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Change "/" to "*" for a better performance.
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@fcyu
fcyu committed Jan 30, 2018
1 parent deb54a5 commit 4f04394
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Showing 6 changed files with 50 additions and 44 deletions.
4 changes: 3 additions & 1 deletion src/main/java/proteomics/Index/BuildIndex.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ public class BuildIndex {
private Map<String, ChainEntry> seq_entry_map = new HashMap<>();
private Map<String, Set<String>> seqProMap;
private final float ms1_bin_size;
private final float inverseMs1BinSize;

public BuildIndex(Map<String, String> parameter_map) throws IOException {
// initialize parameters
Expand All @@ -45,6 +46,7 @@ public BuildIndex(Map<String, String> parameter_map) throws IOException {
} else {
ms1_bin_size = 0.001f;
}
inverseMs1BinSize = 1 / ms1_bin_size;

// Read fix modification
fix_mod_map.put('G', Float.valueOf(parameter_map.get("G")));
Expand Down Expand Up @@ -221,7 +223,7 @@ public float binToRightMass(int bin_idx) {
}

public int massToBin(float mass) {
return (int) Math.floor(mass / ms1_bin_size);
return (int) Math.floor(mass * inverseMs1BinSize);
}

private Map<String, Set<String>> buildSeqProMap(Map<String, String> pro_seq_map, Map<String, boolean[]> seq_term_map, int min_chain_length, int max_chain_length) {
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4 changes: 2 additions & 2 deletions src/main/java/proteomics/Search/CalEValue.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ public class CalEValue {
}

int[] score_histogram = result_entry.getScoreHistogram();
double histogram_bin_size = result_entry.getHistogramBinSize();
double inverseHistogramBinSize = ResultEntry.getInverseHistogramBinSize();

int min_nonzero_idx = 0;
for (int i = 0; i < score_histogram.length; ++i) {
Expand Down Expand Up @@ -179,7 +179,7 @@ public class CalEValue {
result_entry.setEValue(9999);
logger.debug("Estimating E-value failed. Scan: {}, mass: {}, slope: {}, intercept: {}, R square: {}, point num: {}.",scan_num, result_entry.spectrum_mass, optimal_slope, optimal_intercept, max_r_square, result_entry.getScoreCount());
} else {
result_entry.setEValue(Math.exp((optimal_slope * Math.round(result_entry.getScore() / histogram_bin_size) + optimal_intercept) + Math.log((double) result_entry.getCandidateNum() / (double) result_entry.getScoreCount()))); // double point precision limitation.
result_entry.setEValue(Math.exp((optimal_slope * Math.round(result_entry.getScore() * inverseHistogramBinSize) + optimal_intercept) + Math.log((double) result_entry.getCandidateNum() / (double) result_entry.getScoreCount()))); // double point precision limitation.
result_entry.setEValueDetails((float) max_r_square, (float) optimal_slope, (float) optimal_intercept, optimal_start_idx, null_end_idx);
}

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6 changes: 3 additions & 3 deletions src/main/java/proteomics/Search/Search.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@ ResultEntry doSearch(SpectrumEntry spectrumEntry, SparseVector xcorrPL) throws I
if (chain_entry_map.get(chain_score_entry_1.getSeq()).binaryModType == chain_entry_map.get(chain_score_entry_2.getSeq()).binaryModType) {
double score;
if (chain_score_entry_1.getPtmFreeSeq().contentEquals(chain_score_entry_2.getPtmFreeSeq())) {
score = (chain_score_entry_1.getScore() + chain_score_entry_2.getScore()) / 2;
score = (chain_score_entry_1.getScore() + chain_score_entry_2.getScore()) * 0.5;
++candidate_num;
} else {
score = chain_score_entry_1.getScore() + chain_score_entry_2.getScore();
Expand All @@ -142,15 +142,15 @@ ResultEntry doSearch(SpectrumEntry spectrumEntry, SparseVector xcorrPL) throws I
double temp_1 = -1;
if (chain_score_entry_1.getSecondSeq() != null) {
if (chain_score_entry_1.getSecondPtmFreeSeq().contentEquals(chain_score_entry_2.getPtmFreeSeq())) {
temp_1 = (chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore()) / 2;
temp_1 = (chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore()) * 0.5;
} else {
temp_1 = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore();
}
}
double temp_2 = -1;
if (chain_score_entry_2.getSecondSeq() != null) {
if (chain_score_entry_1.getPtmFreeSeq().contentEquals(chain_score_entry_2.getSecondPtmFreeSeq())) {
temp_2 = (chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore()) / 2;
temp_2 = (chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore()) * 0.5;
} else {
temp_2 = chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore();
}
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46 changes: 25 additions & 21 deletions src/main/java/proteomics/TheoSeq/MassTool.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,11 @@ public class MassTool {
private final int missed_cleavage;
private final String cut_site;
private final String protect_site;
private double mz_bin_size = 1.0005;
private double one_minus_bin_offset = 0.4;
private final double inverseMzBinSize;
private final double one_minus_bin_offset;

public MassTool(int missed_cleavage, Map<Character, Float> fix_mod_map, String cut_site, String protect_site, float mz_bin_size, float one_minus_bin_offset) {
this.mz_bin_size = mz_bin_size;
inverseMzBinSize = 1 / mz_bin_size;
this.missed_cleavage = missed_cleavage;
this.cut_site = cut_site;
this.protect_site = protect_site;
Expand Down Expand Up @@ -53,7 +53,7 @@ public MassTool(int missed_cleavage, Map<Character, Float> fix_mod_map, String c
}

public int mzToBin(double mz) {
return (int) (mz / mz_bin_size + one_minus_bin_offset);
return (int) (mz * inverseMzBinSize + one_minus_bin_offset);
}

public float calResidueMass(String seq) { // n and c are also AA.
Expand Down Expand Up @@ -113,58 +113,62 @@ public SparseBooleanVector buildTheoVector(String seq, short linkSite, float add
linkSite = (short) Math.max(1, linkSite);

int localMaxCharge = Math.min(max_charge, Math.max(precursor_charge - 1, 1));
double[] inverseChargeArray = new double[localMaxCharge];
for (int charge = 1; charge <= localMaxCharge; ++charge) {
inverseChargeArray[charge - 1] = (double) 1 / (double) charge;
}

SparseBooleanVector outputVector = new SparseBooleanVector();

AA[] aaArray = seqToAAList(seq);

// traverse the sequence to get b-ion
double bIonMass = mass_table.get(aaArray[0].aa) + aaArray[0].delta_mass; // add N-term modification
for (int i = 1; i < aaArray.length - 2; ++i) {
bIonMass += mass_table.get(aaArray[i].aa) + aaArray[i].delta_mass;
if (i < linkSite) {
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin(bIonMass / charge + 1.00727646688));
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin(bIonMass * inverseCharge + 1.00727646688));
}
} else {
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin((bIonMass + additional_mass) / charge + 1.00727646688));
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin((bIonMass + additional_mass) * inverseCharge + 1.00727646688));
}
}
}
// calculate the last b-ion with C-term modification
bIonMass += mass_table.get(aaArray[aaArray.length - 2].aa) + aaArray[aaArray.length - 2].delta_mass + mass_table.get(aaArray[aaArray.length - 1].aa) + aaArray[aaArray.length - 1].delta_mass;
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin((bIonMass + additional_mass) / charge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin((bIonMass + additional_mass) * inverseCharge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
}

// traverse the sequence with reversed order to get y-ion
// the whole sequence
double yIonMass = bIonMass + H2O;
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin((yIonMass + additional_mass) / charge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688)); // for the fragment containing all amino acids, the additional mass is always included.
}
// delete the first amino acid and N-term modification
yIonMass -= mass_table.get(aaArray[0].aa) + aaArray[0].delta_mass + mass_table.get(aaArray[1].aa) + aaArray[1].delta_mass;
if (1 >= linkSite) {
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin(yIonMass / charge + 1.00727646688));
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin(yIonMass * inverseCharge + 1.00727646688));
}
} else {
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin((yIonMass + additional_mass) / charge + 1.00727646688));
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688));
}
}
// rest of the sequence
for (int i = 2; i < aaArray.length - 2; ++i) {
yIonMass -= mass_table.get(aaArray[i].aa) + aaArray[i].delta_mass;
if (i >= linkSite) { // caution: here, it is different from b-ion
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin(yIonMass / charge + 1.00727646688));
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin(yIonMass * inverseCharge + 1.00727646688));
}
} else {
for (int charge = 1; charge <= localMaxCharge; ++charge) {
outputVector.put(mzToBin((yIonMass + additional_mass) / charge + 1.00727646688));
for (double inverseCharge : inverseChargeArray) {
outputVector.put(mzToBin((yIonMass + additional_mass) * inverseCharge + 1.00727646688));
}
}
}
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/proteomics/Types/ResultEntry.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
public class ResultEntry{

private static final Logger logger = LoggerFactory.getLogger(ResultEntry.class);
public static final double histogram_bin_size = 0.05f;
public static final double inverseHistogramBinSize = 20;
private static final double max_score = 20;

public final String spectrum_id;
Expand Down Expand Up @@ -44,7 +44,7 @@ public class ResultEntry{

public ResultEntry(String spectrum_id, float spectrum_mz, float spectrum_mass, float rt, int charge, boolean cal_evalue, TreeMap<Integer, ChainResultEntry> binChainMap) {
if (cal_evalue) {
score_histogram = new int[(int) Math.round(max_score / histogram_bin_size) + 1]; // start from zero score.
score_histogram = new int[(int) Math.round(max_score * inverseHistogramBinSize) + 1]; // start from zero score.
}
this.spectrum_id = spectrum_id;
this.spectrum_mz = spectrum_mz;
Expand Down Expand Up @@ -88,7 +88,7 @@ public void setCandidateNum(long candidate_num) {

public void addToScoreHistogram(double score) {
try {
++score_histogram[(int) Math.round(score / histogram_bin_size)];
++score_histogram[(int) Math.round(score * inverseHistogramBinSize)];
++score_count;
} catch (ArrayIndexOutOfBoundsException ex) {
logger.warn("Score {} is out of the range [0, {}].", score, max_score);
Expand Down Expand Up @@ -138,8 +138,8 @@ public int[] getScoreHistogram() {
return score_histogram;
}

public double getHistogramBinSize() {
return histogram_bin_size;
public static double getInverseHistogramBinSize() {
return inverseHistogramBinSize;
}

public double getEValue() {
Expand Down
24 changes: 12 additions & 12 deletions src/main/java/proteomics/Validation/CalFDR.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

public class CalFDR {

private final float precision;
private final float inversePrecision;

private double min_score = 999;
private double max_score = -999;
Expand All @@ -17,9 +17,9 @@ public class CalFDR {
public CalFDR(List<FinalResultEntry> results, boolean cal_evalue) {
this.results = results;
if (cal_evalue) {
precision = 0.1f;
inversePrecision = 10;
} else {
precision = 0.001f;
inversePrecision = 1000;
}

// find the max score
Expand All @@ -41,7 +41,7 @@ public CalFDR(List<FinalResultEntry> results, boolean cal_evalue) {
}
}

final int array_length = 1 + (int) Math.ceil((max_score - min_score) / precision);
final int array_length = 1 + (int) Math.ceil((max_score - min_score) * inversePrecision);
float[] decoy_count_vector = new float[array_length];
float[] target_count_vector = new float[array_length];
float[] fuse_count_vector = new float[array_length];
Expand All @@ -52,25 +52,25 @@ public CalFDR(List<FinalResultEntry> results, boolean cal_evalue) {
if (re.hit_type == 1) {
int idx;
if (cal_evalue) {
idx = (int) Math.floor((re.negative_log10_evalue - min_score) / precision);
idx = (int) Math.floor((re.negative_log10_evalue - min_score) * inversePrecision);
} else {
idx = (int) Math.floor((re.score - min_score) / precision);
idx = (int) Math.floor((re.score - min_score) * inversePrecision);
}
++decoy_count_vector[idx];
} else if (re.hit_type == 0) {
int idx;
if (cal_evalue) {
idx = (int) Math.floor((re.negative_log10_evalue - min_score) / precision);
idx = (int) Math.floor((re.negative_log10_evalue - min_score) * inversePrecision);
} else {
idx = (int) Math.floor((re.score - min_score) / precision);
idx = (int) Math.floor((re.score - min_score) * inversePrecision);
}
++target_count_vector[idx];
} else {
int idx;
if (cal_evalue) {
idx = (int) Math.floor((re.negative_log10_evalue - min_score) / precision);
idx = (int) Math.floor((re.negative_log10_evalue - min_score) * inversePrecision);
} else {
idx = (int) Math.floor((re.score - min_score) / precision);
idx = (int) Math.floor((re.score - min_score) * inversePrecision);
}
++fuse_count_vector[idx];
}
Expand Down Expand Up @@ -119,10 +119,10 @@ public List<FinalResultEntry> includeStats(boolean cal_evalue) {
for (FinalResultEntry re : results) {
if (re.hit_type == 0) {
if (cal_evalue) {
int idx = (int) Math.floor((re.negative_log10_evalue - min_score) / precision);
int idx = (int) Math.floor((re.negative_log10_evalue - min_score) * inversePrecision);
re.qvalue = qvalue_array[idx];
} else {
int idx = (int) Math.floor((re.score - min_score) / precision);
int idx = (int) Math.floor((re.score - min_score) * inversePrecision);
re.qvalue = qvalue_array[idx];
}
}
Expand Down

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