From: jprocter Date: Thu, 26 Apr 2007 17:10:05 +0000 (+0000) Subject: total annotation score is a double for maximum precision. X-Git-Tag: Release_2_3~160 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=inline;h=855f7a4bb3e8d5fcfa9059df64262fc73f0164be;p=jalview.git total annotation score is a double for maximum precision. --- diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 1a24509..9ba7919 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -48,7 +48,7 @@ - + diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index 9eb6907..021fa8b 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -98,7 +98,7 @@ public class Annotation implements java.io.Serializable { /** * Field _score */ - private float _score; + private double _score; /** * keeps track of state for field: _score @@ -361,13 +361,13 @@ public class Annotation implements java.io.Serializable { /** * Returns the value of field 'score'. * - * @return float + * @return double * @return the value of field 'score'. */ - public float getScore() + public double getScore() { return this._score; - } //-- float getScore() + } //-- double getScore() /** * Returns the value of field 'scoreOnly'. @@ -657,11 +657,11 @@ public class Annotation implements java.io.Serializable { * * @param score the value of field 'score'. */ - public void setScore(float score) + public void setScore(double score) { this._score = score; this._has_score = true; - } //-- void setScore(float) + } //-- void setScore(double) /** * Sets the value of field 'scoreOnly'. diff --git a/src/jalview/schemabinding/version2/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/AnnotationDescriptor.java index e0061ae..28ceec1 100755 --- a/src/jalview/schemabinding/version2/AnnotationDescriptor.java +++ b/src/jalview/schemabinding/version2/AnnotationDescriptor.java @@ -343,7 +343,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes } desc.setValidator(fieldValidator); //-- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); handler = (new org.exolab.castor.xml.XMLFieldHandler() { public java.lang.Object getValue( java.lang.Object object ) throws IllegalStateException @@ -351,7 +351,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes Annotation target = (Annotation) object; if(!target.hasScore()) return null; - return new java.lang.Float(target.getScore()); + return new java.lang.Double(target.getScore()); } public void setValue( java.lang.Object object, java.lang.Object value) throws IllegalStateException, IllegalArgumentException @@ -363,7 +363,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes target.deleteScore(); return; } - target.setScore( ((java.lang.Float)value).floatValue()); + target.setScore( ((java.lang.Double)value).doubleValue()); } catch (java.lang.Exception ex) { throw new IllegalStateException(ex.toString()); @@ -379,7 +379,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes //-- validation code for: _score fieldValidator = new org.exolab.castor.xml.FieldValidator(); { //-- local scope - FloatValidator typeValidator = new FloatValidator(); + DoubleValidator typeValidator = new DoubleValidator(); fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); diff --git a/src/jalview/schemabinding/version2/PdbidsItem.java b/src/jalview/schemabinding/version2/PdbidsItem.java deleted file mode 100644 index 0c5c10f..0000000 --- a/src/jalview/schemabinding/version2/PdbidsItem.java +++ /dev/null @@ -1,70 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.Serializable; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class PdbidsItem. - * - * @version $Revision$ $Date$ - */ -public class PdbidsItem implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _structureState - */ - private jalview.schemabinding.version2.StructureState _structureState; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbidsItem() { - super(); - } //-- jalview.schemabinding.version2.PdbidsItem() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'structureState'. - * - * @return StructureState - * @return the value of field 'structureState'. - */ - public jalview.schemabinding.version2.StructureState getStructureState() - { - return this._structureState; - } //-- jalview.schemabinding.version2.StructureState getStructureState() - - /** - * Sets the value of field 'structureState'. - * - * @param structureState the value of field 'structureState'. - */ - public void setStructureState(jalview.schemabinding.version2.StructureState structureState) - { - this._structureState = structureState; - } //-- void setStructureState(jalview.schemabinding.version2.StructureState) - -} diff --git a/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java b/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java deleted file mode 100644 index 9128920..0000000 --- a/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java +++ /dev/null @@ -1,207 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class PdbidsItemDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PdbidsItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbidsItemDescriptor() { - super(); - nsURI = "www.jalview.org"; - xmlName = "pdbids"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.xml.XMLFieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _structureState - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureState", "structureState", org.exolab.castor.xml.NodeType.Element); - handler = (new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - PdbidsItem target = (PdbidsItem) object; - return target.getStructureState(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - PdbidsItem target = (PdbidsItem) object; - target.setStructureState( (jalview.schemabinding.version2.StructureState) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new jalview.schemabinding.version2.StructureState(); - } - } ); - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _structureState - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- jalview.schemabinding.version2.PdbidsItemDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.PdbidsItem.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -}