X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbinding%2FJalviewUserColours.java;h=64f5477d50c02bbc1e7b01ccc9958a368ce5c5cd;hb=5964cc48187a5dbf0544f3058c09d553c845afa0;hp=676a62358dc47c9b53aa43d389f357713f9fa214;hpb=5a35786bf1c4219bfa00603036497a18486c6801;p=jalview.git
diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java
old mode 100755
new mode 100644
index 676a623..64f5477
--- a/src/jalview/binding/JalviewUserColours.java
+++ b/src/jalview/binding/JalviewUserColours.java
@@ -1,274 +1,354 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class JalviewUserColours.
- *
- * @version $Revision$ $Date$
- */
-public class JalviewUserColours implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _colourList
- */
- private java.util.Vector _colourList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public JalviewUserColours() {
- super();
- _colourList = new Vector();
- } //-- jalview.binding.JalviewUserColours()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addColour
- *
- *
- *
- * @param vColour
- */
- public void addColour(jalview.binding.Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- _colourList.addElement(vColour);
- } //-- void addColour(jalview.binding.Colour)
-
- /**
- * Method addColour
- *
- *
- *
- * @param index
- * @param vColour
- */
- public void addColour(int index, jalview.binding.Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- _colourList.insertElementAt(vColour, index);
- } //-- void addColour(int, jalview.binding.Colour)
-
- /**
- * Method enumerateColour
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateColour()
- {
- return _colourList.elements();
- } //-- java.util.Enumeration enumerateColour()
-
- /**
- * Method getColour
- *
- *
- *
- * @param index
- * @return Colour
- */
- public jalview.binding.Colour getColour(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _colourList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.binding.Colour) _colourList.elementAt(index);
- } //-- jalview.binding.Colour getColour(int)
-
- /**
- * Method getColour
- *
- *
- *
- * @return Colour
- */
- public jalview.binding.Colour[] getColour()
- {
- int size = _colourList.size();
- jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);
- }
- return mArray;
- } //-- jalview.binding.Colour[] getColour()
-
- /**
- * Method getColourCount
- *
- *
- *
- * @return int
- */
- public int getColourCount()
- {
- return _colourList.size();
- } //-- int getColourCount()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllColour
- *
- */
- public void removeAllColour()
- {
- _colourList.removeAllElements();
- } //-- void removeAllColour()
-
- /**
- * Method removeColour
- *
- *
- *
- * @param index
- * @return Colour
- */
- public jalview.binding.Colour removeColour(int index)
- {
- java.lang.Object obj = _colourList.elementAt(index);
- _colourList.removeElementAt(index);
- return (jalview.binding.Colour) obj;
- } //-- jalview.binding.Colour removeColour(int)
-
- /**
- * Method setColour
- *
- *
- *
- * @param index
- * @param vColour
- */
- public void setColour(int index, jalview.binding.Colour vColour)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _colourList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _colourList.setElementAt(vColour, index);
- } //-- void setColour(int, jalview.binding.Colour)
-
- /**
- * Method setColour
- *
- *
- *
- * @param colourArray
- */
- public void setColour(jalview.binding.Colour[] colourArray)
- {
- //-- copy array
- _colourList.removeAllElements();
- for (int i = 0; i < colourArray.length; i++) {
- _colourList.addElement(colourArray[i]);
- }
- } //-- void setColour(jalview.binding.Colour)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 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("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]); + } + } + + /** + * 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); + } + +}