/*\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.*;\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 javax.swing.event.*;\r
-import java.util.*;\r
-import jalview.datamodel.SequenceGroup;\r
+import java.awt.Dimension;\r
\r
public class AnnotationColourChooser\r
extends JPanel\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
for (int g = 0; g < allGroups.size(); g++)\r
{\r
sg = (SequenceGroup) allGroups.get(g);\r
- oldgroupColours.put(sg, sg.cs);\r
+ if (sg.cs != null)\r
+ {\r
+ oldgroupColours.put(sg, sg.cs);\r
+ }\r
}\r
}\r
this.av = av;\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145, false);\r
+ Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);\r
\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {}\r
\r
slider.addChangeListener(new ChangeListener()\r
{\r
public void stateChanged(ChangeEvent evt)\r
{\r
- thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");\r
- valueChanged();\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
{\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
throws Exception\r
{\r
minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- minColour.setToolTipText("");\r
- minColour.setMargin(new Insets(2, 2, 2, 2));\r
- minColour.setText("Min Colour");\r
- minColour.addActionListener(new ActionListener()\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.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- maxColour.setMargin(new Insets(2, 2, 2, 2));\r
- maxColour.setText("Max Colour");\r
- maxColour.addActionListener(new ActionListener()\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
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(10);\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_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
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.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
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(ActionEvent e)\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
- currentAnnotation = 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
+ {\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
- currentAnnotation.threshold = null;\r
slider.setEnabled(false);\r
thresholdValue.setEnabled(false);\r
thresholdValue.setText("");\r
currentAnnotation.graphMin) / 2f,\r
"Threshold",\r
Color.black));\r
+ }\r
+\r
+ if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)\r
+ {\r
+ adjusting = true;\r
float range = currentAnnotation.graphMax * 1000 -\r
currentAnnotation.graphMin * 1000;\r
\r
slider.setValue( (int) (currentAnnotation.threshold.value * 1000));\r
thresholdValue.setText(currentAnnotation.threshold.value + "");\r
slider.setMajorTickSpacing( (int) (range / 10f));\r
- slider.setMinorTickSpacing( (int) (range / 100f));\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(\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
}\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.repaint();\r
+ ap.paintAlignment(false);\r
}\r
\r
public void ok_actionPerformed(ActionEvent e)\r
{}\r
}\r
\r
-\r
void reset()\r
{\r
av.setGlobalColourScheme(oldcs);\r
for (int g = 0; g < allGroups.size(); g++)\r
{\r
sg = (SequenceGroup) allGroups.get(g);\r
- sg.cs = (ColourSchemeI)oldgroupColours.get(sg);\r
+ sg.cs = (ColourSchemeI) oldgroupColours.get(sg);\r
}\r
}\r
}\r
\r
public void annotations_actionPerformed(ActionEvent e)\r
{\r
- if(currentAnnotation!=null)\r
- currentAnnotation.threshold = null;\r
changeColour();\r
}\r
\r
\r
public void valueChanged()\r
{\r
- currentAnnotation.threshold.value = (float)slider.getValue()/1000f;\r
- ap.repaint();\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
+ if (currentColours.isSelected())\r
{\r
reset();\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