*/
package jalview.analysis;
+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 java.awt.Color;
-import java.util.Enumeration;
-import java.util.Hashtable;
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';
+
SequenceI[] sequences;
int start;
int end;
- Vector seqNums; // vector of int vectors where first is sequence checksum
+ Vector<int[]> seqNums; // vector of int vectors where first is sequence
+ // checksum
int maxLength = 0; // used by quality calcs
boolean seqNumsChanged = false; // updated after any change via calcSeqNum;
- Hashtable[] total;
+ /*
+ * a map per column with {property, conservation} where conservation value is
+ * 1 (property is conserved), 0 (absence of property is conserved) or -1
+ * (property is not conserved i.e. column has residues with and without it)
+ */
+ Map<String, Integer>[] total;
boolean canonicaliseAa = true; // if true then conservation calculation will
// symbol
/** Stores calculated quality values */
- public Vector quality;
+ private Vector<Double> quality;
/** Stores maximum and minimum values of quality values */
- public Double[] qualityRange = new Double[2];
+ private double[] qualityRange = new double[2];
- String consString = "";
+ private Sequence consSequence;
- Sequence consSequence;
-
- Hashtable propHash;
-
- int threshold;
+ /*
+ * percentage of residues in a column to qualify for counting conservation
+ */
+ private int threshold;
- String name = "";
+ private String name = "";
- int[][] cons2;
+ private int[][] cons2;
private String[] consSymbs;
/**
- * Creates a new Conservation object.
+ * Constructor using default threshold of 3%
*
* @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
* @param end
* end residue position
*/
- public Conservation(String name, Hashtable propHash, int threshold,
+ public Conservation(String name, List<SequenceI> 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<SequenceI> sequences, int start, int end)
{
this.name = name;
- this.propHash = propHash;
this.threshold = threshold;
this.start = start;
this.end = end;
}
/**
- * 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 gapIndex = sm.getGapIndex();
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;
maxLength = len;
}
- sqnum = new int[len + 1]; // better to always make a new array -
+ 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)];
+ sqnum[j] = sm.getMatrixIndex(sq.charAt(j - 1));
+ if (sqnum[j] == -1)
+ {
+ sqnum[j] = gapIndex;
+ }
}
seqNums.setElementAt(sqnum, i);
*/
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<String, Integer> resultHash = new TreeMap<String, Integer>();
+ SymbolCounts symbolCounts = values.getSymbolCounts();
+ char[] symbols = symbolCounts.symbols;
+ int[] counts = symbolCounts.values;
+ for (int j = 0; j < symbols.length; j++)
{
- if (sequences[j].getLength() > i)
+ char c = symbols[j];
+ if (counts[j] > thresh)
{
- c = sequences[j].getCharAt(i);
-
- if (canonicaliseAa)
- { // lookup the base aa code symbol
- c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
- .getCharAt(i)];
- if (c > 20)
- {
- c = '-';
- }
- else
- {
- // recover canonical aa symbol
- c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
- }
- }
- else
- {
- // original behaviour - operate on ascii symbols directly
- // No need to check if its a '-'
- if (c == '.' || c == ' ')
- {
- c = '-';
- }
-
- if (!canonicaliseAa && 'a' <= c && c <= 'z')
- {
- c -= (32); // 32 = 'a' - 'A'
- }
- }
- values[c]++;
+ recordConservation(resultHash, String.valueOf(c));
+ }
+ }
+ if (values.getGapCount() > thresh)
+ {
+ recordConservation(resultHash, "-");
+ }
+
+ if (total.length > 0)
+ {
+ total[column - start] = resultHash;
+ }
+ }
+ }
+
+ /**
+ * Updates the conservation results for an observed residue
+ *
+ * @param resultMap
+ * a map of {property, conservation} where conservation value is +1
+ * (all residues have the property), 0 (no residue has the property)
+ * or -1 (some do, some don't)
+ * @param res
+ */
+ protected static void recordConservation(Map<String, Integer> resultMap,
+ String res)
+ {
+ res = res.toUpperCase();
+ for (Entry<String, Map<String, Integer>> property : ResidueProperties.propHash
+ .entrySet())
+ {
+ String propertyName = property.getKey();
+ Integer residuePropertyValue = property.getValue().get(res);
+
+ if (!resultMap.containsKey(propertyName))
+ {
+ /*
+ * first time we've seen this residue - note whether it has this property
+ */
+ if (residuePropertyValue != null)
+ {
+ resultMap.put(propertyName, residuePropertyValue);
}
else
{
- values['-']++;
+ /*
+ * unrecognised residue - use default value for property
+ */
+ resultMap.put(propertyName, property.getValue().get("-"));
}
}
-
- // What is the count threshold to count the residues in residueHash()
- thresh = (threshold * (jSize)) / 100;
-
- // loop over all the found residues
- resultHash = new Hashtable();
- for (char v = '-'; v < 'Z'; v++)
+ else
{
-
- if (values[v] > thresh)
+ Integer currentResult = resultMap.get(propertyName);
+ if (currentResult.intValue() != -1
+ && !currentResult.equals(residuePropertyValue))
{
- res = String.valueOf(v);
+ /*
+ * property is unconserved - residues seen both with and without it
+ */
+ resultMap.put(propertyName, Integer.valueOf(-1));
+ }
+ }
+ }
+ }
- // Now loop over the properties
- enumeration2 = propHash.keys();
+ /**
+ * Counts residues (upper-cased) and gaps in the given column
+ *
+ * @param column
+ * @return
+ */
+ protected ResidueCount countResidues(int column)
+ {
+ ResidueCount values = new ResidueCount(false);
- while (enumeration2.hasMoreElements())
- {
- type = (String) enumeration2.nextElement();
- ht = (Hashtable) propHash.get(type);
-
- // Have we ticked this before?
- if (!resultHash.containsKey(type))
- {
- if (ht.containsKey(res))
- {
- resultHash.put(type, ht.get(res));
- }
- else
- {
- resultHash.put(type, ht.get("-"));
- }
- }
- else if (((Integer) resultHash.get(type)).equals(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);
}
}
-
- if (total.length > 0)
+ else
{
- total[i - start] = resultHash;
+ values.addGap();
}
}
+ return values;
}
- /*****************************************************************************
- * count conservation for the j'th column of the alignment
+ /**
+ * Counts conservation and gaps for a column of the alignment
*
- * @return { gap count, conserved residue count}
+ * @return { 1 if fully conserved, else 0, gap count }
*/
- public int[] countConsNGaps(int j)
+ public int[] countConservationAndGaps(int column)
{
- int count = 0;
- int cons = 0;
- int nres = 0;
- int[] r = new int[2];
- char f = '$';
- int i, iSize = sequences.length;
- char c;
+ int gapCount = 0;
+ boolean fullyConserved = true;
+ int iSize = sequences.length;
- for (i = 0; i < iSize; i++)
+ if (iSize == 0)
+ {
+ 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
consSymbs = new String[end - start + 1];
for (int i = start; i <= end; i++)
{
- gapcons = countConsNGaps(i);
- totGaps = gapcons[1];
- pgaps = ((float) totGaps * 100) / sequences.length;
- consSymbs[i - start] = new String();
+ int[] gapcons = countConservationAndGaps(i);
+ boolean fullyConserved = gapcons[0] == 1;
+ int totGaps = gapcons[1];
+ float pgaps = (totGaps * 100f) / sequences.length;
- if (percentageGaps > pgaps)
+ if (maxPercentageGaps > pgaps)
{
- resultHash = total[i - start];
- // Now find the verdict
- count = 0;
- enumeration = resultHash.keys();
-
- while (enumeration.hasMoreElements())
+ Map<String, Integer> resultHash = total[i - start];
+ int count = 0;
+ StringBuilder positives = new StringBuilder(64);
+ StringBuilder negatives = new StringBuilder(32);
+ for (String type : resultHash.keySet())
{
- type = (String) enumeration.nextElement();
- result = (Integer) resultHash.get(type);
- // Do we want to count +ve conservation or +ve and -ve cons.?
- if (consflag)
+ int result = resultHash.get(type).intValue();
+ if (result == -1)
{
- if (result.intValue() == 1)
- {
- consSymbs[i - start] = type + " " + consSymbs[i - start];
- count++;
- }
+ /*
+ * not conserved (present or absent)
+ */
+ continue;
}
- else
+ count++;
+ if (result == 1)
{
- if (result.intValue() != -1)
- {
- {
- if (result.intValue() == 0)
- {
- consSymbs[i - start] = consSymbs[i - start] + " !" + type;
- }
- else
- {
- consSymbs[i - start] = type + " " + consSymbs[i - start];
- }
- }
-
- 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)
{
}
else
{
- consString.append((gapcons[0] == 1) ? "*" : "+");
+ consString.append(fullyConserved ? "*" : "+");
}
}
else
*
* @return Conservation sequence
*/
- public Sequence getConsSequence()
+ public SequenceI getConsSequence()
{
return consSequence;
}
/**
* DOCUMENT ME!
+ *
+ * @param sm
*/
- private void percentIdentity2()
+ private void percentIdentity(ScoreMatrix sm)
{
- seqNums = new Vector();
- // calcSeqNum(s);
+ seqNums = new Vector<int[]>();
int i = 0, iSize = sequences.length;
// Do we need to calculate this again?
for (i = 0; i < iSize; i++)
{
- calcSeqNum(i);
+ calcSeqNum(i, sm);
}
+ int gapIndex = sm.getGapIndex();
+
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];
- // 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++)
{
for (i = sqnum.length - 1; i < maxLength; i++)
{
- cons2[i][23]++; // gap count
+ cons2[i][gapIndex]++; // 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
+ * @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>();
- double max = -10000;
- int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();
+ double max = -Double.MAX_VALUE;
+ ScoreMatrix blosum62 = ScoreModels.getInstance().getBlosum62();
+ float[][] blosumScores = blosum62.getMatrix();
// Loop over columns // JBPNote Profiling info
// long ts = System.currentTimeMillis();
// long te = System.currentTimeMillis();
- percentIdentity2();
+ percentIdentity(blosum62);
int size = seqNums.size();
int[] lengths = new int[size];
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++)
+ // todo ? remove '*' (unused?) from score matrix and
+ // use getSize() here instead of getSize() - 1 ??
+ final int symbolCount = blosum62.getSize() - 1; // 24;
+ int gapIndex = blosum62.getGapIndex();
+
+ for (j = startRes; j <= endRes; j++)
{
bigtot = 0;
// First Xr = depends on column only
- x = new double[24];
+ x = new double[symbolCount];
- for (ii = 0; ii < 24; ii++)
+ for (ii = 0; ii < symbolCount; ii++)
{
x[ii] = 0;
- for (i2 = 0; i2 < 24; i2++)
+ for (i2 = 0; i2 < symbolCount; i2++)
{
- x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4);
+ x[ii] += (((double) cons2[j][i2] * blosumScores[ii][i2]) + 4);
}
x[ii] /= size;
for (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
+ xx = new double[symbolCount];
+ seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : gapIndex;
+ // Sequence, or gap at the end
// This is a loop over r
- for (i = 0; i < 23; i++)
+ for (i = 0; i < symbolCount - 1; i++)
{
sr = 0;
- sr = (double) BLOSUM62[i][seqNum] + 4;
+ sr = (double) blosumScores[i][seqNum] + 4;
// Calculate X with another loop over residues
// System.out.println("Xi " + i + " " + x[i] + " " + sr);
// Need to normalize by gaps
}
- double newmax = -10000;
+ double newmax = -Double.MAX_VALUE;
- for (j = start; j <= end; j++)
+ for (j = startRes; j <= endRes; j++)
{
- tmp = ((Double) quality.elementAt(j)).doubleValue();
- tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+ tmp = quality.elementAt(j).doubleValue();
+ // tmp = ((max - tmp) * (size - cons2[j][23])) / size;
+ tmp = ((max - tmp) * (size - cons2[j][gapIndex])) / size;
// System.out.println(tmp+ " " + j);
quality.setElementAt(new Double(tmp), j);
}
// System.out.println("Quality " + s);
- qualityRange[0] = new Double(0);
- qualityRange[1] = new Double(newmax);
+ qualityRange[0] = 0D;
+ qualityRange[1] = newmax;
}
/**
- * complete the given consensus and quuality annotation rows. Note: currently
+ * 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.
*
char c;
- if (conservation.annotations != null
+ if (conservation != null && conservation.annotations != null
&& conservation.annotations.length < alWidth)
{
conservation.annotations = new Annotation[alWidth];
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;
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)));
+ 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
*
* @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
+ * @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,
- Hashtable consHash, int threshold, List<SequenceI> 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)
+ List<SequenceI> seqs, int start, int end, boolean positiveOnly,
+ int maxPercentGaps, boolean calcQuality)
{
+ Conservation cons = new Conservation(name, seqs, start, end);
cons.calculate();
- cons.verdict(b, consPercGaps);
+ cons.verdict(positiveOnly, maxPercentGaps);
if (calcQuality)
{
return cons;
}
+
+ /**
+ * Returns the computed tooltip (annotation description) for a given column.
+ * The tip is empty if the conservation score is zero, otherwise holds the
+ * conserved properties (and, optionally, properties whose absence is
+ * conserved).
+ *
+ * @param column
+ * @return
+ */
+ String getTooltip(int column)
+ {
+ char[] sequence = getConsSequence().getSequence();
+ char val = column < sequence.length ? sequence[column] : '-';
+ boolean hasConservation = val != '-' && val != '0';
+ int consp = column - start;
+ String tip = (hasConservation && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]
+ : "";
+ return tip;
+ }
}