Save features

diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
new file mode 100755 (executable)
index 0000000..2ef3731
--- /dev/null
+++ b/src/jalview/binding/FeatureSettings.java
@@ -0,0 +1,274 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class FeatureSettings.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class FeatureSettings implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _settingList\r
+     */\r
+    private java.util.Vector _settingList;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public FeatureSettings() {\r
+        super();\r
+        _settingList = new Vector();\r
+    } //-- jalview.binding.FeatureSettings()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method addSetting\r
+     * \r
+     * \r
+     * \r
+     * @param vSetting\r
+     */\r
+    public void addSetting(jalview.binding.Setting vSetting)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _settingList.addElement(vSetting);\r
+    } //-- void addSetting(jalview.binding.Setting) \r
+\r
+    /**\r
+     * Method addSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSetting\r
+     */\r
+    public void addSetting(int index, jalview.binding.Setting vSetting)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _settingList.insertElementAt(vSetting, index);\r
+    } //-- void addSetting(int, jalview.binding.Setting) \r
+\r
+    /**\r
+     * Method enumerateSetting\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateSetting()\r
+    {\r
+        return _settingList.elements();\r
+    } //-- java.util.Enumeration enumerateSetting() \r
+\r
+    /**\r
+     * Method getSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Setting\r
+     */\r
+    public jalview.binding.Setting getSetting(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _settingList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.binding.Setting) _settingList.elementAt(index);\r
+    } //-- jalview.binding.Setting getSetting(int) \r
+\r
+    /**\r
+     * Method getSetting\r
+     * \r
+     * \r
+     * \r
+     * @return Setting\r
+     */\r
+    public jalview.binding.Setting[] getSetting()\r
+    {\r
+        int size = _settingList.size();\r
+        jalview.binding.Setting[] mArray = new jalview.binding.Setting[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.binding.Setting) _settingList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.binding.Setting[] getSetting() \r
+\r
+    /**\r
+     * Method getSettingCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getSettingCount()\r
+    {\r
+        return _settingList.size();\r
+    } //-- int getSettingCount() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Method removeAllSetting\r
+     * \r
+     */\r
+    public void removeAllSetting()\r
+    {\r
+        _settingList.removeAllElements();\r
+    } //-- void removeAllSetting() \r
+\r
+    /**\r
+     * Method removeSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return Setting\r
+     */\r
+    public jalview.binding.Setting removeSetting(int index)\r
+    {\r
+        java.lang.Object obj = _settingList.elementAt(index);\r
+        _settingList.removeElementAt(index);\r
+        return (jalview.binding.Setting) obj;\r
+    } //-- jalview.binding.Setting removeSetting(int) \r
+\r
+    /**\r
+     * Method setSetting\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vSetting\r
+     */\r
+    public void setSetting(int index, jalview.binding.Setting vSetting)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _settingList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _settingList.setElementAt(vSetting, index);\r
+    } //-- void setSetting(int, jalview.binding.Setting) \r
+\r
+    /**\r
+     * Method setSetting\r
+     * \r
+     * \r
+     * \r
+     * @param settingArray\r
+     */\r
+    public void setSetting(jalview.binding.Setting[] settingArray)\r
+    {\r
+        //-- copy array\r
+        _settingList.removeAllElements();\r
+        for (int i = 0; i < settingArray.length; i++) {\r
+            _settingList.addElement(settingArray[i]);\r
+        }\r
+    } //-- void setSetting(jalview.binding.Setting) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        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
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 4ac40d5..cbb50d5 100755 (executable)
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -60,6 +60,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      */\r
     private java.util.Vector _treeList;\r
 \r
+    /**\r
+     * Field _featureSettings\r
+     */\r
+    private jalview.binding.FeatureSettings _featureSettings;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -275,6 +280,17 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateViewport() \r
 \r
     /**\r
+     * Returns the value of field 'featureSettings'.\r
+     * \r
+     * @return FeatureSettings\r
+     * @return the value of field 'featureSettings'.\r
+     */\r
+    public jalview.binding.FeatureSettings getFeatureSettings()\r
+    {\r
+        return this._featureSettings;\r
+    } //-- jalview.binding.FeatureSettings getFeatureSettings() \r
+\r
+    /**\r
      * Method getJGroup\r
      * \r
      * \r
@@ -681,6 +697,16 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.Viewport removeViewport(int) \r
 \r
     /**\r
+     * Sets the value of field 'featureSettings'.\r
+     * \r
+     * @param featureSettings the value of field 'featureSettings'.\r
+     */\r
+    public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings)\r
+    {\r
+        this._featureSettings = featureSettings;\r
+    } //-- void setFeatureSettings(jalview.binding.FeatureSettings) \r
+\r
+    /**\r
      * Method setJGroup\r
      * \r
      * \r

diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java
new file mode 100755 (executable)
index 0000000..7b56676
--- /dev/null
+++ b/src/jalview/binding/Setting.java
@@ -0,0 +1,253 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Setting.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Setting implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _type\r
+     */\r
+    private java.lang.String _type;\r
+\r
+    /**\r
+     * Field _colour\r
+     */\r
+    private int _colour;\r
+\r
+    /**\r
+     * keeps track of state for field: _colour\r
+     */\r
+    private boolean _has_colour;\r
+\r
+    /**\r
+     * Field _display\r
+     */\r
+    private boolean _display;\r
+\r
+    /**\r
+     * keeps track of state for field: _display\r
+     */\r
+    private boolean _has_display;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public Setting() {\r
+        super();\r
+    } //-- jalview.binding.Setting()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteColour\r
+     * \r
+     */\r
+    public void deleteColour()\r
+    {\r
+        this._has_colour= false;\r
+    } //-- void deleteColour() \r
+\r
+    /**\r
+     * Method deleteDisplay\r
+     * \r
+     */\r
+    public void deleteDisplay()\r
+    {\r
+        this._has_display= false;\r
+    } //-- void deleteDisplay() \r
+\r
+    /**\r
+     * Returns the value of field 'colour'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'colour'.\r
+     */\r
+    public int getColour()\r
+    {\r
+        return this._colour;\r
+    } //-- int getColour() \r
+\r
+    /**\r
+     * Returns the value of field 'display'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'display'.\r
+     */\r
+    public boolean getDisplay()\r
+    {\r
+        return this._display;\r
+    } //-- boolean getDisplay() \r
+\r
+    /**\r
+     * Returns the value of field 'type'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'type'.\r
+     */\r
+    public java.lang.String getType()\r
+    {\r
+        return this._type;\r
+    } //-- java.lang.String getType() \r
+\r
+    /**\r
+     * Method hasColour\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasColour()\r
+    {\r
+        return this._has_colour;\r
+    } //-- boolean hasColour() \r
+\r
+    /**\r
+     * Method hasDisplay\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasDisplay()\r
+    {\r
+        return this._has_display;\r
+    } //-- boolean hasDisplay() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'colour'.\r
+     * \r
+     * @param colour the value of field 'colour'.\r
+     */\r
+    public void setColour(int colour)\r
+    {\r
+        this._colour = colour;\r
+        this._has_colour = true;\r
+    } //-- void setColour(int) \r
+\r
+    /**\r
+     * Sets the value of field 'display'.\r
+     * \r
+     * @param display the value of field 'display'.\r
+     */\r
+    public void setDisplay(boolean display)\r
+    {\r
+        this._display = display;\r
+        this._has_display = true;\r
+    } //-- void setDisplay(boolean) \r
+\r
+    /**\r
+     * Sets the value of field 'type'.\r
+     * \r
+     * @param type the value of field 'type'.\r
+     */\r
+    public void setType(java.lang.String type)\r
+    {\r
+        this._type = type;\r
+    } //-- void setType(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        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
+    } //-- void validate() \r
+\r
+}\r