X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbinding%2FJalviewUserColours.java;h=9a6465b460759bd4587d32ff731f2bebd6c38c38;hb=405376d6d7002b3818d10aebc474f14134d5bbae;hp=7473bc7e8336cbf40df3df330445a75d9c46a44c;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
index 7473bc7..9a6465b 100644
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -1,27 +1,14 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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
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 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(); } - return (Colour) _colourList.get(index); - } - - /** - * Method getColour.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 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; + /** + * 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("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); + } + + 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]); + } } - 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); - } - - /** + + /** + * 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 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("setColour: Index value '" - + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); + public void setVersion( + final java.lang.String version) { + this._version = version; } - 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]); + /** + * 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.JalviewUserColours + */ + public static jalview.binding.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.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); } - } - - /** - * 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.binding.JalviewUserColours - */ - public static jalview.binding.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal( - jalview.binding.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); - } }