From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Dec 2005 13:37:38 +0000 (+0000)
Subject: Save features
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=206907e81392f14925eec7759d16d6cf07460f49;p=jalview.git

Save features
---

diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
new file mode 100755
index 0000000..2ef3731
--- /dev/null
+++ b/src/jalview/binding/FeatureSettings.java
@@ -0,0 +1,274 @@
+/*
+ * 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() 
+
+}
diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java
index 4ac40d5..cbb50d5 100755
--- a/src/jalview/binding/JalviewModelSequence.java
+++ b/src/jalview/binding/JalviewModelSequence.java
@@ -60,6 +60,11 @@ public class JalviewModelSequence implements java.io.Serializable {
      */
     private java.util.Vector _treeList;
 
+    /**
+     * Field _featureSettings
+     */
+    private jalview.binding.FeatureSettings _featureSettings;
+
 
       //----------------/
      //- Constructors -/
@@ -275,6 +280,17 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateViewport() 
 
     /**
+     * Returns the value of field 'featureSettings'.
+     * 
+     * @return FeatureSettings
+     * @return the value of field 'featureSettings'.
+     */
+    public jalview.binding.FeatureSettings getFeatureSettings()
+    {
+        return this._featureSettings;
+    } //-- jalview.binding.FeatureSettings getFeatureSettings() 
+
+    /**
      * Method getJGroup
      * 
      * 
@@ -681,6 +697,16 @@ public class JalviewModelSequence implements java.io.Serializable {
     } //-- jalview.binding.Viewport removeViewport(int) 
 
     /**
+     * Sets the value of field 'featureSettings'.
+     * 
+     * @param featureSettings the value of field 'featureSettings'.
+     */
+    public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings)
+    {
+        this._featureSettings = featureSettings;
+    } //-- void setFeatureSettings(jalview.binding.FeatureSettings) 
+
+    /**
      * Method setJGroup
      * 
      * 
diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java
new file mode 100755
index 0000000..7b56676
--- /dev/null
+++ b/src/jalview/binding/Setting.java
@@ -0,0 +1,253 @@
+/*
+ * 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 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 Setting.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Setting implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _type
+     */
+    private java.lang.String _type;
+
+    /**
+     * Field _colour
+     */
+    private int _colour;
+
+    /**
+     * keeps track of state for field: _colour
+     */
+    private boolean _has_colour;
+
+    /**
+     * Field _display
+     */
+    private boolean _display;
+
+    /**
+     * keeps track of state for field: _display
+     */
+    private boolean _has_display;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Setting() {
+        super();
+    } //-- jalview.binding.Setting()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method deleteColour
+     * 
+     */
+    public void deleteColour()
+    {
+        this._has_colour= false;
+    } //-- void deleteColour() 
+
+    /**
+     * Method deleteDisplay
+     * 
+     */
+    public void deleteDisplay()
+    {
+        this._has_display= false;
+    } //-- void deleteDisplay() 
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return int
+     * @return the value of field 'colour'.
+     */
+    public int getColour()
+    {
+        return this._colour;
+    } //-- int getColour() 
+
+    /**
+     * Returns the value of field 'display'.
+     * 
+     * @return boolean
+     * @return the value of field 'display'.
+     */
+    public boolean getDisplay()
+    {
+        return this._display;
+    } //-- boolean getDisplay() 
+
+    /**
+     * Returns the value of field 'type'.
+     * 
+     * @return String
+     * @return the value of field 'type'.
+     */
+    public java.lang.String getType()
+    {
+        return this._type;
+    } //-- java.lang.String getType() 
+
+    /**
+     * Method hasColour
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasColour()
+    {
+        return this._has_colour;
+    } //-- boolean hasColour() 
+
+    /**
+     * Method hasDisplay
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasDisplay()
+    {
+        return this._has_display;
+    } //-- boolean hasDisplay() 
+
+    /**
+     * 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) 
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(int colour)
+    {
+        this._colour = colour;
+        this._has_colour = true;
+    } //-- void setColour(int) 
+
+    /**
+     * Sets the value of field 'display'.
+     * 
+     * @param display the value of field 'display'.
+     */
+    public void setDisplay(boolean display)
+    {
+        this._display = display;
+        this._has_display = true;
+    } //-- void setDisplay(boolean) 
+
+    /**
+     * Sets the value of field 'type'.
+     * 
+     * @param type the value of field 'type'.
+     */
+    public void setType(java.lang.String type)
+    {
+        this._type = type;
+    } //-- void setType(java.lang.String) 
+
+    /**
+     * 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.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.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() 
+
+}