New Class

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
new file mode 100755 (executable)
index 0000000..71cf688
--- /dev/null
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -0,0 +1,225 @@
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
+package jalview.gui;\r
+\r
+import javax.swing.*;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.BorderLayout;\r
+import java.awt.*;\r
+\r
+import jalview.schemes.*;\r
+\r
+public class AnnotationColourChooser\r
+    extends JPanel\r
+{\r
+  JInternalFrame frame;\r
+  AlignViewport av;\r
+  AlignmentPanel ap;\r
+  ColourSchemeI oldcs;\r
+\r
+  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)\r
+  {\r
+    oldcs = av.getGlobalColourScheme();\r
+    this.av = av;\r
+    this.ap = ap;\r
+    frame = new JInternalFrame();\r
+    frame.setContentPane(this);\r
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 110);\r
+\r
+    try{\r
+      jbInit();\r
+    }catch(Exception ex){}\r
+\r
+    if(av.alignment.getAlignmentAnnotation()==null)\r
+      return;\r
+\r
+    for(int i=0; i<av.alignment.getAlignmentAnnotation().length; i++)\r
+    {\r
+      annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);\r
+    }\r
+\r
+  //  if(av.getGlobalColourScheme() instanceof AnnotationColourGradient)\r
+    {\r
+    //  minColour.\r
+    }\r
+  //  else\r
+    {\r
+      minColour.setBackground(Color.orange);\r
+      maxColour.setBackground(Color.red);\r
+    }\r
+  }\r
+\r
+  public AnnotationColourChooser()\r
+  {\r
+    try\r
+    {\r
+      jbInit();\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+  }\r
+\r
+  private void jbInit()\r
+      throws Exception\r
+  {\r
+    minColour.setBounds(new Rectangle(145, 5, 85, 25));\r
+    minColour.setToolTipText("");\r
+    minColour.setMargin(new Insets(2, 2, 2, 2));\r
+    minColour.setText("Min Colour");\r
+    minColour.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        minColour_actionPerformed(e);\r
+      }\r
+    });\r
+    maxColour.setBounds(new Rectangle(235, 5, 89, 25));\r
+    maxColour.setMargin(new Insets(2, 2, 2, 2));\r
+    maxColour.setText("Max Colour");\r
+    maxColour.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        maxColour_actionPerformed(e);\r
+      }\r
+    });\r
+    thresholdCheck.setOpaque(false);\r
+    thresholdCheck.setHorizontalTextPosition(SwingConstants.LEADING);\r
+    thresholdCheck.setSelectedIcon(null);\r
+    thresholdCheck.setText("Above Threshold");\r
+    thresholdCheck.setBounds(new Rectangle(329, 6, 109, 23));\r
+    apply.setOpaque(false);\r
+    apply.setSelectedIcon(null);\r
+    apply.setText("Apply");\r
+    apply.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        apply_actionPerformed(e);\r
+      }\r
+    });\r
+    ok.setOpaque(false);\r
+    ok.setText("OK");\r
+    ok.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        ok_actionPerformed(e);\r
+      }\r
+    });\r
+    cancel.setOpaque(false);\r
+    cancel.setText("Cancel");\r
+    cancel.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        cancel_actionPerformed(e);\r
+      }\r
+    });\r
+    this.setLayout(borderLayout1);\r
+    jPanel2.setLayout(null);\r
+    annotations.setBounds(new Rectangle(5, 7, 135, 21));\r
+    jPanel1.setBackground(Color.white);\r
+    jPanel2.setBackground(Color.white);\r
+    jPanel1.add(apply);\r
+    jPanel1.add(ok);\r
+    jPanel1.add(cancel);\r
+    jPanel2.add(annotations);\r
+    jPanel2.add(minColour);\r
+    jPanel2.add(maxColour);\r
+    jPanel2.add(thresholdCheck);\r
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+    this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
+  }\r
+\r
+  JComboBox annotations = new JComboBox();\r
+  JButton minColour = new JButton();\r
+  JButton maxColour = new JButton();\r
+  JCheckBox thresholdCheck = new JCheckBox();\r
+  JButton apply = new JButton();\r
+  JButton ok = new JButton();\r
+  JButton cancel = new JButton();\r
+  JPanel jPanel1 = new JPanel();\r
+  JPanel jPanel2 = new JPanel();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+  public void apply_actionPerformed(ActionEvent e)\r
+  {\r
+    changeColour();\r
+  }\r
+\r
+  public void minColour_actionPerformed(ActionEvent e)\r
+  {\r
+    Color col = JColorChooser.showDialog(this,\r
+                                         "Select Colour for Minimum Value",\r
+                                         minColour.getBackground());\r
+    if (col != null)\r
+      minColour.setBackground(col);\r
+    minColour.repaint();\r
+  }\r
+\r
+  public void maxColour_actionPerformed(ActionEvent e)\r
+  {\r
+    Color col = JColorChooser.showDialog(this,\r
+                                         "Select Colour for Maximum Value",\r
+                                         maxColour.getBackground());\r
+    if (col != null)\r
+      maxColour.setBackground(col);\r
+    maxColour.repaint();\r
+  }\r
+\r
+  void changeColour()\r
+  {\r
+    jalview.datamodel.AlignmentAnnotation aa = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];\r
+\r
+    AnnotationColourGradient acg = new AnnotationColourGradient(aa,\r
+     minColour.getBackground(),\r
+     maxColour.getBackground(),\r
+     thresholdCheck.isSelected());\r
+\r
+   if(thresholdCheck.isSelected() && aa.graphLines==null)\r
+   {\r
+     aa.addGraphLine(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));\r
+   }\r
+\r
+   av.setGlobalColourScheme(acg);\r
+   ap.repaint();\r
+\r
+  }\r
+\r
+  public void ok_actionPerformed(ActionEvent e)\r
+  {\r
+    changeColour();\r
+    try{\r
+      frame.setClosed(true);\r
+    }catch(Exception ex){}\r
+  }\r
+\r
+  public void cancel_actionPerformed(ActionEvent e)\r
+  {\r
+    av.setGlobalColourScheme(oldcs);\r
+    try{\r
+      frame.setClosed(true);\r
+    }catch(Exception ex){}\r
+  }\r
+\r
+}\r