X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FFeatureSettings.java;h=029b4f4a12e6b87e9898f43ffebf6a3cc393f7c0;hb=7243db3d99cc1760c2d4802f3005b4f86d1b4bd6;hp=819b05d4c5f2a602757af9582e2568d95dc996a5;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java old mode 100755 new mode 100644 index 819b05d..029b4f4 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ b/src/jalview/schemabinding/version2/FeatureSettings.java @@ -1,477 +1,449 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -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. - *
- * 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 - * know 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. - *
- * 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
- * know 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);
- }
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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
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 know + * 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.
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 know + * 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); + } + +}