X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=98579ebe8af84e31ad1d84d9f24c62f7f3ccacc5;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=f95f84b52ff25701505e0edf1bf9dc38cd038de4;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index f95f84b..98579eb 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -28,6 +28,12 @@ import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SliderPanel
     extends GSliderPanel
 {
@@ -37,6 +43,14 @@ public class SliderPanel
   boolean forConservation = true;
   ColourSchemeI cs;
 
+  /**
+   * Creates a new SliderPanel object.
+   *
+   * @param ap DOCUMENT ME!
+   * @param value DOCUMENT ME!
+   * @param forConserve DOCUMENT ME!
+   * @param cs DOCUMENT ME!
+   */
   public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
                      ColourSchemeI cs)
   {
@@ -50,7 +64,7 @@ public class SliderPanel
     {
       label.setText("Enter value to increase conservation visibility");
       slider.setMinimum(0);
-      slider.setMaximum(50);
+      slider.setMaximum(100);
     }
     else
     {
@@ -72,15 +86,23 @@ public class SliderPanel
     valueField.setText(value + "");
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ap DOCUMENT ME!
+   * @param cs DOCUMENT ME!
+   * @param source DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public static int setConservationSlider(AlignmentPanel ap,
                                           ColourSchemeI cs, String source)
   {
     SliderPanel sp = null;
-    ConservationColourScheme ccs = (ConservationColourScheme) cs;
 
     if (conservationSlider == null)
     {
-      sp = new SliderPanel(ap, ccs.inc, true, cs);
+      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
       conservationSlider = new JInternalFrame();
       conservationSlider.setContentPane(sp);
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -106,6 +128,9 @@ public class SliderPanel
     return sp.getValue();
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   public static void showConservationSlider()
   {
     try
@@ -134,21 +159,21 @@ public class SliderPanel
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param ap DOCUMENT ME!
+   * @param cs DOCUMENT ME!
+   * @param source DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
                                        String source)
   {
     SliderPanel pid = null;
 
-    int threshold = 50;
-
-    if (cs instanceof ResidueColourScheme)
-    {
-      threshold = ( ( (ResidueColourScheme) cs).getThreshold());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      threshold = ( ( (ScoreColourScheme) cs).getThreshold());
-    }
+    int threshold = cs.getThreshold();
 
     if (PIDSlider == null)
     {
@@ -177,6 +202,9 @@ public class SliderPanel
     return pid.getValue();
   }
 
+  /**
+   * DOCUMENT ME!
+   */
   public static void showPIDSlider()
   {
     try
@@ -206,6 +234,11 @@ public class SliderPanel
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
   public void valueChanged(int i)
   {
     if (cs == null)
@@ -232,18 +265,25 @@ public class SliderPanel
       if (allGroups != null)
       {
         toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
+
+        if (toChange == null)
+        {
+          groupIndex--;
+
+          continue;
+        }
       }
 
       if (forConservation)
       {
-        if (toChange instanceof ConservationColourScheme)
+        if (toChange.conservationApplied())
         {
-          ( (ConservationColourScheme) toChange).inc = i;
+          toChange.setConservationInc(i);
         }
       }
       else
       {
-        ( (ResidueColourScheme) toChange).setThreshold(i);
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
       }
 
       groupIndex--;
@@ -252,11 +292,21 @@ public class SliderPanel
     ap.seqPanel.seqCanvas.repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
   public void setAllGroupsCheckEnabled(boolean b)
   {
     allGroupsCheck.setEnabled(b);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
   public void valueField_actionPerformed(ActionEvent e)
   {
     try
@@ -264,19 +314,38 @@ public class SliderPanel
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
     }
-    catch (Exception ex)
+    catch (NumberFormatException ex)
     {
       valueField.setText(slider.getValue() + "");
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param value DOCUMENT ME!
+   */
   public void setValue(int value)
   {
     slider.setValue(value);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public int getValue()
   {
     return Integer.parseInt(valueField.getText());
   }
+
+  public void slider_mouseReleased(MouseEvent e)
+  {
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
+  }
+
 }