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Add a link_same_peptide option.
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@fcyu
fcyu committed Apr 1, 2018
1 parent 8de7ed8 commit 5b6a00d
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Showing 5 changed files with 151 additions and 31 deletions.
2 changes: 1 addition & 1 deletion src/main/java/proteomics/ECL2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,7 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws E
int precursorCharge = sqlResultSet.getInt("precursorCharge");
double massWithoutLinker = sqlResultSet.getDouble("massWithoutLinker");
double precursorMass = sqlResultSet.getDouble("precursorMass");
taskList.add(thread_pool.submit(new SearchWrap(search_obj, build_index_obj, mass_tool_obj, cal_evalue, delta_c_t, flankingPeaks, spectra_parser, lock, scanId, precursorCharge, massWithoutLinker, precursorMass, sqlPath)));
taskList.add(thread_pool.submit(new SearchWrap(search_obj, build_index_obj, mass_tool_obj, cal_evalue, delta_c_t, flankingPeaks, spectra_parser, lock, scanId, precursorCharge, massWithoutLinker, precursorMass, sqlPath, parameter_map.get("link_same_peptide").contentEquals("1"))));
}
sqlResultSet.close();
sqlStatement.close();
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164 changes: 136 additions & 28 deletions src/main/java/proteomics/Search/Search.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package proteomics.Search;

import ProteomicsLibrary.DbTool;
import proteomics.ECL2;
import ProteomicsLibrary.MassTool;
import ProteomicsLibrary.Types.*;
Expand Down Expand Up @@ -42,7 +43,7 @@ public Search(BuildIndex build_index_obj, Map<String, String> parameter_map, dou
}
}

ResultEntry doSearch(SparseVector xcorrPL, TreeMap<Integer, List<Double>> binScoresMap, double massWithoutLinker, int precursorCharge, double precursorMass, String scanId) throws IOException {
ResultEntry doSearch(SparseVector xcorrPL, TreeMap<Integer, List<Double>> binScoresMap, double massWithoutLinker, int precursorCharge, double precursorMass, String scanId, boolean linkSamePeptide) throws IOException {
int max_chain_bin_idx = Math.min(build_index_obj.massToBin(massWithoutLinker) + 1 - bin_seq_map.firstKey(), bin_seq_map.lastKey());
int min_chain_bin_idx = bin_seq_map.firstKey();

Expand Down Expand Up @@ -91,6 +92,7 @@ ResultEntry doSearch(SparseVector xcorrPL, TreeMap<Integer, List<Double>> binSco

if (binChainMap.containsKey(idx_1)) { // There may be no chain with chain score > single_chain_t
ChainResultEntry chain_score_entry_1 = binChainMap.get(idx_1);
String sequence1 = DbTool.getSequenceOnly(chain_score_entry_1.getPtmFreeSeq());
for (int idx_2 : sub_map.keySet()) {
if (!checkedBinSet.contains(idx_2)) {
// this bin hasn't been visited. Linear scan first.
Expand All @@ -106,47 +108,150 @@ ResultEntry doSearch(SparseVector xcorrPL, TreeMap<Integer, List<Double>> binSco

// only two sequences with the same binary mod type can be linked.
if (chain_entry_map.get(chain_score_entry_1.getSeq()).binaryModType == chain_entry_map.get(chain_score_entry_2.getSeq()).binaryModType) {
double score = chain_score_entry_1.getScore() + chain_score_entry_2.getScore();
String sequence2 = DbTool.getSequenceOnly(chain_score_entry_2.getPtmFreeSeq());
++candidate_num;
if (linkSamePeptide || (!sequence1.contains(sequence2) && !sequence2.contains(sequence1))) {
double score = chain_score_entry_1.getScore() + chain_score_entry_2.getScore();
double second_score;

// calculate second score
double second_score = 0;
double temp_1 = -1;
if (chain_score_entry_1.getSecondSeq() != null) {
temp_1 = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore();
}
double temp_2 = -1;
if (chain_score_entry_2.getSecondSeq() != null) {
temp_2 = chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore();
}
// calculate second score
Double[] tempArray = new Double[]{-1d, -1d, -1d};
if (chain_score_entry_1.getSecondSeq() != null) {
String sequence12 = DbTool.getSequenceOnly(chain_score_entry_1.getSecondSeq());
if (linkSamePeptide || (!sequence12.contains(sequence2) && !sequence2.contains(sequence12))) {
tempArray[0] = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore();
}
}
if (chain_score_entry_2.getSecondSeq() != null) {
String sequence22 = DbTool.getSequenceOnly(chain_score_entry_2.getSecondSeq());
if (linkSamePeptide || (!sequence22.contains(sequence1) && !sequence1.contains(sequence22))) {
tempArray[1] = chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore();
}
}
if (chain_score_entry_1.getSecondSeq() != null && chain_score_entry_2.getSecondSeq() != null) {
String sequence12 = DbTool.getSequenceOnly(chain_score_entry_1.getSecondSeq());
String sequence22 = DbTool.getSequenceOnly(chain_score_entry_2.getSecondSeq());
if (linkSamePeptide || (!sequence22.contains(sequence12) && !sequence12.contains(sequence22))) {
tempArray[2] = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getSecondScore();
}
}

Arrays.sort(tempArray, Collections.reverseOrder());
second_score = Math.max(0, tempArray[0]);

if (temp_1 > 0) {
if (temp_1 >= temp_2) {
second_score = temp_1;
// record results
if (score > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), second_score));
resultEntry.setScore(score);
resultEntry.setChain1(chain_score_entry_1.getSeq());
resultEntry.setChain2(chain_score_entry_2.getSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getLinkSite());
} else if (Math.max(score, second_score) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(score, second_score));
}
} else if (temp_2 > 0) {
if (temp_2 > temp_1) {
second_score = temp_2;
} else {
double temp_1 = -1;
if (chain_score_entry_1.getSecondSeq() != null) {
String sequence12 = DbTool.getSequenceOnly(chain_score_entry_1.getSecondSeq());
if (!sequence12.contains(sequence2) && !sequence2.contains(sequence12)) {
temp_1 = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore();
}
}
double temp_2 = -1;
if (chain_score_entry_2.getSecondSeq() != null) {
String sequence22 = DbTool.getSequenceOnly(chain_score_entry_2.getSecondSeq());
if (!sequence22.contains(sequence1) && !sequence1.contains(sequence22)) {
temp_2 = chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore();
}
}
double temp_3 = -1;
if (chain_score_entry_1.getSecondSeq() != null && chain_score_entry_2.getSecondSeq() != null) {
String sequence12 = DbTool.getSequenceOnly(chain_score_entry_1.getSecondSeq());
String sequence22 = DbTool.getSequenceOnly(chain_score_entry_2.getSecondSeq());
if (!sequence12.contains(sequence22) && !sequence22.contains(sequence12)) {
temp_3 = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getSecondScore();
}
}

// record results
if (temp_1 >= temp_2 && temp_2 >= temp_3) {
if (temp_1 > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), temp_2));
resultEntry.setScore(temp_1);
resultEntry.setChain1(chain_score_entry_1.getSecondSeq());
resultEntry.setChain2(chain_score_entry_2.getSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getSecondLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getLinkSite());
} else if (Math.max(temp_1, temp_2) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(temp_1, temp_2));
}
} else if (temp_1 >= temp_3 && temp_3 >= temp_2) {
if (temp_1 > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), temp_3));
resultEntry.setScore(temp_1);
resultEntry.setChain1(chain_score_entry_1.getSecondSeq());
resultEntry.setChain2(chain_score_entry_2.getSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getSecondLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getLinkSite());
} else if (Math.max(temp_1, temp_3) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(temp_1, temp_3));
}
} else if (temp_2 >= temp_3 && temp_3 >= temp_1) {
if (temp_2 > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), temp_3));
resultEntry.setScore(temp_2);
resultEntry.setChain1(chain_score_entry_1.getSeq());
resultEntry.setChain2(chain_score_entry_2.getSecondSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getSecondLinkSite());
} else if (Math.max(temp_2, temp_3) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(temp_2, temp_3));
}
} else if (temp_2 >= temp_1 && temp_1 >= temp_3) {
if (temp_2 > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), temp_1));
resultEntry.setScore(temp_2);
resultEntry.setChain1(chain_score_entry_1.getSeq());
resultEntry.setChain2(chain_score_entry_2.getSecondSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getSecondLinkSite());
} else if (Math.max(temp_1, temp_2) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(temp_1, temp_2));
}
} else if (temp_3 >= temp_1 && temp_1 >= temp_2) {
if (temp_3 > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), temp_1));
resultEntry.setScore(temp_3);
resultEntry.setChain1(chain_score_entry_1.getSecondSeq());
resultEntry.setChain2(chain_score_entry_2.getSecondSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getSecondLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getSecondLinkSite());
} else if (Math.max(temp_1, temp_3) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(temp_1, temp_3));
}
} else if (temp_3 >= temp_2 && temp_2 >= temp_1) {
if (temp_3 > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), temp_2));
resultEntry.setScore(temp_3);
resultEntry.setChain1(chain_score_entry_1.getSecondSeq());
resultEntry.setChain2(chain_score_entry_2.getSecondSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getSecondLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getSecondLinkSite());
} else if (Math.max(temp_2, temp_3) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(temp_2, temp_3));
}
}
}

// record data points if need to calculate e-value;
if (cal_evalue && (resultEntry.getScoreCount() < ECL2.score_point_t)) {
for (double s1 : binScoresMap.get(idx_1)) {
for (double s2 : binScoresMap.get(idx_2)) {
resultEntry.addToScoreHistogram(s1 + s2);
}
}
}
if (score > resultEntry.getScore()) {
resultEntry.setSecondScore(Math.max(resultEntry.getScore(), second_score));
resultEntry.setScore(score);
resultEntry.setChain1(chain_score_entry_1.getSeq());
resultEntry.setChain2(chain_score_entry_2.getSeq());
resultEntry.setLinkSite1(chain_score_entry_1.getLinkSite());
resultEntry.setLinkSite2(chain_score_entry_2.getLinkSite());
} else if (Math.max(score, second_score) > resultEntry.getSecondScore()) {
resultEntry.setSecondScore(Math.max(score, second_score));
}
}
}
}
Expand Down Expand Up @@ -215,19 +320,22 @@ private void linearScan(SparseVector xcorrPL, ChainEntry chainEntry, int binInx,
if (dot_product > chain_result_entry.getScore()) {
chain_result_entry.setSecondScore(chain_result_entry.getScore());
chain_result_entry.setSecondSeq(chain_result_entry.getSeq());
chain_result_entry.setSecondLinkSite(chain_result_entry.getLinkSite());
chain_result_entry.setScore(dot_product);
chain_result_entry.setSeq(chainEntry.seq);
chain_result_entry.setLinkSite(link_site_1);
} else if (dot_product > chain_result_entry.getSecondScore()) {
chain_result_entry.setSecondScore(dot_product);
chain_result_entry.setSecondSeq(chainEntry.seq);
chain_result_entry.setSecondLinkSite(link_site_1);
}
} else {
ChainResultEntry chain_result_entry = new ChainResultEntry();
chain_result_entry.setSeq(chainEntry.seq);
chain_result_entry.setLinkSite(link_site_1);
chain_result_entry.setScore(dot_product);
chain_result_entry.setSecondScore(0);
chain_result_entry.setSecondLinkSite(-1);
binChainMap.put(binInx, chain_result_entry);
}
}
Expand Down
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