X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=98579ebe8af84e31ad1d84d9f24c62f7f3ccacc5;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=dee77d52bc2a6ab4cb3194611cc5d431261106af;hpb=c19a33d7b0583a0f855be33d5640a3158ec77b60;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index dee77d5..98579eb 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,94 +1,351 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.jbgui.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.util.*;
+
 import java.awt.event.*;
+import javax.swing.*;
 import javax.swing.event.*;
 
-public class SliderPanel extends GSliderPanel
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+
+/**
+ * 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)
+  /**
+   * 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)
   {
     this.ap = ap;
     this.cs = cs;
     forConservation = forConserve;
     undoButton.setVisible(false);
     applyButton.setVisible(false);
-    if(forConservation)
+
+    if (forConservation)
     {
-      label.setText("Enter the value by which to decrease conservation colour intensity");
+      label.setText("Enter value to increase conservation visibility");
       slider.setMinimum(0);
-      slider.setMaximum(50);
+      slider.setMaximum(100);
     }
     else
     {
-      label.setText("Enter the percent identity above which to colour residues");
+      label.setText("Enter % identity above which to colour residues");
       slider.setMinimum(0);
       slider.setMaximum(100);
     }
 
-
-
-    slider.addChangeListener( new ChangeListener()
+    slider.addChangeListener(new ChangeListener()
     {
       public void stateChanged(ChangeEvent evt)
       {
-        valueField.setText( slider.getValue()+"" );
-        valueChanged( slider.getValue() );
+        valueField.setText(slider.getValue() + "");
+        valueChanged(slider.getValue());
       }
     });
 
     slider.setValue(value);
-    valueField.setText(value+"");
+    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;
+
+    if (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.setTitle("Conservation Colour Increment  (" +
+                                source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      sp.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sp.setAllGroupsCheckEnabled(false);
+    }
+
+    return sp.getValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showConservationSlider()
+  {
+    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);
+    }
+  }
+
+  /**
+   * 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 = cs.getThreshold();
+
+    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;
+    }
+
+    PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+    if (ap.av.alignment.getGroups() != null)
+    {
+      pid.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      pid.setAllGroupsCheckEnabled(false);
+    }
+
+    return pid.getValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showPIDSlider()
+  {
+    try
+    {
+      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);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
   public void valueChanged(int i)
   {
+    if (cs == null)
+    {
+      return;
+    }
+
+    ColourSchemeI toChange = null;
+    Vector allGroups = null;
+    int groupIndex = 0;
 
-    if(forConservation)
+    if (allGroupsCheck.isSelected())
     {
-      if (cs instanceof ConservationColourScheme)
-        ( (ConservationColourScheme) cs).inc = i;
+      allGroups = ap.av.alignment.getGroups();
+      groupIndex = allGroups.size() - 1;
     }
     else
-     {
-       if( cs instanceof ResidueColourScheme)
-       {
-         ResidueColourScheme rcs = (ResidueColourScheme) cs;
-         rcs.setThreshold(i);
-       }
-       else if( cs instanceof ScoreColourScheme)
-       {
-         ScoreColourScheme scs = (ScoreColourScheme) cs;
-         scs.setThreshold(i);
-       }
-
-     }
-
-    ap.seqPanel.seqCanvas.paintFlag=true;
-    ap.seqPanel.repaint();
+    {
+      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();
   }
 
+  /**
+   * 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{
+    try
+    {
       int i = Integer.parseInt(valueField.getText());
       slider.setValue(i);
     }
-    catch(Exception ex)
+    catch (NumberFormatException ex)
     {
-      valueField.setText( slider.getValue()+"" );
+      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();
+    }
+  }
+
 }