removed explicit 'linkedAlignmentPanel' flag

[jalview.git] / src / jalview / schemabinding / version2 / StructureState.java

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