/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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.
*/
-
package jalview.binding;
- //---------------------------------/
- //- Imported classes and packages -/
//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.util.MessageManager;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;
*
* @version $Revision$ $Date$
*/
-public class JGroup implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private int _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _colour.
- */
- private java.lang.String _colour;
-
- /**
- * Field _consThreshold.
- */
- private int _consThreshold;
-
- /**
- * keeps track of state for field: _consThreshold
- */
- private boolean _has_consThreshold;
-
- /**
- * Field _pidThreshold.
- */
- private int _pidThreshold;
-
- /**
- * keeps track of state for field: _pidThreshold
- */
- private boolean _has_pidThreshold;
-
- /**
- * Field _outlineColour.
- */
- private int _outlineColour;
-
- /**
- * keeps track of state for field: _outlineColour
- */
- private boolean _has_outlineColour;
-
- /**
- * Field _displayBoxes.
- */
- private boolean _displayBoxes;
-
- /**
- * keeps track of state for field: _displayBoxes
- */
- private boolean _has_displayBoxes;
-
- /**
- * Field _displayText.
- */
- private boolean _displayText;
-
- /**
- * keeps track of state for field: _displayText
- */
- private boolean _has_displayText;
-
- /**
- * Field _colourText.
- */
- private boolean _colourText;
-
- /**
- * keeps track of state for field: _colourText
- */
- private boolean _has_colourText;
-
- /**
- * Field _seqList.
- */
- private java.util.Vector _seqList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JGroup() {
- super();
- this._seqList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSeq(
- final int vSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._seqList.addElement(new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addSeq(
- final int index,
- final int vSeq)
- throws java.lang.IndexOutOfBoundsException {
- this._seqList.add(index, new java.lang.Integer(vSeq));
- }
-
- /**
- */
- public void deleteColourText(
- ) {
- this._has_colourText= false;
- }
-
- /**
- */
- public void deleteConsThreshold(
- ) {
- this._has_consThreshold= false;
- }
-
- /**
- */
- public void deleteDisplayBoxes(
- ) {
- this._has_displayBoxes= false;
- }
-
- /**
- */
- public void deleteDisplayText(
- ) {
- this._has_displayText= false;
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteOutlineColour(
- ) {
- this._has_outlineColour= false;
- }
-
- /**
- */
- public void deletePidThreshold(
- ) {
- this._has_pidThreshold= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Method enumerateSeq.
- *
- * @return an Enumeration over all int elements
- */
- public java.util.Enumeration enumerateSeq(
- ) {
- return this._seqList.elements();
- }
-
- /**
- * Returns the value of field 'colour'.
- *
- * @return the value of field 'Colour'.
- */
- public java.lang.String getColour(
- ) {
- return this._colour;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean getColourText(
- ) {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold(
- ) {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean getDisplayBoxes(
- ) {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean getDisplayText(
- ) {
- return this._displayText;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public int getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * Returns the value of field 'outlineColour'.
- *
- * @return the value of field 'OutlineColour'.
- */
- public int getOutlineColour(
- ) {
- return this._outlineColour;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold(
- ) {
- return this._pidThreshold;
- }
-
- /**
- * Method getSeq.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the int at the given index
- */
- public int getSeq(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size()) {
- throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- return ((java.lang.Integer) _seqList.get(index)).intValue();
- }
-
- /**
- * Method getSeq.Returns the contents of the collection in an
- * Array.
- *
- * @return this collection as an Array
- */
- public int[] getSeq(
- ) {
- int size = this._seqList.size();
- int[] array = new int[size];
- java.util.Iterator iter = _seqList.iterator();
- for (int index = 0; index < size; index++) {
- array[index] = ((java.lang.Integer) iter.next()).intValue();
- }
- return array;
- }
-
- /**
- * Method getSeqCount.
- *
- * @return the size of this collection
- */
- public int getSeqCount(
- ) {
- return this._seqList.size();
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public int getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasColourText.
- *
- * @return true if at least one ColourText has been added
- */
- public boolean hasColourText(
- ) {
- return this._has_colourText;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold(
- ) {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasDisplayBoxes.
- *
- * @return true if at least one DisplayBoxes has been added
- */
- public boolean hasDisplayBoxes(
- ) {
- return this._has_displayBoxes;
- }
-
- /**
- * Method hasDisplayText.
- *
- * @return true if at least one DisplayText has been added
- */
- public boolean hasDisplayText(
- ) {
- return this._has_displayText;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasOutlineColour.
- *
- * @return true if at least one OutlineColour has been added
- */
- public boolean hasOutlineColour(
- ) {
- return this._has_outlineColour;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold(
- ) {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * Returns the value of field 'colourText'.
- *
- * @return the value of field 'ColourText'.
- */
- public boolean isColourText(
- ) {
- return this._colourText;
- }
-
- /**
- * Returns the value of field 'displayBoxes'.
- *
- * @return the value of field 'DisplayBoxes'.
- */
- public boolean isDisplayBoxes(
- ) {
- return this._displayBoxes;
- }
-
- /**
- * Returns the value of field 'displayText'.
- *
- * @return the value of field 'DisplayText'.
- */
- public boolean isDisplayText(
- ) {
- return this._displayText;
- }
-
- /**
- * 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 removeAllSeq(
- ) {
- this._seqList.clear();
- }
-
- /**
- * Method removeSeq.
- *
- * @param vSeq
- * @return true if the object was removed from the collection.
- */
- public boolean removeSeq(
- final int vSeq) {
- boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
- return removed;
- }
-
- /**
- * Method removeSeqAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public int removeSeqAt(
- final int index) {
- java.lang.Object obj = this._seqList.remove(index);
- return ((java.lang.Integer) obj).intValue();
- }
-
- /**
- * Sets the value of field 'colour'.
- *
- * @param colour the value of field 'colour'.
- */
- public void setColour(
- final java.lang.String colour) {
- this._colour = colour;
- }
-
- /**
- * Sets the value of field 'colourText'.
- *
- * @param colourText the value of field 'colourText'.
- */
- public void setColourText(
- final boolean colourText) {
- this._colourText = colourText;
- this._has_colourText = true;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold the value of field 'consThreshold'.
- */
- public void setConsThreshold(
- final int consThreshold) {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'displayBoxes'.
- *
- * @param displayBoxes the value of field 'displayBoxes'.
- */
- public void setDisplayBoxes(
- final boolean displayBoxes) {
- this._displayBoxes = displayBoxes;
- this._has_displayBoxes = true;
- }
-
- /**
- * Sets the value of field 'displayText'.
- *
- * @param displayText the value of field 'displayText'.
- */
- public void setDisplayText(
- final boolean displayText) {
- this._displayText = displayText;
- this._has_displayText = true;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final int end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- * Sets the value of field 'outlineColour'.
- *
- * @param outlineColour the value of field 'outlineColour'.
- */
- public void setOutlineColour(
- final int outlineColour) {
- this._outlineColour = outlineColour;
- this._has_outlineColour = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold the value of field 'pidThreshold'.
- */
- public void setPidThreshold(
- final int pidThreshold) {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vSeq
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSeq(
- final int index,
- final int vSeq)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._seqList.size()) {
- throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
- }
-
- this._seqList.set(index, new java.lang.Integer(vSeq));
- }
-
- /**
- *
- *
- * @param vSeqArray
- */
- public void setSeq(
- final int[] vSeqArray) {
- //-- copy array
- _seqList.clear();
-
- for (int i = 0; i < vSeqArray.length; i++) {
- this._seqList.add(new java.lang.Integer(vSeqArray[i]));
- }
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final int start) {
- this._start = start;
- this._has_start = 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.JGroup
- */
- public static jalview.binding.JGroup unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.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);
- }
+public class JGroup implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JGroup()
+ {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSeq(final int index, final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ */
+ public void deleteColourText()
+ {
+ this._has_colourText = false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold()
+ {
+ this._has_consThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes()
+ {
+ this._has_displayBoxes = false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText()
+ {
+ this._has_displayText = false;
+ }
+
+ /**
+ */
+ public void deleteEnd()
+ {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour()
+ {
+ this._has_outlineColour = false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold()
+ {
+ this._has_pidThreshold = false;
+ }
+
+ /**
+ */
+ public void deleteStart()
+ {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateSeq()
+ {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour()
+ {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold()
+ {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour()
+ {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold()
+ {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
+ }
+
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getSeq()
+ {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
+ for (int index = 0; index < size; index++)
+ {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount()
+ {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText()
+ {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold()
+ {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes()
+ {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText()
+ {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour()
+ {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold()
+ {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText()
+ {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes()
+ {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText()
+ {
+ return this._displayText;
+ }
+
+ /**
+ * 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 removeAllSeq()
+ {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(final int vSeq)
+ {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeSeqAt(final int index)
+ {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour
+ * the value of field 'colour'.
+ */
+ public void setColour(final java.lang.String colour)
+ {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText
+ * the value of field 'colourText'.
+ */
+ public void setColourText(final boolean colourText)
+ {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold
+ * the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(final int consThreshold)
+ {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes
+ * the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(final boolean displayBoxes)
+ {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText
+ * the value of field 'displayText'.
+ */
+ public void setDisplayText(final boolean displayText)
+ {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name)
+ {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour
+ * the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(final int outlineColour)
+ {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold
+ * the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(final int pidThreshold)
+ {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSeq(final int index, final int vSeq)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setSeq",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._seqList.size() - 1)).toString()
+ }));
+ }
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(final int[] vSeqArray)
+ {
+ // -- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++)
+ {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final int start)
+ {
+ this._start = start;
+ this._has_start = 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.JGroup
+ */
+ public static jalview.binding.JGroup unmarshal(final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(
+ jalview.binding.JGroup.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