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kohchuanhockkohchuanhock
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Adjust the XML requirements and made attributes as optional if possible
Checked that all Elements and Isotopes used in AminoAcidComposition.xml can be found in ElementMass.xml git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@9030 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent 3991a22 commit ab7a992

10 files changed

Lines changed: 198 additions & 19 deletions

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‎biojava3-aa-prop/TODO.TXT‎

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This file was deleted.

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/IPeptideProperties.java‎

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@@ -34,20 +34,38 @@
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/**
3636
* TODO
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* 13) Definition of the xml in the cook book
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* 2) How to write the formulae for Net Charge where there are summation and power. Likewise for Instability index - Use images if not possible
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*
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* 12) Write an email to in bio-javalist after solving all the above
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*
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*
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* 1) The question I have now is - What is the minimal requirements for defining compound? There should be a test case demonstrating them.
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*
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* Other test cases, and parts of your cookbook should demonstrate how to define
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1) Labelled amino acid.
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2) Phosphorilated or modified in any other way amino acid.
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3) any other compound which is not an amino acid. e.g. Glucose.
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4) Any or all of the above in the peptide chain
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Calculate molecular weight for all of the above.
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Does it all fit well into an XML you have defined for the compound?
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One more thing - what is the minimum requirement for defining an element?
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Which XML attributes are required and which are optional. You should also describe this in you cookbook, perhaps in a separate section to avoid overcomplicating more common use cases.
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I know these are defined in the classes, but the test case and a cookbook entry would be helpful.
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*
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* Meetings
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* Wednesday 6 July
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* Wednesday 13 July
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* Thursday 21 July
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*
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* DONE
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* Added annotations for AminoAcidComposition.java and Element.java.
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* Simplified MolecularWeight.xml and ElementMass.xml.
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* Work around and made the XML files annotated to requirements.
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* Use Hydrogen-1 isotope weight
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* Add CookBook pages on how Net Charge and Instability Index are computed.
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* Defined the standard XML files in the CookBook
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*
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*
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* Question
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*

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/AminoAcidComposition.java‎

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Original file line numberDiff line numberDiff line change
@@ -19,12 +19,12 @@ public class AminoAcidComposition {
1919
/**
2020
* Amino acid short name - three characters
2121
*/
22-
@XmlAttribute(name = "shortname", required = true)
22+
@XmlAttribute(name = "shortname")
2323
private String shortName;
2424
/**
2525
* Amino acid full name
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*/
27-
@XmlAttribute(name = "name", required = true)
27+
@XmlAttribute(name = "name")
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private String name;
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/**
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* Stores the name of the element and the amount this amino acid contains

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/AminoAcidCompositionTable.java‎

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -46,15 +46,21 @@ public void computeMolecularWeight(ElementTable eTable){
4646
if(a.getElementList() != null){
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for(Name2Count element:a.getElementList()){
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element.getName();
49-
eTable.getElement(element.getName());
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if(eTable.getElement(element.getName()) == null){
50+
throw new Error("Element " + element.getName() + " could not be found. " +
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"\r\nPlease ensure that its name is correct in AminoAcidComposition.xml and is defined in ElementMass.xml.");
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}
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eTable.getElement(element.getName()).getMass();
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total += eTable.getElement(element.getName()).getMass() * element.getCount();
5255
}
5356
}
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if(a.getIsotopeList() != null){
5558
for(Name2Count isotope:a.getIsotopeList()){
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isotope.getName();
57-
eTable.getIsotope(isotope.getName());
60+
if(eTable.getIsotope(isotope.getName()) == null){
61+
throw new Error("Isotope " + isotope.getName() + " could not be found. " +
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"\r\nPlease ensure that its name is correct in AminoAcidComposition.xml and is defined in ElementMass.xml.");
63+
}
5864
eTable.getIsotope(isotope.getName()).getWeight();
5965
total += eTable.getIsotope(isotope.getName()).getWeight() * isotope.getCount();
6066
}

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/Element.java‎

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Original file line numberDiff line numberDiff line change
@@ -25,12 +25,12 @@ public class Element {
2525
/**
2626
* Element short name as in periodic table e.g. "H"
2727
*/
28-
@XmlAttribute(name = "symbol", required = true)
28+
@XmlAttribute(name = "symbol")
2929
private String symbol;
3030
/**
3131
* The atomic number of the element = number of protons.
3232
*/
33-
@XmlAttribute(name = "atomicnumber", required = true)
33+
@XmlAttribute(name = "atomicnumber")
3434
private int atomicNumber;
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/**
3636
* The computed mass based on isotopes and their abundances

‎biojava3-aa-prop/src/main/java/org/biojava3/aaproperties/xml/ElementTable.java‎

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Original file line numberDiff line numberDiff line change
@@ -44,8 +44,10 @@ public void populateMaps(){
4444
if(this.element != null){
4545
for(Element e:this.element){
4646
this.elementName2Element.put(e.getName(), e);
47-
for(Isotope i:e.getIsotopes()){
48-
this.isotopeName2Isotope.put(i.name(), i);
47+
if(e.getIsotopes() != null){
48+
for(Isotope i:e.getIsotopes()){
49+
this.isotopeName2Isotope.put(i.name(), i);
50+
}
4951
}
5052
}
5153
}

‎biojava3-aa-prop/src/main/resources/AminoAcidComposition.xsd‎

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@@ -15,8 +15,8 @@
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<xs:element name="isotopes" type="name2Count" minOccurs="0" maxOccurs="unbounded"/>
1616
</xs:sequence>
1717
<xs:attribute name="symbol" type="xs:string" use="required"/>
18-
<xs:attribute name="shortname" type="xs:string" use="required"/>
19-
<xs:attribute name="name" type="xs:string" use="required"/>
18+
<xs:attribute name="shortname" type="xs:string"/>
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<xs:attribute name="name" type="xs:string"/>
2020
</xs:complexType>
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2222
<xs:complexType name="name2Count">

‎biojava3-aa-prop/src/main/resources/MinAminoAcidComposition.xml‎

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@@ -0,0 +1,125 @@
1+
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
2+
<ns2:AminoAcidsTable xmlns:ns2="http://biojava.org">
3+
<aminoacid symbol="A">
4+
<elements count="3" name="Carbon"/>
5+
<elements count="1" name="Nitrogen"/>
6+
<elements count="1" name="Oxygen"/>
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<isotopes count="5" name="Hydrogen"/>
8+
</aminoacid>
9+
<aminoacid symbol="R">
10+
<elements count="6" name="Carbon"/>
11+
<elements count="4" name="Nitrogen"/>
12+
<elements count="1" name="Oxygen"/>
13+
<isotopes count="12" name="Hydrogen"/>
14+
</aminoacid>
15+
<aminoacid symbol="N">
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<elements count="4" name="Carbon"/>
17+
<elements count="2" name="Nitrogen"/>
18+
<elements count="2" name="Oxygen"/>
19+
<isotopes count="6" name="Hydrogen"/>
20+
</aminoacid>
21+
<aminoacid symbol="D">
22+
<elements count="4" name="Carbon"/>
23+
<elements count="1" name="Nitrogen"/>
24+
<elements count="3" name="Oxygen"/>
25+
<isotopes count="5" name="Hydrogen"/>
26+
</aminoacid>
27+
<aminoacid symbol="C">
28+
<elements count="3" name="Carbon"/>
29+
<elements count="1" name="Nitrogen"/>
30+
<elements count="1" name="Oxygen"/>
31+
<elements count="1" name="Sulfur"/>
32+
<isotopes count="5" name="Hydrogen"/>
33+
</aminoacid>
34+
<aminoacid symbol="E">
35+
<elements count="5" name="Carbon"/>
36+
<elements count="1" name="Nitrogen"/>
37+
<elements count="3" name="Oxygen"/>
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<isotopes count="7" name="Hydrogen"/>
39+
</aminoacid>
40+
<aminoacid symbol="Q">
41+
<elements count="5" name="Carbon"/>
42+
<elements count="2" name="Nitrogen"/>
43+
<elements count="2" name="Oxygen"/>
44+
<isotopes count="8" name="Hydrogen"/>
45+
</aminoacid>
46+
<aminoacid symbol="G">
47+
<elements count="2" name="Carbon"/>
48+
<elements count="1" name="Nitrogen"/>
49+
<elements count="1" name="Oxygen"/>
50+
<isotopes count="3" name="Hydrogen"/>
51+
</aminoacid>
52+
<aminoacid symbol="H">
53+
<elements count="6" name="Carbon"/>
54+
<elements count="3" name="Nitrogen"/>
55+
<elements count="1" name="Oxygen"/>
56+
<isotopes count="7" name="Hydrogen"/>
57+
</aminoacid>
58+
<aminoacid symbol="I">
59+
<elements count="6" name="Carbon"/>
60+
<elements count="1" name="Nitrogen"/>
61+
<elements count="1" name="Oxygen"/>
62+
<isotopes count="11" name="Hydrogen"/>
63+
</aminoacid>
64+
<aminoacid symbol="L">
65+
<elements count="6" name="Carbon"/>
66+
<elements count="1" name="Nitrogen"/>
67+
<elements count="1" name="Oxygen"/>
68+
<isotopes count="11" name="Hydrogen"/>
69+
</aminoacid>
70+
<aminoacid symbol="K">
71+
<elements count="6" name="Carbon"/>
72+
<elements count="2" name="Nitrogen"/>
73+
<elements count="1" name="Oxygen"/>
74+
<isotopes count="12" name="Hydrogen"/>
75+
</aminoacid>
76+
<aminoacid symbol="M">
77+
<elements count="5" name="Carbon"/>
78+
<elements count="1" name="Nitrogen"/>
79+
<elements count="1" name="Oxygen"/>
80+
<elements count="1" name="Sulfur"/>
81+
<isotopes count="9" name="Hydrogen"/>
82+
</aminoacid>
83+
<aminoacid symbol="F">
84+
<elements count="9" name="Carbon"/>
85+
<elements count="1" name="Nitrogen"/>
86+
<elements count="1" name="Oxygen"/>
87+
<isotopes count="9" name="Hydrogen"/>
88+
</aminoacid>
89+
<aminoacid symbol="P">
90+
<elements count="5" name="Carbon"/>
91+
<elements count="1" name="Nitrogen"/>
92+
<elements count="1" name="Oxygen"/>
93+
<isotopes count="7" name="Hydrogen"/>
94+
</aminoacid>
95+
<aminoacid symbol="S">
96+
<elements count="3" name="Carbon"/>
97+
<elements count="1" name="Nitrogen"/>
98+
<elements count="2" name="Oxygen"/>
99+
<isotopes count="5" name="Hydrogen"/>
100+
</aminoacid>
101+
<aminoacid symbol="T">
102+
<elements count="4" name="Carbon"/>
103+
<elements count="7" name="Hydrogen"/>
104+
<elements count="1" name="Nitrogen"/>
105+
<elements count="2" name="Oxygen"/>
106+
</aminoacid>
107+
<aminoacid symbol="W">
108+
<elements count="11" name="Carbon"/>
109+
<elements count="2" name="Nitrogen"/>
110+
<elements count="1" name="Oxygen"/>
111+
<isotopes count="10" name="Hydrogen"/>
112+
</aminoacid>
113+
<aminoacid symbol="Y">
114+
<elements count="9" name="Carbon"/>
115+
<elements count="1" name="Nitrogen"/>
116+
<elements count="2" name="Oxygen"/>
117+
<isotopes count="9" name="Hydrogen"/>
118+
</aminoacid>
119+
<aminoacid symbol="V">
120+
<elements count="5" name="Carbon"/>
121+
<elements count="1" name="Nitrogen"/>
122+
<elements count="1" name="Oxygen"/>
123+
<isotopes count="9" name="Hydrogen"/>
124+
</aminoacid>
125+
</ns2:AminoAcidsTable>

‎biojava3-aa-prop/src/main/resources/MinElementMass.xml‎

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@@ -0,0 +1,10 @@
1+
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
2+
<ns2:elements xmlns:ns2="http://biojava.org">
3+
<element mass="1.00794" name="Hydrogen">
4+
<isotope weight="1.00782503207" name="Hydrogen"/>
5+
</element>
6+
<element mass="12.0107" name="Carbon"/>
7+
<element mass="14.0067" name="Nitrogen"/>
8+
<element mass="15.9994" name="Oxygen"/>
9+
<element mass="32.065" name="Sulfur"/>
10+
</ns2:elements>

‎biojava3-aa-prop/src/test/java/org/biojava3/aaproperties/xml/AminoAcidTester.java‎

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,27 @@ public void generateSchema() throws JAXBException, IOException{
2323
context.generateSchema(new SchemaGenerator("./src/main/resources/AminoAcidComposition.xsd"));
2424
}
2525

26+
@Test
27+
public void readMinXml() throws JAXBException, IOException{
28+
ElementTable iTable = new ElementTable();
29+
// Get a JAXB Context for the object we created above
30+
JAXBContext jc = JAXBContext.newInstance(iTable.getClass());
31+
Unmarshaller u = jc.createUnmarshaller();
32+
iTable = (ElementTable)u.unmarshal(new FileInputStream("./src/main/resources/MinElementMass.xml" ) );
33+
iTable.populateMaps();
34+
35+
AminoAcidCompositionTable aTable = new AminoAcidCompositionTable();
36+
// Get a JAXB Context for the object we created above
37+
JAXBContext jc2 = JAXBContext.newInstance(aTable.getClass());
38+
Unmarshaller u2 = jc2.createUnmarshaller();
39+
40+
aTable = (AminoAcidCompositionTable)u2.unmarshal(new FileInputStream("./src/main/resources/MinAminoAcidComposition.xml" ) );
41+
aTable.computeMolecularWeight(iTable);
42+
for(AminoAcidComposition a:aTable.getAminoacid()){
43+
System.out.println(a + ", " + aTable.getMolecularWeight(a.getSymbol()));
44+
}
45+
}
46+
2647
@Test
2748
public void readXml() throws JAXBException, IOException{
2849
ElementTable iTable = new ElementTable();

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