JAL-1483 move show sequence feature and sequence feature height settings to view...

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index a1bb272..9b0412a 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -550,7 +550,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (ap.av.getShowSequenceFeatures())
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index dc0f718..4fd7a35 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -110,7 +110,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   boolean seqColoursReady = false;
 
-  jalview.gui.FeatureRenderer fr;
+  jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   Color backgroundColour = Color.black;
 
@@ -520,7 +520,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (ap.av.getShowSequenceFeatures())
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9409e38..a97f464 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -195,4 +195,8 @@ public interface AlignViewportI
 
   String getSequenceSetId();
 
+  boolean isShowSequenceFeatures();
+
+  void setShowSequenceFeatures(boolean b);
+
 }

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index d98e2aa..7a77935 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -647,7 +647,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
               features, true, ap))
       {
         ap.alignFrame.sequenceFeatures.setState(true);
-        ap.av.showSequenceFeatures(true);
+        ap.av.setShowSequenceFeatures(true);;
         ap.highlightSearchResults(null);
       }
     }

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index cc1703c..e0dad58 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -302,7 +302,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (autoenabledisplay)
       {
-        viewport.showSequenceFeatures = true;
+        viewport.setShowSequenceFeatures(true);
         sequenceFeatures.setState(true);
       }
       if (viewport.featureSettings != null)
@@ -720,7 +720,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (evt.getSource() == sequenceFeatures)
     {
-      viewport.showSequenceFeatures(sequenceFeatures.getState());
+      viewport.setShowSequenceFeatures(sequenceFeatures.getState());
       alignPanel.seqPanel.seqCanvas.repaint();
     }
     else if (evt.getSource() == conservationMenuItem)
@@ -2275,7 +2275,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     FeatureRenderer fr = null;
     this.sequenceFeatures.setState(true);
-    viewport.showSequenceFeatures(true);
+    viewport.setShowSequenceFeatures(true);
     if (alignPanel != null
             && (fr = alignPanel.getFeatureRenderer()) != null)
     {

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index f42f7ba..9a15e10 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -58,8 +58,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
   boolean showAnnotation = true;
 
   boolean upperCasebold = false;
@@ -252,16 +250,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   }
 
-  public void showSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3d1d0fb..0f317ae 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -520,7 +520,7 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -548,7 +548,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
   }
 
   public void updateTitleAndMenus()
@@ -559,7 +559,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
 
     setTitle(jmb.getViewerTitle());
   }

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 650693d..d2a6e6c 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -52,7 +52,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (appletJmolBinding.ap.av.showSequenceFeatures)
+    if (appletJmolBinding.ap.av.isShowSequenceFeatures())
     {
       if (appletJmolBinding.fr == null)
       {
@@ -105,7 +105,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    colourBySequence(ap.av.isShowSequenceFeatures(), ap);
   }
 
   public void showUrl(String url)

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 6389250..1efb971 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -78,7 +78,7 @@ public class ExtJmol extends JalviewJmolBinding
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       return ap.getFeatureRenderer();
     }

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 6ca6ddf..4796bca 100644 (file)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -113,7 +113,7 @@ public class Finder extends Panel implements ActionListener
             features, true, ap))
     {
       ap.alignFrame.sequenceFeatures.setState(true);
-      av.showSequenceFeatures(true);
+      av.setShowSequenceFeatures(true);
       ap.highlightSearchResults(null);
     }
   }

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 2c2c41a..e646051 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -229,7 +229,7 @@ public class OverviewPanel extends Panel implements Runnable,
       return;
     }
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
       fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
@@ -260,7 +260,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int alwidth = av.getAlignment().getWidth();
     int alheight = av.getAlignment().getHeight();
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
@@ -337,7 +337,7 @@ public class OverviewPanel extends Panel implements Runnable,
         {
           color = sr.getResidueBoxColour(seq, lastcol);
 
-          if (av.showSequenceFeatures)
+          if (av.isShowSequenceFeatures())
           {
             color = fr.findFeatureColour(color, seq, lastcol);
           }

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 33caf53..53cca3c 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -589,7 +589,7 @@ public class SeqCanvas extends Panel
       sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
               startRes, endRes, offset + ((i - startSeq) * av.charHeight));
 
-      if (av.showSequenceFeatures)
+      if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
                 + ((i - startSeq) * av.charHeight));

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 4e02984..009d0a2 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1979,7 +1979,7 @@ public class JalviewLite extends Applet implements
         param = applet.getParameter("showFeatureSettings");
         if (param != null && param.equalsIgnoreCase("true"))
         {
-          newAlignFrame.viewport.showSequenceFeatures(true);
+          newAlignFrame.viewport.setShowSequenceFeatures(true);
           new FeatureSettings(newAlignFrame.alignPanel);
         }
 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bf9888c..b958f90 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -739,7 +739,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
-    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    showSeqFeatures.setSelected(av.isShowSequenceFeatures());
     hiddenMarkers.setState(av.showHiddenMarkers);
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
@@ -3021,7 +3021,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
             .isSelected());
-    if (viewport.getShowSequenceFeaturesHeight())
+    if (viewport.isShowSequenceFeaturesHeight())
     {
       // ensure we're actually displaying features
       viewport.setShowSequenceFeatures(true);
@@ -4795,7 +4795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (featuresFile)
     {
-      viewport.showSequenceFeatures = true;
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
       if (alignPanel.seqPanel.seqCanvas.fr != null)
       {

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3254005..a37ded9 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -95,8 +95,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   boolean renderGaps = true;
 
-  boolean showSequenceFeatures = false;
-
   boolean showAnnotation = true;
 
   int charHeight;
@@ -361,22 +359,6 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
-   * set the flag
-   * 
-   * @param b
-   *          features are displayed if true
-   */
-  public void setShowSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
-
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
-
-  /**
    * centre columnar annotation labels in displayed alignment annotation TODO:
    * add to jalviewXML and annotation display settings
    */
@@ -1092,8 +1074,6 @@ public class AlignViewport extends AlignmentViewport implements
     return followSelection;
   }
 
-  boolean showSeqFeaturesHeight;
-
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -1102,16 +1082,6 @@ public class AlignViewport extends AlignmentViewport implements
                     new ColumnSelection(getColumnSelection()), this);
   }
 
-  public void setShowSequenceFeaturesHeight(boolean selected)
-  {
-    showSeqFeaturesHeight = selected;
-  }
-
-  public boolean getShowSequenceFeaturesHeight()
-  {
-    return showSeqFeaturesHeight;
-  }
-
   /**
    * return the alignPanel containing the given viewport. Use this to get the
    * components currently handling the given viewport.

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 6eb6ac3..08b0744 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1020,7 +1020,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
       // Set the colour using the current view for the associated alignframe
       for (AlignmentPanel ap : _colourwith)
       {
-        jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+        jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
       }
     }
   }

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 35abb94..42a2f74 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -58,7 +58,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
             : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
@@ -133,7 +133,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       return;
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
   }
 

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8cad9ca..3ab5a8d 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1064,7 +1064,7 @@ public class Jalview2XML
       view.setShowColourText(av.getColourText());
       view.setShowFullId(av.getShowJVSuffix());
       view.setRightAlignIds(av.rightAlignIds);
-      view.setShowSequenceFeatures(av.showSequenceFeatures);
+      view.setShowSequenceFeatures(av.isShowSequenceFeatures());
       view.setShowText(av.getShowText());
       view.setShowUnconserved(av.getShowUnconserved());
       view.setWrapAlignment(av.getWrapAlignment());
@@ -3432,10 +3432,8 @@ public class Jalview2XML
 
     af.viewport.setColourAppliesToAllGroups(true);
 
-    if (view.getShowSequenceFeatures())
-    {
-      af.viewport.showSequenceFeatures = true;
-    }
+    af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+
     if (view.hasCentreColumnLabels())
     {
       af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 2e3b236..718677c 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -390,7 +390,7 @@ public class Jalview2XML_V1
     }
 
     af.viewport.setColourAppliesToAllGroups(true);
-    af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+    af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 
     if (jms.getFeatureSettings() != null)
     {

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index e8555f7..5edf218 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -254,7 +254,7 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     miniMe = null;
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
@@ -344,7 +344,7 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           color = sr.getResidueBoxColour(seq, lastcol).getRGB();
 
-          if (av.showSequenceFeatures)
+          if (av.isShowSequenceFeatures())
           {
             color = fr.findFeatureColour(color, seq, lastcol);
           }

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d5b81f1..03231c5 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -704,7 +704,7 @@ public class SeqCanvas extends JComponent
       sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
               startRes, endRes, offset + ((i - startSeq) * av.charHeight));
 
-      if (av.showSequenceFeatures)
+      if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
                 + ((i - startSeq) * av.charHeight));

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index bf5ea93..4c2cff2 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -726,7 +726,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     // use aa to see if the mouse pointer is on a
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       int rpos;
       SequenceFeature[] features = findFeaturesAtRes(

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 465a672..2ecaf6c 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -202,7 +202,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
               .getSequenceRenderer();
       FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
-              .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
+              .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
               ((jalview.appletgui.AlignmentPanel) source).av) : null;
       if (fr != null)
       {

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5dd5aa3..cb97ea8 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,7 +20,6 @@
  */
 package jalview.viewmodel;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
@@ -36,7 +35,6 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
@@ -698,6 +696,7 @@ public abstract class AlignmentViewport implements AlignViewportI
     sequenceSetID = new String(newid);
   }
 
+  @Override
   public String getSequenceSetId()
   {
     if (sequenceSetID == null)
@@ -1637,4 +1636,39 @@ public abstract class AlignmentViewport implements AlignViewportI
     return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
   }
 
+  /**
+   * display setting for showing/hiding sequence features on alignment view
+   */
+  boolean showSequenceFeatures = false;
+
+  /**
+   * set the flag
+   * 
+   * @param b
+   *          features are displayed if true
+   */
+  @Override
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
+  @Override
+  public boolean isShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
+
+  boolean showSeqFeaturesHeight;
+
+  public void setShowSequenceFeaturesHeight(boolean selected)
+  {
+    showSeqFeaturesHeight = selected;
+  }
+
+  public boolean isShowSequenceFeaturesHeight()
+  {
+    return showSeqFeaturesHeight;
+  }
+
+
 }