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Merge branch 'pr/38'
# Conflicts: # biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java # biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/package-info.java‎

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@@ -18,13 +18,13 @@
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* http://www.biojava.org/
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*
2020
*/
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/**
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* Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
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*
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* @author Koh Chuan Hock
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*
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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava.nbio.aaproperties;
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/**
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* Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
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*
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* @author Koh Chuan Hock
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*
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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava.nbio.aaproperties;
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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java‎

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@@ -18,21 +18,21 @@
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* http://www.biojava.org/
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*
2020
*/
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/**
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* Set of classes that enable the conversion protein sequences into various attributes.
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* The seven different attributes are<p/>
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* Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
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* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
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* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
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* Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)<br/>
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* Charge (Positive, Neutral, Negative)<br/>
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* Secondary structure (Helix, Strand, Coil)<br/>
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* Solvent accessibility (Buried, Exposed, Intermediate)<br/>
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*
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* @author Koh Chuan Hock
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*
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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava.nbio.aaproperties.profeat.convertor;
38-
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/**
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* Set of classes that enable the conversion protein sequences into various attributes.
23+
* The seven different attributes are<p/>
24+
* Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
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* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
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* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
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* Polarizability (Value 0 - 1.08, 0.128 - 0.186, 0.219 - 0.409)<br/>
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* Charge (Positive, Neutral, Negative)<br/>
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* Secondary structure (Helix, Strand, Coil)<br/>
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* Solvent accessibility (Buried, Exposed, Intermediate)<br/>
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*
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* @author Koh Chuan Hock
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*
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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava.nbio.aaproperties.profeat.convertor;
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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/package-info.java‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -18,15 +18,15 @@
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* http://www.biojava.org/
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*
2020
*/
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/**
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* Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
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* PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
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* http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract
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*
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* @author Koh Chuan Hock
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*
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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava.nbio.aaproperties.profeat;
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/**
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* Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
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* PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
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* http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract
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*
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* @author Koh Chuan Hock
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*
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* @version 2011.08.22
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* @since 3.0.2
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*/
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package org.biojava.nbio.aaproperties.profeat;
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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java‎

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Original file line numberDiff line numberDiff line change
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1-
/*
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* BioJava development code
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*
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* This code may be freely distributed and modified under the
5-
* terms of the GNU Lesser General Public Licence. This should
6-
* be distributed with the code. If you do not have a copy,
7-
* see:
8-
*
9-
* http://www.gnu.org/copyleft/lesser.html
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*
11-
* Copyright for this code is held jointly by the individual
12-
* authors. These should be listed in @author doc comments.
13-
*
14-
* For more information on the BioJava project and its aims,
15-
* or to join the biojava-l mailing list, visit the home page
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* at:
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*
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* http://www.biojava.org/
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*
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*/
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package org.biojava.nbio.aaproperties.xml;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlAttribute;
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import javax.xml.bind.annotation.XmlElement;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* One way to model the elements
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* @author pvtroshin
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*
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*/
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@XmlAccessorType(XmlAccessType.NONE)
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public class Element {
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/**
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* Element name as per periodic table e.g. "Hydrogen"
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*/
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@XmlAttribute(name = "name", required = true)
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private String name;
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/**
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* Element short name as in periodic table e.g. "H"
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*/
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@XmlAttribute(name = "symbol")
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private String symbol;
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/**
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* The atomic number of the element = number of protons.
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*/
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@XmlAttribute(name = "atomicnumber")
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private int atomicNumber;
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/**
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* The computed mass based on isotopes and their abundances
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*/
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@XmlAttribute(name = "mass", required = true)
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private double mass;
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/**
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* List of common isotopes of the element
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*/
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@XmlElement
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private List<Isotope> isotope;
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/**
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* To enable quick retrieval of Isotope from its name
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*/
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private Map<String, Isotope> name2Isotope;
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public Element(){}
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public Element(String name, String symbol, int atomicNumber, List<Isotope> isotopes, double mass){
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if(atomicNumber <= 0){
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throw new Error("Atomic number of Elements must be > 0.");
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}
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if(mass <= 0){
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throw new Error("Mass of Elements must be > 0.");
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}
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this.setName(name);
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this.setSymbol(symbol);
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this.setAtomicNumber(atomicNumber);
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this.setIsotopes(isotopes);
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this.setMass(mass);
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}
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@Override
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public String toString(){
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return symbol + ", " + name + ", " + atomicNumber;
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}
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public void setMass(double mass){
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this.mass = mass;
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}
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public double getMass(){
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return this.mass;
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}
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public void setName(String name) {
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this.name = name;
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}
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public String getName(){
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return this.name;
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}
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public void setSymbol(String symbol) {
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this.symbol = symbol;
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}
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public void setAtomicNumber(int atomicNumber) {
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this.atomicNumber = atomicNumber;
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}
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public List<Isotope> getIsotopes() {
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return isotope;
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}
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public void setIsotopes(List<Isotope> isotopes) {
122-
this.isotope = isotopes;
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this.name2Isotope = new HashMap<String, Isotope>();
124-
if(isotopes != null){
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for(Isotope i:isotopes){
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name2Isotope.put(i.getName(), i);
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}
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}
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}
130-
}
1+
/*
2+
* BioJava development code
3+
*
4+
* This code may be freely distributed and modified under the
5+
* terms of the GNU Lesser General Public Licence. This should
6+
* be distributed with the code. If you do not have a copy,
7+
* see:
8+
*
9+
* http://www.gnu.org/copyleft/lesser.html
10+
*
11+
* Copyright for this code is held jointly by the individual
12+
* authors. These should be listed in @author doc comments.
13+
*
14+
* For more information on the BioJava project and its aims,
15+
* or to join the biojava-l mailing list, visit the home page
16+
* at:
17+
*
18+
* http://www.biojava.org/
19+
*
20+
*/
21+
package org.biojava.nbio.aaproperties.xml;
22+
23+
import javax.xml.bind.annotation.XmlAccessType;
24+
import javax.xml.bind.annotation.XmlAccessorType;
25+
import javax.xml.bind.annotation.XmlAttribute;
26+
import javax.xml.bind.annotation.XmlElement;
27+
import java.util.HashMap;
28+
import java.util.List;
29+
import java.util.Map;
30+
31+
/**
32+
* One way to model the elements
33+
* @author pvtroshin
34+
*
35+
*/
36+
@XmlAccessorType(XmlAccessType.NONE)
37+
public class Element {
38+
39+
/**
40+
* Element name as per periodic table e.g. "Hydrogen"
41+
*/
42+
@XmlAttribute(name = "name", required = true)
43+
private String name;
44+
/**
45+
* Element short name as in periodic table e.g. "H"
46+
*/
47+
@XmlAttribute(name = "symbol")
48+
private String symbol;
49+
/**
50+
* The atomic number of the element = number of protons.
51+
*/
52+
@XmlAttribute(name = "atomicnumber")
53+
private int atomicNumber;
54+
/**
55+
* The computed mass based on isotopes and their abundances
56+
*/
57+
@XmlAttribute(name = "mass", required = true)
58+
private double mass;
59+
/**
60+
* List of common isotopes of the element
61+
*/
62+
@XmlElement
63+
private List<Isotope> isotope;
64+
65+
/**
66+
* To enable quick retrieval of Isotope from its name
67+
*/
68+
private Map<String, Isotope> name2Isotope;
69+
70+
public Element(){}
71+
72+
public Element(String name, String symbol, int atomicNumber, List<Isotope> isotopes, double mass){
73+
if(atomicNumber <= 0){
74+
throw new Error("Atomic number of Elements must be > 0.");
75+
}
76+
if(mass <= 0){
77+
throw new Error("Mass of Elements must be > 0.");
78+
}
79+
this.setName(name);
80+
this.setSymbol(symbol);
81+
this.setAtomicNumber(atomicNumber);
82+
this.setIsotopes(isotopes);
83+
this.setMass(mass);
84+
}
85+
86+
@Override
87+
public String toString(){
88+
return symbol + ", " + name + ", " + atomicNumber;
89+
}
90+
91+
public void setMass(double mass){
92+
this.mass = mass;
93+
}
94+
95+
public double getMass(){
96+
return this.mass;
97+
}
98+
99+
public void setName(String name) {
100+
this.name = name;
101+
}
102+
103+
public String getName(){
104+
return this.name;
105+
}
106+
107+
public void setSymbol(String symbol) {
108+
this.symbol = symbol;
109+
}
110+
111+
public void setAtomicNumber(int atomicNumber) {
112+
this.atomicNumber = atomicNumber;
113+
}
114+
115+
116+
public List<Isotope> getIsotopes() {
117+
return isotope;
118+
}
119+
120+
121+
public void setIsotopes(List<Isotope> isotopes) {
122+
this.isotope = isotopes;
123+
this.name2Isotope = new HashMap<String, Isotope>();
124+
if(isotopes != null){
125+
for(Isotope i:isotopes){
126+
name2Isotope.put(i.getName(), i);
127+
}
128+
}
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}
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}

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/package-info.java‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -18,13 +18,13 @@
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* http://www.biojava.org/
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*
2020
*/
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/**
22-
* Set of classes that handles the reading and writing of xml files.
23-
*
24-
* @author Koh Chuan Hock
25-
*
26-
* @version 2011.08.22
27-
* @since 3.0.2
28-
*/
29-
package org.biojava.nbio.aaproperties.xml;
30-
21+
/**
22+
* Set of classes that handles the reading and writing of xml files.
23+
*
24+
* @author Koh Chuan Hock
25+
*
26+
* @version 2011.08.22
27+
* @since 3.0.2
28+
*/
29+
package org.biojava.nbio.aaproperties.xml;
30+

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