From 24681b2bc3e0cdc0d77dd73cad05deea14264fab Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 5 Oct 2006 16:18:19 +0000 Subject: [PATCH] Sequenceset may be empty, multiple views --- .../version2/SequenceSetDescriptor.java | 3 +- .../version2/SequenceTypeDescriptor.java | 4 - src/jalview/schemabinding/version2/Viewport.java | 105 ++++++++++++++++++ .../schemabinding/version2/ViewportDescriptor.java | 113 ++++++++++++++++++++ 4 files changed, 219 insertions(+), 6 deletions(-) diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java index 1e6c7b5..81946b5 100755 --- a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java +++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java @@ -172,13 +172,12 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe } ); desc.setHandler(handler); desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); desc.setMultivalued(true); addFieldDescriptor(desc); //-- validation code for: _sequenceList fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); + fieldValidator.setMinOccurs(0); { //-- local scope } desc.setValidator(fieldValidator); diff --git a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java index 9977ea3..ef6c636 100755 --- a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java @@ -166,13 +166,11 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD } ); desc.setHandler(handler); desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _sequence fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); { //-- local scope StringValidator typeValidator = new StringValidator(); typeValidator.setWhiteSpace("preserve"); @@ -206,13 +204,11 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD } ); desc.setHandler(handler); desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); desc.setMultivalued(false); addFieldDescriptor(desc); //-- validation code for: _name fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); { //-- local scope StringValidator typeValidator = new StringValidator(); typeValidator.setWhiteSpace("preserve"); diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 557e454..24adba5 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -281,6 +281,26 @@ public class Viewport implements java.io.Serializable { private boolean _has_fontStyle; /** + * Field _viewName + */ + private java.lang.String _viewName; + + /** + * Field _sequenceSetId + */ + private java.lang.String _sequenceSetId; + + /** + * Field _gatheredViews + */ + private boolean _gatheredViews; + + /** + * keeps track of state for field: _gatheredViews + */ + private boolean _has_gatheredViews; + + /** * Field _annotationColours */ private jalview.schemabinding.version2.AnnotationColours _annotationColours; @@ -369,6 +389,15 @@ public class Viewport implements java.io.Serializable { } //-- void deleteFontStyle() /** + * Method deleteGatheredViews + * + */ + public void deleteGatheredViews() + { + this._has_gatheredViews= false; + } //-- void deleteGatheredViews() + + /** * Method deleteHeight * */ @@ -629,6 +658,17 @@ public class Viewport implements java.io.Serializable { } //-- int getFontStyle() /** + * Returns the value of field 'gatheredViews'. + * + * @return boolean + * @return the value of field 'gatheredViews'. + */ + public boolean getGatheredViews() + { + return this._gatheredViews; + } //-- boolean getGatheredViews() + + /** * Returns the value of field 'height'. * * @return int @@ -721,6 +761,17 @@ public class Viewport implements java.io.Serializable { } //-- boolean getRenderGaps() /** + * Returns the value of field 'sequenceSetId'. + * + * @return String + * @return the value of field 'sequenceSetId'. + */ + public java.lang.String getSequenceSetId() + { + return this._sequenceSetId; + } //-- java.lang.String getSequenceSetId() + + /** * Returns the value of field 'showAnnotation'. * * @return boolean @@ -853,6 +904,17 @@ public class Viewport implements java.io.Serializable { } //-- java.lang.String getTitle() /** + * Returns the value of field 'viewName'. + * + * @return String + * @return the value of field 'viewName'. + */ + public java.lang.String getViewName() + { + return this._viewName; + } //-- java.lang.String getViewName() + + /** * Returns the value of field 'width'. * * @return int @@ -945,6 +1007,18 @@ public class Viewport implements java.io.Serializable { } //-- boolean hasFontStyle() /** + * Method hasGatheredViews + * + * + * + * @return boolean + */ + public boolean hasGatheredViews() + { + return this._has_gatheredViews; + } //-- boolean hasGatheredViews() + + /** * Method hasHeight * * @@ -1319,6 +1393,17 @@ public class Viewport implements java.io.Serializable { } //-- void setFontStyle(int) /** + * Sets the value of field 'gatheredViews'. + * + * @param gatheredViews the value of field 'gatheredViews'. + */ + public void setGatheredViews(boolean gatheredViews) + { + this._gatheredViews = gatheredViews; + this._has_gatheredViews = true; + } //-- void setGatheredViews(boolean) + + /** * Sets the value of field 'height'. * * @param height the value of field 'height'. @@ -1397,6 +1482,16 @@ public class Viewport implements java.io.Serializable { } //-- void setRenderGaps(boolean) /** + * Sets the value of field 'sequenceSetId'. + * + * @param sequenceSetId the value of field 'sequenceSetId'. + */ + public void setSequenceSetId(java.lang.String sequenceSetId) + { + this._sequenceSetId = sequenceSetId; + } //-- void setSequenceSetId(java.lang.String) + + /** * Sets the value of field 'showAnnotation'. * * @param showAnnotation the value of field 'showAnnotation'. @@ -1529,6 +1624,16 @@ public class Viewport implements java.io.Serializable { } //-- void setTitle(java.lang.String) /** + * Sets the value of field 'viewName'. + * + * @param viewName the value of field 'viewName'. + */ + public void setViewName(java.lang.String viewName) + { + this._viewName = viewName; + } //-- void setViewName(java.lang.String) + + /** * Sets the value of field 'width'. * * @param width the value of field 'width'. diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java index b98f97b..9f2ad90 100755 --- a/src/jalview/schemabinding/version2/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java @@ -1116,6 +1116,119 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr fieldValidator.setValidator(typeValidator); } desc.setValidator(fieldValidator); + //-- _viewName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = (new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getViewName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setViewName( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + } ); + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _viewName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _sequenceSetId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = (new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getSequenceSetId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setSequenceSetId( (java.lang.String) value); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + } ); + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + StringValidator typeValidator = new StringValidator(); + typeValidator.setWhiteSpace("preserve"); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _gatheredViews + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute); + handler = (new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if(!target.hasGatheredViews()) + return null; + return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGatheredViews(); + return; + } + target.setGatheredViews( ((java.lang.Boolean)value).booleanValue()); + } + catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance( java.lang.Object parent ) { + return null; + } + } ); + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _gatheredViews + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + BooleanValidator typeValidator = new BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); //-- initialize element descriptors //-- _annotationColours -- 1.7.10.2