patch for JAL-542

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 4d58689..13390d9 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -151,7 +151,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
-      displayNonconserved.setState(sg.getShowunconserved());
+      displayNonconserved.setState(sg.getShowNonconserved());
       if (!ap.av.alignment.getGroups().contains(sg))
       {
         groupMenu.remove(unGroupMenuItem);
@@ -992,7 +992,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   public void showNonconserved_itemStateChanged()
   {
-    getGroup().setShowunconserved(this.displayNonconserved.getState());
+    getGroup().setShowNonconserved(this.displayNonconserved.getState());
     refresh();
   }
 

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 56948e3..b8ed2f1 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2866,7 +2866,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     annotationPanelMenuItem.addItemListener(this);
     colourTextMenuItem.setLabel("Colour Text");
     colourTextMenuItem.addItemListener(this);
-    displayNonconservedMenuItem.setLabel("Show non-conserved");
+    displayNonconservedMenuItem.setLabel("Show nonconserved");
     displayNonconservedMenuItem.addItemListener(this);
     alProperties.addActionListener(this);
     overviewMenuItem.setLabel("Overview Window");

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index a954e7b..85c8ab5 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1578,7 +1578,7 @@ public class AlignViewport
   }
 
   /**
-   * @param showUnconserved
+   * @param showNonconserved
    *          the showUnconserved to set
    */
   public void setShowunconserved(boolean displayNonconserved)

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 822e906..e8508b6 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -219,7 +219,7 @@ public class SequenceRenderer
           getBoxColour(currentSequenceGroup.cs, seq, i);
           graphics.setColor(resBoxColour.darker());
         }
-        if (currentSequenceGroup.getShowunconserved())
+        if (currentSequenceGroup.getShowNonconserved())
         {
           // cheat - use this if we have a consensus for each group: s =
           // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9d3e6db..cc71e4a 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -49,7 +49,7 @@ public class SequenceGroup
   /**
    * after Olivier's non-conserved only character display
    */
-  boolean showUnconserved = false;
+  boolean showNonconserved = false;
 
   /**
    * group members
@@ -957,18 +957,18 @@ public class SequenceGroup
   /**
    * @return the showUnconserved
    */
-  public boolean getShowunconserved()
+  public boolean getShowNonconserved()
   {
-    return showUnconserved;
+    return showNonconserved;
   }
 
   /**
-   * @param showUnconserved
+   * @param showNonconserved
    *          the showUnconserved to set
    */
-  public void setShowunconserved(boolean displayNonconserved)
+  public void setShowNonconserved(boolean displayNonconserved)
   {
-    this.showUnconserved = displayNonconserved;
+    this.showNonconserved = displayNonconserved;
   }
 
   AlignmentAnnotation consensus = null, conservation = null;

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2e6ea52..22647a3 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -588,7 +588,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     annotationPanelMenuItem.setState(av.showAnnotation);
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
-    showUnconservedMenuItem.setSelected(av.showUnconserved);
+    showNonconservedMenuItem.setSelected(av.showUnconserved);
     showGroupConsensus.setSelected(av.showGroupConsensus);
     showGroupConservation.setSelected(av.showGroupConservation);
     showConsensusHistogram.setSelected(av.showConsensusHistogram);
@@ -4555,7 +4555,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+    viewport.setShowUnconserved(showNonconservedMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -4638,7 +4638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
-        gps[g].setShowunconserved(viewport.getShowUnconserved());
+        gps[g].setShowNonconserved(viewport.getShowUnconserved());
         gps[g].setIncludeAllConsSymbols(viewport
                 .isIncludeAllConsensusSymbols());
         viewport.alignment.addGroup(gps[g]);

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ba3cef2..8de14b1 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -946,7 +946,7 @@ public class Jalview2XML
         groups[i].setTextCol1(sg.textColour.getRGB());
         groups[i].setTextCol2(sg.textColour2.getRGB());
         groups[i].setTextColThreshold(sg.thresholdTextColour);
-        groups[i].setShowUnconserved(sg.getShowunconserved());
+        groups[i].setShowUnconserved(sg.getShowNonconserved());
         groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
         groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
         groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
@@ -2233,7 +2233,7 @@ public class Jalview2XML
 
         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
-        sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i]
+        sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
                 .isShowUnconserved() : false);
         sg.thresholdTextColour = groups[i].getTextColThreshold();
         if (groups[i].hasShowConsensusHistogram())

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 92e24bf..899a3f8 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -395,7 +395,7 @@ public class PopupMenu extends JPopupMenu
       {
         conservationMenuItem.setSelected(true);
       }
-      displayNonconserved.setSelected(sg.getShowunconserved());
+      displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
@@ -1139,7 +1139,7 @@ public class PopupMenu extends JPopupMenu
 
   protected void showNonconserved_actionPerformed()
   {
-    getGroup().setShowunconserved(displayNonconserved.isSelected());
+    getGroup().setShowNonconserved(displayNonconserved.isSelected());
     refresh();
   }
 

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 86c8490..db66993 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -325,7 +325,7 @@ public class SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
-          if (currentSequenceGroup.getShowunconserved()) // todo optimize
+          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
             s = getDisplayChar(av.consensus, i, s, '.');

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2721fb2..ae5bb46 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -416,7 +416,7 @@ public class AnnotationFile
       text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
       text.append("displayText=" + sg.getDisplayText() + "\t");\r
       text.append("colourText=" + sg.getColourText() + "\t");\r
-      text.append("showUnconserved=" + sg.getShowunconserved() + "\t");\r
+      text.append("showUnconserved=" + sg.getShowNonconserved() + "\t");\r
       if (sg.textColour != java.awt.Color.black)\r
       {\r
         text.append("textCol1="\r
@@ -1253,7 +1253,7 @@ public class AnnotationFile
         }\r
         else if (key.equalsIgnoreCase("showUnconserved"))\r
         {\r
-          sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+          sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());\r
         }\r
         else if (key.equalsIgnoreCase("displayText"))\r
         {\r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 067b3d2..8342609 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -121,7 +121,7 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 
   JMenuItem htmlMenuItem = new JMenuItem();
 
@@ -656,9 +656,9 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    showUnconservedMenuItem.setText("Show Unconserved");
-    showUnconservedMenuItem.setState(false);
-    showUnconservedMenuItem
+    showNonconservedMenuItem.setText("Show nonconserved");
+    showNonconservedMenuItem.setState(false);
+    showNonconservedMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
               public void actionPerformed(ActionEvent e)
@@ -1794,7 +1794,7 @@ public class GAlignFrame extends JInternalFrame
     formatMenu.add(colourTextMenuItem);
     formatMenu.add(renderGapsMenuItem);
     formatMenu.add(centreColumnLabelsMenuItem);
-    formatMenu.add(showUnconservedMenuItem);
+    formatMenu.add(showNonconservedMenuItem);
     selectMenu.add(findMenuItem);
     selectMenu.addSeparator();
     selectMenu.add(selectAllSequenceMenuItem);