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added showUnconserved property to group and view attributes
[jalview.git]
/
src
/
jalview
/
schemabinding
/
version2
/
JalviewUserColours.java
diff --git
a/src/jalview/schemabinding/version2/JalviewUserColours.java
b/src/jalview/schemabinding/version2/JalviewUserColours.java
index
7963596
..
7c059da
100755
(executable)
--- a/
src/jalview/schemabinding/version2/JalviewUserColours.java
+++ b/
src/jalview/schemabinding/version2/JalviewUserColours.java
@@
-1,6
+1,6
@@
/*
\r
* This class was automatically generated with
\r
/*
\r
* This class was automatically generated with
\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
\r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
\r
* Schema.
\r
* $Id$
\r
*/
\r
* Schema.
\r
* $Id$
\r
*/
\r
@@
-11,17
+11,8
@@
package jalview.schemabinding.version2;
//- Imported classes and packages -/
\r
//---------------------------------/
\r
\r
//- Imported classes and packages -/
\r
//---------------------------------/
\r
\r
-import java.io.IOException;
\r
-import java.io.Reader;
\r
-import java.io.Serializable;
\r
-import java.io.Writer;
\r
-import java.util.Enumeration;
\r
-import java.util.Vector;
\r
-import org.exolab.castor.xml.MarshalException;
\r
import org.exolab.castor.xml.Marshaller;
\r
import org.exolab.castor.xml.Unmarshaller;
\r
import org.exolab.castor.xml.Marshaller;
\r
import org.exolab.castor.xml.Unmarshaller;
\r
-import org.exolab.castor.xml.ValidationException;
\r
-import org.xml.sax.ContentHandler;
\r
\r
/**
\r
* Class JalviewUserColours.
\r
\r
/**
\r
* Class JalviewUserColours.
\r
@@
-36,12
+27,12
@@
public class JalviewUserColours implements java.io.Serializable {
//--------------------------/
\r
\r
/**
\r
//--------------------------/
\r
\r
/**
\r
- * Field _schemeName
\r
+ * Field _schemeName.
\r
*/
\r
private java.lang.String _schemeName;
\r
\r
/**
\r
*/
\r
private java.lang.String _schemeName;
\r
\r
/**
\r
- * Field _colourList
\r
+ * Field _colourList.
\r
*/
\r
private java.util.Vector _colourList;
\r
\r
*/
\r
private java.util.Vector _colourList;
\r
\r
@@
-52,8
+43,8
@@
public class JalviewUserColours implements java.io.Serializable {
\r
public JalviewUserColours() {
\r
super();
\r
\r
public JalviewUserColours() {
\r
super();
\r
- _colourList = new Vector();
\r
- } //-- jalview.schemabinding.version2.JalviewUserColours()
\r
+ this._colourList = new java.util.Vector();
\r
+ }
\r
\r
\r
//-----------/
\r
\r
\r
//-----------/
\r
@@
-61,240
+52,248
@@
public class JalviewUserColours implements java.io.Serializable {
//-----------/
\r
\r
/**
\r
//-----------/
\r
\r
/**
\r
- * Method addColour
\r
- *
\r
*
\r
*
\r
* @param vColour
\r
*
\r
*
\r
* @param vColour
\r
+ * @throws java.lang.IndexOutOfBoundsException if the index
\r
+ * given is outside the bounds of the collection
\r
*/
\r
*/
\r
- public void addColour(jalview.schemabinding.version2.Colour vColour)
\r
- throws java.lang.IndexOutOfBoundsException
\r
- {
\r
- _colourList.addElement(vColour);
\r
- } //-- void addColour(jalview.schemabinding.version2.Colour)
\r
+ public void addColour(
\r
+ final Colour vColour)
\r
+ throws java.lang.IndexOutOfBoundsException {
\r
+ this._colourList.addElement(vColour);
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method addColour
\r
- *
\r
*
\r
*
\r
* @param index
\r
* @param vColour
\r
*
\r
*
\r
* @param index
\r
* @param vColour
\r
+ * @throws java.lang.IndexOutOfBoundsException if the index
\r
+ * given is outside the bounds of the collection
\r
*/
\r
*/
\r
- public void addColour(int index, jalview.schemabinding.version2.Colour vColour)
\r
- throws java.lang.IndexOutOfBoundsException
\r
- {
\r
- _colourList.insertElementAt(vColour, index);
\r
- } //-- void addColour(int, jalview.schemabinding.version2.Colour)
\r
+ public void addColour(
\r
+ final int index,
\r
+ final Colour vColour)
\r
+ throws java.lang.IndexOutOfBoundsException {
\r
+ this._colourList.add(index, vColour);
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method enumerateColour
\r
- *
\r
- *
\r
+ * Method enumerateColour.
\r
*
\r
*
\r
- * @return Enumeration
\r
+ * @return an Enumeration over all Colour elements
\r
*/
\r
*/
\r
- public java.util.Enumeration enumerateColour()
\r
- {
\r
- return _colourList.elements();
\r
- } //-- java.util.Enumeration enumerateColour()
\r
+ public java.util.Enumeration enumerateColour(
\r
+ ) {
\r
+ return this._colourList.elements();
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method getColour
\r
- *
\r
- *
\r
+ * Method getColour.
\r
*
\r
* @param index
\r
*
\r
* @param index
\r
- * @return Colour
\r
+ * @throws java.lang.IndexOutOfBoundsException if the index
\r
+ * given is outside the bounds of the collection
\r
+ * @return the value of the Colour at the given index
\r
*/
\r
*/
\r
- public jalview.schemabinding.version2.Colour getColour(int index)
\r
- throws java.lang.IndexOutOfBoundsException
\r
- {
\r
- //-- check bounds for index
\r
- if ((index < 0) || (index > _colourList.size())) {
\r
- throw new IndexOutOfBoundsException();
\r
+ public Colour getColour(
\r
+ final int index)
\r
+ throws java.lang.IndexOutOfBoundsException {
\r
+ // check bounds for index
\r
+ if (index < 0 || index >= this._colourList.size()) {
\r
+ throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
\r
}
\r
\r
}
\r
\r
- return (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
\r
- } //-- jalview.schemabinding.version2.Colour getColour(int)
\r
+ return (Colour) _colourList.get(index);
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method getColour
\r
- *
\r
- *
\r
+ * Method getColour.Returns the contents of the collection in
\r
+ * an Array. <p>Note: Just in case the collection contents
\r
+ * are changing in another thread, we pass a 0-length Array of
\r
+ * the correct type into the API call. This way we <i>know</i>
\r
+ * that the Array returned is of exactly the correct length.
\r
*
\r
*
\r
- * @return Colour
\r
+ * @return this collection as an Array
\r
*/
\r
*/
\r
- public jalview.schemabinding.version2.Colour[] getColour()
\r
- {
\r
- int size = _colourList.size();
\r
- jalview.schemabinding.version2.Colour[] mArray = new jalview.schemabinding.version2.Colour[size];
\r
- for (int index = 0; index < size; index++) {
\r
- mArray[index] = (jalview.schemabinding.version2.Colour) _colourList.elementAt(index);
\r
- }
\r
- return mArray;
\r
- } //-- jalview.schemabinding.version2.Colour[] getColour()
\r
+ public Colour[] getColour(
\r
+ ) {
\r
+ Colour[] array = new Colour[0];
\r
+ return (Colour[]) this._colourList.toArray(array);
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method getColourCount
\r
- *
\r
+ * Method getColourCount.
\r
*
\r
*
\r
- *
\r
- * @return int
\r
+ * @return the size of this collection
\r
*/
\r
*/
\r
- public int getColourCount()
\r
- {
\r
- return _colourList.size();
\r
- } //-- int getColourCount()
\r
+ public int getColourCount(
\r
+ ) {
\r
+ return this._colourList.size();
\r
+ }
\r
\r
/**
\r
* Returns the value of field 'schemeName'.
\r
*
\r
\r
/**
\r
* Returns the value of field 'schemeName'.
\r
*
\r
- * @return String
\r
- * @return the value of field 'schemeName'.
\r
+ * @return the value of field 'SchemeName'.
\r
*/
\r
*/
\r
- public java.lang.String getSchemeName()
\r
- {
\r
+ public java.lang.String getSchemeName(
\r
+ ) {
\r
return this._schemeName;
\r
return this._schemeName;
\r
- } //-- java.lang.String getSchemeName()
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method isValid
\r
- *
\r
+ * Method isValid.
\r
*
\r
*
\r
- *
\r
- * @return boolean
\r
+ * @return true if this object is valid according to the schema
\r
*/
\r
*/
\r
- public boolean isValid()
\r
- {
\r
+ public boolean isValid(
\r
+ ) {
\r
try {
\r
validate();
\r
try {
\r
validate();
\r
- }
\r
- catch (org.exolab.castor.xml.ValidationException vex) {
\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {
\r
return false;
\r
}
\r
return true;
\r
return false;
\r
}
\r
return true;
\r
- } //-- boolean isValid()
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method marshal
\r
- *
\r
*
\r
*
\r
* @param out
\r
*
\r
*
\r
* @param out
\r
+ * @throws org.exolab.castor.xml.MarshalException if object is
\r
+ * null or if any SAXException is thrown during marshaling
\r
+ * @throws org.exolab.castor.xml.ValidationException if this
\r
+ * object is an invalid instance according to the schema
\r
*/
\r
*/
\r
- public void marshal(java.io.Writer out)
\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
- {
\r
-
\r
+ public void marshal(
\r
+ final java.io.Writer out)
\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
Marshaller.marshal(this, out);
\r
Marshaller.marshal(this, out);
\r
- } //-- void marshal(java.io.Writer)
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method marshal
\r
- *
\r
*
\r
*
\r
* @param handler
\r
*
\r
*
\r
* @param handler
\r
+ * @throws java.io.IOException if an IOException occurs during
\r
+ * marshaling
\r
+ * @throws org.exolab.castor.xml.ValidationException if this
\r
+ * object is an invalid instance according to the schema
\r
+ * @throws org.exolab.castor.xml.MarshalException if object is
\r
+ * null or if any SAXException is thrown during marshaling
\r
*/
\r
*/
\r
- public void marshal(org.xml.sax.ContentHandler handler)
\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
- {
\r
-
\r
+ public void marshal(
\r
+ final org.xml.sax.ContentHandler handler)
\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
Marshaller.marshal(this, handler);
\r
Marshaller.marshal(this, handler);
\r
- } //-- void marshal(org.xml.sax.ContentHandler)
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method removeAllColour
\r
- *
\r
*/
\r
*/
\r
- public void removeAllColour()
\r
- {
\r
- _colourList.removeAllElements();
\r
- } //-- void removeAllColour()
\r
+ public void removeAllColour(
\r
+ ) {
\r
+ this._colourList.clear();
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method removeColour
\r
- *
\r
+ * Method removeColour.
\r
*
\r
*
\r
+ * @param vColour
\r
+ * @return true if the object was removed from the collection.
\r
+ */
\r
+ public boolean removeColour(
\r
+ final Colour vColour) {
\r
+ boolean removed = _colourList.remove(vColour);
\r
+ return removed;
\r
+ }
\r
+
\r
+ /**
\r
+ * Method removeColourAt.
\r
*
\r
* @param index
\r
*
\r
* @param index
\r
- * @return Colour
\r
+ * @return the element removed from the collection
\r
*/
\r
*/
\r
- public jalview.schemabinding.version2.Colour removeColour(int index)
\r
- {
\r
- java.lang.Object obj = _colourList.elementAt(index);
\r
- _colourList.removeElementAt(index);
\r
- return (jalview.schemabinding.version2.Colour) obj;
\r
- } //-- jalview.schemabinding.version2.Colour removeColour(int)
\r
+ public Colour removeColourAt(
\r
+ final int index) {
\r
+ java.lang.Object obj = this._colourList.remove(index);
\r
+ return (Colour) obj;
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method setColour
\r
- *
\r
*
\r
*
\r
* @param index
\r
* @param vColour
\r
*
\r
*
\r
* @param index
\r
* @param vColour
\r
+ * @throws java.lang.IndexOutOfBoundsException if the index
\r
+ * given is outside the bounds of the collection
\r
*/
\r
*/
\r
- public void setColour(int index, jalview.schemabinding.version2.Colour vColour)
\r
- throws java.lang.IndexOutOfBoundsException
\r
- {
\r
- //-- check bounds for index
\r
- if ((index < 0) || (index > _colourList.size())) {
\r
- throw new IndexOutOfBoundsException();
\r
+ public void setColour(
\r
+ final int index,
\r
+ final Colour vColour)
\r
+ throws java.lang.IndexOutOfBoundsException {
\r
+ // check bounds for index
\r
+ if (index < 0 || index >= this._colourList.size()) {
\r
+ throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
\r
}
\r
}
\r
- _colourList.setElementAt(vColour, index);
\r
- } //-- void setColour(int, jalview.schemabinding.version2.Colour)
\r
+
\r
+ this._colourList.set(index, vColour);
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method setColour
\r
*
\r
*
\r
*
\r
*
\r
- *
\r
- * @param colourArray
\r
+ * @param vColourArray
\r
*/
\r
*/
\r
- public void setColour(jalview.schemabinding.version2.Colour[] colourArray)
\r
- {
\r
+ public void setColour(
\r
+ final Colour[] vColourArray) {
\r
//-- copy array
\r
//-- copy array
\r
- _colourList.removeAllElements();
\r
- for (int i = 0; i < colourArray.length; i++) {
\r
- _colourList.addElement(colourArray[i]);
\r
+ _colourList.clear();
\r
+
\r
+ for (int i = 0; i < vColourArray.length; i++) {
\r
+ this._colourList.add(vColourArray[i]);
\r
}
\r
}
\r
- } //-- void setColour(jalview.schemabinding.version2.Colour)
\r
+ }
\r
\r
/**
\r
* Sets the value of field 'schemeName'.
\r
*
\r
* @param schemeName the value of field 'schemeName'.
\r
*/
\r
\r
/**
\r
* Sets the value of field 'schemeName'.
\r
*
\r
* @param schemeName the value of field 'schemeName'.
\r
*/
\r
- public void setSchemeName(java.lang.String schemeName)
\r
- {
\r
+ public void setSchemeName(
\r
+ final java.lang.String schemeName) {
\r
this._schemeName = schemeName;
\r
this._schemeName = schemeName;
\r
- } //-- void setSchemeName(java.lang.String)
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method unmarshal
\r
- *
\r
- *
\r
+ * Method unmarshal.
\r
*
\r
* @param reader
\r
*
\r
* @param reader
\r
- * @return Object
\r
+ * @throws org.exolab.castor.xml.MarshalException if object is
\r
+ * null or if any SAXException is thrown during marshaling
\r
+ * @throws org.exolab.castor.xml.ValidationException if this
\r
+ * object is an invalid instance according to the schema
\r
+ * @return the unmarshaled
\r
+ * jalview.schemabinding.version2.JalviewUserColours
\r
*/
\r
*/
\r
- public static java.lang.Object unmarshal(java.io.Reader reader)
\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
\r
- {
\r
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
\r
+ final java.io.Reader reader)
\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
\r
return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
\r
return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewUserColours.class, reader);
\r
- } //-- java.lang.Object unmarshal(java.io.Reader)
\r
+ }
\r
\r
/**
\r
\r
/**
\r
- * Method validate
\r
*
\r
*
\r
+ *
\r
+ * @throws org.exolab.castor.xml.ValidationException if this
\r
+ * object is an invalid instance according to the schema
\r
*/
\r
*/
\r
- public void validate()
\r
- throws org.exolab.castor.xml.ValidationException
\r
- {
\r
+ public void validate(
\r
+ )
\r
+ throws org.exolab.castor.xml.ValidationException {
\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
validator.validate(this);
\r
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
\r
validator.validate(this);
\r
- } //-- void validate()
\r
+ }
\r
\r
}
\r
\r
}
\r