/** @throws BioException */
private void init() throws BioException {
similars = 0;
identicals = 0;
nGapsQ = 0;
nGapsS = 0;
for (int i = 0; i < Math.min(queryEnd - queryStart, subjectEnd - subjectStart); i++) {
Symbol a = query.symbolAt(i + queryStart);
Symbol b = subject.symbolAt(i + subjectStart);
boolean gap = false;
if (a.equals(b)) {
identicals++;
}
// get score for this pair. if it is positive, they are similar...
if (a.equals(query.getAlphabet().getGapSymbol())) {
nGapsQ++;
gap = true;
}
if (b.equals(subject.getAlphabet().getGapSymbol())) {
nGapsS++;
gap = true;
}
if (!gap && subMatrix != null && subMatrix.getValueAt(a, b) > 0) {
similars++;
}
}
}
public ArrayList<Double> mapPDScoresToAlignment(
ArrayList<Double> pdScores, Sequence seq, ArrayList<Integer> indicesOfRowsWithSumZero) {
ArrayList<Double> result = new ArrayList<Double>();
int seqLength = seq.length();
int nonGapPosition = 0;
Symbol gap = seq.getAlphabet().getGapSymbol();
for (int i = 0; i < seqLength; i++) {
double oneScore = Double.MIN_VALUE;
boolean isSumZero = false;
isSumZero = (indicesOfRowsWithSumZero.contains(i));
boolean isGap = false;
isGap =
(seq.symbolAt(i + 1)
== gap); // note: these +1 in indices are because seq starts from one and not zero!
if (isSumZero) {
oneScore = 0.0;
} else {
oneScore = pdScores.get(nonGapPosition);
nonGapPosition++;
}
result.add(oneScore);
}
return result;
} /*mapPDScoresToAlignment*/
public ArrayList<Double> mapViterbiPathToAlignment(
ArrayList<String> viterbiPath, Sequence seq, ArrayList<Integer> indicesOfRowsWithSumZero) {
ArrayList<Double> result = new ArrayList<Double>();
int seqLength = seq.length();
int nonGapPosition = 0;
Symbol gap = seq.getAlphabet().getGapSymbol();
for (int i = 0; i < seqLength; i++) {
double oneScore = Double.MIN_VALUE;
boolean isSumZero = false;
isSumZero = (indicesOfRowsWithSumZero.contains(i));
boolean isGap = false;
isGap =
(seq.symbolAt(i + 1)
== gap); // note: these +1 in indices are because seq and viterbi path start from one
// and not zero!
if (isSumZero) {
oneScore = 0.0;
} else {
if (viterbiPath.get(nonGapPosition).equals("M")) {
oneScore = 0.0;
} else if (viterbiPath.get(nonGapPosition).equals("R")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("r")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("G")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("g")) {
oneScore = 2.0;
} else if (viterbiPath.get(nonGapPosition).equals("E")) {
oneScore = 1.0;
} else if (viterbiPath.get(nonGapPosition).equals("e")) {
oneScore = 1.0;
} else if (viterbiPath.get(nonGapPosition).equals("J")) {
oneScore = 1.5;
} else {
System.err.println("Unknown charecter detected as a state name!");
}
nonGapPosition++;
}
result.add(oneScore);
}
return result;
} /*mapViterbiPathToAlignment*/
public LinkedHashMap<SimpleAlphabet, SimpleSymbolList> getAlphabetAndSimpleSymbolList(
Matrix2D m, Sequence sequence) throws IllegalSymbolException {
LinkedHashMap<SimpleAlphabet, SimpleSymbolList> alphabetAndSymbolList =
new LinkedHashMap<SimpleAlphabet, SimpleSymbolList>();
SimpleAlphabet alphabet = new SimpleAlphabet();
List<AtomicSymbol> listOfSymbols = new ArrayList<AtomicSymbol>();
alphabet.setName("ObservedSequenceAlphabet");
int numberofRows = m.rows();
int seqLength = sequence.length();
if (numberofRows != seqLength) {
System.err.print(
"It was assumed your sequence has a length equal to the number of rows of the matrix, but found a case that is not true!");
}
Symbol gap = sequence.getAlphabet().getGapSymbol();
for (int i = 0; i < numberofRows; i++) {
List<Symbol> oneListOfSymbol = new ArrayList<Symbol>(3);
// red is match, green is flanking and blue is background
double redValue = m.get(i, 0);
double greenValue = m.get(i, 1);
double blueValue = m.get(i, 2);
double onesum = redValue + greenValue + blueValue;
boolean isGap = false;
isGap = (sequence.symbolAt(i + 1) == gap);
if (onesum
== 0) { // sum of this value is supposed to be one, but for some rows it sums up to
// zero, this is to ignore those up to time we found out why these naouthy rows
// sums up to zero!
// continue;
// note these three lines is only a dummy solution for positions where red, green and blue
// are summed up to zero!
redValue = 0.3333;
greenValue = 0.3333;
blueValue = 1 - (redValue + greenValue);
}
// make one triplet symbol from three symbols
Symbol redSymbol = AlphabetManager.createSymbol(Double.toString(redValue));
Symbol greenSymol = AlphabetManager.createSymbol(Double.toString(greenValue));
Symbol blueSymbol = AlphabetManager.createSymbol(Double.toString(blueValue));
oneListOfSymbol.add(redSymbol);
oneListOfSymbol.add(greenSymol);
oneListOfSymbol.add(blueSymbol);
// now create symbol and add it to alphabet
AtomicSymbol oneSym =
(AtomicSymbol)
AlphabetManager.createSymbol(
Annotation.EMPTY_ANNOTATION, oneListOfSymbol, alphabet);
alphabet.addSymbol(oneSym);
listOfSymbols.add(oneSym);
}
SimpleSymbolList ssl = new SimpleSymbolList(alphabet, listOfSymbols);
alphabetAndSymbolList.put(alphabet, ssl);
return alphabetAndSymbolList;
} /*getAlphabetAndSimpleSymbolList*/
/**
* This method provides a BLAST-like formated alignment from the given <code>String</code>s, in
* which the sequence coordinates and the information "Query" or "Sbjct", respectively is added to
* each line. Each line contains <code>width</code> sequence characters including the gap symbols
* plus the meta information. There is one white line between two pairs of sequences.
*
* @param width the number of symbols to be displayed per line.
* @return formated String.
* @throws BioException
*/
public String formatOutput(int width) throws BioException {
int i, j;
/*
* Highlights equal symbols within the alignment, String match/missmatch
* representation
*/
StringBuilder path = new StringBuilder();
for (i = 0; i < Math.min(queryEnd - queryStart, subjectEnd - subjectStart) + 1; i++) {
Symbol a = query.symbolAt(i + queryStart);
Symbol b = subject.symbolAt(i + subjectStart);
if (!a.equals(query.getAlphabet().getGapSymbol())
&& !b.equals(subject.getAlphabet().getGapSymbol())
&& ((subMatrix.getValueAt(a, b) >= 0) || a.equals(b))) {
path.append('|');
} else {
path.append(' ');
}
}
int maxLength = path.length();
/*
* Math.max(queryEnd - queryStart, subjectEnd - subjectStart) + 1;
*/
Formatter output = new Formatter();
output.format("%n Time (ms): %s%n", time);
output.format(" Length: %d%n", maxLength);
output.format(" Score: %d%n", getScore());
output.format(" Query: %s, Length: %d%n", query.getName(), query.length() - nGapsQ);
output.format(" Sbjct: %s, Length: %d%n", subject.getName(), subject.length() - nGapsS);
output.format(
" Identities: %d/%d, i.e., %d %% (query) and %d %% (sbjct)%n",
identicals,
maxLength,
Math.round(getPercentIdentityQuery()),
Math.round(getPercentIdentitySubject()));
output.format(
" Similars: %d/%d, i.e., %d %% (query) and %d %% (sbjct)%n",
similars,
maxLength,
Math.round(getPercentSimilarityQuery()),
Math.round(getPercentSimilaritySubject()));
output.format(
" No. gaps: %d (%d %%) in query and %d (%d %%) in sbjct%n",
nGapsQ, Math.round(getPercentGapsQuery()), nGapsS, Math.round(getPercentGapsTarget()));
int queryLPos = queryStart, queryRPos, pathLPos = 0, pathRPos;
int subjectLPos = subjectStart, subjectRPos;
int ql = queryLPos - 1, qr = queryLPos - 1, qgaps;
int sl = subjectLPos - 1, sr = subjectLPos - 1, sgaps;
int widthLeft = String.valueOf(Math.max(queryStart, queryEnd)).length();
int widthRight = String.valueOf(Math.max(queryEnd, subjectEnd)).length() + 1;
// Take width of the meta information into account.
width = Math.max(width - widthLeft - widthRight - 12, 2);
for (i = 1; i <= Math.ceil((double) maxLength / width); i++) {
// Query
queryRPos =
Math.min(
queryStart + i * width - 1,
Math.min(queryEnd, subjectEnd - subjectStart + queryStart));
qgaps = 0;
for (j = queryLPos; j <= queryRPos; j++) {
if (!query.symbolAt(j).equals(query.getAlphabet().getGapSymbol())) {
qr++;
} else {
qgaps++;
}
}
if (qgaps <= queryRPos - queryLPos) {
ql++;
}
output.format("%nQuery: %" + widthLeft + "d ", ql);
output.format("%s ", query.subStr(queryLPos, queryRPos));
output.format("%-" + widthRight + "d%n", qr);
queryLPos = queryRPos + 1;
ql = qr;
// Path
pathRPos = Math.min(i * width, path.length());
output.format(
"%-" + (widthLeft + 10) + "c%s",
Character.valueOf(' '),
path.substring(pathLPos, pathRPos));
pathLPos = pathRPos;
// Sbjct
subjectRPos =
Math.min(
subjectStart + i * width - 1,
Math.min(queryEnd - queryStart + subjectStart, subjectEnd));
sgaps = 0;
for (j = subjectLPos; j <= subjectRPos; j++) {
if (!subject.symbolAt(j).equals(subject.getAlphabet().getGapSymbol())) {
sr++;
} else {
sgaps++;
}
}
if (sgaps <= subjectRPos - subjectLPos) {
sl++;
}
output.format("%nSbjct: %" + widthLeft + "d ", sl);
output.format("%s ", subject.subStr(subjectLPos, subjectRPos));
output.format("%-" + widthRight + "d%n", sr);
subjectLPos = subjectRPos + 1;
sl = sr;
}
return output.toString();
}