-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.Rectangle;\r
-\r
-public class AnnotationColourChooser\r
- extends Panel implements ActionListener,\r
- AdjustmentListener, ItemListener, MouseListener\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
- slider.addMouseListener(this);\r
-\r
- if (av.alignment.getAlignmentAnnotation() == null)\r
- {\r
- return;\r
- }\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
-\r
- Vector list = new Vector();\r
- int index = 1;\r
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)\r
- {\r
- String label = av.alignment.getAlignmentAnnotation()[i].label;\r
- if (!list.contains(label))\r
- list.addElement(label);\r
- else\r
- list.addElement(label+"_"+(index++));\r
- }\r
-\r
- for (int i = 0; i < list.size(); i++)\r
- {\r
- annotations.addItem(list.elementAt(i).toString());\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
- thresholdIsMin.addItemListener(this);\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(125, 6, 82, 16));\r
- thresholdValue.setEnabled(false);\r
- thresholdValue.setBounds(new Rectangle(211, 4, 56, 22));\r
- thresholdValue.setColumns(5);\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(11, 3, 113, 22));\r
- thresholdIsMin.setBackground(Color.white);\r
- thresholdIsMin.setLabel("Threshold is min/max");\r
- thresholdIsMin.setBounds(new Rectangle(270, 3, 135, 23));\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
- jPanel3.add(thresholdIsMin);\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
- Checkbox thresholdIsMin = new Checkbox();\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
- {\r
- minColour_actionPerformed(null);\r
- }\r
- else if (evt.getSource() == maxColour)\r
- {\r
- maxColour_actionPerformed(null);\r
- }\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.paintAlignment(true);\r
- frame.setVisible(false);\r
- }\r
-\r
- else\r
- {\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.paintAlignment(false);\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
- {\r
- new UserDefinedColours(this, "Min Colour",\r
- minColour.getBackground());\r
- }\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
- {\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
- {\r
- return;\r
- }\r
-\r
-\r
- currentAnnotation = av.alignment.getAlignmentAnnotation()\r
- [annotations.getSelectedIndex()];\r
-\r
- int aboveThreshold = -1;\r
- if (threshold.getSelectedItem().equals("Above Threshold"))\r
- {\r
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
- }\r
- else if (threshold.getSelectedItem().equals("Below Threshold"))\r
- {\r
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;\r
- }\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
- {\r
- acg = new AnnotationColourGradient(\r
- currentAnnotation,\r
- av.getGlobalColourScheme(), aboveThreshold);\r
- }\r
- else\r
- {\r
- acg =\r
- new AnnotationColourGradient(\r
- currentAnnotation,\r
- minColour.getBackground(),\r
- maxColour.getBackground(),\r
- aboveThreshold);\r
- }\r
-\r
- if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)\r
- {\r
- acg.predefinedColours = true;\r
- }\r
-\r
- acg.thresholdIsMinMax = thresholdIsMin.getState();\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
- {\r
- sg.cs = new AnnotationColourGradient(\r
- currentAnnotation,\r
- sg.cs, aboveThreshold);\r
- }\r
- else\r
- {\r
- sg.cs = new AnnotationColourGradient(\r
- currentAnnotation,\r
- minColour.getBackground(),\r
- maxColour.getBackground(),\r
- aboveThreshold);\r
- }\r
-\r
- }\r
- }\r
-\r
- ap.paintAlignment(false);\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.paintAlignment(true);\r
-\r
- }\r
-\r
- public void mouseClicked(MouseEvent evt){}\r
- public void mousePressed(MouseEvent evt){}\r
- public void mouseReleased(MouseEvent evt){ ap.paintAlignment(true);}\r
- public void mouseEntered(MouseEvent evt){}\r
- public void mouseExited(MouseEvent evt){}\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.appletgui;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
+public class AnnotationColourChooser extends Panel implements
+ ActionListener, AdjustmentListener, ItemListener, MouseListener
+{
+ Frame frame;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ ColourSchemeI oldcs;
+
+ Hashtable oldgroupColours;
+
+ jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
+ boolean adjusting = false;
+
+ public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ }
+
+ oldcs = av.getGlobalColourScheme();
+ if (av.getAlignment().getGroups() != null)
+ {
+ oldgroupColours = new Hashtable();
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs != null)
+ {
+ oldgroupColours.put(sg, sg.cs);
+ }
+ else
+ {
+ oldgroupColours.put(sg, "null");
+ }
+ }
+ }
+ this.av = av;
+ this.ap = ap;
+
+ slider.addAdjustmentListener(this);
+ slider.addMouseListener(this);
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ setDefaultMinMax();
+
+ adjusting = true;
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ currentColours.setState(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
+ {
+ minColour.setBackground(acg.getMinColour());
+ maxColour.setBackground(acg.getMaxColour());
+ }
+ // seqAssociated.setState(acg.isSeqAssociated());
+ }
+
+ Vector list = new Vector();
+ int index = 1;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ if (!list.contains(label))
+ {
+ list.addElement(label);
+ }
+ else
+ {
+ list.addElement(label + "_" + (index++));
+ }
+ }
+
+ for (int i = 0; i < list.size(); i++)
+ {
+ annotations.addItem(list.elementAt(i).toString());
+ }
+
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_thereshold"));
+
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ annotations.select(acg.getAnnotation());
+ switch (acg.getAboveThreshold())
+ {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ threshold.select(0);
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ threshold.select(1);
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ threshold.select(1);
+ break;
+ default:
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
+ }
+ thresholdIsMin.setState(acg.thresholdIsMinMax);
+ thresholdValue.setText("" + acg.getAnnotationThreshold());
+ }
+
+ adjusting = false;
+
+ changeColour();
+
+ frame = new Frame();
+ frame.add(this);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 560,
+ 175);
+ validate();
+ }
+
+ private void setDefaultMinMax()
+ {
+ minColour.setBackground(av.applet.getDefaultColourParameter(
+ "ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(av.applet.getDefaultColourParameter(
+ "ANNOTATIONCOLOUR_MAX", Color.red));
+
+ }
+
+ public AnnotationColourChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ minColour.setLabel(MessageManager.getString("label.min_colour"));
+ minColour.addActionListener(this);
+
+ maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ maxColour.setLabel(MessageManager.getString("label.max_colour"));
+ maxColour.addActionListener(this);
+
+ thresholdIsMin.addItemListener(this);
+ ok.setLabel(MessageManager.getString("action.ok"));
+ ok.addActionListener(this);
+
+ cancel.setLabel(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(this);
+
+ defColours.setLabel(MessageManager.getString("action.set_defaults"));
+ defColours.addActionListener(this);
+
+ annotations.addItemListener(this);
+
+ thresholdValue.addActionListener(this);
+ slider.setBackground(Color.white);
+ slider.setPreferredSize(new Dimension(193, 21));
+ slider.setEnabled(false);
+ thresholdValue.setPreferredSize(new Dimension(79, 22));
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(5);
+ currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ currentColours.setLabel(MessageManager
+ .getString("label.use_original_colours"));
+ currentColours.addItemListener(this);
+
+ thresholdIsMin.setBackground(Color.white);
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
+
+ this.setLayout(borderLayout1);
+
+ jPanel1.setBackground(Color.white);
+
+ jPanel2.setLayout(new FlowLayout());
+ jPanel2.setBackground(Color.white);
+ threshold.addItemListener(this);
+ jPanel3.setLayout(new FlowLayout());
+ jPanel3.setBackground(Color.white);
+ Panel jPanel4 = new Panel();
+ jPanel4.setLayout(new BorderLayout());
+ jPanel4.setBackground(Color.white);
+
+ jPanel1.add(ok);
+ jPanel1.add(cancel);
+
+ jPanel2.add(annotations);
+ jPanel2.add(currentColours);
+ jPanel2.add(minColour);
+ jPanel2.add(maxColour);
+
+ jPanel4.add(thresholdIsMin, BorderLayout.WEST);
+ jPanel4.add(slider, BorderLayout.CENTER);
+ jPanel4.add(thresholdValue, BorderLayout.EAST);
+
+ Panel jPanel34 = new Panel();
+ jPanel34.setLayout(new BorderLayout());
+ jPanel34.setBackground(Color.white);
+ jPanel34.add(jPanel2, BorderLayout.NORTH);
+ jPanel34.add(threshold, BorderLayout.WEST);
+ jPanel3.add(defColours);
+ jPanel34.add(jPanel3, BorderLayout.EAST);
+ jPanel34.add(jPanel4, BorderLayout.SOUTH);
+
+ this.add(jPanel34, java.awt.BorderLayout.CENTER);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+
+ }
+
+ Choice annotations = new Choice();
+
+ Button minColour = new Button();
+
+ Button maxColour = new Button();
+
+ Button ok = new Button();
+
+ Button cancel = new Button();
+
+ Button defColours = new Button();
+
+ Panel jPanel1 = new Panel();
+
+ Panel jPanel2 = new Panel();
+
+ Choice threshold = new Choice();
+
+ FlowLayout flowLayout1 = new FlowLayout();
+
+ Panel jPanel3 = new Panel();
+
+ Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
+ TextField thresholdValue = new TextField(20);
+
+ Checkbox currentColours = new Checkbox();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ Checkbox thresholdIsMin = new Checkbox();
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == thresholdValue)
+ {
+ try
+ {
+ float f = new Float(thresholdValue.getText()).floatValue();
+ slider.setValue((int) (f * 1000));
+ adjustmentValueChanged(null);
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+ else if (evt.getSource() == minColour)
+ {
+ minColour_actionPerformed(null);
+ }
+ else if (evt.getSource() == maxColour)
+ {
+ maxColour_actionPerformed(null);
+ }
+ else if (evt.getSource() == defColours)
+ {
+ defColour_actionPerformed();
+ }
+ else if (evt.getSource() == ok)
+ {
+ frame.setVisible(false);
+ }
+ else if (evt.getSource() == cancel)
+ {
+ reset();
+ ap.paintAlignment(true);
+ frame.setVisible(false);
+ }
+
+ else
+ {
+ changeColour();
+ }
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == currentColours)
+ {
+ if (currentColours.getState())
+ {
+ reset();
+ }
+
+ maxColour.setEnabled(!currentColours.getState());
+ minColour.setEnabled(!currentColours.getState());
+
+ }
+
+ changeColour();
+ }
+
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
+ if (currentColours.getState()
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ {
+ changeColour();
+ }
+
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
+ ap.paintAlignment(false);
+ }
+ }
+
+ public void minColour_actionPerformed(Color newCol)
+ {
+ if (newCol != null)
+ {
+ minColour.setBackground(newCol);
+ minColour.repaint();
+ changeColour();
+ }
+ else
+ {
+ new UserDefinedColours(this, "Min Colour", minColour.getBackground());
+ }
+
+ }
+
+ public void maxColour_actionPerformed(Color newCol)
+ {
+ if (newCol != null)
+ {
+ maxColour.setBackground(newCol);
+ maxColour.repaint();
+ changeColour();
+ }
+ else
+ {
+ new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
+ }
+ }
+
+ public void defColour_actionPerformed()
+ {
+ setDefaultMinMax();
+ minColour.repaint();
+ maxColour.repaint();
+ changeColour();
+ }
+
+ void changeColour()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations
+ .getSelectedIndex()];
+
+ int aboveThreshold = -1;
+ if (threshold.getSelectedIndex() == 1)
+ {
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ }
+ else if (threshold.getSelectedIndex() == 2)
+ {
+ aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ }
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+
+ if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdIsMin.setEnabled(false);
+ thresholdValue.setText("");
+ }
+ else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+ && currentAnnotation.threshold == null)
+ {
+ currentAnnotation
+ .setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+ "Threshold", Color.black));
+ }
+
+ if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+
+ slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+ slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+ slider.setValue((int) (currentAnnotation.threshold.value * 1000));
+ thresholdValue.setText(currentAnnotation.threshold.value + "");
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+
+ AnnotationColourGradient acg = null;
+ if (currentColours.getState())
+ {
+ acg = new AnnotationColourGradient(currentAnnotation,
+ av.getGlobalColourScheme(), aboveThreshold);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold);
+ }
+
+ if (currentAnnotation.graphMin == 0f
+ && currentAnnotation.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.thresholdIsMinMax = thresholdIsMin.getState();
+
+ av.setGlobalColourScheme(acg);
+
+ // TODO: per group colour propagation not always desired
+ if (av.getAlignment().getGroups() != null)
+ {
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ if (currentColours.getState())
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+ aboveThreshold);
+ }
+ else
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold);
+ }
+
+ }
+ }
+
+ // update colours in linked windows
+ ap.alignmentChanged();
+ ap.paintAlignment(true);
+ }
+
+ void reset()
+ {
+ av.setGlobalColourScheme(oldcs);
+ if (av.getAlignment().getGroups() != null)
+ {
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ Object cs = oldgroupColours.get(sg);
+ if (cs instanceof ColourSchemeI)
+ {
+ sg.cs = (ColourSchemeI) cs;
+ }
+ else
+ {
+ // probably the "null" string we set it to if it was null originally.
+ sg.cs = null;
+ }
+ }
+ }
+ ap.paintAlignment(true);
+
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ ap.paintAlignment(true);
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff