X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=37ab21974dbe015c9305c4b5e118ccc644f9baa7;hb=69b246bd6330f05271ca15a440c8442b03b7db6c;hp=5a87102af2a83712a64f1783338ff01408d81ae6;hpb=20c71abb4d963ff528c2cbad48d53ce85e7055c5;p=jalview.git

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 5a87102..37ab219 100755
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,233 +1,503 @@
-package jalview.gui;
-
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.datamodel.*;
-import java.awt.event.*;
-import javax.swing.event.*;
-import javax.swing.*;
-import java.util.*;
-
-public class SliderPanel extends GSliderPanel
-{
-  AlignmentPanel ap;
-  boolean forConservation = true;
-  ColourSchemeI cs;
-
-  static JInternalFrame conservationSlider;
-  static JInternalFrame PIDSlider;
-
-  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
-    {
-        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();
-  }
-
-  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);
-    }
-
-  }
-
-  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());
-
-
-     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();
-
-   }
-
-   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);
-    }
-
-   }
-
-
-  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 void valueChanged(int i)
-  {
-    if(cs == null)
-      return;
-
-    ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
-
-    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 (forConservation)
-      {
-        if (toChange instanceof ConservationColourScheme)
-          ( (ConservationColourScheme) toChange).inc = i;
-      }
-      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{
-      int i = Integer.parseInt(valueField.getText());
-      slider.setValue(i);
-    }
-    catch(Exception ex)
-    {
-      valueField.setText( slider.getValue()+"" );
-    }
-  }
-
-  public void setValue(int value)
-  {
-    slider.setValue(value);
-  }
-  public int getValue()
-  {
-    return Integer.parseInt(valueField.getText());
-  }
-
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+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;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel extends GSliderPanel
+{
+  private static final String BACKGROUND = "Background";
+
+  static JInternalFrame conservationSlider;
+
+  static JInternalFrame PIDSlider;
+
+  AlignmentPanel ap;
+
+  boolean forConservation = true;
+
+  ResidueShaderI cs;
+
+  /**
+   * Returns the currently displayed slider panel (or null if none).
+   * 
+   * @return
+   */
+  public static SliderPanel getSliderPanel()
+  {
+    if (conservationSlider != null && conservationSlider.isVisible())
+    {
+      return (SliderPanel) conservationSlider.getContentPane();
+    }
+    if (PIDSlider != null && PIDSlider.isVisible())
+    {
+      return (SliderPanel) PIDSlider.getContentPane();
+    }
+    return null;
+  }
+
+  /**
+   * Creates a new SliderPanel object.
+   * 
+   * @param ap
+   *          DOCUMENT ME!
+   * @param value
+   *          DOCUMENT ME!
+   * @param forConserve
+   *          DOCUMENT ME!
+   * @param scheme
+   *          DOCUMENT ME!
+   */
+  public SliderPanel(final AlignmentPanel ap, int value,
+          boolean forConserve, ResidueShaderI scheme)
+  {
+    this.ap = ap;
+    this.cs = scheme;
+    forConservation = forConserve;
+    undoButton.setVisible(false);
+    applyButton.setVisible(false);
+
+    if (forConservation)
+    {
+      label.setText(MessageManager.getString(
+              "label.enter_value_increase_conservation_visibility"));
+      slider.setMinimum(0);
+      slider.setMaximum(100);
+    }
+    else
+    {
+      label.setText(MessageManager.getString(
+              "label.enter_percentage_identity_above_which_colour_residues"));
+      slider.setMinimum(0);
+      slider.setMaximum(100);
+    }
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      @Override
+      public void stateChanged(ChangeEvent evt)
+      {
+        valueField.setText(String.valueOf(slider.getValue()));
+        valueChanged(slider.getValue());
+      }
+    });
+
+    slider.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mouseReleased(MouseEvent evt)
+      {
+        ap.paintAlignment(true, true);
+      }
+    });
+
+    slider.setValue(value);
+    valueField.setText(String.valueOf(value));
+  }
+
+  /**
+   * Method to 'set focus' of the Conservation slider panel
+   * 
+   * @param ap
+   *          the panel to repaint on change of slider
+   * @param rs
+   *          the colour scheme to update on change of slider
+   * @param source
+   *          a text description for the panel's title
+   * 
+   * @return
+   */
+  public static int setConservationSlider(AlignmentPanel ap,
+          ResidueShaderI rs, String source)
+  {
+    SliderPanel sliderPanel = null;
+
+    if (conservationSlider == null)
+    {
+      sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
+      conservationSlider = new JInternalFrame();
+      conservationSlider.setContentPane(sliderPanel);
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+    else
+    {
+      sliderPanel = (SliderPanel) conservationSlider.getContentPane();
+      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 == null ? BACKGROUND : source }));
+
+    List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+    if (groups != null && !groups.isEmpty())
+    {
+      sliderPanel.setAllGroupsCheckEnabled(true);
+      sliderPanel.allGroupsCheck
+              .setSelected(ap.av.getColourAppliesToAllGroups());
+    }
+    else
+    {
+      sliderPanel.setAllGroupsCheckEnabled(false);
+    }
+
+    return sliderPanel.getValue();
+  }
+
+  /**
+   * Hides the PID slider panel if it is shown
+   */
+  public static void hidePIDSlider()
+  {
+    if (PIDSlider != null)
+    {
+      try
+      {
+        PIDSlider.setClosed(true);
+        PIDSlider = null;
+      } catch (PropertyVetoException ex)
+      {
+      }
+    }
+  }
+
+  /**
+   * Hides the conservation slider panel if it is shown
+   */
+  public static void hideConservationSlider()
+  {
+    if (conservationSlider != null)
+    {
+      try
+      {
+        conservationSlider.setClosed(true);
+        conservationSlider = null;
+      } catch (PropertyVetoException ex)
+      {
+      }
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public static void showConservationSlider()
+  {
+    hidePIDSlider();
+
+    if (!conservationSlider.isVisible())
+    {
+      Desktop.addInternalFrame(conservationSlider,
+              conservationSlider.getTitle(), true, FRAME_WIDTH,
+              FRAME_HEIGHT, false, true);
+      conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
+      {
+        @Override
+        public void internalFrameClosed(InternalFrameEvent e)
+        {
+          conservationSlider = null;
+        }
+      });
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+  }
+
+  /**
+   * Method to 'set focus' of the PID slider panel
+   * 
+   * @param ap
+   *          the panel to repaint on change of slider
+   * @param rs
+   *          the colour scheme to update on change of slider
+   * @param source
+   *          a text description for the panel's title
+   * 
+   * @return
+   */
+  public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
+          String source)
+  {
+    int threshold = rs.getThreshold();
+
+    SliderPanel sliderPanel = null;
+
+    if (PIDSlider == null)
+    {
+      sliderPanel = new SliderPanel(ap, threshold, false, rs);
+      PIDSlider = new JInternalFrame();
+      PIDSlider.setContentPane(sliderPanel);
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+    else
+    {
+      sliderPanel = (SliderPanel) PIDSlider.getContentPane();
+      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 == null ? BACKGROUND : source }));
+
+    if (ap.av.getAlignment().getGroups() != null)
+    {
+      sliderPanel.setAllGroupsCheckEnabled(true);
+    }
+    else
+    {
+      sliderPanel.setAllGroupsCheckEnabled(false);
+    }
+
+    return sliderPanel.getValue();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return
+   */
+  public static JInternalFrame showPIDSlider()
+  {
+    hideConservationSlider();
+
+    if (!PIDSlider.isVisible())
+    {
+      Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), true,
+              FRAME_WIDTH, FRAME_HEIGHT, false, true);
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+      PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
+      {
+        @Override
+        public void internalFrameClosed(InternalFrameEvent e)
+        {
+          PIDSlider = null;
+        }
+      });
+      PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+    }
+    return PIDSlider;
+  }
+
+  /**
+   * Updates the colour scheme with the current (identity threshold or
+   * conservation) percentage value. Also updates all groups if 'apply to all
+   * groups' is selected.
+   * 
+   * @param percent
+   */
+  public void valueChanged(int percent)
+  {
+    if (!forConservation)
+    {
+      ap.av.setThreshold(percent);
+    }
+    updateColourScheme(percent, cs, null);
+
+    if (allGroupsCheck.isSelected())
+    {
+      List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+      for (SequenceGroup sg : groups)
+      {
+        updateColourScheme(percent, sg.getGroupColourScheme(), sg);
+      }
+    }
+
+    ap.getSeqPanel().seqCanvas.repaint();
+  }
+
+  /**
+   * Updates the colour scheme (if not null) with the current (identity
+   * threshold or conservation) percentage value
+   * 
+   * @param percent
+   * @param scheme
+   * @param sg
+   */
+  protected void updateColourScheme(int percent, ResidueShaderI scheme,
+          SequenceGroup sg)
+  {
+    if (scheme == null)
+    {
+      return;
+    }
+    if (forConservation)
+    {
+      if (!scheme.conservationApplied() && sg != null)
+      {
+        /*
+         * 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
+    {
+      scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setAllGroupsCheckEnabled(boolean b)
+  {
+    allGroupsCheck.setEnabled(b);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void valueField_actionPerformed()
+  {
+    try
+    {
+      int i = Integer.parseInt(valueField.getText());
+      slider.setValue(i);
+    } 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());
+  }
+
+  @Override
+  public void slider_mouseReleased(MouseEvent e)
+  {
+    if (ap.overviewPanel != null)
+    {
+      ap.overviewPanel.updateOverviewImage();
+    }
+  }
+
+  public static int getConservationValue()
+  {
+    return getValue(conservationSlider);
+  }
+
+  static int getValue(JInternalFrame slider)
+  {
+    return slider == null ? 0
+            : ((SliderPanel) slider.getContentPane()).getValue();
+  }
+
+  public static int getPIDValue()
+  {
+    return getValue(PIDSlider);
+  }
+
+  /**
+   * Answers true if the SliderPanel is for Conservation, false if it is for PID
+   * threshold
+   * 
+   * @return
+   */
+  public boolean isForConservation()
+  {
+    return forConservation;
+  }
+
+  /**
+   * Answers the title for the slider panel; this may include 'Background' if
+   * for the alignment, or the group id if for a group
+   * 
+   * @return
+   */
+  public String getTitle()
+  {
+    String title = null;
+    if (isForConservation())
+    {
+      if (conservationSlider != null)
+      {
+        title = conservationSlider.getTitle();
+      }
+    }
+    else if (PIDSlider != null)
+    {
+      title = PIDSlider.getTitle();
+    }
+    return title;
+  }
+}