package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-public class Colour implements java.io.Serializable {
+public class Colour implements java.io.Serializable
+{
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * Single letter residue code for an alignment colour scheme, or feature type
+ * for a feature colour scheme
+ */
+ private java.lang.String _name;
- /**
- * Field _name.
- */
- private java.lang.String _name;
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
- /**
- * Field _RGB.
- */
- private java.lang.String _RGB;
+ /**
+ * Field _minRGB.
+ */
+ private java.lang.String _minRGB;
+ /**
+ * Field _noValueColour.
+ */
+ private jalview.binding.types.NoValueColour _noValueColour = jalview.binding.types.NoValueColour
+ .valueOf("Min");
- //----------------/
- //- Constructors -/
- //----------------/
+ /**
+ * Field _threshType.
+ */
+ private jalview.binding.types.ColourThreshTypeType _threshType;
- public Colour() {
- super();
- }
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
- //-----------/
- //- Methods -/
- //-----------/
+ /**
+ * Field _max.
+ */
+ private float _max;
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
- /**
- * Returns the value of field 'RGB'.
- *
- * @return the value of field 'RGB'.
- */
- public java.lang.String getRGB(
- ) {
- return this._RGB;
- }
+ /**
+ * Field _min.
+ */
+ private float _min;
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+ /**
+ * name of feature attribute to colour by, or attribute and sub-attribute
+ */
+ private java.util.Vector _attributeNameList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Colour()
+ {
+ super();
+ setNoValueColour(jalview.binding.types.NoValueColour.valueOf("Min"));
+ this._attributeNameList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAttributeName
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttributeName(final java.lang.String vAttributeName)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._attributeNameList.size() >= 2)
+ {
+ throw new IndexOutOfBoundsException(
+ "addAttributeName has a maximum of 2");
}
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
+ this._attributeNameList.addElement(vAttributeName);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttributeName
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttributeName(final int index,
+ final java.lang.String vAttributeName)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check for the maximum size
+ if (this._attributeNameList.size() >= 2)
+ {
+ throw new IndexOutOfBoundsException(
+ "addAttributeName has a maximum of 2");
}
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
+ this._attributeNameList.add(index, vAttributeName);
+ }
+
+ /**
+ */
+ public void deleteAutoScale()
+ {
+ this._has_autoScale = false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel()
+ {
+ this._has_colourByLabel = false;
+ }
+
+ /**
+ */
+ public void deleteMax()
+ {
+ this._has_max = false;
+ }
+
+ /**
+ */
+ public void deleteMin()
+ {
+ this._has_min = false;
+ }
+
+ /**
+ */
+ public void deleteThreshold()
+ {
+ this._has_threshold = false;
+ }
+
+ /**
+ * Method enumerateAttributeName.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateAttributeName()
+ {
+ return this._attributeNameList.elements();
+ }
+
+ /**
+ * Method getAttributeName.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getAttributeName(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._attributeNameList.size())
+ {
+ throw new IndexOutOfBoundsException("getAttributeName: Index value '"
+ + index + "' not in range [0.."
+ + (this._attributeNameList.size() - 1) + "]");
}
- /**
- * Sets the value of field 'RGB'.
- *
- * @param RGB the value of field 'RGB'.
- */
- public void setRGB(
- final java.lang.String RGB) {
- this._RGB = RGB;
+ return (java.lang.String) _attributeNameList.get(index);
+ }
+
+ /**
+ * Method getAttributeName.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getAttributeName()
+ {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._attributeNameList.toArray(array);
+ }
+
+ /**
+ * Method getAttributeNameCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAttributeNameCount()
+ {
+ return this._attributeNameList.size();
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax()
+ {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin()
+ {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'minRGB'.
+ *
+ * @return the value of field 'MinRGB'.
+ */
+ public java.lang.String getMinRGB()
+ {
+ return this._minRGB;
+ }
+
+ /**
+ * Returns the value of field 'name'. The field 'name' has the following
+ * description: Single letter residue code for an alignment colour scheme, or
+ * feature type for a feature colour scheme
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'noValueColour'.
+ *
+ * @return the value of field 'NoValueColour'.
+ */
+ public jalview.binding.types.NoValueColour getNoValueColour()
+ {
+ return this._noValueColour;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB()
+ {
+ return this._RGB;
+ }
+
+ /**
+ * Returns the value of field 'threshType'.
+ *
+ * @return the value of field 'ThreshType'.
+ */
+ public jalview.binding.types.ColourThreshTypeType getThreshType()
+ {
+ return this._threshType;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold()
+ {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale()
+ {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel()
+ {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax()
+ {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin()
+ {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold()
+ {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale()
+ {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel()
+ {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid()
+ {
+ try
+ {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex)
+ {
+ return false;
}
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException,
+ org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAttributeName()
+ {
+ this._attributeNameList.clear();
+ }
+
+ /**
+ * Method removeAttributeName.
+ *
+ * @param vAttributeName
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAttributeName(final java.lang.String vAttributeName)
+ {
+ boolean removed = _attributeNameList.remove(vAttributeName);
+ return removed;
+ }
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Colour
- */
- public static jalview.binding.Colour unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
+ /**
+ * Method removeAttributeNameAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeAttributeNameAt(final int index)
+ {
+ java.lang.Object obj = this._attributeNameList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttributeName
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAttributeName(final int index,
+ final java.lang.String vAttributeName)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._attributeNameList.size())
+ {
+ throw new IndexOutOfBoundsException("setAttributeName: Index value '"
+ + index + "' not in range [0.."
+ + (this._attributeNameList.size() - 1) + "]");
}
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ this._attributeNameList.set(index, vAttributeName);
+ }
+
+ /**
+ *
+ *
+ * @param vAttributeNameArray
+ */
+ public void setAttributeName(final java.lang.String[] vAttributeNameArray)
+ {
+ // -- copy array
+ _attributeNameList.clear();
+
+ for (int i = 0; i < vAttributeNameArray.length; i++)
+ {
+ this._attributeNameList.add(vAttributeNameArray[i]);
}
+ }
+
+ /**
+ * Sets the value of field 'autoScale'.
+ *
+ * @param autoScale
+ * the value of field 'autoScale'.
+ */
+ public void setAutoScale(final boolean autoScale)
+ {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel
+ * the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(final boolean colourByLabel)
+ {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max
+ * the value of field 'max'.
+ */
+ public void setMax(final float max)
+ {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min
+ * the value of field 'min'.
+ */
+ public void setMin(final float min)
+ {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'minRGB'.
+ *
+ * @param minRGB
+ * the value of field 'minRGB'.
+ */
+ public void setMinRGB(final java.lang.String minRGB)
+ {
+ this._minRGB = minRGB;
+ }
+
+ /**
+ * Sets the value of field 'name'. The field 'name' has the following
+ * description: Single letter residue code for an alignment colour scheme, or
+ * feature type for a feature colour scheme
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'noValueColour'.
+ *
+ * @param noValueColour
+ * the value of field 'noValueColour'.
+ */
+ public void setNoValueColour(
+ final jalview.binding.types.NoValueColour noValueColour)
+ {
+ this._noValueColour = noValueColour;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB
+ * the value of field 'RGB'.
+ */
+ public void setRGB(final java.lang.String RGB)
+ {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Sets the value of field 'threshType'.
+ *
+ * @param threshType
+ * the value of field 'threshType'.
+ */
+ public void setThreshType(
+ final jalview.binding.types.ColourThreshTypeType threshType)
+ {
+ this._threshType = threshType;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold
+ * the value of field 'threshold'.
+ */
+ public void setThreshold(final float threshold)
+ {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Colour
+ */
+ public static jalview.binding.Colour unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.Colour) Unmarshaller
+ .unmarshal(jalview.binding.Colour.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
git://source.jalview.org / jalview.git / blobdiff