X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=4b29f53bb8cbec1c18ece29f89349125f1aec0d6;hb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;hp=cd11a35ad92d3f6b0bb7c4fb3394194d11c8de3e;hpb=70fd4c40d0b2046c6d402e365e4d04f9cfbb68ef;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index cd11a35..4b29f53 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -21,7 +21,7 @@
 package jalview.appletgui;
 
 import java.util.*;
-
+import java.util.List;
 import java.awt.*;
 import java.awt.event.*;
 
@@ -50,8 +50,6 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   ScrollPane scrollPane;
 
-  boolean alignmentHasFeatures = false;
-
   Image linkImage;
 
   Scrollbar transparency;
@@ -64,9 +62,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();
 
     transparency = new Scrollbar(Scrollbar.HORIZONTAL,
-            100 - (int) (fr.transparency * 100), 1, 1, 100);
+            100 - (int) (fr.getTransparency() * 100), 1, 1, 100);
 
-    if (fr.transparencySetter != null)
+    if (fr.isTransparencyAvailable())
     {
       transparency.addAdjustmentListener(this);
     }
@@ -81,9 +79,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       linkImage = java.awt.Toolkit.getDefaultToolkit().getImage(url);
     }
 
-    if (av.featuresDisplayed == null)
+    if (av.isShowSequenceFeatures() || !fr.hasRenderOrder())
     {
-      fr.findAllFeatures();
+      fr.findAllFeatures(true); // was default - now true to make all visible
     }
 
     setTableData();
@@ -91,7 +89,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     this.setLayout(new BorderLayout());
     scrollPane = new ScrollPane();
     scrollPane.add(featurePanel);
-    if (alignmentHasFeatures)
+    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
     {
       add(scrollPane, BorderLayout.CENTER);
     }
@@ -104,7 +102,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     Panel tPanel = new Panel(new BorderLayout());
 
-    if (fr.transparencySetter != null)
+    if (fr.isTransparencyAvailable())
     {
       tPanel.add(transparency, BorderLayout.CENTER);
       tPanel.add(new Label("Transparency"), BorderLayout.EAST);
@@ -124,8 +122,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     {
       groupPanel
               .setLayout(new GridLayout(
-                      (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1,
-                      4));
+                      (fr.getFeatureGroupsSize()) / 4 + 1,
+                      4)); // JBPNote - this was scaled on number of visible groups. seems broken
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
@@ -185,7 +183,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       public void actionPerformed(ActionEvent e)
       {
-        me.sortByScore(new String[]
+        me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
         { type });
       }
 
@@ -197,7 +195,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       public void actionPerformed(ActionEvent e)
       {
-        me.sortByDens(new String[]
+        me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
         { type });
       }
 
@@ -253,8 +251,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   public void setTableData()
   {
-    alignmentHasFeatures = fr.buildGroupHash();
-    if (alignmentHasFeatures)
+    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
     {
       rebuildGroups();
 
@@ -279,18 +276,17 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     // TODO: JAL-964 - smoothly incorporate new group entries if panel already
     // displayed and new groups present
-    Enumeration gps = fr.featureGroups.keys();
-    while (gps.hasMoreElements())
+    for (String group:(List<String>)fr.getFeatureGroups())
     {
-      String group = (String) gps.nextElement();
-      Boolean vis = (Boolean) fr.featureGroups.get(group);
-      Checkbox check = new MyCheckbox(group, vis.booleanValue(),
+      boolean vis = fr.checkGroupVisibility(group, false);
+      Checkbox check = new MyCheckbox(group, vis,
               (fr.featureLinks != null && fr.featureLinks
                       .containsKey(group)));
       check.addMouseListener(this);
       check.setFont(new Font("Serif", Font.BOLD, 12));
-      check.addItemListener(this);
-      check.setVisible(fr.hiddenGroups.contains(group));
+      check.addItemListener(groupItemListener);
+      // note - visibility seems to correlate with displayed. ???wtf ??
+      check.setVisible(vis);
       groupPanel.add(check);
     }
     if (rdrw)
@@ -298,7 +294,6 @@ public class FeatureSettings extends Panel implements ItemListener,
       groupPanel.validate();
     }
   }
-
   // This routine adds and removes checkboxes depending on
   // Group selection states
   void resetTable(boolean groupsChanged)
@@ -320,8 +315,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       {
         group = tmpfeatures[index].featureGroup;
 
-        if (group == null || fr.featureGroups.get(group) == null
-                || ((Boolean) fr.featureGroups.get(group)).booleanValue())
+        if (group == null || fr.checkGroupVisibility(group, true))
         {
           type = tmpfeatures[index].getType();
           if (!visibleChecks.contains(type))
@@ -350,13 +344,14 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
     }
 
-    if (fr.renderOrder != null)
+    if (fr.getRenderOrder() != null)
     {
       // First add the checks in the previous render order,
       // in case the window has been closed and reopened
-      for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
+      List<String> rol = fr.getRenderOrder();
+      for (int ro = rol.size() - 1; ro > -1; ro--)
       {
-        String item = fr.renderOrder[ro];
+        String item = rol.get(ro);
 
         if (!visibleChecks.contains(item))
         {
@@ -418,7 +413,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     if (addCheck)
     {
       boolean selected = false;
-      if (groupsChanged || av.featuresDisplayed.containsKey(type))
+      if (groupsChanged || av.getFeaturesDisplayed().isVisible(type))
       {
         selected = true;
       }
@@ -455,26 +450,22 @@ public class FeatureSettings extends Panel implements ItemListener,
     selectionChanged();
   }
 
-  public void itemStateChanged(ItemEvent evt)
-  {
-    if (evt != null)
-    {
-      // Is the source a top level featureGroup?
+  private ItemListener groupItemListener = new ItemListener() {
+    public void itemStateChanged(ItemEvent evt) {
       Checkbox source = (Checkbox) evt.getSource();
-      if (fr.featureGroups.containsKey(source.getLabel()))
+      fr.setGroupVisibility(source.getLabel(),
+              source.getState());
+      ap.seqPanel.seqCanvas.repaint();
+      if (ap.overviewPanel != null)
       {
-        fr.featureGroups.put(source.getLabel(),
-                new Boolean(source.getState()));
-        ap.seqPanel.seqCanvas.repaint();
-        if (ap.overviewPanel != null)
-        {
-          ap.overviewPanel.updateOverviewImage();
-        }
-
-        resetTable(true);
-        return;
+        ap.overviewPanel.updateOverviewImage();
       }
-    }
+      resetTable(true);
+      return;
+    };
+  };
+  public void itemStateChanged(ItemEvent evt)
+  {
     selectionChanged();
   }
 
@@ -617,7 +608,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     MyCheckbox check = (MyCheckbox) evt.getSource();
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
     {
-      this.popupSort(check, fr.minmax, evt.getX(), evt.getY());
+      this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
     }
     if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
     {
@@ -657,7 +648,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    fr.transparency = ((float) (100 - transparency.getValue()) / 100f);
+    fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
     ap.seqPanel.seqCanvas.repaint();
 
   }
@@ -771,81 +762,4 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
-  protected void sortByDens(String[] typ)
-  {
-    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
-  }
-
-  private String[] getDisplayedFeatureTypes()
-  {
-    String[] typ = null;
-    if (fr != null)
-    {
-      synchronized (fr.renderOrder)
-      {
-        typ = new String[fr.renderOrder.length];
-        System.arraycopy(fr.renderOrder, 0, typ, 0, typ.length);
-        for (int i = 0; i < typ.length; i++)
-        {
-          if (av.featuresDisplayed.get(typ[i]) == null)
-          {
-            typ[i] = null;
-          }
-        }
-      }
-    }
-    return typ;
-  }
-
-  protected void sortBy(String[] typ, String methodText, final String method)
-  {
-    if (typ == null)
-    {
-      typ = getDisplayedFeatureTypes();
-    }
-    String gps[] = null;
-    gps = fr.getGroups(true);
-    if (typ != null)
-    {
-      for (int i = 0; i < typ.length; i++)
-      {
-        System.err.println("Sorting on Types:" + typ[i]);
-      }
-    }
-    if (gps != null)
-    {
-
-      for (int i = 0; i < gps.length; i++)
-      {
-        System.err.println("Sorting on groups:" + gps[i]);
-      }
-    }
-    AlignmentPanel alignPanel = ap;
-    AlignmentI al = alignPanel.av.getAlignment();
-
-    int start, stop;
-    SequenceGroup sg = alignPanel.av.getSelectionGroup();
-    if (sg != null)
-    {
-      start = sg.getStartRes();
-      stop = sg.getEndRes();
-    }
-    else
-    {
-      start = 0;
-      stop = al.getWidth();
-    }
-    SequenceI[] oldOrder = al.getSequencesArray();
-    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
-    this.ap.alignFrame.addHistoryItem(new OrderCommand(methodText,
-            oldOrder, alignPanel.av.getAlignment()));
-    alignPanel.paintAlignment(true);
-
-  }
-
-  protected void sortByScore(String[] typ)
-  {
-    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
-  }
-
 }