X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FFeatureSettings.java;h=ec7001d9b458981fdbd727e229581d69e15073cb;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=2ef3731d228d11a975dc00ebc7652f9ac7411a88;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
old mode 100755
new mode 100644
index 2ef3731..ec7001d
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -1,274 +1,292 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, 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 FeatureSettings.
- * 
- * @version $Revision$ $Date$
- */
-public class FeatureSettings implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _settingList
-     */
-    private java.util.Vector _settingList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public FeatureSettings() {
-        super();
-        _settingList = new Vector();
-    } //-- jalview.binding.FeatureSettings()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addSetting
-     * 
-     * 
-     * 
-     * @param vSetting
-     */
-    public void addSetting(jalview.binding.Setting vSetting)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _settingList.addElement(vSetting);
-    } //-- void addSetting(jalview.binding.Setting) 
-
-    /**
-     * Method addSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     */
-    public void addSetting(int index, jalview.binding.Setting vSetting)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _settingList.insertElementAt(vSetting, index);
-    } //-- void addSetting(int, jalview.binding.Setting) 
-
-    /**
-     * Method enumerateSetting
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateSetting()
-    {
-        return _settingList.elements();
-    } //-- java.util.Enumeration enumerateSetting() 
-
-    /**
-     * Method getSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @return Setting
-     */
-    public jalview.binding.Setting getSetting(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _settingList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.Setting) _settingList.elementAt(index);
-    } //-- jalview.binding.Setting getSetting(int) 
-
-    /**
-     * Method getSetting
-     * 
-     * 
-     * 
-     * @return Setting
-     */
-    public jalview.binding.Setting[] getSetting()
-    {
-        int size = _settingList.size();
-        jalview.binding.Setting[] mArray = new jalview.binding.Setting[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.Setting) _settingList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.Setting[] getSetting() 
-
-    /**
-     * Method getSettingCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getSettingCount()
-    {
-        return _settingList.size();
-    } //-- int getSettingCount() 
-
-    /**
-     * 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 removeAllSetting
-     * 
-     */
-    public void removeAllSetting()
-    {
-        _settingList.removeAllElements();
-    } //-- void removeAllSetting() 
-
-    /**
-     * Method removeSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @return Setting
-     */
-    public jalview.binding.Setting removeSetting(int index)
-    {
-        java.lang.Object obj = _settingList.elementAt(index);
-        _settingList.removeElementAt(index);
-        return (jalview.binding.Setting) obj;
-    } //-- jalview.binding.Setting removeSetting(int) 
-
-    /**
-     * Method setSetting
-     * 
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     */
-    public void setSetting(int index, jalview.binding.Setting vSetting)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _settingList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _settingList.setElementAt(vSetting, index);
-    } //-- void setSetting(int, jalview.binding.Setting) 
-
-    /**
-     * Method setSetting
-     * 
-     * 
-     * 
-     * @param settingArray
-     */
-    public void setSetting(jalview.binding.Setting[] settingArray)
-    {
-        //-- copy array
-        _settingList.removeAllElements();
-        for (int i = 0; i < settingArray.length; i++) {
-            _settingList.addElement(settingArray[i]);
-        }
-    } //-- void setSetting(jalview.binding.Setting) 
-
-    /**
-     * 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.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.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 2.7)
+ * 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 <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+  //---------------------------------/
+ //- 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;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public FeatureSettings() {
+        super();
+        this._settingList = new java.util.Vector();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * 
+     * 
+     * @param vSetting
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addSetting(
+            final jalview.binding.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.binding.Setting vSetting)
+    throws java.lang.IndexOutOfBoundsException {
+        this._settingList.add(index, vSetting);
+    }
+
+    /**
+     * Method enumerateSetting.
+     * 
+     * @return an Enumeration over all jalview.binding.Setting
+     * elements
+     */
+    public java.util.Enumeration enumerateSetting(
+    ) {
+        return this._settingList.elements();
+    }
+
+    /**
+     * 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.binding.Setting at the
+     * given index
+     */
+    public jalview.binding.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.binding.Setting) _settingList.get(index);
+    }
+
+    /**
+     * Method getSetting.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 jalview.binding.Setting[] getSetting(
+    ) {
+        jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+        return (jalview.binding.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 removeAllSetting(
+    ) {
+        this._settingList.clear();
+    }
+
+    /**
+     * Method removeSetting.
+     * 
+     * @param vSetting
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeSetting(
+            final jalview.binding.Setting vSetting) {
+        boolean removed = _settingList.remove(vSetting);
+        return removed;
+    }
+
+    /**
+     * Method removeSettingAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.Setting removeSettingAt(
+            final int index) {
+        java.lang.Object obj = this._settingList.remove(index);
+        return (jalview.binding.Setting) obj;
+    }
+
+    /**
+     * 
+     * 
+     * @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.binding.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.binding.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.binding.FeatureSettings
+     */
+    public static jalview.binding.FeatureSettings unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.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);
+    }
+
+}