Add the reader.close() missed by e960094.

Other minor refactors and improvements.

Author: fcyu

MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java

@@ -64,7 +64,7 @@ public class Skyline {
 
   // convert our names to Skyline names
   // names from Skyline cmd documentation (version 24.0-daily, 7/19/2024)
-  private final static HashMap<String, String> enzymesMap = new HashMap<>();
+  private final static Map<String, String> enzymesMap = new HashMap<>();
   static {
     enzymesMap.put("trypsin", "Trypsin");
     enzymesMap.put("stricttrypsin", "Trypsin/P");
@@ -103,8 +103,8 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
       PropsFile pf = new PropsFile(workflowPath, "for Skyline");
       pf.load();
 
-      TreeSet<String> lcmsFiles = new TreeSet<>();
-      TreeSet<String> ddaAndDIAfiles = new TreeSet<>();
+      Set<String> lcmsFiles = new TreeSet<>();
+      Set<String> ddaAndDIAfiles = new TreeSet<>();
 
       String dataType = "DDA";
       String line;
@@ -141,7 +141,7 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
       reader.close();
 
       List<Path> speclibFiles = Files.walk(wd).filter(p -> p.getFileName().toString().endsWith(".speclib")).collect(Collectors.toList());
-      TreeSet<Path> psmTsvFiles = Files.walk(wd).filter(p -> p.getFileName().toString().startsWith("psm.tsv") && p.getFileName().toString().endsWith("psm.tsv")).collect(Collectors.toCollection(TreeSet::new));
+      Set<Path> psmTsvFiles = Files.walk(wd).filter(p -> p.getFileName().toString().startsWith("psm.tsv") && p.getFileName().toString().endsWith("psm.tsv")).collect(Collectors.toCollection(TreeSet::new));
 
       if (useSpeclib && speclibFiles.isEmpty()) {
         System.out.println("No DIA-NN .speclib files found in " + wd + " but Skyline was set to use the spectral library as input and DIA-NN was enabled. Did the DIA-NN run fail? No Skyline document will be generated.");
@@ -156,7 +156,7 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
 
       Path peptideListPath = skylineOutputDir.resolve("peptide_list.txt").toAbsolutePath();
       WritePeptideList pepWriter = new WritePeptideList();
-      HashMap<String, HashSet<String>> addedMods = pepWriter.writePeptideList(psmTsvFiles, peptideListPath);
+      Map<String, Set<String>> addedMods = pepWriter.writePeptideList(psmTsvFiles, peptideListPath);
 
       Path modXmlPath = wd.resolve("mod.xml");
       WriteSkyMods writeSkyMods = new WriteSkyMods(modXmlPath, pf, modsMode, matchUnimod, !useSpeclib, addedMods);

MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/WritePeptideList.java

@@ -7,7 +7,7 @@
 import java.util.regex.Pattern;
 
 public class WritePeptideList {
-    private static HashMap<String, Integer> columns;
+    private static Map<String, Integer> columns;
     private static final Pattern sitePattern = Pattern.compile("(\\d+)\\w\\(");
     private static final Pattern massPattern = Pattern.compile("(\\([\\d.]+\\))");
     private static final Pattern AApattern = Pattern.compile("\\d?([\\w-]+)\\(");
@@ -18,9 +18,9 @@ public class WritePeptideList {
     public static final String COL_PROTEIN = "Protein";
 
 
-    public HashMap<String, HashSet<String>> writePeptideList(TreeSet<Path> psmtsvFiles, Path outputPath) throws IOException {
-        HashMap<String, Set<String>> proteinMap = new HashMap<>();
-        HashMap<String, HashSet<String>> additiveMods = new HashMap<>();
+    public Map<String, Set<String>> writePeptideList(Set<Path> psmtsvFiles, Path outputPath) throws IOException {
+        Map<String, Set<String>> proteinMap = new HashMap<>();
+        Map<String, Set<String>> additiveMods = new HashMap<>();
 
         for (Path psmtsv: psmtsvFiles) {
             BufferedReader reader = new BufferedReader(new FileReader(psmtsv.toFile()));
@@ -35,11 +35,13 @@ public HashMap<String, HashSet<String>> writePeptideList(TreeSet<Path> psmtsvFil
                     proteinMap.get(protein).add(modpep);
                 } else {
                     // initialize new protein and peptide
-                    HashSet<String> peptides = new HashSet<>();
+                    Set<String> peptides = new HashSet<>();
                     peptides.add(modpep);
                     proteinMap.put(protein, peptides);
                 }
             }
+
+            reader.close();
         }
 
         // write output
@@ -60,11 +62,11 @@ public HashMap<String, HashSet<String>> writePeptideList(TreeSet<Path> psmtsvFil
      * of "+" characters.
      * @return
      */
-    public static String generateModifiedPeptide(String[] psmSplits, HashMap<String, Integer> columns, boolean addCharge, HashMap<String, HashSet<String>> additiveMods) {
+    public static String generateModifiedPeptide(String[] psmSplits, Map<String, Integer> columns, boolean addCharge, Map<String, Set<String>> additiveMods) {
         String peptide = psmSplits[columns.get(COL_PEPTIDE)];
 
         String[] mods = psmSplits[columns.get(COL_ASSIGNED_MODS)].split(",");
-        HashMap<Integer, String> modMap = new HashMap<>();
+        Map<Integer, String> modMap = new TreeMap<>();
         for (String mod : mods) {
             Matcher siteMatch = sitePattern.matcher(mod);
             int site;
@@ -94,15 +96,14 @@ public static String generateModifiedPeptide(String[] psmSplits, HashMap<String,
     /**
      * Generate a modified peptide String with all Assigned modifications placed within it
      */
-    private static String insertMods(String peptide, HashMap<Integer, String> modMap) {
-        TreeMap<Integer, String> sortedMods = new TreeMap<>(modMap);
+    private static String insertMods(String peptide, Map<Integer, String> modMap) {
         StringBuilder modifiedPeptide = new StringBuilder(peptide);
 
         // Offset to account for insertions
         int offset = 0;
 
         // Iterate through the sorted entries and insert the mods
-        for (Map.Entry<Integer, String> entry : sortedMods.entrySet()) {
+        for (Map.Entry<Integer, String> entry : modMap.entrySet()) {
             int position = entry.getKey() + offset;
             String mod = entry.getValue();
 

MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/WriteSSL.java

@@ -8,7 +8,7 @@
 
 public class WriteSSL {
 
-    private static HashMap<String, Integer> columns;
+    private static Map<String, Integer> columns;
     public static final String COL_SCANID = "Spectrum";
     public static final String COL_CHARGE = "Charge";
     public static final String COL_SCORE = "Probability";
@@ -23,13 +23,13 @@ public class WriteSSL {
      * file     scan    charge  sequence    score-type  score   RT  IM
      * Sequence includes all mods. IM is optional. Score-type can be PERCOLATOR QVALUE or PEPTIDE PROPHET SOMETHING
      */
-    public void writeSSL(TreeSet<Path> psmtsvFiles, Path outputPath, boolean isPercolator, TreeSet<String> lcmsFiles, boolean useIonQuantPeaks) throws IOException {
+    public void writeSSL(Set<Path> psmtsvFiles, Path outputPath, boolean isPercolator, Set<String> lcmsFiles, boolean useIonQuantPeaks) throws IOException {
         ArrayList<String> output = new ArrayList<>();
         boolean isIM = false;
         boolean checkIM = true;
 
         // map file paths to the file names that will be in the psm.tsv
-        HashMap<String, String> lcmsFileNames = new HashMap<>();
+        Map<String, String> lcmsFileNames = new HashMap<>();
         for (String lcmsFile : lcmsFiles) {
             Path path = Paths.get(lcmsFile);
             String fileName = path.getFileName().toString();
@@ -86,6 +86,8 @@ public void writeSSL(TreeSet<Path> psmtsvFiles, Path outputPath, boolean isPerco
                 }
                 output.add(sslLine.toString());
             }
+
+            reader.close();
         }
 
         // write output

MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/WriteSkyMods.java

@@ -72,7 +72,7 @@ public class WriteSkyMods {
     }
   }
 
-  public WriteSkyMods(Path path, PropsFile pf, int modsMode, boolean matchUnimod, boolean isSSL, HashMap<String, HashSet<String>> addedMods) throws Exception {
+  public WriteSkyMods(Path path, PropsFile pf, int modsMode, boolean matchUnimod, boolean isSSL, Map<String, Set<String>> addedMods) throws Exception {
     List<Mod> mods = new ArrayList<>(4);
 
     String fixModStr = pf.getProperty("msfragger.table.fix-mods");
@@ -113,7 +113,7 @@ public WriteSkyMods(Path path, PropsFile pf, int modsMode, boolean matchUnimod,
     }
 
     // add any combined mods (multiple at one site) found during peptide list generation
-    for (Map.Entry<String, HashSet<String>> entry : addedMods.entrySet()) {
+    for (Map.Entry<String, Set<String>> entry : addedMods.entrySet()) {
       mass = Float.parseFloat(entry.getKey());
       mods.addAll(convertMods(String.join("", entry.getValue()), true, mass, mass, new ArrayList<>(), new ArrayList<>(), false));
     }