Add functionality to support carrying over specific additional cvPara…

…ms from mzML to mzid. Adding upon request from Matt Chambers to support some IMS-specific CV params.
MSGFPlus · Jul 9, 2018 · c17cdc2 · c17cdc2
1 parent 049de36
commit c17cdc2
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Showing 4 changed files with 102 additions and 0 deletions.
diff --git a/src/main/java/edu/ucsd/msjava/msutil/CvParamInfo.java b/src/main/java/edu/ucsd/msjava/msutil/CvParamInfo.java
@@ -0,0 +1,53 @@
+package edu.ucsd.msjava.msutil;
+
+/**
+ * Stored information for a cvParam, for "copying" cvParams from mzML( and potentially other formats) to mzIdentML
+ * @author Bryson Gibbons
+ */
+public class CvParamInfo {
+    private String accession;
+    private String name;
+    private String value;
+    private String unitAccession;
+    private String unitName;
+    private Boolean hasUnit;
+
+    public CvParamInfo(String accession, String name, String value) {
+        this.accession = accession;
+        this.name = name;
+        this.value = value;
+    }
+
+    public CvParamInfo(String accession, String name, String value, String unitAccession, String unitName) {
+        this.accession = accession;
+        this.name = name;
+        this.value = value;
+        this.hasUnit = true;
+        this.unitAccession = unitAccession;
+        this.unitName = unitName;
+    }
+
+    public String getAccession() {
+        return this.accession;
+    }
+
+    public String getName() {
+        return this.name;
+    }
+
+    public String getValue() {
+        return this.value;
+    }
+
+    public Boolean getHasUnit() {
+        return this.hasUnit;
+    }
+
+    public String getUnitAccession() {
+        return this.unitAccession;
+    }
+
+    public String getUnitName() {
+        return this.unitName;
+    }
+}
diff --git a/src/main/java/edu/ucsd/msjava/msutil/Spectrum.java b/src/main/java/edu/ucsd/msjava/msutil/Spectrum.java
@@ -47,6 +47,8 @@ public class Spectrum extends ArrayList<Peak> implements Comparable<Spectrum> {
 //	private Float fractionIonCurrent = null;
 //	private Integer numMS1Features = null;
 
+    private ArrayList<CvParamInfo> addlCvParams;
+
     private Float isolationWindowTargetMz = null;
 
     /***** CONSTRUCTORS *****/
@@ -268,6 +270,14 @@ public int getMSLevel() {
         return this.msLevel;
     }
 
+    /**
+     * Gets additional cvParams to output as cvParams under the mzIdentML SpectrumIdentificationResult
+     * @return cvParam necessary info
+     */
+    public ArrayList<CvParamInfo> getAddlCvParams() {
+        return this.addlCvParams;
+    }
+
     /***** SETTERS *****/
 
     /**
@@ -495,6 +505,18 @@ public void setChargeIfSinglyCharged() {
         if (ticBelowPrecursor / tic > 0.9f)
             precursor.setCharge(1);
     }
+
+    /**
+     * Add an additional cvParam to output as a cvParam under the mzIdentML SpectrumIdentificationResult
+     * @param cvParam
+     */
+    public void addAddlCvParam(CvParamInfo cvParam) {
+        if (addlCvParams == null){
+            addlCvParams = new ArrayList<CvParamInfo>();
+        }
+
+        addlCvParams.add(cvParam);
+    }
 
     /****** FUNCTIONS *****/
     @Override

diff --git a/src/main/java/edu/ucsd/msjava/mzid/MZIdentMLGen.java b/src/main/java/edu/ucsd/msjava/mzid/MZIdentMLGen.java
@@ -298,6 +298,18 @@ public synchronized void addSpectrumIdentificationResults(List<MSGFPlusMatch> re
                 sir.getCvParam().add(cvParam);
             }
 
+            if (spec.getAddlCvParams() != null) {
+                for (CvParamInfo cvParamInfo : spec.getAddlCvParams()) {
+                    CvParam cvParam = Constants.makeCvParam(cvParamInfo.getAccession(), cvParamInfo.getName());
+                    cvParam.setValue(cvParamInfo.getValue());
+                    if (cvParamInfo.getHasUnit()) {
+                        cvParam.setUnitCv(Constants.unitCV);
+                        cvParam.setUnitAccession(cvParamInfo.getUnitAccession());
+                        cvParam.setUnitName(cvParamInfo.getUnitName());
+                    }
+                    sir.getCvParam().add(cvParam);
+                }
+            }
 
             int rank = 0;
             int resultCount = 0;

diff --git a/src/main/java/edu/ucsd/msjava/mzml/SpectrumConverter.java b/src/main/java/edu/ucsd/msjava/mzml/SpectrumConverter.java
@@ -1,6 +1,7 @@
 package edu.ucsd.msjava.mzml;
 
 import edu.ucsd.msjava.msutil.ActivationMethod;
+import edu.ucsd.msjava.msutil.CvParamInfo;
 import edu.ucsd.msjava.msutil.Peak;
 import uk.ac.ebi.jmzml.model.mzml.*;
 
@@ -58,6 +59,20 @@ public static edu.ucsd.msjava.msutil.Spectrum getSpectrumFromJMzMLSpec(uk.ac.ebi
                         scanStartTimeIsSeconds = true;
                     }
                 }
+                // is_a: MS:1002892 ! ion mobility attribute cvParams
+                else if (cvParam.getAccession().equals("MS:1001581")      // FAIMS compensation voltage
+                        || cvParam.getAccession().equals("MS:1002476")    // ion mobility drift time
+                        || cvParam.getAccession().equals("MS:1002815")) { // inverse reduced ion mobility
+                    CvParamInfo cvParamInfo;
+                    if (cvParam.getUnitAccession() != null && !cvParam.getUnitAccession().isEmpty()) {
+                        cvParamInfo = new CvParamInfo(cvParam.getAccession(), cvParam.getName(), cvParam.getValue(), cvParam.getUnitAccession(), cvParam.getUnitName());
+                    }
+                    else {
+                        cvParamInfo = new CvParamInfo(cvParam.getAccession(), cvParam.getName(), cvParam.getValue());
+                    }
+
+                    spec.addAddlCvParam(cvParamInfo);
+                }
             }
             for (UserParam param : scanList.getScan().get(0).getUserParam()) {
                 if (param.getName().equals("[Thermo Trailer Extra]Monoisotopic M/Z:")) {