JAL-1690 scaleProteinAsCdna new optional attribute on Viewport in

project file

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index f60bb6a..850b223 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -430,6 +430,7 @@
                                                <xs:attribute name="fontName" type="xs:string" />
                                                <xs:attribute name="fontSize" type="xs:int" />
                                                <xs:attribute name="fontStyle" type="xs:int" />
+                                               <xs:attribute name="scaleProteinAsCdna" type="xs:boolean" use="optional" default="true" />
                                                <xs:attribute name="viewName" type="xs:string" />
                                                <xs:attribute name="sequenceSetId" type="xs:string" />
                                                <xs:attribute name="gatheredViews" type="xs:boolean" />

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 23b09de..2f90e91 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.ViewStyleI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -1149,6 +1150,7 @@ public class Jalview2XML
       view.setFontName(av.font.getName());
       view.setFontSize(av.font.getSize());
       view.setFontStyle(av.font.getStyle());
+      view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
       view.setRenderGaps(av.isRenderGaps());
       view.setShowAnnotation(av.isShowAnnotation());
       view.setShowBoxes(av.getShowBoxes());
@@ -4194,6 +4196,9 @@ public class Jalview2XML
     af.viewport.setFont(
             new java.awt.Font(view.getFontName(), view.getFontStyle(), view
                     .getFontSize()), true);
+    ViewStyleI vs = af.viewport.getViewStyle();
+    vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
+    af.viewport.setViewStyle(vs);
     // TODO: allow custom charWidth/Heights to be restored by updating them
     // after setting font - which means set above to false
     af.viewport.setRenderGaps(view.getRenderGaps());

diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr
index e01bbd4..361fb7c 100644 (file)
--- a/src/jalview/schemabinding/version2/.castor.cdr
+++ b/src/jalview/schemabinding/version2/.castor.cdr
@@ -1,4 +1,4 @@
-#Fri Jun 26 14:22:47 BST 2015
+#Thu Sep 03 10:55:37 BST 2015
 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
 jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 136a3b3..e3a19de 100644 (file)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -332,6 +332,16 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontStyle;
 
     /**
+     * Field _scaleProteinAsCdna.
+     */
+    private boolean _scaleProteinAsCdna = true;
+
+    /**
+     * keeps track of state for field: _scaleProteinAsCdna
+     */
+    private boolean _has_scaleProteinAsCdna;
+
+    /**
      * Field _viewName.
      */
     private java.lang.String _viewName;
@@ -631,6 +641,13 @@ public class Viewport implements java.io.Serializable {
 
     /**
      */
+    public void deleteScaleProteinAsCdna(
+    ) {
+        this._has_scaleProteinAsCdna= false;
+    }
+
+    /**
+     */
     public void deleteShowAnnotation(
     ) {
         this._has_showAnnotation= false;
@@ -1107,6 +1124,16 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'scaleProteinAsCdna'.
+     * 
+     * @return the value of field 'ScaleProteinAsCdna'.
+     */
+    public boolean getScaleProteinAsCdna(
+    ) {
+        return this._scaleProteinAsCdna;
+    }
+
+    /**
      * Returns the value of field 'sequenceSetId'.
      * 
      * @return the value of field 'SequenceSetId'.
@@ -1510,6 +1537,16 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Method hasScaleProteinAsCdna.
+     * 
+     * @return true if at least one ScaleProteinAsCdna has been adde
+     */
+    public boolean hasScaleProteinAsCdna(
+    ) {
+        return this._has_scaleProteinAsCdna;
+    }
+
+    /**
      * Method hasShowAnnotation.
      * 
      * @return true if at least one ShowAnnotation has been added
@@ -1834,6 +1871,16 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Returns the value of field 'scaleProteinAsCdna'.
+     * 
+     * @return the value of field 'ScaleProteinAsCdna'.
+     */
+    public boolean isScaleProteinAsCdna(
+    ) {
+        return this._scaleProteinAsCdna;
+    }
+
+    /**
      * Returns the value of field 'showAnnotation'.
      * 
      * @return the value of field 'ShowAnnotation'.
@@ -2382,6 +2429,18 @@ public class Viewport implements java.io.Serializable {
     }
 
     /**
+     * Sets the value of field 'scaleProteinAsCdna'.
+     * 
+     * @param scaleProteinAsCdna the value of field
+     * 'scaleProteinAsCdna'.
+     */
+    public void setScaleProteinAsCdna(
+            final boolean scaleProteinAsCdna) {
+        this._scaleProteinAsCdna = scaleProteinAsCdna;
+        this._has_scaleProteinAsCdna = true;
+    }
+
+    /**
      * Sets the value of field 'sequenceSetId'.
      * 
      * @param sequenceSetId the value of field 'sequenceSetId'.

diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index 0044f5b..cea458c 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -1375,6 +1375,47 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
             typeValidator.setMaxInclusive(2147483647);
         }
         desc.setValidator(fieldValidator);
+        //-- _scaleProteinAsCdna
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleProteinAsCdna", "scaleProteinAsCdna", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if (!target.hasScaleProteinAsCdna()) { return null; }
+                return (target.getScaleProteinAsCdna() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteScaleProteinAsCdna();
+                        return;
+                    }
+                    target.setScaleProteinAsCdna( ((java.lang.Boolean) value).booleanValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _scaleProteinAsCdna
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
         //-- _viewName
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute);
         desc.setImmutable(true);