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Complete lazy computation for PSMFile class, speeds up parsing by avo…
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…iding unnecessary string splitting
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@danielgeiszler
danielgeiszler committed Apr 13, 2024
1 parent 8d7c324 commit 85cee56
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Showing 2 changed files with 101 additions and 10 deletions.
66 changes: 61 additions & 5 deletions src/edu/umich/andykong/ptmshepherd/PSMFile.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,8 @@ public class PSM {

PSM(int lineNum, String line) {
this.lineNum = lineNum;
this.spLine = new ArrayList<>(StringParsingUtils.splitStringByTab(line.replace("\n","")));
this.spLine = new ArrayList<>(StringParsingUtils.splitStringByTab(
line.replace("\n","")));
this.fileName = null;
this.spec = null;
this.specNum = -1;
Expand All @@ -81,29 +82,58 @@ public class PSM {
this.dMass = null;
}

PSM(int lineNum) {
this.lineNum = lineNum;
this.spLine = null;
this.fileName = null;
this.spec = null;
this.specNum = -1;
this.pep = null;
this.mods = null;
this.modArr = null;
this.dMass = null;
}

private void calculateSpLine() {
this.spLine = new ArrayList<>(StringParsingUtils.splitStringByTab(
data.get(this.lineNum).replace("\n","")));
}

public void addValAtColumn(int colIdx, String val){
if (this.spLine == null)
this.calculateSpLine();
this.spLine.add(colIdx, val);
}

public void addValAtColumn(String colName, String val){
if (this.spLine == null)
this.calculateSpLine();
this.spLine.add(getColumn(colName), val);
}

public void replaceValAtColumn(int colIdx, String val){
if (this.spLine == null)
this.calculateSpLine();
this.spLine.set(colIdx, val);
}

public void replaceValAtColumn(String colName, String val){
if (this.spLine == null)
this.calculateSpLine();
this.spLine.set(getColumn(colName), val);
}

public String getSpec() {
if (this.spLine == null)
this.calculateSpLine();
if (this.spec == null)
this.spec = reNormName(spLine.get(getColumn("Spectrum")));
return this.spec;
}

public int getSpecNum() {
if (this.spLine == null)
this.calculateSpLine();
if (this.specNum == -1) {
if (this.spec == null) {
this.getSpec();
Expand All @@ -115,18 +145,24 @@ public int getSpecNum() {
}

public String getFileName() {
if (this.spLine == null)
this.calculateSpLine();
if (this.fileName == null)
this.fileName = this.getSpec().substring(0, this.getSpec().indexOf("."));
return this.fileName;
}

public String getPep() {
if (this.spLine == null)
this.calculateSpLine();
if (this.pep == null)
this.pep = spLine.get(getColumn("Peptide"));
return this.pep;
}

public ArrayList<ImmutablePair<Integer,Float>> getMods() {
if (this.spLine == null)
this.calculateSpLine();
if (this.mods == null) {
this.mods = new ArrayList<>();
String strMods = spLine.get(getColumn("Assigned Modifications"));
Expand All @@ -152,6 +188,8 @@ else if (spos.equals("c"))
}

public float [] getModsAsArray() {
if (this.spLine == null)
this.calculateSpLine();
if (this.modArr == null) {
this.modArr = new float[this.getPep().length()];
Arrays.fill(this.modArr, 0.0f);
Expand All @@ -166,15 +204,25 @@ else if (spos.equals("c"))
}

public float getDMass() {
if (this.spLine == null)
this.calculateSpLine();
if (this.dMass == null)
this.dMass = Float.parseFloat(this.spLine.get(getColumn("Delta Mass")));
return this.dMass;
}

public String getColumnValue(String colName) {
if (this.spLine == null)
this.calculateSpLine();
return this.spLine.get(getColumn(colName));
}

public ArrayList<String> getSpLine() {
if (this.spLine == null)
this.calculateSpLine();
return this.spLine;
}

public String toString() {
String newStr = String.join("\t", this.spLine);
return newStr;
Expand Down Expand Up @@ -223,7 +271,7 @@ public static String getCRC32(File f) throws Exception {
* @return PSM
*/
private PSM getRawLine(int i) {
PSM psm = new PSM(i, data.get(i));
PSM psm = new PSM(i);
return psm;
}

Expand Down Expand Up @@ -809,15 +857,19 @@ public PSMFile(File f) throws Exception {
}
in.close();

// Build index of PSM file lines to spectrum names and pre parse spec names
this.scanToLine = new HashMap<>();
// Prefill PSM array with dummy variables so they can be constructed upon being called
for (int i = 0; i < this.data.size(); i++) {
PSM tPSM = this.getRawLine(i);
psms.add(tPSM);
this.scanToLine.put(tPSM.getSpec(), i);
}
}

private void constructScanToLineMap() {
this.scanToLine = new HashMap<>();
for (int i = 0; i < this.psms.size(); i++)
this.scanToLine.put(this.psms.get(i).getSpec(), i);
}

public void annotateMassDiffs(String [] annotations) throws IOException {
/* find column to modify, overwrite Observed Modifications col if exists */
int annoCol = getColumn("Observed Modifications");
Expand Down Expand Up @@ -936,6 +988,10 @@ public void addColumn(int colIndx, String newHead, ArrayList<String> keys, Array
"editing PSM table will fail\n");
}

// Check that the scan to line mapping has been constructed
if (this.scanToLine == null)
constructScanToLineMap();

//TODO if column not found and inserting to the right, it will insert at the beginning of the table
// This fixes it, but the error message should be different. Not sure how to check colIndx
if (colIndx == 0)
Expand Down
45 changes: 40 additions & 5 deletions src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,8 @@ public class IterativeLocalizer {
static int scanNum;

Map<String, LocalizationLikelihood> localizationLikelihoodMap;
Map<String, HashMap<String, ArrayList<Integer>>> psmToRunToLine;
Map<String, HashSet<Integer>> convergedPsmsMap;
static boolean debugFlag;
boolean printIonDistribution = true; // TODO make this a parameter
boolean poissonBinomialDistribution = true; // TODO make this a parameter
Expand Down Expand Up @@ -197,6 +199,12 @@ private void calculateLocalizationProbabilities() throws Exception {
// Set up likelihood store so that values can be accessed without recomputing
this.localizationLikelihoodMap = new HashMap<>();

// Set up converged scans map so that PSMs are reprocessed if not necessary
this.convergedPsmsMap = new HashMap<>();

// Set up run -> line mapping so that the whole PSM table doesn't get parsed every iteration
this.psmToRunToLine = new HashMap<>();

// Faster access to zero bin spectra to be ignored
double zbL = this.peaks[1][this.zeroBin]; // TODO: set up custom bounds?
double zbR = this.peaks[2][this.zeroBin]; // TODO: set up custom bounds?
Expand All @@ -216,8 +224,18 @@ private void calculateLocalizationProbabilities() throws Exception {

// Loop through PSM files
for (int i = 0; i < dsData.size(); i++) {
PSMFile psmf = new PSMFile(new File(dsData.get(i)[0]));
HashMap<String, ArrayList<Integer>> runToLine = psmf.getRunMappings();
String psmfStr = dsData.get(i)[0];
PSMFile psmf = new PSMFile(psmfStr);

// Get run to line mappings, if first run calculate, else get preprocessed list to prevent extra parsing
HashMap<String, ArrayList<Integer>> runToLine;
if (epoch == 1) {//todo simplify logic
runToLine = psmf.getRunMappings(); //TODO this is what's parsing it every time
this.psmToRunToLine.put(psmfStr, runToLine);
} else
runToLine = this.psmToRunToLine.get(psmfStr);

// These hold the output to insert into the PSM table //todo only need to be declared on final run
ArrayList<String> specNames = new ArrayList<>();
ArrayList<String> strOutputProbs = new ArrayList<>();
ArrayList<String> strMaxProbs = new ArrayList<>();
Expand All @@ -237,6 +255,15 @@ private void calculateLocalizationProbabilities() throws Exception {
this.scanNum = -1;
debugFlag = false;

// First, check if we can skip this line because the bin is converged
if (!finalPass) {
if (this.convergedPsmsMap.containsKey(cf)) { // check if run is in map
if (this.convergedPsmsMap.get(cf).contains(j)) { // check if scan is in converged bin
continue;
}
}
}

PSMFile.PSM psm = psmf.getLine(j);
float dMass = psm.getDMass();
String pep = psm.getPep();
Expand Down Expand Up @@ -268,9 +295,18 @@ private void calculateLocalizationProbabilities() throws Exception {
continue;
}

// If converged skip unless final round
if (!finalPass && this.priorProbs[cBin].getIsConverged()) // Safe because left is first
// If converged, skip. Unless final round, then calculate final values.
// If converged and not in converged map, add to converged map.
if (!finalPass && this.priorProbs[cBin].getIsConverged()) { // safe because left is first

if (!finalPass) {
if (!this.convergedPsmsMap.containsKey(cf)) // check if run is in map
this.convergedPsmsMap.put(cf, new HashSet<>(runToLine.get(cf).size()+1,1.0f));
if (!this.convergedPsmsMap.get(cf).contains(j)) // check if scan is in converged bin
this.convergedPsmsMap.get(cf).add(j); // add scan to list of converged scans
}
continue;
}

// todo this logic is getting way too complex, need to handle execution states in a static context
Spectrum spec = null;
Expand Down Expand Up @@ -1139,5 +1175,4 @@ private double safeDivide(int x, int y) {
else
return (double) x / (double) y;
}

}

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