-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.schemabinding.version2;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class FeatureSettings.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class FeatureSettings implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _settingList.\r
- */\r
- private java.util.Vector _settingList;\r
-\r
- /**\r
- * Field _groupList.\r
- */\r
- private java.util.Vector _groupList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public FeatureSettings()\r
- {\r
- super();\r
- this._settingList = new java.util.Vector();\r
- this._groupList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addGroup(final jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._groupList.addElement(vGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addGroup(final int index,\r
- final jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._groupList.add(index, vGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSetting\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSetting(\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._settingList.addElement(vSetting);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSetting\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addSetting(final int index,\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._settingList.add(index, vSetting);\r
- }\r
-\r
- /**\r
- * Method enumerateGroup.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Group\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateGroup()\r
- {\r
- return this._groupList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateSetting.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Setting\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateSetting()\r
- {\r
- return this._settingList.elements();\r
- }\r
-\r
- /**\r
- * Method getGroup.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.Group at the given\r
- * index\r
- */\r
- public jalview.schemabinding.version2.Group getGroup(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._groupList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getGroup: Index value '" + index\r
- + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Group) _groupList.get(index);\r
- }\r
-\r
- /**\r
- * Method getGroup.Returns the contents of the collection in an Array.\r
- * <p>\r
- * Note: Just in case the collection contents are changing in another thread,\r
- * we pass a 0-length Array of the correct type into the API call. This way we\r
- * <i>know</i> that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.Group[] getGroup()\r
- {\r
- jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];\r
- return (jalview.schemabinding.version2.Group[]) this._groupList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getGroupCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getGroupCount()\r
- {\r
- return this._groupList.size();\r
- }\r
-\r
- /**\r
- * Method getSetting.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.Setting at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Setting getSetting(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._settingList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getSetting: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._settingList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Setting) _settingList.get(index);\r
- }\r
-\r
- /**\r
- * Method getSetting.Returns the contents of the collection in an Array.\r
- * <p>\r
- * Note: Just in case the collection contents are changing in another thread,\r
- * we pass a 0-length Array of the correct type into the API call. This way we\r
- * <i>know</i> that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.Setting[] getSetting()\r
- {\r
- jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];\r
- return (jalview.schemabinding.version2.Setting[]) this._settingList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getSettingCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getSettingCount()\r
- {\r
- return this._settingList.size();\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- */\r
- public void marshal(final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException\r
- * if an IOException occurs during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- */\r
- public void marshal(final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException,\r
- org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllGroup()\r
- {\r
- this._groupList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllSetting()\r
- {\r
- this._settingList.clear();\r
- }\r
-\r
- /**\r
- * Method removeGroup.\r
- * \r
- * @param vGroup\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeGroup(\r
- final jalview.schemabinding.version2.Group vGroup)\r
- {\r
- boolean removed = _groupList.remove(vGroup);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeGroupAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Group removeGroupAt(final int index)\r
- {\r
- java.lang.Object obj = this._groupList.remove(index);\r
- return (jalview.schemabinding.version2.Group) obj;\r
- }\r
-\r
- /**\r
- * Method removeSetting.\r
- * \r
- * @param vSetting\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeSetting(\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- {\r
- boolean removed = _settingList.remove(vSetting);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeSettingAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Setting removeSettingAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._settingList.remove(index);\r
- return (jalview.schemabinding.version2.Setting) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vGroup\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setGroup(final int index,\r
- final jalview.schemabinding.version2.Group vGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._groupList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setGroup: Index value '" + index\r
- + "' not in range [0.." + (this._groupList.size() - 1) + "]");\r
- }\r
-\r
- this._groupList.set(index, vGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vGroupArray\r
- */\r
- public void setGroup(\r
- final jalview.schemabinding.version2.Group[] vGroupArray)\r
- {\r
- // -- copy array\r
- _groupList.clear();\r
-\r
- for (int i = 0; i < vGroupArray.length; i++)\r
- {\r
- this._groupList.add(vGroupArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vSetting\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setSetting(final int index,\r
- final jalview.schemabinding.version2.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._settingList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setSetting: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._settingList.size() - 1) + "]");\r
- }\r
-\r
- this._settingList.set(index, vSetting);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSettingArray\r
- */\r
- public void setSetting(\r
- final jalview.schemabinding.version2.Setting[] vSettingArray)\r
- {\r
- // -- copy array\r
- _settingList.clear();\r
-\r
- for (int i = 0; i < vSettingArray.length; i++)\r
- {\r
- this._settingList.add(vSettingArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- * @return the unmarshaled jalview.schemabinding.version2.FeatureSettings\r
- */\r
- public static jalview.schemabinding.version2.FeatureSettings unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.FeatureSettings.class,\r
- reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the schema\r
- */\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class FeatureSettings.
+ *
+ * @version $Revision$ $Date$
+ */
+public class FeatureSettings implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _settingList.
+ */
+ private java.util.Vector _settingList;
+
+ /**
+ * Field _groupList.
+ */
+ private java.util.Vector _groupList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public FeatureSettings()
+ {
+ super();
+ this._settingList = new java.util.Vector();
+ this._groupList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addGroup(final jalview.schemabinding.version2.Group vGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._groupList.addElement(vGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addGroup(final int index,
+ final jalview.schemabinding.version2.Group vGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._groupList.add(index, vGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final jalview.schemabinding.version2.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._settingList.addElement(vSetting);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addSetting(final int index,
+ final jalview.schemabinding.version2.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._settingList.add(index, vSetting);
+ }
+
+ /**
+ * Method enumerateGroup.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Group
+ * elements
+ */
+ public java.util.Enumeration enumerateGroup()
+ {
+ return this._groupList.elements();
+ }
+
+ /**
+ * Method enumerateSetting.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.Setting
+ * elements
+ */
+ public java.util.Enumeration enumerateSetting()
+ {
+ return this._settingList.elements();
+ }
+
+ /**
+ * Method getGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Group at the given
+ * index
+ */
+ public jalview.schemabinding.version2.Group getGroup(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._groupList.size())
+ {
+ throw new IndexOutOfBoundsException("getGroup: Index value '" + index
+ + "' not in range [0.." + (this._groupList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Group) _groupList.get(index);
+ }
+
+ /**
+ * Method getGroup.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 jalview.schemabinding.version2.Group[] getGroup()
+ {
+ jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0];
+ return (jalview.schemabinding.version2.Group[]) this._groupList
+ .toArray(array);
+ }
+
+ /**
+ * Method getGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getGroupCount()
+ {
+ return this._groupList.size();
+ }
+
+ /**
+ * Method getSetting.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the jalview.schemabinding.version2.Setting at the
+ * given index
+ */
+ public jalview.schemabinding.version2.Setting getSetting(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size())
+ {
+ throw new IndexOutOfBoundsException("getSetting: Index value '"
+ + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Setting) _settingList.get(index);
+ }
+
+ /**
+ * Method getSetting.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 jalview.schemabinding.version2.Setting[] getSetting()
+ {
+ jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0];
+ return (jalview.schemabinding.version2.Setting[]) this._settingList
+ .toArray(array);
+ }
+
+ /**
+ * Method getSettingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSettingCount()
+ {
+ return this._settingList.size();
+ }
+
+ /**
+ * 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 removeAllGroup()
+ {
+ this._groupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSetting()
+ {
+ this._settingList.clear();
+ }
+
+ /**
+ * Method removeGroup.
+ *
+ * @param vGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeGroup(
+ final jalview.schemabinding.version2.Group vGroup)
+ {
+ boolean removed = _groupList.remove(vGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Group removeGroupAt(final int index)
+ {
+ java.lang.Object obj = this._groupList.remove(index);
+ return (jalview.schemabinding.version2.Group) obj;
+ }
+
+ /**
+ * Method removeSetting.
+ *
+ * @param vSetting
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSetting(
+ final jalview.schemabinding.version2.Setting vSetting)
+ {
+ boolean removed = _settingList.remove(vSetting);
+ return removed;
+ }
+
+ /**
+ * Method removeSettingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Setting removeSettingAt(
+ final int index)
+ {
+ java.lang.Object obj = this._settingList.remove(index);
+ return (jalview.schemabinding.version2.Setting) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vGroup
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setGroup(final int index,
+ final jalview.schemabinding.version2.Group vGroup)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._groupList.size())
+ {
+ throw new IndexOutOfBoundsException("setGroup: Index value '" + index
+ + "' not in range [0.." + (this._groupList.size() - 1) + "]");
+ }
+
+ this._groupList.set(index, vGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vGroupArray
+ */
+ public void setGroup(
+ final jalview.schemabinding.version2.Group[] vGroupArray)
+ {
+ // -- copy array
+ _groupList.clear();
+
+ for (int i = 0; i < vGroupArray.length; i++)
+ {
+ this._groupList.add(vGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setSetting(final int index,
+ final jalview.schemabinding.version2.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size())
+ {
+ throw new IndexOutOfBoundsException("setSetting: Index value '"
+ + index + "' not in range [0.."
+ + (this._settingList.size() - 1) + "]");
+ }
+
+ this._settingList.set(index, vSetting);
+ }
+
+ /**
+ *
+ *
+ * @param vSettingArray
+ */
+ public void setSetting(
+ final jalview.schemabinding.version2.Setting[] vSettingArray)
+ {
+ // -- copy array
+ _settingList.clear();
+
+ for (int i = 0; i < vSettingArray.length; i++)
+ {
+ this._settingList.add(vSettingArray[i]);
+ }
+ }
+
+ /**
+ * 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.schemabinding.version2.FeatureSettings
+ */
+ public static jalview.schemabinding.version2.FeatureSettings unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.FeatureSettings.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