X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotationElement.java;h=3c6eba4053d9deb192726137bbf134cb36ca0603;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=211810dcb59a9c7078b4fc32e25d035a4a501908;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java index 211810d..3c6eba4 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -4,7 +4,6 @@ * Schema. * $Id$ */ - /* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle @@ -23,33 +22,32 @@ * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ - package jalview.binding; - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; import org.exolab.castor.xml.MarshalException; import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; import org.exolab.castor.xml.ValidationException; + import org.xml.sax.ContentHandler; +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; + + /** * Class AnnotationElement. * * @version $Revision$ $Date$ */ public class AnnotationElement implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -87,37 +85,28 @@ public class AnnotationElement implements java.io.Serializable { */ private boolean _has_value; - - //----------------/ - //- Constructors -/ //----------------/ - + //- Constructors -/ + //----------------/ public AnnotationElement() { super(); - } //-- jalview.binding.AnnotationElement() - - - //-----------/ - //- Methods -/ - //-----------/ + } + //-- jalview.binding.AnnotationElement() + //-----------/ - /** - * Method deletePosition - * - */ - public void deletePosition() - { - this._has_position= false; - } //-- void deletePosition() + public void deletePosition() { + this._has_position = false; + } + //-- void deletePosition() /** * Method deleteValue * */ - public void deleteValue() - { - this._has_value= false; - } //-- void deleteValue() + public void deleteValue() { + this._has_value = false; + } + //-- void deleteValue() /** * Returns the value of field 'description'. @@ -125,10 +114,10 @@ public class AnnotationElement implements java.io.Serializable { * @return String * @return the value of field 'description'. */ - public java.lang.String getDescription() - { + public java.lang.String getDescription() { return this._description; - } //-- java.lang.String getDescription() + } + //-- java.lang.String getDescription() /** * Returns the value of field 'displayCharacter'. @@ -136,10 +125,10 @@ public class AnnotationElement implements java.io.Serializable { * @return String * @return the value of field 'displayCharacter'. */ - public java.lang.String getDisplayCharacter() - { + public java.lang.String getDisplayCharacter() { return this._displayCharacter; - } //-- java.lang.String getDisplayCharacter() + } + //-- java.lang.String getDisplayCharacter() /** * Returns the value of field 'position'. @@ -147,10 +136,10 @@ public class AnnotationElement implements java.io.Serializable { * @return int * @return the value of field 'position'. */ - public int getPosition() - { + public int getPosition() { return this._position; - } //-- int getPosition() + } + //-- int getPosition() /** * Returns the value of field 'secondaryStructure'. @@ -158,10 +147,10 @@ public class AnnotationElement implements java.io.Serializable { * @return String * @return the value of field 'secondaryStructure'. */ - public java.lang.String getSecondaryStructure() - { + public java.lang.String getSecondaryStructure() { return this._secondaryStructure; - } //-- java.lang.String getSecondaryStructure() + } + //-- java.lang.String getSecondaryStructure() /** * Returns the value of field 'value'. @@ -169,10 +158,10 @@ public class AnnotationElement implements java.io.Serializable { * @return float * @return the value of field 'value'. */ - public float getValue() - { + public float getValue() { return this._value; - } //-- float getValue() + } + //-- float getValue() /** * Method hasPosition @@ -181,10 +170,10 @@ public class AnnotationElement implements java.io.Serializable { * * @return boolean */ - public boolean hasPosition() - { + public boolean hasPosition() { return this._has_position; - } //-- boolean hasPosition() + } + //-- boolean hasPosition() /** * Method hasValue @@ -193,10 +182,10 @@ public class AnnotationElement implements java.io.Serializable { * * @return boolean */ - public boolean hasValue() - { + public boolean hasValue() { return this._has_value; - } //-- boolean hasValue() + } + //-- boolean hasValue() /** * Method isValid @@ -205,16 +194,16 @@ public class AnnotationElement implements java.io.Serializable { * * @return boolean */ - public boolean isValid() - { + public boolean isValid() { try { validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { + } catch (org.exolab.castor.xml.ValidationException vex) { return false; } + return true; - } //-- boolean isValid() + } + //-- boolean isValid() /** * Method marshal @@ -224,11 +213,11 @@ public class AnnotationElement implements java.io.Serializable { * @param out */ public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + } + //-- void marshal(java.io.Writer) /** * Method marshal @@ -238,42 +227,42 @@ public class AnnotationElement implements java.io.Serializable { * @param handler */ public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - + throws java.io.IOException, org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } + //-- void marshal(org.xml.sax.ContentHandler) /** * Sets the value of field 'description'. * * @param description the value of field 'description'. */ - public void setDescription(java.lang.String description) - { + public void setDescription(java.lang.String description) { this._description = description; - } //-- void setDescription(java.lang.String) + } + //-- void setDescription(java.lang.String) /** * Sets the value of field 'displayCharacter'. * * @param displayCharacter the value of field 'displayCharacter' */ - public void setDisplayCharacter(java.lang.String displayCharacter) - { + public void setDisplayCharacter(java.lang.String displayCharacter) { this._displayCharacter = displayCharacter; - } //-- void setDisplayCharacter(java.lang.String) + } + //-- void setDisplayCharacter(java.lang.String) /** * Sets the value of field 'position'. * * @param position the value of field 'position'. */ - public void setPosition(int position) - { + public void setPosition(int position) { this._position = position; this._has_position = true; - } //-- void setPosition(int) + } + //-- void setPosition(int) /** * Sets the value of field 'secondaryStructure'. @@ -281,21 +270,21 @@ public class AnnotationElement implements java.io.Serializable { * @param secondaryStructure the value of field * 'secondaryStructure'. */ - public void setSecondaryStructure(java.lang.String secondaryStructure) - { + public void setSecondaryStructure(java.lang.String secondaryStructure) { this._secondaryStructure = secondaryStructure; - } //-- void setSecondaryStructure(java.lang.String) + } + //-- void setSecondaryStructure(java.lang.String) /** * Sets the value of field 'value'. * * @param value the value of field 'value'. */ - public void setValue(float value) - { + public void setValue(float value) { this._value = value; this._has_value = true; - } //-- void setValue(float) + } + //-- void setValue(float) /** * Method unmarshal @@ -306,20 +295,20 @@ public class AnnotationElement implements java.io.Serializable { * @return Object */ public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException { + return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, + reader); + } + //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate * */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { + public void validate() throws org.exolab.castor.xml.ValidationException { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } //-- void validate() - + } + //-- void validate() }