-/*
- * 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.appletgui;
-
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.Font;
-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;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-import javax.swing.JScrollBar;
-import javax.swing.JTextField;
-
-public class AnnotationColourChooser extends JPanel implements
- ActionListener, AdjustmentListener, ItemListener, MouseListener
-{
- JFrame frame;
-
- AlignViewport av;
-
- AlignmentPanel ap;
-
- ColourSchemeI oldcs;
-
- Hashtable oldgroupColours;
-
- 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.setSelected(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.setSelected(acg.thresholdIsMinMax);
- thresholdValue.setText("" + acg.getAnnotationThreshold());
- }
-
- adjusting = false;
-
- changeColour();
-
- frame = new JFrame();
- frame.add(this);
- 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);
- JPanel jPanel4 = new JPanel();
- 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);
-
- JPanel jPanel34 = new JPanel();
- 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();
-
- JButton minColour = new JButton();
-
- JButton maxColour = new JButton();
-
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JButton defColours = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- Choice threshold = new Choice();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- JPanel jPanel3 = new JPanel();
-
- JScrollBar slider = new JScrollBar(JScrollBar.HORIZONTAL);
-
- JTextField thresholdValue = new JTextField(20);
-
- JCheckBox currentColours = new JCheckBox();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- 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)
- {
- changeColour();
- 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.isSelected())
- {
- reset();
- }
-
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
-
- }
-
- changeColour();
- }
-
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText((slider.getValue() / 1000f) + "");
- if (currentColours.isSelected()
- && !(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 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.isSelected())
- {
- 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.isSelected();
-
- 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.isSelected())
- {
- 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)
- {
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.bin.JalviewLite;\r
+import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.GraphLine;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.schemes.AnnotationColourGradient;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.util.MessageManager;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Color;\r
+import java.awt.Dimension;\r
+import java.awt.FlowLayout;\r
+import java.awt.Font;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.AdjustmentEvent;\r
+import java.awt.event.AdjustmentListener;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
+import javax.swing.JButton;\r
+import javax.swing.JCheckBox;\r
+import javax.swing.JComboBox;\r
+import javax.swing.JFrame;\r
+import javax.swing.JPanel;\r
+import javax.swing.JScrollBar;\r
+import javax.swing.JTextField;\r
+\r
+public class AnnotationColourChooser extends JPanel implements\r
+ ActionListener, AdjustmentListener, ItemListener, MouseListener\r
+{\r
+ JFrame frame;\r
+\r
+ AlignViewport av;\r
+\r
+ AlignmentPanel ap;\r
+\r
+ ColourSchemeI oldcs;\r
+\r
+ Hashtable oldgroupColours;\r
+\r
+ AlignmentAnnotation currentAnnotation;\r
+\r
+ boolean adjusting = false;\r
+\r
+ public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ oldcs = av.getGlobalColourScheme();\r
+ if (av.getAlignment().getGroups() != null)\r
+ {\r
+ oldgroupColours = new Hashtable();\r
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())\r
+ {\r
+ if (sg.cs != null)\r
+ {\r
+ oldgroupColours.put(sg, sg.cs);\r
+ }\r
+ else\r
+ {\r
+ oldgroupColours.put(sg, "null");\r
+ }\r
+ }\r
+ }\r
+ this.av = av;\r
+ this.ap = ap;\r
+\r
+ slider.addAdjustmentListener(this);\r
+ slider.addMouseListener(this);\r
+\r
+ if (av.getAlignment().getAlignmentAnnotation() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ setDefaultMinMax();\r
+\r
+ adjusting = true;\r
+ if (oldcs instanceof AnnotationColourGradient)\r
+ {\r
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;\r
+ currentColours.setSelected(acg.isPredefinedColours()\r
+ || acg.getBaseColour() != null);\r
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)\r
+ {\r
+ minColour.setBackground(acg.getMinColour());\r
+ maxColour.setBackground(acg.getMaxColour());\r
+ }\r
+ // seqAssociated.setState(acg.isSeqAssociated());\r
+ }\r
+\r
+ Vector list = new Vector();\r
+ int index = 1;\r
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)\r
+ {\r
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;\r
+ if (!list.contains(label))\r
+ {\r
+ list.addElement(label);\r
+ }\r
+ else\r
+ {\r
+ list.addElement(label + "_" + (index++));\r
+ }\r
+ }\r
+\r
+ for (int i = 0; i < list.size(); i++)\r
+ {\r
+ annotations.addItem(list.elementAt(i).toString());\r
+ }\r
+\r
+ threshold.addItem(MessageManager\r
+ .getString("label.threshold_feature_no_thereshold"));\r
+ threshold.addItem(MessageManager\r
+ .getString("label.threshold_feature_above_thereshold"));\r
+ threshold.addItem(MessageManager\r
+ .getString("label.threshold_feature_below_thereshold"));\r
+\r
+ if (oldcs instanceof AnnotationColourGradient)\r
+ {\r
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;\r
+ annotations.select(acg.getAnnotation());\r
+ switch (acg.getAboveThreshold())\r
+ {\r
+ case AnnotationColourGradient.NO_THRESHOLD:\r
+ threshold.select(0);\r
+ break;\r
+ case AnnotationColourGradient.ABOVE_THRESHOLD:\r
+ threshold.select(1);\r
+ break;\r
+ case AnnotationColourGradient.BELOW_THRESHOLD:\r
+ threshold.select(1);\r
+ break;\r
+ default:\r
+ throw new Error(\r
+ MessageManager\r
+ .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));\r
+ }\r
+ thresholdIsMin.setSelected(acg.thresholdIsMinMax);\r
+ thresholdValue.setText("" + acg.getAnnotationThreshold());\r
+ }\r
+\r
+ adjusting = false;\r
+\r
+ changeColour();\r
+\r
+ frame = new JFrame();\r
+ frame.add(this);\r
+ JalviewLite.addFrame(frame,\r
+ MessageManager.getString("label.colour_by_annotation"), 560,\r
+ 175);\r
+ validate();\r
+ }\r
+\r
+ private void setDefaultMinMax()\r
+ {\r
+ minColour.setBackground(av.applet.getDefaultColourParameter(\r
+ "ANNOTATIONCOLOUR_MIN", Color.orange));\r
+ maxColour.setBackground(av.applet.getDefaultColourParameter(\r
+ "ANNOTATIONCOLOUR_MAX", Color.red));\r
+\r
+ }\r
+\r
+ public AnnotationColourChooser()\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+ minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ minColour.setLabel(MessageManager.getString("label.min_colour"));\r
+ minColour.addActionListener(this);\r
+\r
+ maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ maxColour.setLabel(MessageManager.getString("label.max_colour"));\r
+ maxColour.addActionListener(this);\r
+\r
+ thresholdIsMin.addItemListener(this);\r
+ ok.setLabel(MessageManager.getString("action.ok"));\r
+ ok.addActionListener(this);\r
+\r
+ cancel.setLabel(MessageManager.getString("action.cancel"));\r
+ cancel.addActionListener(this);\r
+\r
+ defColours.setLabel(MessageManager.getString("action.set_defaults"));\r
+ defColours.addActionListener(this);\r
+\r
+ annotations.addItemListener(this);\r
+\r
+ thresholdValue.addActionListener(this);\r
+ slider.setBackground(Color.white);\r
+ slider.setPreferredSize(new Dimension(193, 21));\r
+ slider.setEnabled(false);\r
+ thresholdValue.setPreferredSize(new Dimension(79, 22));\r
+ thresholdValue.setEnabled(false);\r
+ thresholdValue.setColumns(5);\r
+ currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ currentColours.setLabel(MessageManager\r
+ .getString("label.use_original_colours"));\r
+ currentColours.addItemListener(this);\r
+\r
+ thresholdIsMin.setBackground(Color.white);\r
+ thresholdIsMin.setLabel(MessageManager\r
+ .getString("label.threshold_minmax"));\r
+\r
+ this.setLayout(borderLayout1);\r
+\r
+ jPanel1.setBackground(Color.white);\r
+\r
+ jPanel2.setLayout(new FlowLayout());\r
+ jPanel2.setBackground(Color.white);\r
+ threshold.addItemListener(this);\r
+ jPanel3.setLayout(new FlowLayout());\r
+ jPanel3.setBackground(Color.white);\r
+ JPanel jPanel4 = new JPanel();\r
+ jPanel4.setLayout(new BorderLayout());\r
+ jPanel4.setBackground(Color.white);\r
+\r
+ jPanel1.add(ok);\r
+ jPanel1.add(cancel);\r
+\r
+ jPanel2.add(annotations);\r
+ jPanel2.add(currentColours);\r
+ jPanel2.add(minColour);\r
+ jPanel2.add(maxColour);\r
+\r
+ jPanel4.add(thresholdIsMin, BorderLayout.WEST);\r
+ jPanel4.add(slider, BorderLayout.CENTER);\r
+ jPanel4.add(thresholdValue, BorderLayout.EAST);\r
+\r
+ JPanel jPanel34 = new JPanel();\r
+ jPanel34.setLayout(new BorderLayout());\r
+ jPanel34.setBackground(Color.white);\r
+ jPanel34.add(jPanel2, BorderLayout.NORTH);\r
+ jPanel34.add(threshold, BorderLayout.WEST);\r
+ jPanel3.add(defColours);\r
+ jPanel34.add(jPanel3, BorderLayout.EAST);\r
+ jPanel34.add(jPanel4, BorderLayout.SOUTH);\r
+\r
+ this.add(jPanel34, java.awt.BorderLayout.CENTER);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+\r
+ }\r
+\r
+ Choice annotations = new Choice();\r
+\r
+ JButton minColour = new JButton();\r
+\r
+ JButton maxColour = new JButton();\r
+\r
+ JButton ok = new JButton();\r
+\r
+ JButton cancel = new JButton();\r
+\r
+ JButton defColours = new JButton();\r
+\r
+ JPanel jPanel1 = new JPanel();\r
+\r
+ JPanel jPanel2 = new JPanel();\r
+\r
+ Choice threshold = new Choice();\r
+\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+\r
+ JPanel jPanel3 = new JPanel();\r
+\r
+ JScrollBar slider = new JScrollBar(JScrollBar.HORIZONTAL);\r
+\r
+ JTextField thresholdValue = new JTextField(20);\r
+\r
+ JCheckBox currentColours = new JCheckBox();\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ JCheckBox thresholdIsMin = new JCheckBox();\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
+ } catch (NumberFormatException ex)\r
+ {\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
+ else if (evt.getSource() == defColours)\r
+ {\r
+ defColour_actionPerformed();\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.isSelected())\r
+ {\r
+ reset();\r
+ }\r
+\r
+ maxColour.setEnabled(!currentColours.isSelected());\r
+ minColour.setEnabled(!currentColours.isSelected());\r
+\r
+ }\r
+\r
+ changeColour();\r
+ }\r
+\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ if (!adjusting)\r
+ {\r
+ thresholdValue.setText((slider.getValue() / 1000f) + "");\r
+ if (currentColours.isSelected()\r
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))\r
+ {\r
+ changeColour();\r
+ }\r
+\r
+ currentAnnotation.threshold.value = 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", 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", maxColour.getBackground());\r
+ }\r
+ }\r
+\r
+ public void defColour_actionPerformed()\r
+ {\r
+ setDefaultMinMax();\r
+ minColour.repaint();\r
+ maxColour.repaint();\r
+ changeColour();\r
+ }\r
+\r
+ void changeColour()\r
+ {\r
+ // Check if combobox is still adjusting\r
+ if (adjusting)\r
+ {\r
+ return;\r
+ }\r
+\r
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations\r
+ .getSelectedIndex()];\r
+\r
+ int aboveThreshold = -1;\r
+ if (threshold.getSelectedIndex() == 1)\r
+ {\r
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
+ }\r
+ else if (threshold.getSelectedIndex() == 2)\r
+ {\r
+ aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;\r
+ }\r
+\r
+ slider.setEnabled(true);\r
+ thresholdValue.setEnabled(true);\r
+ thresholdIsMin.setEnabled(true);\r
+\r
+ if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ slider.setEnabled(false);\r
+ thresholdValue.setEnabled(false);\r
+ thresholdIsMin.setEnabled(false);\r
+ thresholdValue.setText("");\r
+ }\r
+ else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD\r
+ && currentAnnotation.threshold == null)\r
+ {\r
+ currentAnnotation\r
+ .setThreshold(new GraphLine(\r
+ (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,\r
+ "Threshold", 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.isSelected())\r
+ {\r
+ acg = new AnnotationColourGradient(currentAnnotation,\r
+ av.getGlobalColourScheme(), aboveThreshold);\r
+ }\r
+ else\r
+ {\r
+ acg = new AnnotationColourGradient(currentAnnotation,\r
+ minColour.getBackground(), maxColour.getBackground(),\r
+ aboveThreshold);\r
+ }\r
+\r
+ if (currentAnnotation.graphMin == 0f\r
+ && currentAnnotation.graphMax == 0f)\r
+ {\r
+ acg.setPredefinedColours(true);\r
+ }\r
+\r
+ acg.thresholdIsMinMax = thresholdIsMin.isSelected();\r
+\r
+ av.setGlobalColourScheme(acg);\r
+\r
+ // TODO: per group colour propagation not always desired\r
+ if (av.getAlignment().getGroups() != null)\r
+ {\r
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())\r
+ {\r
+\r
+ if (sg.cs == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (currentColours.isSelected())\r
+ {\r
+ sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,\r
+ aboveThreshold);\r
+ }\r
+ else\r
+ {\r
+ sg.cs = new AnnotationColourGradient(currentAnnotation,\r
+ minColour.getBackground(), maxColour.getBackground(),\r
+ aboveThreshold);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ // update colours in linked windows\r
+ ap.alignmentChanged();\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ void reset()\r
+ {\r
+ av.setGlobalColourScheme(oldcs);\r
+ if (av.getAlignment().getGroups() != null)\r
+ {\r
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())\r
+ {\r
+ Object cs = oldgroupColours.get(sg);\r
+ if (cs instanceof ColourSchemeI)\r
+ {\r
+ sg.cs = (ColourSchemeI) cs;\r
+ }\r
+ else\r
+ {\r
+ // probably the "null" string we set it to if it was null originally.\r
+ sg.cs = null;\r
+ }\r
+ }\r
+ }\r
+ ap.paintAlignment(true);\r
+\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff