X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FJalviewUserColours.java;h=67ee5a2cb1cafd8ef08c167596622abbc545ce1a;hb=bb620cae1e4c44ae9efaf975c7bbbc63b0558db3;hp=822392e1b18582be50c840629b2768ba8b84a3b7;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java old mode 100755 new mode 100644 index 822392e..67ee5a2 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,26 +1,15 @@ /* - * 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 + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -43,10 +32,21 @@ public class JalviewUserColours implements java.io.Serializable private java.lang.String _schemeName; /** + * Jalview colour scheme document version. + * + */ + private java.lang.String _version; + + /** * Field _colourList. */ private java.util.Vector _colourList; + /** + * Field _filterList. + */ + private java.util.Vector _filterList; + // ----------------/ // - Constructors -/ // ----------------/ @@ -55,6 +55,7 @@ public class JalviewUserColours implements java.io.Serializable { super(); this._colourList = new java.util.Vector(); + this._filterList = new java.util.Vector(); } // -----------/ @@ -66,7 +67,7 @@ public class JalviewUserColours implements java.io.Serializable * * @param vColour * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addColour(final Colour vColour) throws java.lang.IndexOutOfBoundsException @@ -80,7 +81,7 @@ public class JalviewUserColours implements java.io.Serializable * @param index * @param vColour * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addColour(final int index, final Colour vColour) throws java.lang.IndexOutOfBoundsException @@ -89,6 +90,33 @@ public class JalviewUserColours implements java.io.Serializable } /** + * + * + * @param vFilter + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addFilter(final Filter vFilter) + throws java.lang.IndexOutOfBoundsException + { + this._filterList.addElement(vFilter); + } + + /** + * + * + * @param index + * @param vFilter + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addFilter(final int index, final Filter vFilter) + throws java.lang.IndexOutOfBoundsException + { + this._filterList.add(index, vFilter); + } + + /** * Method enumerateColour. * * @return an Enumeration over all Colour elements @@ -99,11 +127,21 @@ public class JalviewUserColours implements java.io.Serializable } /** + * Method enumerateFilter. + * + * @return an Enumeration over all Filter elements + */ + public java.util.Enumeration enumerateFilter() + { + return this._filterList.elements(); + } + + /** * Method getColour. * * @param index * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * 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) @@ -112,9 +150,9 @@ public class JalviewUserColours implements java.io.Serializable // check bounds for index if (index < 0 || index >= this._colourList.size()) { - throw new IndexOutOfBoundsException("getColour: Index value '" - + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); + throw new IndexOutOfBoundsException( + "getColour: Index value '" + index + "' not in range [0.." + + (this._colourList.size() - 1) + "]"); } return (Colour) _colourList.get(index); @@ -146,6 +184,53 @@ public class JalviewUserColours implements java.io.Serializable } /** + * Method getFilter. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the Filter at the given index + */ + public Filter getFilter(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._filterList.size()) + { + throw new IndexOutOfBoundsException( + "getFilter: Index value '" + index + "' not in range [0.." + + (this._filterList.size() - 1) + "]"); + } + + return (Filter) _filterList.get(index); + } + + /** + * Method getFilter.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 Filter[] getFilter() + { + Filter[] array = new Filter[0]; + return (Filter[]) this._filterList.toArray(array); + } + + /** + * Method getFilterCount. + * + * @return the size of this collection + */ + public int getFilterCount() + { + return this._filterList.size(); + } + + /** * Returns the value of field 'schemeName'. * * @return the value of field 'SchemeName'. @@ -156,6 +241,18 @@ public class JalviewUserColours implements java.io.Serializable } /** + * 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 @@ -177,11 +274,10 @@ public class JalviewUserColours implements java.io.Serializable * * @param out * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * 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 + * 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, @@ -195,13 +291,12 @@ public class JalviewUserColours implements java.io.Serializable * * @param handler * @throws java.io.IOException - * if an IOException occurs during marshaling + * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * 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 + * 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, @@ -219,6 +314,13 @@ public class JalviewUserColours implements java.io.Serializable } /** + */ + public void removeAllFilter() + { + this._filterList.clear(); + } + + /** * Method removeColour. * * @param vColour @@ -243,12 +345,36 @@ public class JalviewUserColours implements java.io.Serializable } /** + * Method removeFilter. + * + * @param vFilter + * @return true if the object was removed from the collection. + */ + public boolean removeFilter(final Filter vFilter) + { + boolean removed = _filterList.remove(vFilter); + return removed; + } + + /** + * Method removeFilterAt. + * + * @param index + * @return the element removed from the collection + */ + public Filter removeFilterAt(final int index) + { + java.lang.Object obj = this._filterList.remove(index); + return (Filter) obj; + } + + /** * * * @param index * @param vColour * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void setColour(final int index, final Colour vColour) throws java.lang.IndexOutOfBoundsException @@ -256,9 +382,9 @@ public class JalviewUserColours implements java.io.Serializable // 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) + "]"); + throw new IndexOutOfBoundsException( + "setColour: Index value '" + index + "' not in range [0.." + + (this._colourList.size() - 1) + "]"); } this._colourList.set(index, vColour); @@ -281,10 +407,48 @@ public class JalviewUserColours implements java.io.Serializable } /** + * + * + * @param index + * @param vFilter + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setFilter(final int index, final Filter vFilter) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._filterList.size()) + { + throw new IndexOutOfBoundsException( + "setFilter: Index value '" + index + "' not in range [0.." + + (this._filterList.size() - 1) + "]"); + } + + this._filterList.set(index, vFilter); + } + + /** + * + * + * @param vFilterArray + */ + public void setFilter(final Filter[] vFilterArray) + { + // -- copy array + _filterList.clear(); + + for (int i = 0; i < vFilterArray.length; i++) + { + this._filterList.add(vFilterArray[i]); + } + } + + /** * Sets the value of field 'schemeName'. * * @param schemeName - * the value of field 'schemeName'. + * the value of field 'schemeName'. */ public void setSchemeName(final java.lang.String schemeName) { @@ -292,15 +456,27 @@ public class JalviewUserColours implements java.io.Serializable } /** + * 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 + * 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 + * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.binding.JalviewUserColours */ public static jalview.binding.JalviewUserColours unmarshal( @@ -308,16 +484,15 @@ public class JalviewUserColours implements java.io.Serializable throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal( - jalview.binding.JalviewUserColours.class, reader); + 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 + * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException {