From 627834dc46a79d74dec14c3d7a64a529f2337f6f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 30 Jan 2006 14:46:40 +0000
Subject: [PATCH] New Class

---
 src/jalview/gui/AnnotationColourChooser.java |  225 ++++++++++++++++++++++++++
 1 file changed, 225 insertions(+)
 create mode 100755 src/jalview/gui/AnnotationColourChooser.java

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
new file mode 100755
index 0000000..71cf688
--- /dev/null
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -0,0 +1,225 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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 javax.swing.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.awt.BorderLayout;
+import java.awt.*;
+
+import jalview.schemes.*;
+
+public class AnnotationColourChooser
+    extends JPanel
+{
+  JInternalFrame frame;
+  AlignViewport av;
+  AlignmentPanel ap;
+  ColourSchemeI oldcs;
+
+  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
+  {
+    oldcs = av.getGlobalColourScheme();
+    this.av = av;
+    this.ap = ap;
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 110);
+
+    try{
+      jbInit();
+    }catch(Exception ex){}
+
+    if(av.alignment.getAlignmentAnnotation()==null)
+      return;
+
+    for(int i=0; i<av.alignment.getAlignmentAnnotation().length; i++)
+    {
+      annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
+    }
+
+  //  if(av.getGlobalColourScheme() instanceof AnnotationColourGradient)
+    {
+    //  minColour.
+    }
+  //  else
+    {
+      minColour.setBackground(Color.orange);
+      maxColour.setBackground(Color.red);
+    }
+  }
+
+  public AnnotationColourChooser()
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    minColour.setBounds(new Rectangle(145, 5, 85, 25));
+    minColour.setToolTipText("");
+    minColour.setMargin(new Insets(2, 2, 2, 2));
+    minColour.setText("Min Colour");
+    minColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        minColour_actionPerformed(e);
+      }
+    });
+    maxColour.setBounds(new Rectangle(235, 5, 89, 25));
+    maxColour.setMargin(new Insets(2, 2, 2, 2));
+    maxColour.setText("Max Colour");
+    maxColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        maxColour_actionPerformed(e);
+      }
+    });
+    thresholdCheck.setOpaque(false);
+    thresholdCheck.setHorizontalTextPosition(SwingConstants.LEADING);
+    thresholdCheck.setSelectedIcon(null);
+    thresholdCheck.setText("Above Threshold");
+    thresholdCheck.setBounds(new Rectangle(329, 6, 109, 23));
+    apply.setOpaque(false);
+    apply.setSelectedIcon(null);
+    apply.setText("Apply");
+    apply.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        apply_actionPerformed(e);
+      }
+    });
+    ok.setOpaque(false);
+    ok.setText("OK");
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setOpaque(false);
+    cancel.setText("Cancel");
+    cancel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(null);
+    annotations.setBounds(new Rectangle(5, 7, 135, 21));
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+    jPanel1.add(apply);
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel2.add(annotations);
+    jPanel2.add(minColour);
+    jPanel2.add(maxColour);
+    jPanel2.add(thresholdCheck);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    this.add(jPanel2, java.awt.BorderLayout.CENTER);
+  }
+
+  JComboBox annotations = new JComboBox();
+  JButton minColour = new JButton();
+  JButton maxColour = new JButton();
+  JCheckBox thresholdCheck = new JCheckBox();
+  JButton apply = new JButton();
+  JButton ok = new JButton();
+  JButton cancel = new JButton();
+  JPanel jPanel1 = new JPanel();
+  JPanel jPanel2 = new JPanel();
+  BorderLayout borderLayout1 = new BorderLayout();
+  public void apply_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
+  public void minColour_actionPerformed(ActionEvent e)
+  {
+    Color col = JColorChooser.showDialog(this,
+                                         "Select Colour for Minimum Value",
+                                         minColour.getBackground());
+    if (col != null)
+      minColour.setBackground(col);
+    minColour.repaint();
+  }
+
+  public void maxColour_actionPerformed(ActionEvent e)
+  {
+    Color col = JColorChooser.showDialog(this,
+                                         "Select Colour for Maximum Value",
+                                         maxColour.getBackground());
+    if (col != null)
+      maxColour.setBackground(col);
+    maxColour.repaint();
+  }
+
+  void changeColour()
+  {
+    jalview.datamodel.AlignmentAnnotation aa = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
+
+    AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+     minColour.getBackground(),
+     maxColour.getBackground(),
+     thresholdCheck.isSelected());
+
+   if(thresholdCheck.isSelected() && aa.graphLines==null)
+   {
+     aa.addGraphLine(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));
+   }
+
+   av.setGlobalColourScheme(acg);
+   ap.repaint();
+
+  }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+    try{
+      frame.setClosed(true);
+    }catch(Exception ex){}
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    av.setGlobalColourScheme(oldcs);
+    try{
+      frame.setClosed(true);
+    }catch(Exception ex){}
+  }
+
+}
-- 
1.7.10.2