Annotation colours added to applet

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
new file mode 100755 (executable)
index 0000000..1c73f7b
--- /dev/null
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -0,0 +1,403 @@
+/*\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.appletgui;\r
+\r
+import java.awt.event.*;\r
+import java.awt.*;\r
+\r
+import jalview.schemes.*;\r
+import java.util.*;\r
+import jalview.datamodel.SequenceGroup;\r
+\r
+public class AnnotationColourChooser extends Panel implements ActionListener,\r
+    AdjustmentListener, ItemListener\r
+{\r
+  Frame frame;\r
+  AlignViewport av;\r
+  AlignmentPanel ap;\r
+  ColourSchemeI oldcs;\r
+  Hashtable oldgroupColours;\r
+  jalview.datamodel.AlignmentAnnotation currentAnnotation;\r
+  boolean adjusting = false;\r
+\r
+  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)\r
+  {\r
+    try\r
+    {\r
+      jbInit();\r
+    }\r
+    catch (Exception ex)\r
+    {}\r
+\r
+    oldcs = av.getGlobalColourScheme();\r
+    if (av.alignment.getGroups() != null)\r
+    {\r
+      oldgroupColours = new Hashtable();\r
+      Vector allGroups = ap.av.alignment.getGroups();\r
+      SequenceGroup sg;\r
+      for (int g = 0; g < allGroups.size(); g++)\r
+      {\r
+        sg = (SequenceGroup) allGroups.elementAt(g);\r
+        oldgroupColours.put(sg, sg.cs);\r
+      }\r
+    }\r
+    this.av = av;\r
+    this.ap = ap;\r
+\r
+    slider.addAdjustmentListener(this);\r
+\r
+    if (av.alignment.getAlignmentAnnotation() == null)\r
+      return;\r
+\r
+    if (oldcs instanceof AnnotationColourGradient)\r
+    {\r
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;\r
+      minColour.setBackground(acg.getMinColour());\r
+      maxColour.setBackground(acg.getMaxColour());\r
+    }\r
+    else\r
+    {\r
+      minColour.setBackground(Color.orange);\r
+      maxColour.setBackground(Color.red);\r
+    }\r
+\r
+    adjusting = true;\r
+    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)\r
+    {\r
+      if (av.alignment.getAlignmentAnnotation()[i].graph > 0)\r
+        annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);\r
+    }\r
+\r
+    threshold.addItem("No Threshold");\r
+    threshold.addItem("Above Threshold");\r
+    threshold.addItem("Below Threshold");\r
+\r
+    adjusting = false;\r
+\r
+    changeColour();\r
+\r
+    frame = new Frame();\r
+    frame.add(this);\r
+    jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145);\r
+    validate();\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.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    minColour.setLabel("Min Colour");\r
+    minColour.addActionListener(this);\r
+\r
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    maxColour.setLabel("Max Colour");\r
+    maxColour.addActionListener(this);\r
+\r
+    ok.setLabel("OK");\r
+    ok.addActionListener(this);\r
+\r
+    cancel.setLabel("Cancel");\r
+    cancel.addActionListener(this);\r
+\r
+    this.setLayout(borderLayout1);\r
+    jPanel2.setLayout(flowLayout1);\r
+    annotations.addItemListener(this);\r
+\r
+    jPanel1.setBackground(Color.white);\r
+    jPanel2.setBackground(Color.white);\r
+    threshold.addItemListener(this);\r
+    jPanel3.setLayout(null);\r
+    thresholdValue.addActionListener(this);\r
+\r
+    slider.setBackground(Color.white);\r
+    slider.setEnabled(false);\r
+    slider.setBounds(new Rectangle(172, 7, 120, 16));\r
+    thresholdValue.setEnabled(false);\r
+    thresholdValue.setBounds(new Rectangle(295, 4, 83, 22));\r
+    thresholdValue.setColumns(10);\r
+    jPanel3.setBackground(Color.white);\r
+    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    currentColours.setLabel("Use Original Colours");\r
+    currentColours.addItemListener(this);\r
+\r
+    threshold.setBounds(new Rectangle(19, 4, 141, 22));\r
+    jPanel1.add(ok);\r
+    jPanel1.add(cancel);\r
+    jPanel2.add(annotations);\r
+    jPanel2.add(currentColours);\r
+    jPanel2.add(minColour);\r
+    jPanel2.add(maxColour);\r
+    jPanel3.add(threshold);\r
+    jPanel3.add(slider);\r
+    jPanel3.add(thresholdValue);\r
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);\r
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+  }\r
+\r
+  Choice annotations = new Choice();\r
+  Button minColour = new Button();\r
+  Button maxColour = new Button();\r
+  Button ok = new Button();\r
+  Button cancel = new Button();\r
+  Panel jPanel1 = new Panel();\r
+  Panel jPanel2 = new Panel();\r
+  Choice threshold = new Choice();\r
+  FlowLayout flowLayout1 = new FlowLayout();\r
+  Panel jPanel3 = new Panel();\r
+  Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);\r
+  TextField thresholdValue = new TextField(20);\r
+  Checkbox currentColours = new Checkbox();\r
+  BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+\r
+  public void actionPerformed(ActionEvent evt)\r
+  {\r
+    if(evt.getSource() == thresholdValue)\r
+    {\r
+      try\r
+      {\r
+        float f = new Float(thresholdValue.getText()).floatValue();\r
+        slider.setValue( (int) (f * 1000));\r
+        adjustmentValueChanged(null);\r
+      }\r
+      catch (NumberFormatException ex)\r
+      {}\r
+    }\r
+    else if (evt.getSource() == minColour)\r
+      minColour_actionPerformed(null);\r
+    else if (evt.getSource() == maxColour)\r
+      maxColour_actionPerformed(null);\r
+\r
+    else if (evt.getSource() == ok)\r
+    {\r
+      changeColour();\r
+      frame.setVisible(false);\r
+    }\r
+    else if (evt.getSource() == cancel)\r
+    {\r
+      reset();\r
+      ap.repaint();\r
+      frame.setVisible(false);\r
+    }\r
+\r
+    else\r
+      changeColour();\r
+  }\r
+\r
+\r
+  public void itemStateChanged(ItemEvent evt)\r
+  {\r
+    if (evt.getSource() == currentColours)\r
+    {\r
+      if (currentColours.getState())\r
+      {\r
+        reset();\r
+      }\r
+\r
+      maxColour.setEnabled(!currentColours.getState());\r
+      minColour.setEnabled(!currentColours.getState());\r
+\r
+    }\r
+\r
+    changeColour();\r
+  }\r
+\r
+  public void adjustmentValueChanged(AdjustmentEvent evt)\r
+  {\r
+    if (!adjusting)\r
+    {\r
+      thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");\r
+      if (currentColours.getState()\r
+          && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))\r
+      {\r
+        changeColour();\r
+      }\r
+\r
+      currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;\r
+      ap.repaint();\r
+    }\r
+  }\r
+\r
+  public void minColour_actionPerformed(Color newCol)\r
+  {\r
+    if (newCol != null)\r
+    {\r
+      minColour.setBackground(newCol);\r
+      minColour.repaint();\r
+      changeColour();\r
+    }\r
+    else\r
+      new UserDefinedColours(this, "Min Colour",\r
+                              minColour.getBackground());\r
+\r
+  }\r
+\r
+  public void maxColour_actionPerformed(Color newCol)\r
+  {\r
+    if (newCol != null)\r
+    {\r
+      maxColour.setBackground(newCol);\r
+      maxColour.repaint();\r
+      changeColour();\r
+    }\r
+    else\r
+      new UserDefinedColours(this, "Max Colour",\r
+                              maxColour.getBackground());\r
+  }\r
+\r
+\r
+  void changeColour()\r
+  {\r
+    // Check if combobox is still adjusting\r
+    if (adjusting)\r
+      return;\r
+\r
+    // We removed the non-graph annotations when filling the combobox\r
+    // so allow for them again here\r
+    int nograph = 0, graph = -1;\r
+    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)\r
+    {\r
+      if (av.alignment.getAlignmentAnnotation()[i].graph == 0)\r
+        nograph++;\r
+      else\r
+        graph++;\r
+\r
+      if (graph == annotations.getSelectedIndex())\r
+        break;\r
+    }\r
+\r
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];\r
+\r
+    int aboveThreshold = -1;\r
+    if (threshold.getSelectedItem().equals("Above Threshold"))\r
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
+    else if (threshold.getSelectedItem().equals("Below Threshold"))\r
+      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;\r
+\r
+    slider.setEnabled(true);\r
+    thresholdValue.setEnabled(true);\r
+\r
+    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)\r
+    {\r
+      slider.setEnabled(false);\r
+      thresholdValue.setEnabled(false);\r
+      thresholdValue.setText("");\r
+    }\r
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&\r
+             currentAnnotation.threshold == null)\r
+    {\r
+      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine\r
+                                     ( (currentAnnotation.graphMax -\r
+                                        currentAnnotation.graphMin) / 2f,\r
+                                      "Threshold",\r
+                                      Color.black));\r
+    }\r
+\r
+    if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)\r
+    {\r
+      adjusting = true;\r
+\r
+      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));\r
+      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));\r
+      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));\r
+      thresholdValue.setText(currentAnnotation.threshold.value + "");\r
+      slider.setEnabled(true);\r
+      thresholdValue.setEnabled(true);\r
+      adjusting = false;\r
+    }\r
+\r
+    AnnotationColourGradient acg = null;\r
+    if (currentColours.getState())\r
+      acg = new AnnotationColourGradient(\r
+          currentAnnotation,\r
+          av.getGlobalColourScheme(), aboveThreshold);\r
+    else\r
+      acg =\r
+          new AnnotationColourGradient(\r
+              currentAnnotation,\r
+              minColour.getBackground(),\r
+              maxColour.getBackground(),\r
+              aboveThreshold);\r
+\r
+    av.setGlobalColourScheme(acg);\r
+\r
+    if (av.alignment.getGroups() != null)\r
+    {\r
+      Vector allGroups = ap.av.alignment.getGroups();\r
+      SequenceGroup sg;\r
+      for (int g = 0; g < allGroups.size(); g++)\r
+      {\r
+        sg = (SequenceGroup) allGroups.elementAt(g);\r
+\r
+        if (sg.cs == null)\r
+        {\r
+          continue;\r
+        }\r
+\r
+        if (currentColours.getState())\r
+          sg.cs = new AnnotationColourGradient(\r
+              currentAnnotation,\r
+              sg.cs, aboveThreshold);\r
+        else\r
+          sg.cs = new AnnotationColourGradient(\r
+              currentAnnotation,\r
+              minColour.getBackground(),\r
+              maxColour.getBackground(),\r
+              aboveThreshold);\r
+\r
+      }\r
+    }\r
+\r
+    ap.repaint();\r
+  }\r
+\r
+\r
+  void reset()\r
+  {\r
+    av.setGlobalColourScheme(oldcs);\r
+    if (av.alignment.getGroups() != null)\r
+    {\r
+      Vector allGroups = ap.av.alignment.getGroups();\r
+      SequenceGroup sg;\r
+      for (int g = 0; g < allGroups.size(); g++)\r
+      {\r
+        sg = (SequenceGroup) allGroups.elementAt(g);\r
+        sg.cs = (ColourSchemeI)oldgroupColours.get(sg);\r
+      }\r
+    }\r
+    ap.repaint();\r
+\r
+  }\r
+\r
+\r
+\r
+}\r