X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=b830d5db30bbc25c5cb115dfb108acf3818deada;hb=69e9cd54dcfd25dd3067f353bc53eb6b4d7e27af;hp=1a62fffee304c1f46c14ec316d1cbbacf6caffc4;hpb=813abcbd234db6ac665bf43ffc17759f33667015;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 1a62fff..b830d5d 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -18,270 +18,328 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
 
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
 
-public class SliderPanel
-    extends GSliderPanel
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel extends GSliderPanel
 {
-  static JInternalFrame conservationSlider;
-  static JInternalFrame PIDSlider;
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
-                     ColourSchemeI cs)
-  {
-    this.ap = ap;
-    this.cs = cs;
-    forConservation = forConserve;
-    undoButton.setVisible(false);
-    applyButton.setVisible(false);
-
-    if (forConservation)
-    {
-      label.setText("Enter value to increase conservation visibility");
-      slider.setMinimum(0);
-      slider.setMaximum(50);
-    }
-    else
-    {
-      label.setText("Enter % identity above which to colour residues");
-      slider.setMinimum(0);
-      slider.setMaximum(100);
-    }
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        valueField.setText(slider.getValue() + "");
-        valueChanged(slider.getValue());
-      }
-    });
-
-    slider.setValue(value);
-    valueField.setText(value + "");
-  }
-
-  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);
-      conservationSlider = new JInternalFrame();
-      conservationSlider.setContentPane(sp);
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-    else
+    static JInternalFrame conservationSlider;
+    static JInternalFrame PIDSlider;
+    AlignmentPanel ap;
+    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)
     {
-      sp = (SliderPanel) conservationSlider.getContentPane();
-      sp.cs = cs;
-    }
+        this.ap = ap;
+        this.cs = cs;
+        forConservation = forConserve;
+        undoButton.setVisible(false);
+        applyButton.setVisible(false);
 
-    conservationSlider.setTitle("Conservation Colour Increment  (" +
-                                source + ")");
+        if (forConservation)
+        {
+            label.setText("Enter value to increase conservation visibility");
+            slider.setMinimum(0);
+            slider.setMaximum(100);
+        }
+        else
+        {
+            label.setText("Enter % identity above which to colour residues");
+            slider.setMinimum(0);
+            slider.setMaximum(100);
+        }
 
-    if (ap.av.alignment.getGroups() != null)
-    {
-      sp.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      sp.setAllGroupsCheckEnabled(false);
+        slider.addChangeListener(new ChangeListener()
+            {
+                public void stateChanged(ChangeEvent evt)
+                {
+                    valueField.setText(slider.getValue() + "");
+                    valueChanged(slider.getValue());
+                }
+            });
+
+        slider.setValue(value);
+        valueField.setText(value + "");
     }
 
-    return sp.getValue();
-  }
 
-  public static void showConservationSlider()
-  {
-    try
+    /**
+     * 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)
     {
-      PIDSlider.setClosed(true);
-      PIDSlider = null;
-    }
-    catch (Exception ex)
-    {
-    }
+        SliderPanel sp = null;
 
-    if (!conservationSlider.isVisible())
-    {
-      Desktop.addInternalFrame(conservationSlider,
-                               conservationSlider.getTitle(), 420, 90, false);
-      conservationSlider.addInternalFrameListener(new javax.swing.event.
-                                                  InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
+        if (conservationSlider == null)
         {
-          conservationSlider = null;
+            sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+            conservationSlider = new JInternalFrame();
+            conservationSlider.setContentPane(sp);
+            conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        }
+        else
+        {
+            sp = (SliderPanel) conservationSlider.getContentPane();
+            sp.cs = cs;
         }
-      });
-      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-    }
-  }
 
-  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
-                                       String source)
-  {
-    SliderPanel pid = null;
+        conservationSlider.setTitle("Conservation Colour Increment  (" +
+            source + ")");
 
-    int threshold = 50;
+        if (ap.av.alignment.getGroups() != null)
+        {
+            sp.setAllGroupsCheckEnabled(true);
+        }
+        else
+        {
+            sp.setAllGroupsCheckEnabled(false);
+        }
 
-    if (cs instanceof ResidueColourScheme)
-    {
-      threshold = ( ( (ResidueColourScheme) cs).getThreshold());
-    }
-    else if (cs instanceof ScoreColourScheme)
-    {
-      threshold = ( ( (ScoreColourScheme) cs).getThreshold());
+        return sp.getValue();
     }
 
-    if (PIDSlider == null)
+    /**
+     * DOCUMENT ME!
+     */
+    public static void showConservationSlider()
     {
-      pid = new SliderPanel(ap, threshold, false, cs);
-      PIDSlider = new JInternalFrame();
-      PIDSlider.setContentPane(pid);
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        try
+        {
+            PIDSlider.setClosed(true);
+            PIDSlider = null;
+        }
+        catch (Exception ex)
+        {
+        }
+
+        if (!conservationSlider.isVisible())
+        {
+            Desktop.addInternalFrame(conservationSlider,
+                conservationSlider.getTitle(), 420, 90, false);
+            conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                {
+                    public void internalFrameClosed(
+                        javax.swing.event.InternalFrameEvent e)
+                    {
+                        conservationSlider = null;
+                    }
+                });
+            conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        }
     }
-    else
+
+    /**
+     * 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)
     {
-      pid = (SliderPanel) PIDSlider.getContentPane();
-      pid.cs = cs;
-    }
+        SliderPanel pid = null;
 
-    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+        int threshold = cs.getThreshold();
 
-    if (ap.av.alignment.getGroups() != null)
-    {
-      pid.setAllGroupsCheckEnabled(true);
-    }
-    else
-    {
-      pid.setAllGroupsCheckEnabled(false);
-    }
+        if (PIDSlider == null)
+        {
+            pid = new SliderPanel(ap, threshold, false, cs);
+            PIDSlider = new JInternalFrame();
+            PIDSlider.setContentPane(pid);
+            PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+        }
+        else
+        {
+            pid = (SliderPanel) PIDSlider.getContentPane();
+            pid.cs = cs;
+        }
 
-    return pid.getValue();
-  }
+        PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-  public static void showPIDSlider()
-  {
-    try
-    {
-      conservationSlider.setClosed(true);
-      conservationSlider = null;
-    }
-    catch (Exception ex)
-    {
+        if (ap.av.alignment.getGroups() != null)
+        {
+            pid.setAllGroupsCheckEnabled(true);
+        }
+        else
+        {
+            pid.setAllGroupsCheckEnabled(false);
+        }
+
+        return pid.getValue();
     }
 
-    if (!PIDSlider.isVisible())
+    /**
+     * DOCUMENT ME!
+     */
+    public static void showPIDSlider()
     {
-      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
-                               false);
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
-      PIDSlider.addInternalFrameListener(new javax.swing.event.
-                                         InternalFrameAdapter()
-      {
-        public void internalFrameClosed(
-            javax.swing.event.InternalFrameEvent e)
+        try
         {
-          PIDSlider = null;
+            conservationSlider.setClosed(true);
+            conservationSlider = null;
+        }
+        catch (Exception ex)
+        {
+        }
+
+        if (!PIDSlider.isVisible())
+        {
+            Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
+                false);
+            PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+            PIDSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+                {
+                    public void internalFrameClosed(
+                        javax.swing.event.InternalFrameEvent e)
+                    {
+                        PIDSlider = null;
+                    }
+                });
+            PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
         }
-      });
-      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
     }
-  }
 
-  public void valueChanged(int i)
-  {
-    if (cs == null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void valueChanged(int i)
     {
-      return;
-    }
+        if (cs == null)
+        {
+            return;
+        }
 
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
+        ColourSchemeI toChange = null;
+        Vector allGroups = null;
+        int groupIndex = 0;
 
-    if (allGroupsCheck.isSelected())
-    {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
+        if (allGroupsCheck.isSelected())
+        {
+            allGroups = ap.av.alignment.getGroups();
+            groupIndex = allGroups.size() - 1;
+        }
+        else
+        {
+            toChange = cs;
+        }
+
+
+        while (groupIndex > -1)
+        {
+            if (allGroups != null)
+            {
+                toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
+
+                if (toChange == null)
+                {
+                    groupIndex--;
+
+                    continue;
+                }
+            }
+
+            if (forConservation)
+            {
+                if (toChange.conservationApplied())
+                {
+                    toChange.setConservationInc(i);
+                }
+            }
+            else
+            {
+                toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+            }
+
+            groupIndex--;
+        }
+
+        ap.seqPanel.seqCanvas.repaint();
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAllGroupsCheckEnabled(boolean b)
     {
-      toChange = cs;
+        allGroupsCheck.setEnabled(b);
     }
 
-    while (groupIndex > -1)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void valueField_actionPerformed(ActionEvent e)
     {
-      if (allGroups != null)
-      {
-        toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;
-        if(toChange==null)
+        try
         {
-          groupIndex--;
-          continue;
+            int i = Integer.parseInt(valueField.getText());
+            slider.setValue(i);
         }
-      }
-
-      if (forConservation)
-      {
-        if (toChange instanceof ConservationColourScheme)
+        catch (NumberFormatException ex)
         {
-          ( (ConservationColourScheme) toChange).inc = i;
+            valueField.setText(slider.getValue() + "");
         }
-      }
-      else
-      {
-        ( (ResidueColourScheme) toChange).setThreshold(i);
-      }
-
-      groupIndex--;
     }
 
-    ap.seqPanel.seqCanvas.repaint();
-  }
-
-  public void setAllGroupsCheckEnabled(boolean b)
-  {
-    allGroupsCheck.setEnabled(b);
-  }
-
-  public void valueField_actionPerformed(ActionEvent e)
-  {
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param value DOCUMENT ME!
+     */
+    public void setValue(int value)
     {
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
+        slider.setValue(value);
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getValue()
     {
-      valueField.setText(slider.getValue() + "");
+        return Integer.parseInt(valueField.getText());
     }
-  }
-
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
 }