Output raw spectrum, normalized spectrum, xcorr spectrum, and two cha…

…ins' theoretical spectra in debug mode.
fcyu · May 18, 2017 · a133aee · a133aee
1 parent 608dee3
commit a133aee
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Showing 5 changed files with 70 additions and 9 deletions.
diff --git a/src/main/java/proteomics/Search/SearchWrap.java b/src/main/java/proteomics/Search/SearchWrap.java
@@ -6,11 +6,11 @@
 import proteomics.Index.BuildIndex;
 import proteomics.Spectrum.PreSpectrum;
 import proteomics.TheoSeq.MassTool;
-import proteomics.Types.FinalResultEntry;
-import proteomics.Types.ResultEntry;
-import proteomics.Types.SparseVector;
-import proteomics.Types.SpectrumEntry;
+import proteomics.Types.*;
 
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
 import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.Callable;
@@ -40,8 +40,38 @@ public SearchWrap(Search search_obj, SpectrumEntry spectrumEntry, BuildIndex bui
     @Override
     public FinalResultEntry call() {
         SparseVector xcorrPL = preSpectrumObj.prepareXcorr(spectrumEntry.originalPlMap, spectrumEntry.precursor_mass);
+        if (ECL2.debug) {
+            try (BufferedWriter writer = new BufferedWriter(new FileWriter(spectrumEntry.scan_num + ".xcorr.spectrum.csv"))) {
+                writer.write("bin_idx,intensity\n");
+                for (int idx : xcorrPL.getIdxSet()) {
+                    writer.write(idx + "," + xcorrPL.get(idx) + "\n");
+                }
+            } catch (IOException ex) {
+                ex.printStackTrace();
+                logger.error(ex.getMessage());
+                System.exit(1);
+            }
+        }
         ResultEntry resultEntry =  search_obj.doSearch(spectrumEntry, xcorrPL);
         if (resultEntry != null) {
+            if (ECL2.debug) {
+                SparseBooleanVector chainVector1 = mass_tool_obj.buildTheoVector(MassTool.seqToAAList(resultEntry.getChain1()), (short) resultEntry.getLinkSite1(), spectrumEntry.precursor_mass - mass_tool_obj.calResidueMass(MassTool.seqToAAList(resultEntry.getChain1())), spectrumEntry.precursor_charge, max_common_ion_charge);
+                SparseBooleanVector chainVector2 = mass_tool_obj.buildTheoVector(MassTool.seqToAAList(resultEntry.getChain2()), (short) resultEntry.getLinkSite2(), spectrumEntry.precursor_mass - mass_tool_obj.calResidueMass(MassTool.seqToAAList(resultEntry.getChain2())), spectrumEntry.precursor_charge, max_common_ion_charge);
+                try (BufferedWriter writer = new BufferedWriter(new FileWriter(spectrumEntry.scan_num + ".chain.spectrum.csv"))) {
+                    writer.write("chain1 bin idx\n");
+                    for (int idx : chainVector1.getIdxSet()) {
+                        writer.write(idx + "\n");
+                    }
+                    writer.write("chain2 bin idx\n");
+                    for (int idx : chainVector2.getIdxSet()) {
+                        writer.write(idx + "\n");
+                    }
+                } catch (IOException ex) {
+                    ex.printStackTrace();
+                    logger.error(ex.getMessage());
+                    System.exit(1);
+                }
+            }
             if (1 - (resultEntry.getSecondScore() / resultEntry.getScore()) > ECL2.delta_c_t) {
                 if (ECL2.cal_evalue) {
                     float e_value_precursor_mass_tol;

diff --git a/src/main/java/proteomics/Spectrum/PreSpectra.java b/src/main/java/proteomics/Spectrum/PreSpectra.java
@@ -11,9 +11,7 @@
 import uk.ac.ebi.pride.tools.mzxml_parser.MzXMLParsingException;
 import uk.ac.ebi.pride.tools.mzxml_parser.mzxml.model.Scan;
 
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintStream;
+import java.io.*;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -84,12 +82,41 @@ public void write(int b) throws IOException {}
 
                 Map<Double, Double> raw_mz_intensity_map = spectrum.getPeakList();
 
+                if (ECL2.debug) {
+                    try (BufferedWriter writer = new BufferedWriter(new FileWriter(Integer.valueOf(spectrum.getId()) + ".raw.spectrum.csv"))) {
+                        writer.write("mz,intensity\n");
+                        for (double mz : raw_mz_intensity_map.keySet()) {
+                            if (Math.abs(raw_mz_intensity_map.get(mz)) > 1e-6) {
+                                writer.write(mz + "," + raw_mz_intensity_map.get(mz) + "\n");
+                            }
+                        }
+                    } catch (IOException ex) {
+                        ex.printStackTrace();
+                        logger.error(ex.getMessage());
+                        System.exit(1);
+                    }
+                }
+
                 if (raw_mz_intensity_map.size() < min_peak_num) {
                     logger.debug("Scan {} doesn't contain enough peak number ({}). Skip.", spectrum.getId(), min_peak_num);
                     continue;
                 }
 
                 TreeMap<Float, Float> originalPlMap = pre_spectrum_obj.preSpectrum(raw_mz_intensity_map, precursor_mass);
+
+                if (ECL2.debug) {
+                    try (BufferedWriter writer = new BufferedWriter(new FileWriter(Integer.valueOf(spectrum.getId()) + ".normalized.spectrum.csv"))) {
+                        writer.write("mz,intensity\n");
+                        for (float mz : originalPlMap.keySet()) {
+                            writer.write(mz + "," + originalPlMap.get(mz) + "\n");
+                        }
+                    } catch (IOException ex) {
+                        ex.printStackTrace();
+                        logger.error(ex.getMessage());
+                        System.exit(1);
+                    }
+                }
+
                 if (originalPlMap.size() <= min_peak_num) {
                     continue;
                 }

diff --git a/src/main/java/proteomics/Types/SparseBooleanVector.java b/src/main/java/proteomics/Types/SparseBooleanVector.java
@@ -47,6 +47,10 @@ public boolean contains(int v) {
         return sparse_vector.contains(v);
     }
 
+    public Set<Integer> getIdxSet() {
+        return sparse_vector;
+    }
+
     public boolean equals(Object other) {
         if (other instanceof SparseBooleanVector) {
             SparseBooleanVector temp = (SparseBooleanVector) other;

diff --git a/src/main/java/proteomics/Types/SparseVector.java b/src/main/java/proteomics/Types/SparseVector.java
@@ -38,7 +38,7 @@ public float get(int i) {
         }
     }
 
-    Set<Integer> idxSet() {
+    public Set<Integer> getIdxSet() {
         return sparse_vector.keySet();
     }
 

diff --git a/src/test/java/proteomics/Types/SparseVectorTest.java b/src/test/java/proteomics/Types/SparseVectorTest.java
@@ -48,7 +48,7 @@ public void get() throws Exception {
 
     @Test
     public void idxSet() throws Exception {
-        Set<Integer> result = vector.idxSet();
+        Set<Integer> result = vector.getIdxSet();
         Set<Integer> ground_truth = new HashSet<>();
         ground_truth.add(1);
         ground_truth.add(3);