-/*\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 JalviewUserColours.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewUserColours implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _schemeName.\r
- */\r
- private java.lang.String _schemeName;\r
-\r
- /**\r
- * Jalview colour scheme document version.\r
- * \r
- */\r
- private java.lang.String _version;\r
-\r
- /**\r
- * Field _colourList.\r
- */\r
- private java.util.Vector _colourList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public JalviewUserColours()\r
- {\r
- super();\r
- this._colourList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vColour\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addColour(final Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._colourList.addElement(vColour);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vColour\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addColour(final int index, final Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._colourList.add(index, vColour);\r
- }\r
-\r
- /**\r
- * Method enumerateColour.\r
- * \r
- * @return an Enumeration over all Colour elements\r
- */\r
- public java.util.Enumeration enumerateColour()\r
- {\r
- return this._colourList.elements();\r
- }\r
-\r
- /**\r
- * Method getColour.\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 Colour at the given index\r
- */\r
- public Colour getColour(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._colourList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getColour: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._colourList.size() - 1) + "]");\r
- }\r
-\r
- return (Colour) _colourList.get(index);\r
- }\r
-\r
- /**\r
- * Method getColour.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 Colour[] getColour()\r
- {\r
- Colour[] array = new Colour[0];\r
- return (Colour[]) this._colourList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getColourCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getColourCount()\r
- {\r
- return this._colourList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'schemeName'.\r
- * \r
- * @return the value of field 'SchemeName'.\r
- */\r
- public java.lang.String getSchemeName()\r
- {\r
- return this._schemeName;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'version'. The field 'version' has the following\r
- * description: Jalview colour scheme document version.\r
- * \r
- * \r
- * @return the value of field 'Version'.\r
- */\r
- public java.lang.String getVersion()\r
- {\r
- return this._version;\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 removeAllColour()\r
- {\r
- this._colourList.clear();\r
- }\r
-\r
- /**\r
- * Method removeColour.\r
- * \r
- * @param vColour\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeColour(final Colour vColour)\r
- {\r
- boolean removed = _colourList.remove(vColour);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeColourAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public Colour removeColourAt(final int index)\r
- {\r
- java.lang.Object obj = this._colourList.remove(index);\r
- return (Colour) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vColour\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setColour(final int index, final Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._colourList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setColour: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._colourList.size() - 1) + "]");\r
- }\r
-\r
- this._colourList.set(index, vColour);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vColourArray\r
- */\r
- public void setColour(final Colour[] vColourArray)\r
- {\r
- // -- copy array\r
- _colourList.clear();\r
-\r
- for (int i = 0; i < vColourArray.length; i++)\r
- {\r
- this._colourList.add(vColourArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'schemeName'.\r
- * \r
- * @param schemeName\r
- * the value of field 'schemeName'.\r
- */\r
- public void setSchemeName(final java.lang.String schemeName)\r
- {\r
- this._schemeName = schemeName;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'version'. The field 'version' has the following\r
- * description: Jalview colour scheme document version.\r
- * \r
- * \r
- * @param version\r
- * the value of field 'version'.\r
- */\r
- public void setVersion(final java.lang.String version)\r
- {\r
- this._version = version;\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.JalviewUserColours\r
- */\r
- public static jalview.schemabinding.version2.JalviewUserColours 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.JalviewUserColours) Unmarshaller\r
- .unmarshal(\r
- jalview.schemabinding.version2.JalviewUserColours.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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.util.MessageManager;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewUserColours.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JalviewUserColours implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _schemeName.
+ */
+ private java.lang.String _schemeName;
+
+ /**
+ * Jalview colour scheme document version.
+ *
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _colourList.
+ */
+ private java.util.Vector _colourList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public JalviewUserColours()
+ {
+ super();
+ this._colourList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addColour(final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._colourList.addElement(vColour);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addColour(final int index, final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._colourList.add(index, vColour);
+ }
+
+ /**
+ * Method enumerateColour.
+ *
+ * @return an Enumeration over all Colour elements
+ */
+ public java.util.Enumeration enumerateColour()
+ {
+ return this._colourList.elements();
+ }
+
+ /**
+ * Method getColour.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the Colour at the given index
+ */
+ public Colour getColour(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getColour",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._colourList.size() - 1)).toString()
+ }));
+ }
+
+ return (Colour) _colourList.get(index);
+ }
+
+ /**
+ * Method getColour.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 Colour[] getColour()
+ {
+ Colour[] array = new Colour[0];
+ return (Colour[]) this._colourList.toArray(array);
+ }
+
+ /**
+ * Method getColourCount.
+ *
+ * @return the size of this collection
+ */
+ public int getColourCount()
+ {
+ return this._colourList.size();
+ }
+
+ /**
+ * Returns the value of field 'schemeName'.
+ *
+ * @return the value of field 'SchemeName'.
+ */
+ public java.lang.String getSchemeName()
+ {
+ return this._schemeName;
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion()
+ {
+ return this._version;
+ }
+
+ /**
+ * 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 removeAllColour()
+ {
+ this._colourList.clear();
+ }
+
+ /**
+ * Method removeColour.
+ *
+ * @param vColour
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeColour(final Colour vColour)
+ {
+ boolean removed = _colourList.remove(vColour);
+ return removed;
+ }
+
+ /**
+ * Method removeColourAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Colour removeColourAt(final int index)
+ {
+ java.lang.Object obj = this._colourList.remove(index);
+ return (Colour) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setColour(final int index, final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size())
+ {
+ throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setColour",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._colourList.size() - 1)).toString()
+ }));
+ }
+
+ this._colourList.set(index, vColour);
+ }
+
+ /**
+ *
+ *
+ * @param vColourArray
+ */
+ public void setColour(final Colour[] vColourArray)
+ {
+ // -- copy array
+ _colourList.clear();
+
+ for (int i = 0; i < vColourArray.length; i++)
+ {
+ this._colourList.add(vColourArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'schemeName'.
+ *
+ * @param schemeName
+ * the value of field 'schemeName'.
+ */
+ public void setSchemeName(final java.lang.String schemeName)
+ {
+ this._schemeName = schemeName;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Jalview colour scheme document version.
+ *
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version)
+ {
+ this._version = version;
+ }
+
+ /**
+ * 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.JalviewUserColours
+ */
+ public static jalview.schemabinding.version2.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller
+ .unmarshal(
+ jalview.schemabinding.version2.JalviewUserColours.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