git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2609 enabled (still broken/incomplete) fast paint
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
diff --git
a/src/jalview/analysis/Conservation.java
b/src/jalview/analysis/Conservation.java
index
d1a3c37
..
f94a658
100755
(executable)
--- a/
src/jalview/analysis/Conservation.java
+++ b/
src/jalview/analysis/Conservation.java
@@
-52,14
+52,19
@@
public class Conservation
private static final int TOUPPERCASE = 'a' - 'A';
private static final int TOUPPERCASE = 'a' - 'A';
+ private static final int GAP_INDEX = -1;
+
SequenceI[] sequences;
int start;
int end;
SequenceI[] sequences;
int start;
int end;
- Vector<int[]> 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<int[]> seqNums;
int maxLength = 0; // used by quality calcs
int maxLength = 0; // used by quality calcs
@@
-72,17
+77,17
@@
public class Conservation
*/
Map<String, Integer>[] total;
*/
Map<String, Integer>[] total;
- boolean canonicaliseAa = true; // if true then conservation calculation will
-
- // map all symbols to canonical aa numbering
- // rather than consider conservation of that
- // symbol
+ /*
+ * if true then conservation calculation will map all symbols to canonical aa
+ * numbering rather than consider conservation of that symbol
+ */
+ boolean canonicaliseAa = true;
- /** Stores calculated quality values */
private Vector<Double> quality;
private Vector<Double> quality;
- /** Stores maximum and minimum values of quality values */
- private double[] qualityRange = new double[2];
+ private double qualityMinimum;
+
+ private double qualityMaximum;
private Sequence consSequence;
private Sequence consSequence;
@@
-93,8
+98,16
@@
public class Conservation
private String name = "";
private String name = "";
+ /*
+ * an array, for each column, of counts of symbols (by score matrix index)
+ */
private int[][] cons2;
private int[][] cons2;
+ /*
+ * gap counts for each column
+ */
+ private int[] cons2GapCounts;
+
private String[] consSymbs;
/**
private String[] consSymbs;
/**
@@
-172,7
+185,6
@@
public class Conservation
*/
private void calcSeqNum(int i, ScoreMatrix sm)
{
*/
private void calcSeqNum(int i, ScoreMatrix sm)
{
- int gapIndex = sm.getMatrixIndex(' ');
int sSize = sequences.length;
if ((i > -1) && (i < sSize))
int sSize = sequences.length;
if ((i > -1) && (i < sSize))
@@
-207,10
+219,18
@@
public class Conservation
for (j = 1; j <= len; j++)
{
// sqnum[j] = ResidueProperties.aaIndex[sq.charAt(j - 1)];
for (j = 1; j <= len; j++)
{
// sqnum[j] = ResidueProperties.aaIndex[sq.charAt(j - 1)];
- sqnum[j] = sm.getMatrixIndex(sq.charAt(j - 1));
- if (sqnum[j] == -1)
+ char residue = sq.charAt(j - 1);
+ if (Comparison.isGap(residue))
{
{
- sqnum[j] = gapIndex;
+ sqnum[j] = GAP_INDEX;
+ }
+ else
+ {
+ sqnum[j] = sm.getMatrixIndex(residue);
+ if (sqnum[j] == -1)
+ {
+ sqnum[j] = GAP_INDEX;
+ }
}
}
}
}
@@
-536,7
+556,7
@@
public class Conservation
// From Alignment.java in jalview118
public void findQuality()
{
// From Alignment.java in jalview118
public void findQuality()
{
- findQuality(0, maxLength - 1);
+ findQuality(0, maxLength - 1, ScoreModels.getInstance().getBlosum62());
}
/**
}
/**
@@
-554,13
+574,12
@@
public class Conservation
calcSeqNum(i, sm);
}
calcSeqNum(i, sm);
}
- int gapIndex = sm.getMatrixIndex(' ');
-
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];
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;
int j = 0;
@@
-570,12
+589,21
@@
public class Conservation
for (i = 1; i < sqnum.length; i++)
{
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++)
{
for (i = sqnum.length - 1; i < maxLength; i++)
{
- cons2[i][gapIndex]++; // gap count
+ cons2GapCounts[i]++;
}
j++;
}
}
j++;
}
@@
-583,78
+611,78
@@
public class Conservation
}
/**
}
/**
- * 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 startRes
- * Start residue
- * @param endRes
- * End residue
+ * @param startCol
+ * @param endCol
+ * @param scoreMatrix
*/
*/
- public void findQuality(int startRes, int endRes)
+ protected void findQuality(int startCol, int endCol, ScoreMatrix scoreMatrix)
{
quality = new Vector<Double>();
double max = -Double.MAX_VALUE;
{
quality = new Vector<Double>();
double max = -Double.MAX_VALUE;
- ScoreMatrix blosum62 = ScoreModels.getInstance().getBlosum62();
- float[][] blosumScores = blosum62.getMatrix();
- int gapIndex = blosum62.getMatrixIndex(' ');
+ float[][] scores = scoreMatrix.getMatrix();
- // Loop over columns // JBPNote Profiling info
- // long ts = System.currentTimeMillis();
- // long te = System.currentTimeMillis();
- percentIdentity(blosum62);
+ percentIdentity(scoreMatrix);
int size = seqNums.size();
int[] lengths = new int[size];
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] = seqNums.elementAt(l).length - 1;
}
{
lengths[l] = seqNums.elementAt(l).length - 1;
}
- // todo ? remove '*' (unused?) from score matrix and
- // use getSize() here instead of getSize() - 1 ??
- final int symbolCount = blosum62.getSize() - 1; // 24;
+ final int symbolCount = scoreMatrix.getSize();
- for (j = startRes; j <= endRes; j++)
+ for (int j = startCol; j <= endCol; j++)
{
{
- bigtot = 0;
+ double bigtot = 0;
// First Xr = depends on column only
// First Xr = depends on column only
- x = new double[symbolCount];
+ double[] x = new double[symbolCount];
- for (ii = 0; ii < symbolCount; ii++)
+ for (int ii = 0; ii < symbolCount; ii++)
{
x[ii] = 0;
{
x[ii] = 0;
- for (i2 = 0; i2 < symbolCount; 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] * blosumScores[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
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[symbolCount];
- seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : gapIndex;
- // 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 < symbolCount - 1; i++)
+ for (int i = 0; i < symbolCount - 1; i++)
{
{
- sr = 0;
-
- sr = (double) blosumScores[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]);
xx[i] = x[i] - sr;
tot += (xx[i] * xx[i]);
@@
-663,25
+691,18
@@
public class Conservation
bigtot += Math.sqrt(tot);
}
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));
quality.addElement(new Double(bigtot));
-
- // Need to normalize by gaps
}
double newmax = -Double.MAX_VALUE;
}
double newmax = -Double.MAX_VALUE;
- for (j = startRes; j <= endRes; j++)
+ for (int j = startCol; j <= endCol; j++)
{
{
- tmp = quality.elementAt(j).doubleValue();
+ double tmp = quality.elementAt(j).doubleValue();
// tmp = ((max - tmp) * (size - cons2[j][23])) / size;
// tmp = ((max - tmp) * (size - cons2[j][23])) / size;
- tmp = ((max - tmp) * (size - cons2[j][gapIndex])) / size;
+ tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
// System.out.println(tmp+ " " + j);
quality.setElementAt(new Double(tmp), j);
// System.out.println(tmp+ " " + j);
quality.setElementAt(new Double(tmp), j);
@@
-692,9
+713,8
@@
public class Conservation
}
}
}
}
- // System.out.println("Quality " + s);
- qualityRange[0] = 0D;
- qualityRange[1] = newmax;
+ qualityMinimum = 0D;
+ qualityMaximum = newmax;
}
/**
}
/**
@@
-714,28
+734,23
@@
public class Conservation
public void completeAnnotations(AlignmentAnnotation conservation,
AlignmentAnnotation quality2, int istart, int alWidth)
{
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
+ 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;
float min = 0f;
float max = 11f;
float qmin = 0f;
float qmax = 0f;
- char c;
-
if (conservation != null && conservation.annotations != null
&& conservation.annotations.length < alWidth)
{
if (conservation != null && conservation.annotations != null
&& conservation.annotations.length < alWidth)
{
@@
-744,21
+759,21
@@
public class Conservation
if (quality2 != null)
{
if (quality2 != null)
{
- quality2.graphMax = (float) qualityRange[1];
+ quality2.graphMax = (float) qualityMaximum;
if (quality2.annotations != null
&& quality2.annotations.length < alWidth)
{
quality2.annotations = new Annotation[alWidth];
}
if (quality2.annotations != null
&& quality2.annotations.length < alWidth)
{
quality2.annotations = new Annotation[alWidth];
}
- qmin = (float) qualityRange[0];
- qmax = (float) qualityRange[1];
+ qmin = (float) qualityMinimum;
+ qmax = (float) qualityMaximum;
}
for (int i = istart; i < alWidth; i++)
{
float value = 0;
}
for (int i = istart; i < alWidth; i++)
{
float value = 0;
- c = sequence[i];
+ char c = cons.getCharAt(i);
if (Character.isDigit(c))
{
if (Character.isDigit(c))
{
@@
-845,8
+860,8
@@
public class Conservation
*/
String getTooltip(int column)
{
*/
String getTooltip(int column)
{
- char[] sequence = getConsSequence().getSequence();
- char val = column < sequence.length ? sequence[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]
boolean hasConservation = val != '-' && val != '0';
int consp = column - start;
String tip = (hasConservation && consp > -1 && consp < consSymbs.length) ? consSymbs[consp]