/*\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
+ * 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.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.util.*;\r
+\r
import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
\r
+import jalview.datamodel.*;\r
import jalview.schemes.*;\r
+import java.awt.Dimension;\r
\r
public class AnnotationColourChooser\r
extends JPanel\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
+ public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)\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.get(g);\r
+ if (sg.cs != null)\r
+ {\r
+ oldgroupColours.put(sg, sg.cs);\r
+ }\r
+ }\r
+ }\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, false);\r
+ Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);\r
\r
- try{\r
- jbInit();\r
- }catch(Exception ex){}\r
\r
- if(av.alignment.getAlignmentAnnotation()==null)\r
+ slider.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ if (!adjusting)\r
+ {\r
+ thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");\r
+ valueChanged();\r
+ }\r
+ }\r
+ });\r
+ slider.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ ap.paintAlignment(true);\r
+ }\r
+ });\r
+\r
+ if (av.alignment.getAlignmentAnnotation() == null)\r
+ {\r
return;\r
+ }\r
\r
- if(oldcs instanceof AnnotationColourGradient)\r
+ if (oldcs instanceof AnnotationColourGradient)\r
{\r
- AnnotationColourGradient acg = (AnnotationColourGradient)oldcs;\r
- minColour.setBackground( acg.getMinColour() );\r
- maxColour.setBackground( acg.getMaxColour() );\r
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;\r
+ minColour.setBackground(acg.getMinColour());\r
+ maxColour.setBackground(acg.getMaxColour());\r
}\r
else\r
{\r
maxColour.setBackground(Color.red);\r
}\r
\r
+ adjusting = true;\r
+ Vector list = new Vector();\r
+ int index = 1;\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
+ 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
+ annotations = new JComboBox(list);\r
+\r
threshold.addItem("No Threshold");\r
threshold.addItem("Above Threshold");\r
threshold.addItem("Below Threshold");\r
\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+\r
+ adjusting = false;\r
+\r
+ changeColour();\r
+\r
}\r
\r
public AnnotationColourChooser()\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
+ minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ minColour.setBorder(BorderFactory.createEtchedBorder());\r
+ minColour.setPreferredSize(new Dimension(40, 20));\r
+ minColour.setToolTipText("Minimum Colour");\r
+ minColour.addMouseListener(new MouseAdapter()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void mousePressed(MouseEvent e)\r
{\r
- minColour_actionPerformed(e);\r
+ if (minColour.isEnabled())\r
+ {\r
+ minColour_actionPerformed();\r
+ }\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
+ maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ maxColour.setBorder(BorderFactory.createEtchedBorder());\r
+ maxColour.setPreferredSize(new Dimension(40, 20));\r
+ maxColour.setToolTipText("Maximum Colour");\r
+ maxColour.addMouseListener(new MouseAdapter()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void mousePressed(MouseEvent e)\r
{\r
- maxColour_actionPerformed(e);\r
+ if (maxColour.isEnabled())\r
+ {\r
+ maxColour_actionPerformed();\r
+ }\r
}\r
});\r
ok.setOpaque(false);\r
}\r
});\r
this.setLayout(borderLayout1);\r
- jPanel2.setLayout(null);\r
- annotations.setBounds(new Rectangle(5, 7, 135, 21));\r
+ jPanel2.setLayout(flowLayout1);\r
annotations.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
});\r
jPanel1.setBackground(Color.white);\r
jPanel2.setBackground(Color.white);\r
- threshold.setBounds(new Rectangle(328, 6, 125, 22));\r
threshold.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
threshold_actionPerformed(e);\r
}\r
});\r
+ jPanel3.setLayout(flowLayout2);\r
+ thresholdValue.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ thresholdValue_actionPerformed(e);\r
+ }\r
+ });\r
+ slider.setPaintLabels(false);\r
+ slider.setPaintTicks(true);\r
+ slider.setBackground(Color.white);\r
+ slider.setEnabled(false);\r
+ slider.setOpaque(false);\r
+ slider.setPreferredSize(new Dimension(100, 32));\r
+ thresholdValue.setEnabled(false);\r
+ thresholdValue.setColumns(7);\r
+ jPanel3.setBackground(Color.white);\r
+ currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ currentColours.setOpaque(false);\r
+ currentColours.setText("Use Original Colours");\r
+ currentColours.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ currentColours_actionPerformed(e);\r
+ }\r
+ });\r
+ thresholdIsMin.setBackground(Color.white);\r
+ thresholdIsMin.setText("Threshold is Min/Max");\r
+ thresholdIsMin.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ thresholdIsMin_actionPerformed(actionEvent);\r
+ }\r
+ });\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
- jPanel2.add(threshold);\r
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
+ jPanel3.add(threshold);\r
+ jPanel3.add(slider);\r
+ jPanel3.add(thresholdValue);\r
+ jPanel3.add(thresholdIsMin);\r
this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
- this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
+ this.add(jPanel2, java.awt.BorderLayout.NORTH);\r
}\r
\r
- JComboBox annotations = new JComboBox();\r
- JButton minColour = new JButton();\r
- JButton maxColour = new JButton();\r
+ JComboBox annotations;\r
+ JPanel minColour = new JPanel();\r
+ JPanel maxColour = new JPanel();\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
JComboBox threshold = new JComboBox();\r
-\r
- public void minColour_actionPerformed(ActionEvent e)\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ JPanel jPanel3 = new JPanel();\r
+ FlowLayout flowLayout2 = new FlowLayout();\r
+ JSlider slider = new JSlider();\r
+ JTextField thresholdValue = new JTextField(20);\r
+ JCheckBox currentColours = new JCheckBox();\r
+ JCheckBox thresholdIsMin = new JCheckBox();\r
+\r
+ public void minColour_actionPerformed()\r
{\r
Color col = JColorChooser.showDialog(this,\r
"Select Colour for Minimum Value",\r
minColour.getBackground());\r
if (col != null)\r
+ {\r
minColour.setBackground(col);\r
+ }\r
minColour.repaint();\r
changeColour();\r
}\r
\r
- public void maxColour_actionPerformed(ActionEvent e)\r
+ public void maxColour_actionPerformed()\r
{\r
Color col = JColorChooser.showDialog(this,\r
"Select Colour for Maximum Value",\r
maxColour.getBackground());\r
if (col != null)\r
+ {\r
maxColour.setBackground(col);\r
+ }\r
maxColour.repaint();\r
changeColour();\r
}\r
void changeColour()\r
{\r
// Check if combobox is still adjusting\r
- if(threshold.getSelectedIndex()==-1)\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
+ if (adjusting)\r
{\r
- if (av.alignment.getAlignmentAnnotation()[i].graph == 0)\r
- nograph ++;\r
- else\r
- graph ++;\r
-\r
- if(graph==annotations.getSelectedIndex())\r
- break;\r
+ return;\r
}\r
\r
- jalview.datamodel.AlignmentAnnotation aa\r
- = av.alignment.getAlignmentAnnotation()[graph+nograph];\r
\r
+ currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];\r
\r
int aboveThreshold = -1;\r
- if(threshold.getSelectedItem().equals("Above Threshold"))\r
+ if (threshold.getSelectedItem().equals("Above Threshold"))\r
+ {\r
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
- else if(threshold.getSelectedItem().equals("Below 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 && aa.threshold==null)\r
- {\r
- aa.setThreshold(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));\r
- }\r
+ if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ adjusting = true;\r
+ float range = currentAnnotation.graphMax * 1000 -\r
+ currentAnnotation.graphMin * 1000;\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.setMajorTickSpacing( (int) (range / 10f));\r
+ slider.setEnabled(true);\r
+ thresholdValue.setEnabled(true);\r
+ adjusting = false;\r
+ }\r
\r
- AnnotationColourGradient acg = new AnnotationColourGradient(aa,\r
- minColour.getBackground(),\r
- maxColour.getBackground(),\r
- aboveThreshold );\r
+ AnnotationColourGradient acg = null;\r
+ if (currentColours.isSelected())\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.isSelected();\r
\r
+ av.setGlobalColourScheme(acg);\r
\r
- av.setGlobalColourScheme(acg);\r
- ap.repaint();\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.get(g);\r
+\r
+ if (sg.cs == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (currentColours.isSelected())\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
public void ok_actionPerformed(ActionEvent e)\r
{\r
changeColour();\r
- try{\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
}\r
\r
public void cancel_actionPerformed(ActionEvent e)\r
{\r
- av.setGlobalColourScheme(oldcs);\r
- try{\r
+ reset();\r
+ try\r
+ {\r
frame.setClosed(true);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\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.get(g);\r
+ sg.cs = (ColourSchemeI) oldgroupColours.get(sg);\r
+ }\r
+ }\r
}\r
\r
public void thresholdCheck_actionPerformed(ActionEvent e)\r
changeColour();\r
}\r
\r
+ public void thresholdValue_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ float f = Float.parseFloat(thresholdValue.getText());\r
+ slider.setValue( (int) (f * 1000));\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
+ }\r
+\r
+ public void valueChanged()\r
+ {\r
+ if (currentColours.isSelected()\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
+ public void currentColours_actionPerformed(ActionEvent e)\r
+ {\r
+ if (currentColours.isSelected())\r
+ {\r
+ reset();\r
+ }\r
+\r
+ maxColour.setEnabled(!currentColours.isSelected());\r
+ minColour.setEnabled(!currentColours.isSelected());\r
+\r
+ changeColour();\r
+ }\r
+\r
+ public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ changeColour();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff