(String name, int threshold, List sequences,
+ int start, int end)
+ {
+ this.name = name;
+ this.threshold = threshold;
+ this.start = start;
+ this.end = end;
+
+ maxLength = end - start + 1; // default width includes bounds of
+ // calculation
+
+ int s, sSize = sequences.size();
+ SequenceI[] sarray = new SequenceI[sSize];
+ this.sequences = sarray;
+ try
+ {
+ for (s = 0; s < sSize; s++)
+ {
+ 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 score matrix indices and store it in the i'th
+ * position of the seqNums array.
+ *
+ * @param i
+ * @param sm
+ */
+ private void calcSeqNum(int i, ScoreMatrix sm)
+ {
+ int sSize = sequences.length;
+
+ if ((i > -1) && (i < sSize))
+ {
+ String sq = sequences[i].getSequenceAsString();
+
+ if (seqNums.size() <= i)
+ {
+ seqNums.addElement(new int[sq.length() + 1]);
+ }
+
+ /*
+ * 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;
+ seqNumsChanged = true;
+ len = sq.length();
+
+ if (maxLength < len)
+ {
+ maxLength = len;
+ }
+
+ 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] = 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);
+ }
+ else
+ {
+ System.out.println("SEQUENCE HAS BEEN DELETED!!!");
+ }
+ }
+ else
+ {
+ // JBPNote INFO level debug
+ System.err.println(
+ "ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
+ }
+ }
+
+ /**
+ * Calculates the conservation values for given set of sequences
+ */
+ public void calculate()
+ {
+ int height = sequences.length;
+
+ total = new Map[maxLength];
+
+ for (int column = start; column <= end; column++)
+ {
+ ResidueCount values = countResidues(column);
+
+ /*
+ * 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
+ */
+ SortedMap resultHash = new TreeMap<>();
+ SymbolCounts symbolCounts = values.getSymbolCounts();
+ char[] symbols = symbolCounts.symbols;
+ int[] counts = symbolCounts.values;
+ for (int j = 0; j < symbols.length; j++)
+ {
+ char c = symbols[j];
+ if (counts[j] > thresh)
+ {
+ 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 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
+ {
+ /*
+ * unrecognised residue - use default value for property
+ */
+ resultMap.put(propertyName, property.getValue().get("-"));
+ }
+ }
+ else
+ {
+ Integer currentResult = resultMap.get(propertyName);
+ if (currentResult.intValue() != -1
+ && !currentResult.equals(residuePropertyValue))
+ {
+ /*
+ * property is unconserved - residues seen both with and without it
+ */
+ resultMap.put(propertyName, Integer.valueOf(-1));
+ }
+ }
+ }
+ }
+
+ /**
+ * Counts residues (upper-cased) and gaps in the given column
+ *
+ * @param column
+ * @return
+ */
+ protected ResidueCount countResidues(int column)
+ {
+ ResidueCount values = new ResidueCount(false);
+
+ 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);
+ }
+ }
+ else
+ {
+ values.addGap();
+ }
+ }
+ return values;
+ }
+
+ /**
+ * Counts conservation and gaps for a column of the alignment
+ *
+ * @return { 1 if fully conserved, else 0, gap count }
+ */
+ public int[] countConservationAndGaps(int column)
+ {
+ int gapCount = 0;
+ boolean fullyConserved = true;
+ int iSize = sequences.length;
+
+ if (iSize == 0)
+ {
+ return new int[] { 0, 0 };
+ }
+
+ char lastRes = '0';
+ for (int i = 0; i < iSize; i++)
+ {
+ if (column >= sequences[i].getLength())
+ {
+ gapCount++;
+ continue;
+ }
+
+ char c = sequences[i].getCharAt(column); // gaps do not have upper/lower
+ // case
+
+ if (Comparison.isGap((c)))
+ {
+ gapCount++;
+ }
+ else
+ {
+ c = toUpperCase(c);
+ if (lastRes == '0')
+ {
+ lastRes = c;
+ }
+ if (c != lastRes)
+ {
+ fullyConserved = false;
+ }
+ }
+ }
+
+ 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 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 positiveOnly, float maxPercentageGaps)
+ {
+ // 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
+ // 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++)
+ {
+ int[] gapcons = countConservationAndGaps(i);
+ boolean fullyConserved = gapcons[0] == 1;
+ int totGaps = gapcons[1];
+ float pgaps = (totGaps * 100f) / sequences.length;
+
+ if (maxPercentageGaps > pgaps)
+ {
+ Map resultHash = total[i - start];
+ int count = 0;
+ StringBuilder positives = new StringBuilder(64);
+ StringBuilder negatives = new StringBuilder(32);
+ for (String type : resultHash.keySet())
+ {
+ int result = resultHash.get(type).intValue();
+ if (result == -1)
+ {
+ /*
+ * not conserved (present or absent)
+ */
+ continue;
+ }
+ count++;
+ if (result == 1)
+ {
+ /*
+ * 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)
+ {
+ consString.append(count); // Conserved props!=Identity
+ }
+ else
+ {
+ consString.append(fullyConserved ? "*" : "+");
+ }
+ }
+ else
+ {
+ consString.append('-');
+ }
+ }
+
+ consSequence = new Sequence(name, consString.toString(), start, end);
+ }
+
+ /**
+ *
+ *
+ * @return Conservation sequence
+ */
+ public SequenceI getConsSequence()
+ {
+ return consSequence;
+ }
+
+ // From Alignment.java in jalview118
+ public void findQuality()
+ {
+ findQuality(0, maxLength - 1, ScoreModels.getInstance().getBlosum62());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sm
+ */
+ private void percentIdentity(ScoreMatrix sm)
+ {
+ seqNums = new Vector<>();
+ int i = 0, iSize = sequences.length;
+ // Do we need to calculate this again?
+ for (i = 0; i < iSize; 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];
+
+ int j = 0;
+
+ while (j < sequences.length)
+ {
+ int[] sqnum = seqNums.elementAt(j);
+
+ for (i = 1; i < sqnum.length; 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++)
+ {
+ cons2GapCounts[i]++;
+ }
+ j++;
+ }
+ }
+ }
+
+ /**
+ * Calculates the quality of the set of sequences over the given inclusive
+ * column range, using the specified substitution score matrix
+ *
+ * @param startCol
+ * @param endCol
+ * @param scoreMatrix
+ */
+ protected void findQuality(int startCol, int endCol,
+ ScoreMatrix scoreMatrix)
+ {
+ quality = new Vector<>();
+
+ double max = -Double.MAX_VALUE;
+ float[][] scores = scoreMatrix.getMatrix();
+
+ percentIdentity(scoreMatrix);
+
+ int size = seqNums.size();
+ int[] lengths = new int[size];
+
+ for (int l = 0; l < size; l++)
+ {
+ lengths[l] = seqNums.elementAt(l).length - 1;
+ }
+
+ final int symbolCount = scoreMatrix.getSize();
+
+ for (int j = startCol; j <= endCol; j++)
+ {
+ double bigtot = 0;
+
+ // First Xr = depends on column only
+ double[] x = new double[symbolCount];
+
+ for (int ii = 0; ii < symbolCount; ii++)
+ {
+ x[ii] = 0;
+
+ /*
+ * 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] * scores[ii][i2]) + 4D);
+ }
+ x[ii] += 4D + cons2GapCounts[j] * scoreMatrix.getMinimumScore();
+
+ x[ii] /= size;
+ }
+
+ // Now calculate D for each position and sum
+ for (int k = 0; k < size; k++)
+ {
+ 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;
+
+ for (int i = 0; i < symbolCount - 1; i++)
+ {
+ double sr = 4D;
+ if (seqNum == GAP_INDEX)
+ {
+ sr += scoreMatrix.getMinimumScore();
+ }
+ else
+ {
+ sr += scores[i][seqNum];
+ }
+
+ xx[i] = x[i] - sr;
+
+ tot += (xx[i] * xx[i]);
+ }
+
+ bigtot += Math.sqrt(tot);
+ }
+
+ max = Math.max(max, bigtot);
+
+ quality.addElement(Double.valueOf(bigtot));
+ }
+
+ double newmax = -Double.MAX_VALUE;
+
+ for (int j = startCol; j <= endCol; j++)
+ {
+ 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(Double.valueOf(tmp), j);
+
+ if (tmp > newmax)
+ {
+ newmax = tmp;
+ }
+ }
+
+ 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;
+ }
+}