/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
*/
+
package jalview.binding;
//---------------------------------/
// --------------------------/
/**
- * Field _name.
+ * Single letter residue code for an alignment colour scheme, or feature type
+ * for a feature colour scheme
*/
private java.lang.String _name;
private java.lang.String _minRGB;
/**
- * loosely specified enumeration: NONE,ABOVE, or BELOW
+ * Field _noValueColour.
+ */
+ private jalview.binding.types.NoValueColour _noValueColour = jalview.binding.types.NoValueColour
+ .valueOf("Min");
+
+ /**
+ * Field _threshType.
*/
- private java.lang.String _threshType;
+ private jalview.binding.types.ColourThreshTypeType _threshType;
/**
* Field _threshold.
*/
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();
}
// -----------/
// -----------/
/**
- */
+ *
+ *
+ * @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");
+ }
+
+ 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");
+ }
+
+ 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) + "]");
+ }
+
+ 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'.
}
/**
- * Returns the value of field 'name'.
+ * 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'.
*/
}
/**
+ * 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'.
}
/**
- * Returns the value of field 'threshType'. The field 'threshType' has the
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+ * Returns the value of field 'threshType'.
*
* @return the value of field 'ThreshType'.
*/
- public java.lang.String getThreshType()
+ public jalview.binding.types.ColourThreshTypeType getThreshType()
{
return this._threshType;
}
}
/**
+ */
+ 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 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) + "]");
+ }
+
+ 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
}
/**
- * Sets the value of field 'name'.
+ * 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'.
}
/**
+ * 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
}
/**
- * Sets the value of field 'threshType'. The field 'threshType' has the
- * following description: loosely specified enumeration: NONE,ABOVE, or BELOW
+ * Sets the value of field 'threshType'.
*
* @param threshType
* the value of field 'threshType'.
*/
- public void setThreshType(final java.lang.String threshType)
+ public void setThreshType(
+ final jalview.binding.types.ColourThreshTypeType threshType)
{
this._threshType = threshType;
}
* 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)
+ 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);
+ return (jalview.binding.Colour) Unmarshaller
+ .unmarshal(jalview.binding.Colour.class, reader);
}
/**
git://source.jalview.org / jalview.git / blobdiff