JAL-1640 JAL-966 is for boolean getter on AlignViewportI

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 5d3f89d..fe49488 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -77,9 +77,9 @@ public interface AlignViewportI
 
   Hashtable[] getRnaStructureConsensusHash();
 
-  boolean getIgnoreGapsConsensus();
 
   boolean getCentreColumnLabels();
+  boolean isIgnoreGapsConsensus();
 
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index e688177..3b37b62 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1023,7 +1023,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
-      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
 
@@ -1031,7 +1031,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     else
     // remove PIDColouring
     {
-      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     refresh();

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 566be33..fdbf1ff 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -482,7 +482,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
                     MessageManager.getString("label.ignore_gaps_consensus"),
                     (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                             .getIgnoreGapsConsensus() : ap.av
-                            .getIgnoreGapsConsensus());
+                            .isIgnoreGapsConsensus());
             final AlignmentAnnotation aaa = aa[selectedRow];
             cbmi.addItemListener(new ItemListener()
             {

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 220a7fb..2a4d582 100644 (file)
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -215,7 +215,7 @@ public class SliderPanel extends Panel implements ActionListener,
       }
       else
       {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+        toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
       }
       if (allGroups != null && allGroups.hasNext())
       {

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 745520b..da8f91e 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -639,7 +639,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.getIgnoreGapsConsensus());
+                  av.isIgnoreGapsConsensus());
         }
       }
       // TODO: cs used to be initialized with a sequence collection and

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index afa6419..6d8933c 100644 (file)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -489,7 +489,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     UserColourScheme ucs = new UserColourScheme(newColours);
     if (ap != null)
     {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     if (ap != null)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 974dbad..2b6795b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3361,11 +3361,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
       }
       else
       {
-        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
       }
 
       if (viewport.getConservationSelected())
@@ -3428,7 +3428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 || cs instanceof PIDColourScheme
                 || cs instanceof Blosum62ColourScheme)
         {
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
 
           sg.cs.setConsensus(AAFrequency.calculate(
                   sg.getSequences(viewport.getHiddenRepSequences()),
@@ -3436,7 +3436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         else
         {
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
         }
 
         if (viewport.getConservationSelected())

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d6bfaf3..a54f9e8 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -296,7 +296,7 @@ public class AlignViewport extends AlignmentViewport implements
       {
         globalColourScheme = UserDefinedColours.loadDefaultColours();
         ((UserColourScheme) globalColourScheme).setThreshold(0,
-                getIgnoreGapsConsensus());
+                isIgnoreGapsConsensus());
       }
 
       if (globalColourScheme != null)

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 49ff2e0..f9a9e7e 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -686,7 +686,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                        MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                         .getIgnoreGapsConsensus() : ap.av
-                        .getIgnoreGapsConsensus());
+                        .isIgnoreGapsConsensus());
         final AlignmentAnnotation aaa = aa[selectedRow];
         cbmi.addActionListener(new ActionListener()
         {

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ce2dd81..1d59ce0 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1119,7 +1119,7 @@ public class Jalview2XML
       view.setShowDbRefTooltip(av.isShowDbRefs());
       view.setFollowHighlight(av.followHighlight);
       view.setFollowSelection(av.followSelection);
-      view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+      view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
       if (av.getFeaturesDisplayed() != null)
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 8565f9f..bccbf8c 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2190,14 +2190,14 @@ public class PopupMenu extends JPopupMenu
       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
               .getName());
 
-      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
     }
     else
     // remove PIDColouring
     {
-      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     refresh();

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index cbd0d58..f536efc 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -286,13 +286,15 @@ public class SliderPanel extends GSliderPanel
       }
       else
       {
-        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+        toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
       }
       if (allGroups != null && allGroups.hasNext())
       {
         while ((toChange = allGroups.next().cs) == null
                 && allGroups.hasNext())
+        {
           ;
+        }
       }
       else
       {

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index c5650f5..d921ba4 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -916,7 +916,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.getIgnoreGapsConsensus());
+                  av.isIgnoreGapsConsensus());
         }
       }
       sg.cs = cs;

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 37824fe..44a633b 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -556,7 +556,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (ap != null)
     {
-      ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
     }
 
     return ucs;

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index d5b2f49..f4e9b1f 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -302,7 +302,7 @@ public class AnnotationRenderer
     columnSelection = av.getColumnSelection();
     hconsensus = av.getSequenceConsensusHash();// hconsensus;
     hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
-    av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
+    av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
   }
 
   public int[] getProfileFor(AlignmentAnnotation aa, int column)

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index d94fa5d..152f155 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -530,12 +530,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
                 || cs instanceof Blosum62ColourScheme)
         {
           sg.cs.setThreshold(viewStyle.getThreshold(),
-                  getIgnoreGapsConsensus());
+                  isIgnoreGapsConsensus());
           recalc = true;
         }
         else
         {
-          sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+          sg.cs.setThreshold(0, isIgnoreGapsConsensus());
         }
 
         if (getConservationSelected())
@@ -1055,7 +1055,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
-  public boolean getIgnoreGapsConsensus()
+  public boolean isIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensusCalculation;
   }

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index c754ee3..f940450 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -158,7 +158,7 @@ public class ConsensusThread extends AlignCalcWorker implements
             && hconsensus != null)
     {
       AAFrequency.completeConsensus(consensus, hconsensus, 0,
-              hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
+              hconsensus.length, alignViewport.isIgnoreGapsConsensus(),
               alignViewport.isShowSequenceLogo(), nseq);
     }
   }

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 3230a36..2249081 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -166,7 +166,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     {
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
-              alignViewport.getIgnoreGapsConsensus(),
+              alignViewport.isIgnoreGapsConsensus(),
               alignViewport.isShowSequenceLogo(), nseq);
     }
   }