removed explicit 'linkedAlignmentPanel' flag

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index d179ab2..8ba8b4b 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -52,17 +52,17 @@
                                                                                                                                                viewId will appear for each instance.</xs:documentation>
                                                                                                                                        </xs:annotation>
                                                                                                                                </xs:attribute>
-                                                                                                                               <xs:attribute name="linkAlignPanel" type="xs:boolean" use="optional" default="true">
+                                                                                                                               <xs:attribute name="alignwithAlignPanel" type="xs:boolean" use="optional" default="true">
                                                                                                                                <xs:annotation>
                                                                                                                                <xs:documentation>
-                                                                                                                                       Flag set if the alignment panel containing this JSeq should be explicitly linked to the Jmol view referred to/created by this structureState (since Jalview 2.7).
+                                                                                                                                       Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7).
                                                                                                                                </xs:documentation>
                                                                                                                                </xs:annotation>
                                                                                                                                </xs:attribute>
-                                                                                                                               <xs:attribute name="alignwithAlignPanel" type="xs:boolean" use="optional" default="true">
+                                                                                                                               <xs:attribute name="colourwithAlignPanel" type="xs:boolean" use="optional" default="true">
                                                                                                                                <xs:annotation>
                                                                                                                                <xs:documentation>
-                                                                                                                                       Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7).
+                                                                                                                                       Flag set if the alignment panel containing this JSeq should be included in those used to colour its associated sequences in this structureState(since Jalview 2.7).
                                                                                                                                </xs:documentation>
                                                                                                                                </xs:annotation>
                                                                                                                                </xs:attribute>

diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr
index e54b627..d1be982 100644 (file)
--- a/src/jalview/schemabinding/version2/.castor.cdr
+++ b/src/jalview/schemabinding/version2/.castor.cdr
@@ -1,4 +1,4 @@
-#Tue Feb 15 17:12:42 GMT 2011\r
+#Thu Feb 17 18:45:28 GMT 2011\r
 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
 jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 7a2b076..4432971 100644 (file)
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -95,29 +95,29 @@ public class StructureState implements java.io.Serializable {
 
     /**
      * Flag set if the alignment panel containing this JSeq should
-     * be explicitly linked to the Jmol view referred to/created by
-     * this structureState (since Jalview 2.7).
+     * be included in those used to perform a structure
+     * superposition (since Jalview 2.7).
      *  
      */
-    private boolean _linkAlignPanel = true;
+    private boolean _alignwithAlignPanel = true;
 
     /**
-     * keeps track of state for field: _linkAlignPanel
+     * keeps track of state for field: _alignwithAlignPanel
      */
-    private boolean _has_linkAlignPanel;
+    private boolean _has_alignwithAlignPanel;
 
     /**
      * Flag set if the alignment panel containing this JSeq should
-     * be included in those used to perform a structure
-     * superposition (since Jalview 2.7).
+     * be included in those used to colour its associated sequences
+     * in this structureState(since Jalview 2.7).
      *  
      */
-    private boolean _alignwithAlignPanel = true;
+    private boolean _colourwithAlignPanel = true;
 
     /**
-     * keeps track of state for field: _alignwithAlignPanel
+     * keeps track of state for field: _colourwithAlignPanel
      */
-    private boolean _has_alignwithAlignPanel;
+    private boolean _has_colourwithAlignPanel;
 
 
       //----------------/
@@ -143,16 +143,16 @@ public class StructureState implements java.io.Serializable {
 
     /**
      */
-    public void deleteHeight(
+    public void deleteColourwithAlignPanel(
     ) {
-        this._has_height= false;
+        this._has_colourwithAlignPanel= false;
     }
 
     /**
      */
-    public void deleteLinkAlignPanel(
+    public void deleteHeight(
     ) {
-        this._has_linkAlignPanel= false;
+        this._has_height= false;
     }
 
     /**
@@ -199,6 +199,21 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'colourwithAlignPanel'. The field
+     * 'colourwithAlignPanel' has the following description: Flag
+     * set if the alignment panel containing this JSeq should be
+     * included in those used to colour its associated sequences in
+     * this structureState(since Jalview 2.7).
+     *  
+     * 
+     * @return the value of field 'ColourwithAlignPanel'.
+     */
+    public boolean getColourwithAlignPanel(
+    ) {
+        return this._colourwithAlignPanel;
+    }
+
+    /**
      * Returns the value of field 'content'. The field 'content'
      * has the following description: internal content storage
      * 
@@ -220,21 +235,6 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
-     * Returns the value of field 'linkAlignPanel'. The field
-     * 'linkAlignPanel' has the following description: Flag set if
-     * the alignment panel containing this JSeq should be
-     * explicitly linked to the Jmol view referred to/created by
-     * this structureState (since Jalview 2.7).
-     *  
-     * 
-     * @return the value of field 'LinkAlignPanel'.
-     */
-    public boolean getLinkAlignPanel(
-    ) {
-        return this._linkAlignPanel;
-    }
-
-    /**
      * Returns the value of field 'viewId'. The field 'viewId' has
      * the following description: additional identifier which
      * properly disambiguates
@@ -305,23 +305,24 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
-     * Method hasHeight.
+     * Method hasColourwithAlignPanel.
      * 
-     * @return true if at least one Height has been added
+     * @return true if at least one ColourwithAlignPanel has been
+     * added
      */
-    public boolean hasHeight(
+    public boolean hasColourwithAlignPanel(
     ) {
-        return this._has_height;
+        return this._has_colourwithAlignPanel;
     }
 
     /**
-     * Method hasLinkAlignPanel.
+     * Method hasHeight.
      * 
-     * @return true if at least one LinkAlignPanel has been added
+     * @return true if at least one Height has been added
      */
-    public boolean hasLinkAlignPanel(
+    public boolean hasHeight(
     ) {
-        return this._has_linkAlignPanel;
+        return this._has_height;
     }
 
     /**
@@ -380,18 +381,18 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
-     * Returns the value of field 'linkAlignPanel'. The field
-     * 'linkAlignPanel' has the following description: Flag set if
-     * the alignment panel containing this JSeq should be
-     * explicitly linked to the Jmol view referred to/created by
-     * this structureState (since Jalview 2.7).
+     * Returns the value of field 'colourwithAlignPanel'. The field
+     * 'colourwithAlignPanel' has the following description: Flag
+     * set if the alignment panel containing this JSeq should be
+     * included in those used to colour its associated sequences in
+     * this structureState(since Jalview 2.7).
      *  
      * 
-     * @return the value of field 'LinkAlignPanel'.
+     * @return the value of field 'ColourwithAlignPanel'.
      */
-    public boolean isLinkAlignPanel(
+    public boolean isColourwithAlignPanel(
     ) {
-        return this._linkAlignPanel;
+        return this._colourwithAlignPanel;
     }
 
     /**
@@ -469,6 +470,23 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'colourwithAlignPanel'. The field
+     * 'colourwithAlignPanel' has the following description: Flag
+     * set if the alignment panel containing this JSeq should be
+     * included in those used to colour its associated sequences in
+     * this structureState(since Jalview 2.7).
+     *  
+     * 
+     * @param colourwithAlignPanel the value of field
+     * 'colourwithAlignPanel'.
+     */
+    public void setColourwithAlignPanel(
+            final boolean colourwithAlignPanel) {
+        this._colourwithAlignPanel = colourwithAlignPanel;
+        this._has_colourwithAlignPanel = true;
+    }
+
+    /**
      * Sets the value of field 'content'. The field 'content' has
      * the following description: internal content storage
      * 
@@ -491,22 +509,6 @@ public class StructureState implements java.io.Serializable {
     }
 
     /**
-     * Sets the value of field 'linkAlignPanel'. The field
-     * 'linkAlignPanel' has the following description: Flag set if
-     * the alignment panel containing this JSeq should be
-     * explicitly linked to the Jmol view referred to/created by
-     * this structureState (since Jalview 2.7).
-     *  
-     * 
-     * @param linkAlignPanel the value of field 'linkAlignPanel'.
-     */
-    public void setLinkAlignPanel(
-            final boolean linkAlignPanel) {
-        this._linkAlignPanel = linkAlignPanel;
-        this._has_linkAlignPanel = true;
-    }
-
-    /**
      * Sets the value of field 'viewId'. The field 'viewId' has the
      * following description: additional identifier which properly
      * disambiguates

diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
index 3db3b4c..fe61eb9 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
@@ -346,15 +346,15 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
             typeValidator.setWhiteSpace("preserve");\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _linkAlignPanel\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_linkAlignPanel", "linkAlignPanel", org.exolab.castor.xml.NodeType.Attribute);\r
+        //-- _alignwithAlignPanel\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
                 StructureState target = (StructureState) object;\r
-                if (!target.hasLinkAlignPanel()) { return null; }\r
-                return (target.getLinkAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+                if (!target.hasAlignwithAlignPanel()) { return null; }\r
+                return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
@@ -363,10 +363,10 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
                     StructureState target = (StructureState) object;\r
                     // if null, use delete method for optional primitives \r
                     if (value == null) {\r
-                        target.deleteLinkAlignPanel();\r
+                        target.deleteAlignwithAlignPanel();\r
                         return;\r
                     }\r
-                    target.setLinkAlignPanel( ((java.lang.Boolean) value).booleanValue());\r
+                    target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue());\r
                 } catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
@@ -379,7 +379,7 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
         desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
-        //-- validation code for: _linkAlignPanel\r
+        //-- validation code for: _alignwithAlignPanel\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         { //-- local scope\r
             org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
@@ -387,15 +387,15 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _alignwithAlignPanel\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);\r
+        //-- _colourwithAlignPanel\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourwithAlignPanel", "colourwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
                 StructureState target = (StructureState) object;\r
-                if (!target.hasAlignwithAlignPanel()) { return null; }\r
-                return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+                if (!target.hasColourwithAlignPanel()) { return null; }\r
+                return (target.getColourwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
@@ -404,10 +404,10 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
                     StructureState target = (StructureState) object;\r
                     // if null, use delete method for optional primitives \r
                     if (value == null) {\r
-                        target.deleteAlignwithAlignPanel();\r
+                        target.deleteColourwithAlignPanel();\r
                         return;\r
                     }\r
-                    target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue());\r
+                    target.setColourwithAlignPanel( ((java.lang.Boolean) value).booleanValue());\r
                 } catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
@@ -420,7 +420,7 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
         desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
-        //-- validation code for: _alignwithAlignPanel\r
+        //-- validation code for: _colourwithAlignPanel\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         { //-- local scope\r
             org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r