\r
for (int i = 0; i < aa.length; i++)\r
{\r
+ Annotation an = new Annotation();\r
+\r
if (aa[i].label.equals("Quality") ||\r
aa[i].label.equals("Conservation") ||\r
aa[i].label.equals("Consensus"))\r
{\r
+ an.setLabel(aa[i].label);\r
+ an.setGraph(true);\r
+ vamsasSet.addAnnotation(an);\r
continue;\r
}\r
\r
- Annotation an = new Annotation();\r
+\r
an.setDescription(aa[i].description);\r
\r
if(aa[i].sequenceRef!=null)\r
{\r
an.setGraph(true);\r
an.setGraphType(aa[i].graph);\r
+ an.setGraphGroup(aa[i].graphGroup);\r
if(aa[i].getThreshold()!=null)\r
{\r
ThresholdLine line = new ThresholdLine();\r
ae.setPosition(a);\r
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
"");\r
+\r
+ if(aa[i].annotations[a].colour!=java.awt.Color.black)\r
+ ae.setColour(aa[i].annotations[a].colour.getRGB());\r
+\r
an.addAnnotationElement(ae);\r
}\r
\r
}\r
}\r
\r
+\r
/////////////////////////////////\r
//////////////////////////////////\r
//LOAD ANNOTATIONS\r
+ boolean hideQuality = true,\r
+ hideConservation = true,\r
+ hideConsensus = true;\r
+\r
if (vamsasSet.getAnnotation() != null)\r
{\r
Annotation[] an = vamsasSet.getAnnotation();\r
\r
for (int i = 0; i < an.length; i++)\r
{\r
+ if (an[i].getLabel().equals("Quality"))\r
+ {\r
+ hideQuality = false;\r
+ continue;\r
+ }\r
+ else if(an[i].getLabel().equals("Conservation"))\r
+ {\r
+ hideConservation = false;\r
+ continue;\r
+ }\r
+ else if(an[i].getLabel().equals("Consensus"))\r
+ {\r
+ hideConsensus = false;\r
+ continue;\r
+ }\r
+\r
AnnotationElement[] ae = an[i].getAnnotationElement();\r
jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
\r
ae[aa].getDescription(),\r
ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
ae[aa].getValue());\r
+ anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
}\r
\r
jalview.datamodel.AlignmentAnnotation jaa = null;\r
an[i].getDescription(), anot, 0, 0,\r
an[i].getGraphType());\r
\r
+ jaa.graphGroup = an[i].getGraphGroup();\r
+\r
if (an[i].getThresholdLine() != null)\r
{\r
jaa.setThreshold(new jalview.datamodel.GraphLine(\r
}\r
\r
\r
- /////////////////////////////////\r
- // LOAD VIEWPORT\r
- Viewport[] views = jms.getViewport();\r
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
-\r
- AlignFrame af = new AlignFrame(al);\r
-\r
-\r
// af.changeColour() );\r
/////////////////////////\r
//LOAD GROUPS\r
}\r
\r
\r
+ /////////////////////////////////\r
+ // LOAD VIEWPORT\r
+ Viewport[] views = jms.getViewport();\r
+ Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
+\r
+ AlignFrame af = new AlignFrame(al);\r
+ int hSize = al.getAlignmentAnnotation().length;\r
+ for (int h = 0; h < hSize; h++)\r
+ {\r
+ if (\r
+ (hideConsensus &&\r
+ al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
+ ||\r
+ (hideQuality && al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
+ ||\r
+ (hideConservation &&\r
+ al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
+ {\r
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
+ hSize --;\r
+ h--;\r
+ }\r
+ }\r
\r
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
view.getHeight());\r
private java.lang.String _sequenceRef;\r
\r
/**\r
+ * Field _graphColour\r
+ */\r
+ private int _graphColour;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphColour\r
+ */\r
+ private boolean _has_graphColour;\r
+\r
+ /**\r
+ * Field _graphGroup\r
+ */\r
+ private int _graphGroup;\r
+\r
+ /**\r
+ * keeps track of state for field: _graphGroup\r
+ */\r
+ private boolean _has_graphGroup;\r
+\r
+ /**\r
* Field _annotationElementList\r
*/\r
private java.util.Vector _annotationElementList;\r
} //-- void deleteGraph() \r
\r
/**\r
+ * Method deleteGraphColour\r
+ * \r
+ */\r
+ public void deleteGraphColour()\r
+ {\r
+ this._has_graphColour= false;\r
+ } //-- void deleteGraphColour() \r
+\r
+ /**\r
+ * Method deleteGraphGroup\r
+ * \r
+ */\r
+ public void deleteGraphGroup()\r
+ {\r
+ this._has_graphGroup= false;\r
+ } //-- void deleteGraphGroup() \r
+\r
+ /**\r
* Method deleteGraphType\r
* \r
*/\r
} //-- boolean getGraph() \r
\r
/**\r
+ * Returns the value of field 'graphColour'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'graphColour'.\r
+ */\r
+ public int getGraphColour()\r
+ {\r
+ return this._graphColour;\r
+ } //-- int getGraphColour() \r
+\r
+ /**\r
+ * Returns the value of field 'graphGroup'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'graphGroup'.\r
+ */\r
+ public int getGraphGroup()\r
+ {\r
+ return this._graphGroup;\r
+ } //-- int getGraphGroup() \r
+\r
+ /**\r
* Returns the value of field 'graphType'.\r
* \r
* @return int\r
} //-- boolean hasGraph() \r
\r
/**\r
+ * Method hasGraphColour\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasGraphColour()\r
+ {\r
+ return this._has_graphColour;\r
+ } //-- boolean hasGraphColour() \r
+\r
+ /**\r
+ * Method hasGraphGroup\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasGraphGroup()\r
+ {\r
+ return this._has_graphGroup;\r
+ } //-- boolean hasGraphGroup() \r
+\r
+ /**\r
* Method hasGraphType\r
* \r
* \r
} //-- void setGraph(boolean) \r
\r
/**\r
+ * Sets the value of field 'graphColour'.\r
+ * \r
+ * @param graphColour the value of field 'graphColour'.\r
+ */\r
+ public void setGraphColour(int graphColour)\r
+ {\r
+ this._graphColour = graphColour;\r
+ this._has_graphColour = true;\r
+ } //-- void setGraphColour(int) \r
+\r
+ /**\r
+ * Sets the value of field 'graphGroup'.\r
+ * \r
+ * @param graphGroup the value of field 'graphGroup'.\r
+ */\r
+ public void setGraphGroup(int graphGroup)\r
+ {\r
+ this._graphGroup = graphGroup;\r
+ this._has_graphGroup = true;\r
+ } //-- void setGraphGroup(int) \r
+\r
+ /**\r
* Sets the value of field 'graphType'.\r
* \r
* @param graphType the value of field 'graphType'.\r
fieldValidator.setValidator(typeValidator);\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _graphColour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if(!target.hasGraphColour())\r
+ return null;\r
+ return new java.lang.Integer(target.getGraphColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphColour();\r
+ return;\r
+ }\r
+ target.setGraphColour( ((java.lang.Integer)value).intValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphColour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ IntegerValidator typeValidator= new IntegerValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _graphGroup\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Annotation target = (Annotation) object;\r
+ if(!target.hasGraphGroup())\r
+ return null;\r
+ return new java.lang.Integer(target.getGraphGroup());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Annotation target = (Annotation) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteGraphGroup();\r
+ return;\r
+ }\r
+ target.setGraphGroup( ((java.lang.Integer)value).intValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _graphGroup\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ IntegerValidator typeValidator= new IntegerValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
//-- _annotationElementList\r
} );\r
desc.setHandler(handler);\r
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
desc.setMultivalued(true);\r
addFieldDescriptor(desc);\r
\r
//-- validation code for: _annotationElementList\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
+ fieldValidator.setMinOccurs(0);\r
{ //-- local scope\r
}\r
desc.setValidator(fieldValidator);\r
} );\r
desc.setHandler(handler);\r
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
//-- validation code for: _description\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
{ //-- local scope\r
StringValidator typeValidator = new StringValidator();\r
typeValidator.setWhiteSpace("preserve");\r
private boolean _has_position;\r
\r
/**\r
+ * Field _colour\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\r
+\r
+ /**\r
* Field _displayCharacter\r
*/\r
private java.lang.String _displayCharacter;\r
//-----------/\r
\r
/**\r
+ * Method deleteColour\r
+ * \r
+ */\r
+ public void deleteColour()\r
+ {\r
+ this._has_colour= false;\r
+ } //-- void deleteColour() \r
+\r
+ /**\r
* Method deletePosition\r
* \r
*/\r
} //-- void deleteValue() \r
\r
/**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'colour'.\r
+ */\r
+ public int getColour()\r
+ {\r
+ return this._colour;\r
+ } //-- int getColour() \r
+\r
+ /**\r
* Returns the value of field 'description'.\r
* \r
* @return String\r
} //-- float getValue() \r
\r
/**\r
+ * Method hasColour\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasColour()\r
+ {\r
+ return this._has_colour;\r
+ } //-- boolean hasColour() \r
+\r
+ /**\r
* Method hasPosition\r
* \r
* \r
} //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(int colour)\r
+ {\r
+ this._colour = colour;\r
+ this._has_colour = true;\r
+ } //-- void setColour(int) \r
+\r
+ /**\r
* Sets the value of field 'description'.\r
* \r
* @param description the value of field 'description'.\r
fieldValidator.setValidator(typeValidator);\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _colour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ if(!target.hasColour())\r
+ return null;\r
+ return new java.lang.Integer(target.getColour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AnnotationElement target = (AnnotationElement) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteColour();\r
+ return;\r
+ }\r
+ target.setColour( ((java.lang.Integer)value).intValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _colour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ IntegerValidator typeValidator= new IntegerValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
//-- _displayCharacter\r
} );\r
desc.setHandler(handler);\r
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
//-- validation code for: _displayCharacter\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
{ //-- local scope\r
StringValidator typeValidator = new StringValidator();\r
typeValidator.setWhiteSpace("preserve");\r
} );\r
desc.setHandler(handler);\r
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
//-- validation code for: _description\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
{ //-- local scope\r
StringValidator typeValidator = new StringValidator();\r
typeValidator.setWhiteSpace("preserve");\r
} );\r
desc.setHandler(handler);\r
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
//-- validation code for: _secondaryStructure\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
{ //-- local scope\r
StringValidator typeValidator = new StringValidator();\r
typeValidator.setLength(1);\r
{\r
try {\r
AnnotationElement target = (AnnotationElement) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteValue();\r
+ return;\r
+ }\r
target.setValue( ((java.lang.Float)value).floatValue());\r
}\r
catch (java.lang.Exception ex) {\r
} );\r
desc.setHandler(handler);\r
desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
- desc.setRequired(true);\r
desc.setMultivalued(false);\r
addFieldDescriptor(desc);\r
\r
//-- validation code for: _value\r
fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
{ //-- local scope\r
FloatValidator typeValidator = new FloatValidator();\r
fieldValidator.setValidator(typeValidator);\r