Changeset 4545

Timestamp:

Feb 26, 2014, 4:55:01 PM (9 years ago)

Author:

Fredrik Levander

Message:

Updates to Modification to give diff formula. Updates to contrib library expeort with msp library peak annotation.

Location:

trunk

Files:

• api/core/src/org/proteios/core/Modification.java (modified) (2 diffs)
• api/external/Proteins-1.1.0.jar (added)
• contrib/SpectrumLibraryExport/src/satoshi/CreateLibraryExportJob.java (modified) (3 diffs)
• contrib/SpectrumLibraryExport/src/satoshi/LibraryExportForm.java (modified) (4 diffs)
• contrib/SpectrumLibraryExport/src/satoshi/LibraryExportPlugin.java (modified) (14 diffs)

trunk/api/core/src/org/proteios/core/Modification.java

@@ -168 +168 @@
   public String getDiffFormula()
   {
-    return getData().getDiffFormula();
+    if (getData().getDiffFormula()!=null)
+      return getData().getDiffFormula();
+    else {
+      return getDiffFormulaFromModificationName(this);
+    }
   }
 
@@ -313 +317 @@
     mod.setPosition(mod.getPosition() + 1);
   }
+  
+  protected static String getDiffFormulaFromModificationName(Modification<?> mod)
+  {
+    Map<String, String> modMap = new HashMap<String, String>();
+    modMap.put("Carbamidomethyl", "H(3) C(2) N(1) O(1)");
+    modMap.put("Phospho", "H(1) O(3) P(1)");
+    modMap.put("Oxidation", "O(1)");
+    modMap.put("Acetyl", "H(2) C(2) O(1)");
+    modMap.put("Deamidation", "H(-1) N(-1) O(1)");
+    modMap.put("Pyro_glu", "H(-2) O(-1)");
+    modMap.put("Pyro-glu", "H(-3) N(-1)");
+    return modMap.get(mod.getName());     
+  }
 }

trunk/contrib/SpectrumLibraryExport/src/satoshi/CreateLibraryExportJob.java

@@ -34 +34 @@
     // List<Integer> files = getValidIntegerList(FormFactory.VID);
     Float fdr = getValidFloat(LibraryExportForm.FDRCUTOFF);
+    Float fragTol = getValidFloat(LibraryExportForm.FRAGMENTTOL);
     String prefix2 = getValidString(LibraryExportForm.OUTFILENAME);
     String prefix3 = getValidString(LibraryExportForm.OUTFILENAME2);
     Boolean ssl = getValidBoolean(LibraryExportForm.SSLFORMAT);
     Boolean msp = getValidBoolean(LibraryExportForm.MSPFORMAT);
+    Boolean eValue = getValidBoolean(LibraryExportForm.EVALUE);
+    if (eValue == null)
+      eValue = new Boolean(false);
     if (ssl == null)
       ssl = new Boolean(false);
     if (msp == null)
       msp = new Boolean(false);
-    if (msp == null && ssl == null)
-    {
-      throw new NullPointerException(
-        "Failed to initialize job. Missing values");
+    if (!msp.booleanValue() && !ssl.booleanValue()){
+      throw new ActionException(
+        "Failed to initialize job. Missing output format");
     }
 
@@ -64 +67 @@
     Job job = factory.createJob(plugin, null);
     job.setName(plugin.getName()); // pass the name of the plugin
-    // Tell the job which file to work with
-    // File file = factory.getById(File.class, fileId);
-    job.setDescription("Library export");
-    // Tell the job which file to work with
-    // FileParameterType fileParam = new FileParameterType();
-    // job.setParameterValue(ImportXFile.FILEPARAM, fileParam, file);
-
-    // Tell the job which prefix to add
     FloatParameterType prefixParam = new FloatParameterType();
     job.setParameterValue(LibraryExportPlugin.FDRCUTOFFPARAM, prefixParam,
       fdr);
+    job.setParameterValue(LibraryExportPlugin.FRAGMENTTOLERANCEPARAM, new FloatParameterType(),
+      fragTol);
     StringParameterType prefixParam2 = new StringParameterType();
     job.setParameterValue(LibraryExportPlugin.OUTFILEPARAM, prefixParam2,
@@ -85 +82 @@
     BooleanParameterType prefixParam5 = new BooleanParameterType();
     job.setParameterValue(LibraryExportPlugin.MSPPARAM, prefixParam5, msp);
-
+    job.setParameterValue(LibraryExportPlugin.EVALUEPARAM, new BooleanParameterType(), eValue);
     Project project = isProjectActive(dc); // returns the active project if
     // any
     Directory dir = project.getProjectDirectory(); // returns the project
     // directory path
+    job.setDescription("Library export "+ project.getName());
     ItemParameterType<Directory> dirParam = new ItemParameterType<Directory>(
       Directory.class, null);

trunk/contrib/SpectrumLibraryExport/src/satoshi/LibraryExportForm.java

@@ -6 +6 @@
 import org.proteios.TableToolbarContext;
 import org.proteios.action.ProteiosAction;
-import org.proteios.action.feature.FeatureHitMatchForm;
-import org.proteios.action.hit.CreateProteinAssemblyJob;
 import org.proteios.core.Hit;
 import org.proteios.gui.Title;
@@ -45 +43 @@
   public static final VBoolean SSLFORMAT = new VBoolean("sslON", false);
   public static final VBoolean MSPFORMAT = new VBoolean("mspON", false);
+  public static final VBoolean EVALUE = new VBoolean("evalueON", false);
+  public static final VFloat FRAGMENTTOL = new VFloat("fragTol", 0f, 1f);
 
 
@@ -64 +64 @@
     fdrCutOff.setValue("0.01");
     fieldSet.add(fdrCutOff);
+
+    Checkbox<VBoolean> eON = new Checkbox<VBoolean>(EVALUE);
+    eON.setValue("true");
+    eON.isChecked(false);
+    eON.setLabel(getLocale().get("E-value"));
+    eON.setHelp("E-value instead of FDR cutoff");
+    fieldSet.add(eON);
 
     TextField<String> filename = new TextField<String>(OUTFILENAME);
@@ -86 +93 @@
     mspON.setLabel(getLocale().get(".msp format as output"));
     fieldSet.add(mspON);
+    
+    TextField<String> fragTolF = new TextField<String>(FRAGMENTTOL);
+    fragTolF.setLabel(getLocale().get("Fragment m/z tolerance"));
+    fragTolF.setValue("0.5");
+    fieldSet.add(fragTolF);
 
     /*

trunk/contrib/SpectrumLibraryExport/src/satoshi/LibraryExportPlugin.java

@@ -9 +9 @@
 import org.proteios.core.ItemFactory;
 import org.proteios.core.ItemQuery;
-import org.proteios.core.ItemResultIterator;
 import org.proteios.core.ItemResultList;
 import org.proteios.core.ObservedModification;
@@ -19 +18 @@
 import org.proteios.core.SearchModification;
 import org.proteios.core.SessionControl;
-import org.proteios.core.SpectrumSearch;
-import org.proteios.core.SearchModification.TerminalSpecificity;
 import org.proteios.core.plugin.About;
 import org.proteios.core.plugin.AboutImpl;
@@ -39 +36 @@
 import org.proteios.io.SpectrumPrecursor;
 
+import se.lth.immun.chem.Ion;
+import se.lth.immun.chem.ModifiedAminoAcid;
+import se.lth.immun.chem.Modifier;
+import se.lth.immun.chem.PeptideFragment;
+import se.lth.immun.chem.PeptideUtil;
+
 import java.io.BufferedWriter;
 import java.io.IOException;
@@ -73 +76 @@
   public static final String SSLPARAM = "sslFormat";
   public static final String MSPPARAM = "mspFormat";
+  public static final String EVALUEPARAM = "eValue";
+  public static final String FRAGMENTTOLERANCEPARAM = "fragTol";
   private static final Double MONOISTOPIC_PROTON_MASS = 1.007276035;
 
@@ -87 +92 @@
   private boolean mspFormat = true; // to be used for SpectraSt
   private boolean sslFormat = true;
+  private boolean eValue = false;
   // other variables
   private Project project = null;
@@ -92 +98 @@
   private boolean fileNameAssigned2 = false;
   private int spectrumNumber = 1;
+  private double mzTolerance = 0.5d;
 
   // SessionControl sc; // instantiated below
@@ -139 +146 @@
       String filename2 = (String) job.getValue(OUTFILEPARAM2); // for .msp
       fdrCutOff = ((Float) job.getValue(FDRCUTOFFPARAM)).doubleValue();
+      mzTolerance = ((Float) job.getValue(FRAGMENTTOLERANCEPARAM)).doubleValue();
       mgfFormat = false;
       sslFormat = ((Boolean) job.getValue(SSLPARAM)).booleanValue();
       mspFormat = ((Boolean) job.getValue(MSPPARAM)).booleanValue();
-
+      eValue = ((Boolean) job.getValue(EVALUEPARAM)).booleanValue();
       if (filename == null && filename2 == null) // stop
       {
@@ -401 +409 @@
           Expressions.parameter("protein")));
       hitQuery.setPermanentParameter("protein", false, null);
-      hitQuery.restrict(Restrictions.lteq(Hql.property("combinedFDR"),
+      if (!eValue)
+      {
+        hitQuery.restrict(Restrictions.lteq(Hql.property("combinedFDR"),
           Expressions.aFloat((float) fdrCutOff)));
+      }
+      else
+      {
+        hitQuery.restrict(Restrictions.lteq(Hql.property("expectationValue"),
+          Expressions.aFloat((float) fdrCutOff)));
+        
+      }
       hitQuery.restrict(Restrictions.neq(Hql.property("scoreType"),
           Expressions.string("Proteios aligned")));
       hitQuery.order(Orders.asc(Hql.property("charge")));
       hitQuery.order(Orders.asc(Hql.property("description")));
-      hitQuery.order(Orders.asc(Hql.property("combinedFDR")));
+      if (!eValue) hitQuery.order(Orders.asc(Hql.property("combinedFDR")));
       hitQuery.order(Orders.asc(Hql.property("expectationValue")));
       List<String> sequencesForCharge = new ArrayList<String>();
@@ -413 +430 @@
       ItemResultList<Hit> hitlist = hitQuery.list(dc);
       int currentCharge = 0;
+      log.debug("Number of hits:"+hitlist.size());
       for (Hit h : hitlist) {
         if (currentCharge != h.getCharge().intValue()) {
@@ -433 +451 @@
       while (hitit.hasNext()) {
         Hit currentHit = hitit.next();
-        if (hitit.hasNext()) {
-          // log.debug(">" + pklFile + "\t" + output + "\t" +
-          // output2 + "\t" + peptidelist + "\n");
-          if (pklFile != null
-              && currentHit.getPeakListFile() != pklFile) {
-            // start retrieving all necessary info.
-            // including spectrum for each hit
-            retrieveAndWriteSpectra(pklFile, hitList, output,
+        if (pklFile == null)
+        {
+          pklFile = currentHit.getPeakListFile(); 
+        }
+        if (pklFile != currentHit.getPeakListFile())
+        {
+          retrieveAndWriteSpectra(pklFile, hitList, output,
                 output2, dc);
-            // empty hitList and store the currentHit
-            hitList.clear();
-            hitList.add(currentHit);
-            pklFile = currentHit.getPeakListFile();
-          } else {
-            hitList.add(currentHit);
-            pklFile = currentHit.getPeakListFile(); // get the
-            // file name
-            // even if it is the same as before
-          }
-        } else {
-          // log.debug(">2" + pklFile + "\t" + output + "\t" +
-          // output2 + "\t" + peptidelist + "\n");
-          retrieveAndWriteSpectra(pklFile, hitList, output, output2,
-              dc);
+          // empty hitList
           hitList.clear();
-          hitList.add(currentHit);
-        }
-      }
+          pklFile = currentHit.getPeakListFile();
+        } 
+        log.debug("Adding hit:"+currentHit.getDescription());
+        hitList.add(currentHit);
+      }
+      log.debug("At final");
+      if (!hitList.isEmpty()) retrieveAndWriteSpectra(pklFile, hitList, output, output2,dc);
       if (output != null) {
         // log.debug(">3 output closed\n");
@@ -597 +604 @@
       // correct only unique ones
       int requestSpectraNr = 0;
+      log.debug("PKL file:"+pklFile.getName()+" hits:"+peptideHits.size());
       for (Hit phit : peptideHits) {
         // make sure the file format and its interface
@@ -603 +611 @@
           requestSpectraStringID.add(phit.getSpectrumStringId());
           String[] s1 = phit.getDescription().split(" ", 2);
+          if (s1.length == 2 && s1[1].contains(">"))
+          {
+            log.debug("Sequence:"+s1[0]+" mod:"+s1[1]);
+            String[] parts = s1[1].split(" ");
+            String newString = null;
+            for (String s2:parts)
+            {
+              if (s2.contains(">"))
+              {
+                int pos = Integer.parseInt(s2.substring(s2.indexOf('@')+2,s2.indexOf('('))); 
+                char newchar = s2.charAt(s2.indexOf('>')+1);
+                if (pos>0) --pos;
+                String newSeq = s1[0].substring(0,pos)+newchar+s1[0].substring(pos+1);
+                s1[0]=newSeq;
+                log.debug("new Sequence:"+newSeq);
+              }
+              else
+              {
+                if (newString == null) newString=s2;
+                else newString+=" "+s2;
+              }
+            }
+            s1[1]=newString;
+          }
+          
           requestSpectraSEQ.add(s1[0]); // sequence
           if (s1.length == 2) {
@@ -958 +991 @@
               requestSpectraSEQ.get(i),
               requestSpectraModification.get(i), fixedMods);
+          List<ObservedModification> obsMods = ObservedModification.getModList(requestSpectraSEQ.get(i), requestSpectraModification.get(i),
+            fixedMods, factory);
+          se.lth.immun.chem.Peptide pep = PeptideUtil.standardPeptideFromString(requestSpectraSEQ.get(i));
+          for (ObservedModification om : obsMods)
+          {
+            int pos = om.getPosition();
+            ModifiedAminoAcid maa = new ModifiedAminoAcid(pep.aminoAcids[pos],Modifier.parseMolecule(om.getDiffFormula()));
+            pep.aminoAcids[pos]=maa;
+          }
+          List<Ion<PeptideFragment>> ions = PeptideUtil.possibleYAndBIons(pep, 2);
           output2.write(charge + "\n" + "MW: " + mass + "\n");
           // List<Double> parent = new ArrayList<Double>();
@@ -1047 +1090 @@
           for (int l = 0; l < mzs.size(); l++) {
             output2.write(fourDecimals.format(mzs.get(l)) + "\t"
-                + ints.get(l) + "\t\"?\"\n");
+                + ints.get(l) + "\t\"");
+            String s = PeptideUtil.matchedIonsAsString(PeptideUtil.matchingIons(ions, mzs.get(l), mzTolerance));
+            if (s!=null && s.length()>0)
+            {
+              output2.write(s+"\"\n");
+            }
+            else
+            {
+              output2.write("?\"\n");
+            }
           }
           output2.write("\n");