Using ProteomicsLibrary's methods.

fcyu · Mar 15, 2018 · 6b88a18 · 6b88a18
1 parent 9031e71
commit 6b88a18
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Showing 3 changed files with 12 additions and 903 deletions.
diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
@@ -1,5 +1,6 @@
 package proteomics;
 
+import ProteomicsLibrary.IsotopeDistribution;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import proteomics.Index.BuildIndex;
@@ -145,11 +146,11 @@ private ECL2(String parameter_path, String spectra_path, String dbName) throws E
         if (dev && parameter_map.get("C13_correction").contentEquals("1")) {
             BufferedWriter writer = new BufferedWriter(new FileWriter("spectrum.dev.csv"));
             writer.write("scanNum,charge,finalIsotopeCorrectionNum,isotopeCorrectionNum,pearsonCorrelationCoefficient,expMz1,expMz2,expMz3,expInt1,expInt2,expInt3,theoMz1,theoMz2,theoMz3,theoInt1,theoInt2,theoInt3\n");
-            Map<Integer, TreeMap<Integer, TreeSet<PreSpectra.DevEntry>>> scanDevEntryMap = preSpectra.getScanDevEntryMap();
+            Map<Integer, TreeMap<Integer, TreeSet<IsotopeDistribution.DevEntry>>> scanDevEntryMap = preSpectra.getScanDevEntryMap();
             for (int scanNum : scanDevEntryMap.keySet()) {
-                TreeMap<Integer, TreeSet<PreSpectra.DevEntry>> chargeDevEntryMap = scanDevEntryMap.get(scanNum);
+                TreeMap<Integer, TreeSet<IsotopeDistribution.DevEntry>> chargeDevEntryMap = scanDevEntryMap.get(scanNum);
                 for (int charge : chargeDevEntryMap.keySet()) {
-                    for (PreSpectra.DevEntry devEntry : chargeDevEntryMap.get(charge)) {
+                    for (IsotopeDistribution.DevEntry devEntry : chargeDevEntryMap.get(charge)) {
                         writer.write(String.format(Locale.US, "%d,%d,%d,%d,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f,%f\n", scanNum, charge, devEntry.isotopeCorrectionNum, devEntry.isotopeCorrectionNum, devEntry.pearsonCorrelationCoefficient, devEntry.expMatrix[0][0], devEntry.expMatrix[1][0], devEntry.expMatrix[2][0], devEntry.expMatrix[0][1], devEntry.expMatrix[1][1], devEntry.expMatrix[2][1], devEntry.theoMatrix[0][0], devEntry.theoMatrix[1][0], devEntry.theoMatrix[2][0], devEntry.theoMatrix[0][1], devEntry.theoMatrix[1][1], devEntry.theoMatrix[2][1]));
                     }
                 }