/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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.appletgui;\r
\r
-import java.awt.event.*;\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.util.*;\r
-import jalview.datamodel.SequenceGroup;\r
+import java.awt.Rectangle;\r
\r
-public class AnnotationColourChooser extends Panel implements ActionListener,\r
- AdjustmentListener, ItemListener\r
+public class AnnotationColourChooser\r
+ extends Panel implements ActionListener,\r
+ AdjustmentListener, ItemListener, MouseListener\r
{\r
Frame frame;\r
AlignViewport 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
}\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
- 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
+ for (int i = 0; i < list.size(); i++)\r
+ {\r
+ annotations.addItem(list.elementAt(i).toString());\r
}\r
\r
threshold.addItem("No Threshold");\r
maxColour.setLabel("Max Colour");\r
maxColour.addActionListener(this);\r
\r
+ thresholdIsMin.addItemListener(this);\r
ok.setLabel("OK");\r
ok.addActionListener(this);\r
\r
\r
slider.setBackground(Color.white);\r
slider.setEnabled(false);\r
- slider.setBounds(new Rectangle(172, 7, 120, 16));\r
+ slider.setBounds(new Rectangle(153, 3, 93, 21));\r
thresholdValue.setEnabled(false);\r
- thresholdValue.setBounds(new Rectangle(295, 4, 83, 22));\r
- thresholdValue.setColumns(10);\r
+ thresholdValue.setBounds(new Rectangle(248, 2, 79, 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(19, 4, 141, 22));\r
+ threshold.setBounds(new Rectangle(11, 3, 139, 22));\r
+ thresholdIsMin.setBackground(Color.white);\r
+ thresholdIsMin.setLabel("Threshold is min/max");\r
+ thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));\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(jPanel2, java.awt.BorderLayout.NORTH);\r
this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
TextField thresholdValue = new TextField(20);\r
Checkbox currentColours = new Checkbox();\r
BorderLayout borderLayout1 = new BorderLayout();\r
-\r
+ Checkbox thresholdIsMin = new Checkbox();\r
\r
public void actionPerformed(ActionEvent evt)\r
{\r
- if(evt.getSource() == thresholdValue)\r
+ if (evt.getSource() == thresholdValue)\r
{\r
try\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
\r
else if (evt.getSource() == ok)\r
{\r
else if (evt.getSource() == cancel)\r
{\r
reset();\r
- ap.repaint();\r
+ ap.paintAlignment(true);\r
frame.setVisible(false);\r
}\r
\r
else\r
+ {\r
changeColour();\r
+ }\r
}\r
\r
-\r
public void itemStateChanged(ItemEvent evt)\r
{\r
if (evt.getSource() == currentColours)\r
}\r
\r
currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;\r
- ap.repaint();\r
+ ap.paintAlignment(false);\r
}\r
}\r
\r
changeColour();\r
}\r
else\r
+ {\r
new UserDefinedColours(this, "Min Colour",\r
- minColour.getBackground());\r
+ minColour.getBackground());\r
+ }\r
\r
}\r
\r
changeColour();\r
}\r
else\r
+ {\r
new UserDefinedColours(this, "Max Colour",\r
- maxColour.getBackground());\r
+ maxColour.getBackground());\r
+ }\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
+ return;\r
}\r
\r
- currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];\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
Color.black));\r
}\r
\r
- if(aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)\r
+ if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)\r
{\r
adjusting = true;\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
}\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.repaint();\r
+ ap.paintAlignment(false);\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.elementAt(g);\r
- sg.cs = (ColourSchemeI)oldgroupColours.get(sg);\r
+ sg.cs = (ColourSchemeI) oldgroupColours.get(sg);\r
}\r
}\r
- ap.repaint();\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
git://source.jalview.org / jalview.git / blobdiff