Update MzId to use all Doubles instead of Floats

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/jaxb/standard/FragmentArrayType.java

@@ -50,7 +50,7 @@
 public class FragmentArrayType {
 
     @XmlAttribute(name = "values", required = true)
-    protected List<Float> values;
+    protected List<Double> values;
     @XmlAttribute(name = "measure_ref", required = true)
     protected String measureRef;
 
@@ -72,13 +72,13 @@ public class FragmentArrayType {
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link Float }
+     * {@link Double }
      * 
      * 
      */
-    public List<Float> getValues() {
+    public List<Double> getValues() {
         if (values == null) {
-            values = new ArrayList<Float>(1);
+            values = new ArrayList<Double>(1);
         }
         return this.values;
     }

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/jaxb/standard/ResidueType.java

@@ -33,7 +33,7 @@
  *   <complexContent>
  *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
  *       <attribute name="code" use="required" type="{http://psidev.info/psi/pi/mzIdentML/1.2}chars" />
- *       <attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       <attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
  *     </restriction>
  *   </complexContent>
  * </complexType>
@@ -48,7 +48,7 @@ public class ResidueType {
     @XmlAttribute(name = "code", required = true)
     protected String code;
     @XmlAttribute(name = "mass", required = true)
-    protected float mass;
+    protected double mass;
 
     /**
      * Gets the value of the code property.
@@ -78,15 +78,15 @@ public void setCode(String value) {
      * Gets the value of the mass property.
      * 
      */
-    public float getMass() {
+    public double getMass() {
         return mass;
     }
 
     /**
      * Sets the value of the mass property.
      * 
      */
-    public void setMass(float value) {
+    public void setMass(double value) {
         this.mass = value;
     }
 

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/jaxb/standard/SearchModificationType.java

@@ -42,7 +42,7 @@
  *         <element name="cvParam" type="{http://psidev.info/psi/pi/mzIdentML/1.2}CVParamType" maxOccurs="unbounded"/>
  *       </sequence>
  *       <attribute name="fixedMod" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       <attribute name="massDelta" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       <attribute name="massDelta" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
  *       <attribute name="residues" use="required" type="{http://psidev.info/psi/pi/mzIdentML/1.2}listOfCharsOrAny" />
  *     </restriction>
  *   </complexContent>
@@ -65,7 +65,7 @@ public class SearchModificationType {
     @XmlAttribute(name = "fixedMod", required = true)
     protected boolean fixedMod;
     @XmlAttribute(name = "massDelta", required = true)
-    protected float massDelta;
+    protected double massDelta;
     @XmlAttribute(name = "residues", required = true)
     protected List<String> residues;
 
@@ -147,15 +147,15 @@ public void setFixedMod(boolean value) {
      * Gets the value of the massDelta property.
      * 
      */
-    public float getMassDelta() {
+    public double getMassDelta() {
         return massDelta;
     }
 
     /**
      * Sets the value of the massDelta property.
      * 
      */
-    public void setMassDelta(float value) {
+    public void setMassDelta(double value) {
         this.massDelta = value;
     }
 

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/jaxb/standard/SpectrumIdentificationItemType.java

@@ -47,7 +47,7 @@
  *       <attribute name="chargeState" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
  *       <attribute name="experimentalMassToCharge" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
  *       <attribute name="calculatedMassToCharge" type="{http://www.w3.org/2001/XMLSchema}double" />
- *       <attribute name="calculatedPI" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       <attribute name="calculatedPI" type="{http://www.w3.org/2001/XMLSchema}double" />
  *       <attribute name="peptide_ref" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  *       <attribute name="rank" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
  *       <attribute name="passThreshold" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
@@ -86,7 +86,7 @@ public class SpectrumIdentificationItemType
     @XmlAttribute(name = "calculatedMassToCharge")
     protected Double calculatedMassToCharge;
     @XmlAttribute(name = "calculatedPI")
-    protected Float calculatedPI;
+    protected Double calculatedPI;
     @XmlAttribute(name = "peptide_ref", required = true)
     protected String peptideRef;
     @XmlAttribute(name = "rank", required = true)
@@ -242,10 +242,10 @@ public void setCalculatedMassToCharge(Double value) {
      * 
      * @return
      *     possible object is
-     *     {@link Float }
+     *     {@link Double }
      *     
      */
-    public Float getCalculatedPI() {
+    public Double getCalculatedPI() {
         return calculatedPI;
     }
 
@@ -254,10 +254,10 @@ public Float getCalculatedPI() {
      * 
      * @param value
      *     allowed object is
-     *     {@link Float }
+     *     {@link Double }
      *     
      */
-    public void setCalculatedPI(Float value) {
+    public void setCalculatedPI(Double value) {
         this.calculatedPI = value;
     }
 

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/jaxb/standard/package-info.java

@@ -0,0 +1,18 @@
+/*
+ * Copyright (c) 2017 Dmitry Avtonomov
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+@javax.xml.bind.annotation.XmlSchema()
+package umich.ms.fileio.filetypes.mzidentml.jaxb.standard;

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/resources/README.md

@@ -2,12 +2,11 @@
 These schemas are much better than pepxml, they actually compile without errors with _xjc_.
 
 # Generated with
+Using xjc.exe from Oracle JDK 8.
 * `cd BatMass\MSFTBX\MSFileToolbox\src\umich\ms\fileio\filetypes\mzidentml\resources`
 
 * Standard:
-`"C:\Programs\Java\oracle-jdk-8\bin\xjc.exe" -b bindings_mzidml_standard.xml -no-header -encoding UTF-8 -extension -p umich.ms.fileio.filetypes.mzidentml.jaxb.standard -d "C:\projects\batmass\MSFTBX\MSFileToolbox\src" mzIdentML1.2.0.xsd`
-  * Old version: `"D:\tmp\jaxb-ri-2.2.11\jaxb-ri\bin\xjc.bat" -b bindings_mzidml_standard.xml -no-header -extension -p umich.ms.fileio.filetypes.mzidentml.jaxb.standard -d "D:\projects\BatMass\MSFTBX\MSFileToolbox\src" mzIdentML1.2.0.xsd`
-
+`xjc -b bindings_mzidml_standard.xml -no-header -encoding UTF-8 -extension -p umich.ms.fileio.filetypes.mzidentml.jaxb.standard -d "C:\projects\batmass\MSFTBX\MSFileToolbox\src" mzIdentML1.2.0_fixed-double.xsd`
 
 * Primitive (deprecated):
 ~~`"C:\Programs\Java\oracle-jdk-8\bin\xjc.exe" -b bindings_mzidml_primitive.xml -no-header -encoding UTF-8 -extension -p umich.ms.fileio.filetypes.mzidentml.jaxb.primitive -d "C:\projects\batmass\MSFTBX\MSFileToolbox\src" mzIdentML1.2.0.xsd`~~

MSFileToolbox/src/umich/ms/fileio/filetypes/mzidentml/resources/bindings_mzidml_standard.xml

@@ -8,23 +8,25 @@
         <jaxb:globalBindings localScoping="toplevel">
         <!-- No nonsense like BigDecimal and the likes -->
         <jaxb:javaType name="java.lang.Double"
-                       xmlType="xs:decimal"
+                       xmlType="xsd:decimal"
                        parseMethod="javax.xml.bind.DatatypeConverter.parseDouble"
                        printMethod="javax.xml.bind.DatatypeConverter.printDouble" />
 
         <jaxb:javaType name="java.lang.Integer"
-                       xmlType="xs:integer"
+                       xmlType="xsd:integer"
                        parseMethod="javax.xml.bind.DatatypeConverter.parseInt"
                        printMethod="javax.xml.bind.DatatypeConverter.printInt" />
 
+        <!--<jaxb:javaType name="java.lang.Double"-->
+                       <!--xmlType="xsd:float"-->
+                       <!--parseMethod="javax.xml.bind.DatatypeConverter.parseDouble"-->
+                       <!--printMethod="javax.xml.bind.DatatypeConverter.printDouble" />-->
+
         <!--<jaxb:javaType name="java.lang.Double"-->
         <!--xmlType="xs:double"-->
         <!--parseMethod="javax.xml.bind.DatatypeConverter.parseDouble"-->
         <!--printMethod="javax.xml.bind.DatatypeConverter.printDouble" />-->
-        <!--<jaxb:javaType name="java.lang.Float"-->
-        <!--xmlType="xs:float"-->
-        <!--parseMethod="javax.xml.bind.DatatypeConverter.parseFloat"-->
-        <!--printMethod="javax.xml.bind.DatatypeConverter.printFloat" />-->
+
         <!--<jaxb:javaType name="java.lang.Integer"-->
         <!--xmlType="xs:int"-->
         <!--parseMethod="javax.xml.bind.DatatypeConverter.parseInt"-->
@@ -40,7 +42,8 @@
 
     </jaxb:globalBindings>
 
-    <jaxb:bindings schemaLocation="mzIdentML1.2.0.xsd" node="/xs:schema">
+    <!--<jaxb:bindings schemaLocation="mzIdentML1.2.0.xsd" node="/xs:schema">-->
+    <jaxb:bindings schemaLocation="mzIdentML1.2.0_fixed-double.xsd" node="/xs:schema">
 
     </jaxb:bindings>