qvals determination

deprecated/Ms2Hit_.java

@@ -335,8 +335,8 @@ public Ms2Hit_ isIsotopeErr(Range<Integer> range, Tolerance tol)
   public Integer hashcodeByYBmz()
   {
     int hash=0;
-    if (getY()!=null) hash+=getY().hashcodeByTrackMz();
-    if (getB()!=null) hash+=getB().hashcodeByTrackMz();
+    if (getY()!=null) hash+=getY().hashcodeByTrackMz(2);
+    if (getB()!=null) hash+=getB().hashcodeByTrackMz(2);
 
     return hash;
   }

src/org/ms2ms/algo/Spectra.java

@@ -3,20 +3,23 @@
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.Range;
+import org.expasy.mzjava.core.io.ms.spectrum.MgfWriter;
 import org.expasy.mzjava.core.ms.Tolerance;
 import org.expasy.mzjava.core.ms.peaklist.*;
 import org.expasy.mzjava.core.ms.spectrum.MsnSpectrum;
 import org.expasy.mzjava.core.ms.spectrum.RetentionTime;
 import org.expasy.mzjava.core.ms.spectrum.RetentionTimeList;
 import org.ms2ms.data.ms.IsoEnvelope;
 import org.ms2ms.data.ms.OffsetPpmTolerance;
+import org.ms2ms.io.MsReaders;
 import org.ms2ms.math.Histogram;
 import org.ms2ms.math.Stats;
 import org.ms2ms.mzjava.AnnotatedPeak;
 import org.ms2ms.mzjava.IsotopePeakAnnotation;
 import org.ms2ms.utils.Strs;
 import org.ms2ms.utils.Tools;
 
+import java.io.IOException;
 import java.util.*;
 
 /**
@@ -801,4 +804,21 @@ public static MsnSpectrum purgeC13(MsnSpectrum ms)
     }
     return ms;
   }
+  // -2.3,2.9
+  public static MsnSpectrum setIsolationComment(MsnSpectrum ms, double left, double right, MsnSpectrum ms10, MsnSpectrum ms11)
+  {
+    // parse the isolated m/z. It maybe different from the precursor m/z
+    String[] strs = ms.getComment().split("@")[0].split(" ");
+    double center = (Tools.isSet(strs)? Stats.toDouble(strs[strs.length-1]):ms.getPrecursor().getMz());
+
+    // save the precursor isolation region
+    String isolation = "isolation/"+ms10.getScanNumbers().getFirst().getValue()+"/"+center+
+        (ms11!=null?("/"+ms11.getScanNumbers().getFirst().getValue()):""),
+        line = MsReaders.Peaks2Str(Peaks.isolate(ms10, center+left, center+right)) +
+            (ms11!=null?(","+MsReaders.Peaks2Str(Peaks.isolate(ms11, center+left, center+right))):"");
+
+    if (Strs.isSet(line)) ms.setComment(isolation+","+line);
+
+    return ms;
+  }
 }

src/org/ms2ms/data/ms/FpmEntry.java

@@ -218,15 +218,23 @@ public int hashcodeByTrack()
 
     return hash;
   }
-  public int hashcodeByTrackMz()
+  public int hashcodeByTrackMz(int precision)
   {
-    int hash=0;
+    int hash=0; double multi = Math.pow(10d, precision);
     if (Tools.isSet(getTrack()))
       for (int i=0; i<getTrack().size(); i++)
-        hash+=getTrack().get(i).getMz()*1000;
+        // grab the obs m/z rather than the ppm
+        hash+=Math.round(getTrack().get(i).getIntensity()*multi);
 
     return hash;
   }
+  public Collection<Double> fillMz(Collection<Double> data)
+  {
+    if (Tools.isSet(getTrack()))
+      for (AnnotatedPeak p : getTrack()) data.add(p.getIntensity());
+
+    return data;
+  }
   @Override
   public FpmEntry clone()
   {

src/org/ms2ms/data/ms/OffsetPpmTolerance.java

@@ -9,6 +9,7 @@
 public class OffsetPpmTolerance extends PpmTolerance
 {
   private double mScale=1d, mOffset=0d, mTol=0d, mTransitionMass=0, mOffsetSlope=0, mTolSlope=0, mZval=0;
+  private boolean mIsIncremental=false;
 
   public OffsetPpmTolerance() { super(0d); }
   public OffsetPpmTolerance(double tol) { super(tol); mTol=tol; }
@@ -17,6 +18,9 @@ public OffsetPpmTolerance(double tol, double offset)
     super(tol); mOffset=offset; mTol=tol;
   }
 
+  public OffsetPpmTolerance isIncremental(boolean s) { mIsIncremental=s; return this; }
+  public boolean            isIncremental()          { return mIsIncremental; }
+
   public OffsetPpmTolerance setOffsetParams(double transition, double intercept, double slope)
   {
     mTransitionMass=transition; mOffsetSlope=slope; mOffset=intercept; return this;
@@ -33,6 +37,7 @@ public double getOffset(double m)
   }
   // 2-sigma to cover the 95% interval
   public double getPpmTol(double m) { return mTolSlope!=0?Math.exp(mTol+mTolSlope*m)*mZval*mScale : (mTol*mScale); }
+  public double getPpmTol() { return mTol; }
 
   public OffsetPpmTolerance scale( double s) { mScale =s; return this; }
   public OffsetPpmTolerance offset(double s) { mOffset=s; return this; }
@@ -60,7 +65,7 @@ public Location check(double expected, double actual)
 
   public OffsetPpmTolerance clone()
   {
-    return new OffsetPpmTolerance().setOffsetParams(mTransitionMass, mOffset, mOffsetSlope).setTolParams(mTol, mTolSlope, 3d);
+    return new OffsetPpmTolerance().setOffsetParams(mTransitionMass, mOffset, mOffsetSlope).setTolParams(mTol, mTolSlope, mZval).isIncremental(mIsIncremental);
   }
   private double calcError( double expectedMass) { return expectedMass * (getPpmTol(expectedMass)/1000000d); }
   private double calcOffset(double expectedMass) { return expectedMass * (getOffset(expectedMass)/1000000d); }

src/org/ms2ms/data/ms/ProteinID.java

@@ -27,6 +27,7 @@ public class ProteinID implements Comparable<ProteinID>
 
   public Double getBestQVal() { return mBestQVal; }
   public String getSequence() { return mSequence; }
+  public String getAccession() { return mAccessionId; }
   public Multimap<String, PeptideMatch> getSeqMatch() { return mSeqMatch; }
 
   public ProteinID updateBestQVal(Double s) { if (mBestQVal==null || (s!=null && mBestQVal>s)) mBestQVal=s; return this; }
@@ -69,7 +70,7 @@ public static TreeMultimap<Float, ProteinID> toAbundanceRanks(Collection<Protein
       if (Tools.isSet(protein.getSeqMatch()) && protein.getSequence()!=null)
       {
 //        Float abund = (float )protein.getSeqMatch().values().size() / (float )protein.getSequence().length();
-        Float abund = (float )protein.getSeqMatch().values().size();
+        Float abund = (float )protein.getSeqMatch().keySet().size();
         peptide_protein.put(abund, protein);
       }
 

src/org/ms2ms/io/CustomFastaProteinReader.java

@@ -26,6 +26,7 @@ public CustomFastaProteinReader(File file) throws FileNotFoundException
   protected void parseHeader(String header, Protein.Builder builder)
   {
     int left = header.indexOf('>')+1, right = header.indexOf(' ');
-    builder.setAccessionId((right>0?header.substring(left, right):header.substring(left)).replaceAll("\\|", "_"));
+//    builder.setAccessionId((right>0?header.substring(left, right):header.substring(left)).replaceAll("\\|", "_"));
+    builder.setAccessionId(header.substring(left).replaceAll("\\|", "_"));
   }
 }