<xs:attribute name="colour" type="xs:int" use="required"/>
<xs:attribute name="display" type="xs:boolean" use="required"/>
<xs:attribute name="order" type="xs:float" use="optional"/>
- </xs:complexType>
+ <xs:attribute name="mincolour" type="xs:int" use="optional">
+ <xs:annotation><xs:documentation>Optional minimum colour for graduated feature colour</xs:documentation>
+ </xs:annotation></xs:attribute>
+ <xs:attribute name="threshold" type="xs:float" use="optional">
+ <xs:annotation><xs:documentation>threshold value for graduated feature colour</xs:documentation>
+ </xs:annotation></xs:attribute>
+ <xs:attribute name="threshstate" type="xs:int" use="optional">
+ <xs:annotation><xs:documentation>threshold type for graduated feature colour</xs:documentation>
+ </xs:annotation></xs:attribute>
+ </xs:complexType>
</xs:element>
<xs:element name="group" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
-
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ if (setting.hasMincolour())
+ {
+ // TODO: determine how to set data independent bounds for a graduated colour scheme's range.
+ GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()),
+ 0,1);
+ if (setting.hasThreshold()) {
+ gc.setThresh(setting.getThreshold());
+ gc.setThreshType(setting.getThreshstate());
+ }
+ } else {
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), new java.awt.Color(setting.getColour()));
+ }
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
-#Fri Feb 06 14:21:53 GMT 2009\r
+#Tue Mar 31 17:21:18 BST 2009\r
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
*/\r
private boolean _has_order;\r
\r
+ /**\r
+ * Optional minimum colour for graduated feature colour\r
+ */\r
+ private int _mincolour;\r
+\r
+ /**\r
+ * keeps track of state for field: _mincolour\r
+ */\r
+ private boolean _has_mincolour;\r
+\r
+ /**\r
+ * threshold value for graduated feature colour\r
+ */\r
+ private float _threshold;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshold\r
+ */\r
+ private boolean _has_threshold;\r
+\r
+ /**\r
+ * threshold type for graduated feature colour\r
+ */\r
+ private int _threshstate;\r
+\r
+ /**\r
+ * keeps track of state for field: _threshstate\r
+ */\r
+ private boolean _has_threshstate;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
\r
/**\r
*/\r
+ public void deleteMincolour(\r
+ ) {\r
+ this._has_mincolour= false;\r
+ }\r
+\r
+ /**\r
+ */\r
public void deleteOrder(\r
) {\r
this._has_order= false;\r
}\r
\r
/**\r
+ */\r
+ public void deleteThreshold(\r
+ ) {\r
+ this._has_threshold= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteThreshstate(\r
+ ) {\r
+ this._has_threshstate= false;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'colour'.\r
* \r
* @return the value of field 'Colour'.\r
}\r
\r
/**\r
+ * Returns the value of field 'mincolour'. The field\r
+ * 'mincolour' has the following description: Optional minimum\r
+ * colour for graduated feature colour\r
+ * \r
+ * @return the value of field 'Mincolour'.\r
+ */\r
+ public int getMincolour(\r
+ ) {\r
+ return this._mincolour;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'order'.\r
* \r
* @return the value of field 'Order'.\r
}\r
\r
/**\r
+ * Returns the value of field 'threshold'. The field\r
+ * 'threshold' has the following description: threshold value\r
+ * for graduated feature colour\r
+ * \r
+ * @return the value of field 'Threshold'.\r
+ */\r
+ public float getThreshold(\r
+ ) {\r
+ return this._threshold;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'threshstate'. The field\r
+ * 'threshstate' has the following description: threshold type\r
+ * for graduated feature colour\r
+ * \r
+ * @return the value of field 'Threshstate'.\r
+ */\r
+ public int getThreshstate(\r
+ ) {\r
+ return this._threshstate;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'type'.\r
* \r
* @return the value of field 'Type'.\r
}\r
\r
/**\r
+ * Method hasMincolour.\r
+ * \r
+ * @return true if at least one Mincolour has been added\r
+ */\r
+ public boolean hasMincolour(\r
+ ) {\r
+ return this._has_mincolour;\r
+ }\r
+\r
+ /**\r
* Method hasOrder.\r
* \r
* @return true if at least one Order has been added\r
}\r
\r
/**\r
+ * Method hasThreshold.\r
+ * \r
+ * @return true if at least one Threshold has been added\r
+ */\r
+ public boolean hasThreshold(\r
+ ) {\r
+ return this._has_threshold;\r
+ }\r
+\r
+ /**\r
+ * Method hasThreshstate.\r
+ * \r
+ * @return true if at least one Threshstate has been added\r
+ */\r
+ public boolean hasThreshstate(\r
+ ) {\r
+ return this._has_threshstate;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'display'.\r
* \r
* @return the value of field 'Display'.\r
}\r
\r
/**\r
+ * Sets the value of field 'mincolour'. The field 'mincolour'\r
+ * has the following description: Optional minimum colour for\r
+ * graduated feature colour\r
+ * \r
+ * @param mincolour the value of field 'mincolour'.\r
+ */\r
+ public void setMincolour(\r
+ final int mincolour) {\r
+ this._mincolour = mincolour;\r
+ this._has_mincolour = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'order'.\r
* \r
* @param order the value of field 'order'.\r
}\r
\r
/**\r
+ * Sets the value of field 'threshold'. The field 'threshold'\r
+ * has the following description: threshold value for graduated\r
+ * feature colour\r
+ * \r
+ * @param threshold the value of field 'threshold'.\r
+ */\r
+ public void setThreshold(\r
+ final float threshold) {\r
+ this._threshold = threshold;\r
+ this._has_threshold = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'threshstate'. The field\r
+ * 'threshstate' has the following description: threshold type\r
+ * for graduated feature colour\r
+ * \r
+ * @param threshstate the value of field 'threshstate'.\r
+ */\r
+ public void setThreshstate(\r
+ final int threshstate) {\r
+ this._threshstate = threshstate;\r
+ this._has_threshstate = true;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'type'.\r
* \r
* @param type the value of field 'type'.\r
typeValidator.setMaxInclusive((float) 3.4028235E38);\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _mincolour\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_mincolour", "mincolour", 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
+ Setting target = (Setting) object;\r
+ if (!target.hasMincolour()) { return null; }\r
+ return new java.lang.Integer(target.getMincolour());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteMincolour();\r
+ return;\r
+ }\r
+ target.setMincolour( ((java.lang.Integer) value).intValue());\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
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mincolour\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshold\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", 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
+ Setting target = (Setting) object;\r
+ if (!target.hasThreshold()) { return null; }\r
+ return new java.lang.Float(target.getThreshold());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshold();\r
+ return;\r
+ }\r
+ target.setThreshold( ((java.lang.Float) value).floatValue());\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
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshold\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.FloatValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.FloatValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive((float) -3.4028235E38);\r
+ typeValidator.setMaxInclusive((float) 3.4028235E38);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _threshstate\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", 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
+ Setting target = (Setting) object;\r
+ if (!target.hasThreshstate()) { return null; }\r
+ return new java.lang.Integer(target.getThreshstate());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Setting target = (Setting) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteThreshstate();\r
+ return;\r
+ }\r
+ target.setThreshstate( ((java.lang.Integer) value).intValue());\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
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _threshstate\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
}\r
git://source.jalview.org / jalview.git / commitdiff