X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=ec53e93e1e96e0db1b879ff24b694a46a8674ac6;hb=cfa90577b4ddcb2e163a9bac0b2786d45de57933;hp=1793a9be9edb27fa88adead5581c1d42762ea561;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 1793a9b..ec53e93 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.SequenceGroup;
 import jalview.jbgui.GSliderPanel;
 import jalview.renderer.ResidueShaderI;
@@ -28,6 +29,7 @@ import jalview.util.MessageManager;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
+import java.util.List;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
@@ -44,6 +46,8 @@ import javax.swing.event.InternalFrameEvent;
  */
 public class SliderPanel extends GSliderPanel
 {
+  private static final String BACKGROUND = "Background";
+
   static JInternalFrame conservationSlider;
 
   static JInternalFrame PIDSlider;
@@ -54,16 +58,22 @@ public class SliderPanel extends GSliderPanel
 
   ResidueShaderI cs;
 
-  private static SliderPanel sliderPanel;
-
   /**
-   * Returns the currently active slider panel (or null if none).
+   * Returns the currently displayed slider panel (or null if none).
    * 
    * @return
    */
   public static SliderPanel getSliderPanel()
   {
-    return sliderPanel;
+    if (conservationSlider != null && conservationSlider.isVisible())
+    {
+      return (SliderPanel) conservationSlider.getContentPane();
+    }
+    if (PIDSlider != null && PIDSlider.isVisible())
+    {
+      return (SliderPanel) PIDSlider.getContentPane();
+    }
+    return null;
   }
 
   /**
@@ -126,25 +136,25 @@ public class SliderPanel extends GSliderPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Method to 'set focus' of the Conservation slider panel
    * 
    * @param ap
-   *          DOCUMENT ME!
-   * @param ccs
-   *          DOCUMENT ME!
+   *          the panel to repaint on change of slider
+   * @param rs
+   *          the colour scheme to update on change of slider
    * @param source
-   *          DOCUMENT ME!
+   *          a text description for the panel's title
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   public static int setConservationSlider(AlignmentPanel ap,
-          ResidueShaderI ccs, String source)
+          ResidueShaderI rs, String source)
   {
-    sliderPanel = null;
+    SliderPanel sliderPanel = null;
 
     if (conservationSlider == null)
     {
-      sliderPanel = new SliderPanel(ap, ccs.getConservationInc(), true, ccs);
+      sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
       conservationSlider = new JInternalFrame();
       conservationSlider.setContentPane(sliderPanel);
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -152,16 +162,18 @@ public class SliderPanel extends GSliderPanel
     else
     {
       sliderPanel = (SliderPanel) conservationSlider.getContentPane();
-      sliderPanel.valueField.setText(String.valueOf(ccs.getConservationInc()));
-      sliderPanel.cs = ccs;
+      sliderPanel.valueField.setText(String.valueOf(rs.getConservationInc()));
+      sliderPanel.cs = rs;
+      sliderPanel.ap = ap;
+      sliderPanel.slider.setValue(rs.getConservationInc());
     }
 
-    conservationSlider
-            .setTitle(MessageManager.formatMessage(
-                    "label.conservation_colour_increment",
-                    new String[] { source }));
+    conservationSlider.setTitle(MessageManager.formatMessage(
+            "label.conservation_colour_increment",
+            new String[] { source == null ? BACKGROUND : source }));
 
-    if (ap.av.getAlignment().getGroups() != null)
+    List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+    if (groups != null && !groups.isEmpty())
     {
       sliderPanel.setAllGroupsCheckEnabled(true);
     }
@@ -232,25 +244,27 @@ public class SliderPanel extends GSliderPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Method to 'set focus' of the PID slider panel
    * 
    * @param ap
-   *          DOCUMENT ME!
-   * @param ccs
-   *          DOCUMENT ME!
+   *          the panel to repaint on change of slider
+   * @param rs
+   *          the colour scheme to update on change of slider
    * @param source
-   *          DOCUMENT ME!
+   *          a text description for the panel's title
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   public static int setPIDSliderSource(AlignmentPanel ap,
-          ResidueShaderI ccs, String source)
+          ResidueShaderI rs, String source)
   {
-    int threshold = ccs.getThreshold();
+    int threshold = rs.getThreshold();
+
+    SliderPanel sliderPanel = null;
 
     if (PIDSlider == null)
     {
-      sliderPanel = new SliderPanel(ap, threshold, false, ccs);
+      sliderPanel = new SliderPanel(ap, threshold, false, rs);
       PIDSlider = new JInternalFrame();
       PIDSlider.setContentPane(sliderPanel);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -258,14 +272,15 @@ public class SliderPanel extends GSliderPanel
     else
     {
       sliderPanel = (SliderPanel) PIDSlider.getContentPane();
-      sliderPanel.cs = ccs;
-      sliderPanel.valueField.setText(String.valueOf(ccs.getThreshold()));
+      sliderPanel.cs = rs;
+      sliderPanel.ap = ap;
+      sliderPanel.valueField.setText(String.valueOf(rs.getThreshold()));
+      sliderPanel.slider.setValue(rs.getThreshold());
     }
 
-    PIDSlider
-            .setTitle(MessageManager.formatMessage(
-                    "label.percentage_identity_threshold",
-                    new String[] { source }));
+    PIDSlider.setTitle(MessageManager.formatMessage(
+            "label.percentage_identity_threshold",
+            new String[] { source == null ? BACKGROUND : source }));
 
     if (ap.av.getAlignment().getGroups() != null)
     {
@@ -319,13 +334,14 @@ public class SliderPanel extends GSliderPanel
     {
       ap.av.setThreshold(percent);
     }
-    updateColourScheme(percent, cs);
+    updateColourScheme(percent, cs, null);
 
     if (allGroupsCheck.isSelected())
     {
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+      for (SequenceGroup sg : groups)
       {
-        updateColourScheme(percent, sg.getGroupColourScheme());
+        updateColourScheme(percent, sg.getGroupColourScheme(), sg);
       }
     }
 
@@ -338,8 +354,10 @@ public class SliderPanel extends GSliderPanel
    * 
    * @param percent
    * @param scheme
+   * @param sg
    */
-  protected void updateColourScheme(int percent, ResidueShaderI scheme)
+  protected void updateColourScheme(int percent, ResidueShaderI scheme,
+          SequenceGroup sg)
   {
     if (scheme == null)
     {
@@ -347,6 +365,20 @@ public class SliderPanel extends GSliderPanel
     }
     if (forConservation)
     {
+      if (!scheme.conservationApplied())
+      {
+        /*
+         * first time the colour scheme has had Conservation shading applied
+         * - compute conservation
+         */
+        Conservation c = new Conservation("Group", sg.getSequences(null),
+                sg.getStartRes(), sg.getEndRes());
+        c.calculate();
+        c.verdict(false, ap.av.getConsPercGaps());
+        sg.cs.setConservation(c);
+
+      }
+      scheme.setConservationApplied(true);
       scheme.setConservationInc(percent);
     }
     else
@@ -364,6 +396,7 @@ public class SliderPanel extends GSliderPanel
   public void setAllGroupsCheckEnabled(boolean b)
   {
     allGroupsCheck.setEnabled(b);
+    allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups());
   }
 
   /**