/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\r
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
import java.io.*;\r
-\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
-\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class UserDefinedColours extends GUserDefinedColours\r
- implements ChangeListener\r
+public class UserDefinedColours\r
+ extends GUserDefinedColours implements ChangeListener\r
{\r
- AlignmentPanel ap;\r
- SequenceGroup seqGroup;\r
- Vector selectedButtons;\r
- ColourSchemeI oldColourScheme;\r
- JInternalFrame frame;\r
-\r
- /**\r
- * Creates a new UserDefinedColours object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param sg DOCUMENT ME!\r
- */\r
- public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
- {\r
- super();\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
-\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- frame.setSize(760, 370);\r
- }\r
+ AlignmentPanel ap;\r
+ SequenceGroup seqGroup;\r
+ Vector selectedButtons;\r
+ ColourSchemeI oldColourScheme;\r
+ JInternalFrame frame;\r
+ MCview.PDBCanvas pdbcanvas;\r
+ Vector upperCaseButtons;\r
+ Vector lowerCaseButtons;\r
+\r
+ /**\r
+ * Creates a new UserDefinedColours object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
+ {\r
+ super();\r
+\r
+ lcaseColour.setEnabled(false);\r
+\r
+ this.ap = ap;\r
+ seqGroup = sg;\r
+\r
+ if (seqGroup != null)\r
+ {\r
+ oldColourScheme = seqGroup.cs;\r
+ }\r
+ else\r
+ {\r
+ oldColourScheme = ap.av.getGlobalColourScheme();\r
+ }\r
\r
- if (sg != null)\r
- {\r
- frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");\r
- }\r
+ if (oldColourScheme instanceof UserColourScheme)\r
+ {\r
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+ if ( ( (UserColourScheme) oldColourScheme).getLowerCaseColours() != null)\r
+ {\r
+ caseSensitive.setSelected(true);\r
+ lcaseColour.setEnabled(true);\r
+ resetButtonPanel(true);\r
+ }\r
+ else\r
+ {\r
+ resetButtonPanel(false);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ resetButtonPanel(false);\r
+ }\r
\r
- colorChooser.getSelectionModel().addChangeListener(this);\r
+ showFrame();\r
+ }\r
\r
- this.ap = ap;\r
- seqGroup = sg;\r
+ public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
+ {\r
+ super();\r
+ pdbcanvas = pdb;\r
\r
- if (seqGroup != null)\r
- {\r
- oldColourScheme = seqGroup.cs;\r
- }\r
- else\r
- {\r
- oldColourScheme = ap.av.getGlobalColourScheme();\r
- }\r
+ colorChooser.getSelectionModel().addChangeListener(this);\r
\r
- if (oldColourScheme instanceof UserColourScheme)\r
- {\r
- schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
- }\r
- for (int i = 0; i < 20; i++)\r
- {\r
- makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
- "", ResidueProperties.aa[i]);\r
- }\r
+ oldColourScheme = oldcs;\r
\r
- makeButton("B", "B");\r
- makeButton("Z", "Z");\r
- makeButton("X", "X");\r
- makeButton("Gap", "-");\r
+ if (oldColourScheme instanceof UserColourScheme)\r
+ {\r
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void stateChanged(ChangeEvent evt)\r
+ resetButtonPanel(false);\r
+\r
+ showFrame();\r
+\r
+ }\r
+\r
+ void showFrame()\r
+ {\r
+ colorChooser.getSelectionModel().addChangeListener(this);\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
+\r
+ if (seqGroup != null)\r
{\r
- if (selectedButtons != null)\r
- {\r
- JButton button;\r
- for(int i=0; i<selectedButtons.size(); i++)\r
- {\r
- button = (JButton)selectedButtons.elementAt(i);\r
- button.setBackground(colorChooser.getColor());\r
- button.setForeground( button.getBackground().brighter().brighter().brighter());\r
- }\r
- }\r
+ frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void colourButtonPressed(MouseEvent e)\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
{\r
- if(selectedButtons == null)\r
- selectedButtons = new Vector();\r
+ frame.setSize(760, 370);\r
+ }\r
+ }\r
\r
- JButton pressed = (JButton) e.getSource();\r
+ void resetButtonPanel(boolean caseSensitive)\r
+ {\r
+ buttonPanel.removeAll();\r
\r
- if(e.isShiftDown())\r
+ if (upperCaseButtons == null)\r
+ {\r
+ upperCaseButtons = new Vector();\r
+ }\r
+\r
+ JButton button;\r
+ String label;\r
+ for (int i = 0; i < 20; i++)\r
+ {\r
+ if (caseSensitive)\r
{\r
- JButton start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);\r
- JButton end = (JButton) e.getSource();\r
- int startIndex=0, endIndex=0;\r
- for(int b=0; b<buttonPanel.getComponentCount(); b++)\r
- {\r
- if(buttonPanel.getComponent(b)==start)\r
- startIndex = b;\r
- if(buttonPanel.getComponent(b)==end)\r
- endIndex = b;\r
- }\r
+ label = ResidueProperties.aa[i];\r
+ }\r
+ else\r
+ {\r
+ label = ResidueProperties.aa2Triplet.get\r
+ (ResidueProperties.aa[i]).toString();\r
+ }\r
\r
- if(startIndex > endIndex)\r
- {\r
- int temp = startIndex;\r
- startIndex = endIndex;\r
- endIndex = temp;\r
- }\r
+ button = makeButton(label,\r
+ ResidueProperties.aa[i],\r
+ upperCaseButtons, i);\r
\r
- for(int b=startIndex; b<=endIndex; b++)\r
- {\r
- JButton button = (JButton)buttonPanel.getComponent(b);\r
- if(!selectedButtons.contains(button))\r
- {\r
- button.setForeground(button.getBackground().brighter().brighter());\r
- selectedButtons.add(button);\r
- }\r
- }\r
+ buttonPanel.add(button);\r
+ }\r
+\r
+ buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));\r
+ buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));\r
+ buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));\r
+ buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));\r
+\r
+ if (!caseSensitive)\r
+ {\r
+ gridLayout.setRows(6);\r
+ gridLayout.setColumns(4);\r
+ }\r
+ else\r
+ {\r
+ gridLayout.setRows(7);\r
+ int cols = 7;\r
+ gridLayout.setColumns(cols + 1);\r
+\r
+ if (lowerCaseButtons == null)\r
+ {\r
+ lowerCaseButtons = new Vector();\r
}\r
- else if(!e.isControlDown())\r
+\r
+ for (int i = 0; i < 20; i++)\r
{\r
- for(int b=0; b<selectedButtons.size(); b++)\r
- {\r
- JButton button = (JButton)selectedButtons.elementAt(b);\r
- button.setForeground(button.getBackground().darker().darker());\r
- }\r
- selectedButtons.clear();\r
- pressed.setForeground( pressed.getBackground().brighter().brighter());\r
- selectedButtons.addElement(pressed);\r
+ int row = i / cols + 1;\r
+ int index = (row * cols) + i;\r
+ button = makeButton(\r
+ ResidueProperties.aa[i].toLowerCase(),\r
+ ResidueProperties.aa[i].toLowerCase(),\r
+ lowerCaseButtons,\r
+ i);\r
+\r
+ buttonPanel.add(button, index);\r
+ }\r
+ }\r
\r
+ if (caseSensitive)\r
+ {\r
+ buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));\r
+ buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));\r
+ buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));\r
+ }\r
+\r
+ buttonPanel.validate();\r
+ validate();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ if (selectedButtons != null)\r
+ {\r
+ JButton button = null;\r
+ for (int i = 0; i < selectedButtons.size(); i++)\r
+ {\r
+ button = (JButton) selectedButtons.elementAt(i);\r
+ button.setBackground(colorChooser.getColor());\r
+ button.setForeground(button.getBackground().brighter().brighter().\r
+ brighter());\r
}\r
- else if(e.isControlDown())\r
+ if (button == lcaseColour)\r
{\r
- if(selectedButtons.contains(pressed))\r
+ for (int i = 0; i < lowerCaseButtons.size(); i++)\r
{\r
- pressed.setForeground(pressed.getBackground().darker().darker());\r
- selectedButtons.remove(pressed);\r
- }\r
- else\r
- {\r
- pressed.setForeground( pressed.getBackground().brighter().brighter());\r
- selectedButtons.addElement(pressed);\r
+ button = (JButton) lowerCaseButtons.elementAt(i);\r
+ button.setBackground(colorChooser.getColor());\r
+ button.setForeground(button.getBackground().brighter().brighter().\r
+ brighter());\r
}\r
}\r
-\r
- if(selectedButtons.size()>0)\r
- colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void colourButtonPressed(MouseEvent e)\r
+ {\r
+ if (selectedButtons == null)\r
+ {\r
+ selectedButtons = new Vector();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param label DOCUMENT ME!\r
- * @param aa DOCUMENT ME!\r
- */\r
- void makeButton(String label, String aa)\r
+ JButton pressed = (JButton) e.getSource();\r
+\r
+ if (e.isShiftDown())\r
{\r
- final JButton button = new JButton();\r
- Color col = Color.white;\r
+ JButton start, end = (JButton) e.getSource();\r
+ if (selectedButtons.size() > 0)\r
+ {\r
+ start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);\r
+ }\r
+ else\r
+ {\r
+ start = (JButton) e.getSource();\r
+ }\r
\r
- try\r
+ int startIndex = 0, endIndex = 0;\r
+ for (int b = 0; b < buttonPanel.getComponentCount(); b++)\r
+ {\r
+ if (buttonPanel.getComponent(b) == start)\r
{\r
- col = oldColourScheme.findColour(aa, -1);\r
+ startIndex = b;\r
}\r
- catch (Exception ex)\r
+ if (buttonPanel.getComponent(b) == end)\r
{\r
- // ex.printStackTrace();\r
+ endIndex = b;\r
}\r
+ }\r
\r
- button.setBackground(col);\r
- button.setText(label);\r
- button.setForeground(col.darker().darker().darker());\r
- button.setFont(new java.awt.Font("Verdana", 1, 10));\r
- button.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- colourButtonPressed(e);\r
- }\r
- });\r
+ if (startIndex > endIndex)\r
+ {\r
+ int temp = startIndex;\r
+ startIndex = endIndex;\r
+ endIndex = temp;\r
+ }\r
\r
- buttonPanel.add(button, null);\r
+ for (int b = startIndex; b <= endIndex; b++)\r
+ {\r
+ JButton button = (JButton) buttonPanel.getComponent(b);\r
+ if (!selectedButtons.contains(button))\r
+ {\r
+ button.setForeground(button.getBackground().brighter().brighter());\r
+ selectedButtons.add(button);\r
+ }\r
+ }\r
}\r
+ else if (!e.isControlDown())\r
+ {\r
+ for (int b = 0; b < selectedButtons.size(); b++)\r
+ {\r
+ JButton button = (JButton) selectedButtons.elementAt(b);\r
+ button.setForeground(button.getBackground().darker().darker());\r
+ }\r
+ selectedButtons.clear();\r
+ pressed.setForeground(pressed.getBackground().brighter().brighter());\r
+ selectedButtons.addElement(pressed);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void okButton_actionPerformed(ActionEvent e)\r
+ }\r
+ else if (e.isControlDown())\r
{\r
- applyButton_actionPerformed(null);\r
+ if (selectedButtons.contains(pressed))\r
+ {\r
+ pressed.setForeground(pressed.getBackground().darker().darker());\r
+ selectedButtons.remove(pressed);\r
+ }\r
+ else\r
+ {\r
+ pressed.setForeground(pressed.getBackground().brighter().brighter());\r
+ selectedButtons.addElement(pressed);\r
+ }\r
+ }\r
\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
+ if (selectedButtons.size() > 0)\r
+ {\r
+ colorChooser.setColor( ( (JButton) selectedButtons.elementAt(0)).\r
+ getBackground());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param label DOCUMENT ME!\r
+ * @param aa DOCUMENT ME!\r
+ */\r
+ JButton makeButton(String label,\r
+ String aa,\r
+ Vector caseSensitiveButtons,\r
+ int buttonIndex)\r
+ {\r
+ final JButton button;\r
+ Color col;\r
+\r
+ if (buttonIndex < caseSensitiveButtons.size())\r
+ {\r
+ button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);\r
+ col = button.getBackground();\r
+ }\r
+ else\r
+ {\r
+ button = new JButton();\r
+ button.addMouseListener(new java.awt.event.MouseAdapter()\r
+ {\r
+ public void mouseClicked(MouseEvent e)\r
{\r
+ colourButtonPressed(e);\r
}\r
+ });\r
+\r
+ caseSensitiveButtons.addElement(button);\r
+\r
+ col = Color.white;\r
+\r
+ try\r
+ {\r
+ col = oldColourScheme.findColour(aa.charAt(0), -1);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void applyButton_actionPerformed(ActionEvent e)\r
+ if (caseSensitive.isSelected())\r
+ {\r
+ button.setMargin(new java.awt.Insets(2, 2, 2, 2));\r
+ }\r
+ else\r
{\r
- UserColourScheme ucs = getSchemeFromGUI();\r
- ucs.setName(schemeName.getText());\r
+ button.setMargin(new java.awt.Insets(2, 14, 2, 14));\r
+ }\r
\r
- if (seqGroup != null)\r
- {\r
- seqGroup.cs = ucs;\r
- ap.repaint();\r
- }\r
- else\r
- {\r
- ap.alignFrame.changeColour(ucs);\r
- }\r
+ button.setBackground(col);\r
+ button.setText(label);\r
+ button.setForeground(col.darker().darker().darker());\r
+ button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));\r
+\r
+ return button;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void okButton_actionPerformed(ActionEvent e)\r
+ {\r
+ applyButton_actionPerformed(null);\r
+\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void applyButton_actionPerformed(ActionEvent e)\r
+ {\r
+ UserColourScheme ucs = getSchemeFromButtons();\r
+ ucs.setName(schemeName.getText());\r
+\r
+ if (seqGroup != null)\r
+ {\r
+ seqGroup.cs = ucs;\r
+ ap.repaint();\r
+ }\r
+ else if (ap != null)\r
+ {\r
+ ap.alignFrame.changeColour(ucs);\r
+ }\r
+ else if (pdbcanvas != null)\r
+ {\r
+ pdbcanvas.pdb.setColours(ucs);\r
+ pdbcanvas.updateSeqColours();\r
}\r
+ }\r
\r
- UserColourScheme getSchemeFromGUI()\r
+ UserColourScheme getSchemeFromButtons()\r
+ {\r
+\r
+ Color[] newColours = new Color[24];\r
+\r
+ for (int i = 0; i < 24; i++)\r
{\r
- Color[] newColours = new Color[24];\r
+ JButton button = (JButton) upperCaseButtons.elementAt(i);\r
+ newColours[i] = button.getBackground();\r
+ }\r
\r
- for (int i = 0; i < 24; i++)\r
+ UserColourScheme ucs = new UserColourScheme(newColours);\r
+\r
+ if (caseSensitive.isSelected())\r
+ {\r
+ newColours = new Color[23];\r
+ for (int i = 0; i < 23; i++)\r
{\r
- JButton button = (JButton) buttonPanel.getComponent(i);\r
+ JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
newColours[i] = button.getBackground();\r
}\r
+ ucs.setLowerCaseColours(newColours);\r
+ }\r
\r
- UserColourScheme ucs = new UserColourScheme(newColours);\r
+ if (ap != null)\r
+ {\r
ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
-\r
- return ucs;\r
}\r
\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void loadbutton_actionPerformed(ActionEvent e)\r
+ return ucs;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void loadbutton_actionPerformed(ActionEvent e)\r
+ {\r
+ upperCaseButtons = new Vector();\r
+ lowerCaseButtons = new Vector();\r
+\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jc"},\r
+ new String[]\r
+ {"Jalview User Colours"}, "Jalview User Colours");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Load colour scheme");\r
+ chooser.setToolTipText("Load");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jc" },\r
- new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Load colour scheme");\r
- chooser.setToolTipText("Load");\r
+ File choice = chooser.getSelectedFile();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+ String defaultColours = jalview.bin.Cache.getDefault(\r
+ "USER_DEFINED_COLOURS",\r
+ choice.getPath());\r
+ if (defaultColours.indexOf(choice.getPath()) == -1)\r
+ {\r
+ defaultColours = defaultColours.concat("|").concat(choice.getPath());\r
+ }\r
\r
- int value = chooser.showOpenDialog(this);\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ UserColourScheme ucs = loadColours(choice.getAbsolutePath());\r
+ Color[] colors = ucs.getColours();\r
+ schemeName.setText(ucs.getName());\r
+\r
+ if (ucs.getLowerCaseColours() != null)\r
+ {\r
+ caseSensitive.setSelected(true);\r
+ lcaseColour.setEnabled(true);\r
+ resetButtonPanel(true);\r
+ for (int i = 0; i < lowerCaseButtons.size(); i++)\r
{\r
- File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",\r
- choice.getPath());\r
- if (defaultColours.indexOf(choice.getPath()) == -1)\r
- defaultColours = defaultColours.concat("|").concat(choice.getPath());\r
+ JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
+ button.setBackground(ucs.getLowerCaseColours()[i]);\r
+ }\r
\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
+ }\r
+ else\r
+ {\r
+ caseSensitive.setSelected(false);\r
+ lcaseColour.setEnabled(false);\r
+ resetButtonPanel(false);\r
+ }\r
\r
+ for (int i = 0; i < upperCaseButtons.size(); i++)\r
+ {\r
+ JButton button = (JButton) upperCaseButtons.elementAt(i);\r
+ button.setBackground(colors[i]);\r
+ }\r
\r
- UserColourScheme ucs = loadColours(choice.getAbsolutePath());\r
- Color[] colors = ucs.getColours();\r
- schemeName.setText(ucs.getName());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static UserColourScheme loadDefaultColours()\r
+ {\r
+ UserColourScheme ret = null;\r
+\r
+ String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
+ if (colours != null)\r
+ {\r
+ if (colours.indexOf("|") > -1)\r
+ {\r
+ colours = colours.substring(0, colours.indexOf("|"));\r
+ }\r
\r
- for (int i = 0; i < colors.length; i++)\r
- {\r
- JButton button = (JButton) buttonPanel.getComponent(i);\r
- button.setBackground(colors[i]);\r
- }\r
- }\r
+ ret = loadColours(colours);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static UserColourScheme loadDefaultColours()\r
+ if (ret == null)\r
{\r
- UserColourScheme ret = null;\r
+ Color[] newColours = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColours[i] = Color.white;\r
+ }\r
+ ret = new UserColourScheme(newColours);\r
+ }\r
\r
- String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
- if ( colours != null )\r
- {\r
- if(colours.indexOf("|")>-1)\r
- colours = colours.substring(0, colours.indexOf("|"));\r
+ return ret;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ static UserColourScheme loadColours(String file)\r
+ {\r
+ UserColourScheme ucs = null;\r
+ Color[] newColours = null;\r
+ try\r
+ {\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
+\r
+ jalview.schemabinding.version2.JalviewUserColours jucs\r
+ = new jalview.schemabinding.version2.JalviewUserColours();\r
+\r
+ org.exolab.castor.xml.Unmarshaller unmar\r
+ = new org.exolab.castor.xml.Unmarshaller(jucs);\r
+ jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.\r
+ unmarshal(in);\r
\r
- ret = loadColours(colours);\r
+ newColours = new Color[24];\r
+\r
+ Color[] lowerCase = null;\r
+ boolean caseSensitive = false;\r
+\r
+ String name;\r
+ int index;\r
+ for (int i = 0; i < jucs.getColourCount(); i++)\r
+ {\r
+ name = jucs.getColour(i).getName();\r
+ if (ResidueProperties.aa3Hash.containsKey(name))\r
+ {\r
+ index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();\r
+ }\r
+ else\r
+ {\r
+ index = ResidueProperties.aaIndex[name.charAt(0)];\r
+ }\r
+ if (index == -1)\r
+ {\r
+ continue;\r
}\r
\r
- if(ret == null)\r
+ if (name.toLowerCase().equals(name))\r
{\r
- Color[] newColours = new Color[24];\r
- for (int i = 0; i < 24; i++)\r
+ if (lowerCase == null)\r
{\r
- newColours[i] = Color.white;\r
+ lowerCase = new Color[23];\r
}\r
- ret = new UserColourScheme(newColours);\r
+ caseSensitive = true;\r
+ lowerCase[index] = new Color(Integer.parseInt(\r
+ jucs.getColour(i).getRGB(), 16));\r
}\r
+ else\r
+ {\r
+ newColours[index] = new Color(Integer.parseInt(\r
+ jucs.getColour(i).getRGB(), 16));\r
+ }\r
+ }\r
\r
- return ret;\r
- }\r
+ if (newColours != null)\r
+ {\r
+ ucs = new UserColourScheme(newColours);\r
+ ucs.setName(jucs.getSchemeName());\r
+ if (caseSensitive)\r
+ {\r
+ ucs.setLowerCaseColours(lowerCase);\r
+ }\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- static UserColourScheme loadColours(String file)\r
+ }\r
+ catch (Exception ex)\r
{\r
- UserColourScheme ucs = null;\r
- Color[] newColours = null;\r
-\r
- try\r
- {\r
- InputStreamReader in = new InputStreamReader(new FileInputStream(\r
- file), "UTF-8");\r
+ //Could be Archive Jalview format\r
+ try\r
+ {\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
\r
- jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();\r
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
+ jalview.binding.JalviewUserColours jucs\r
+ = new jalview.binding.JalviewUserColours();\r
\r
- newColours = new Color[jucs.getColourCount()];\r
+ jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
\r
- for (int i = 0; i < 24; i++)\r
- {\r
- newColours[i] = new Color(Integer.parseInt(\r
- jucs.getColour(i).getRGB(), 16));\r
- }\r
- if (newColours != null)\r
- {\r
- ucs = new UserColourScheme(newColours);\r
- ucs.setName( jucs.getSchemeName() );\r
- }\r
+ newColours = new Color[jucs.getColourCount()];\r
\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColours[i] = new Color(Integer.parseInt(\r
+ jucs.getColour(i).getRGB(), 16));\r
}\r
- catch (Exception ex)\r
+ if (newColours != null)\r
{\r
- System.out.println("Error loading User ColourFile\n"+ex);\r
+ ucs = new UserColourScheme(newColours);\r
+ ucs.setName(jucs.getSchemeName());\r
}\r
+ }\r
+ catch (Exception ex2)\r
+ {\r
+ ex2.printStackTrace();\r
+ }\r
\r
+ if (newColours == null)\r
+ {\r
+ System.out.println("Error loading User ColourFile\n" + ex);\r
+ }\r
+ }\r
\r
- return ucs;\r
+ return ucs;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void savebutton_actionPerformed(ActionEvent e)\r
+ {\r
+ if (schemeName.getText().trim().length() < 1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "User colour scheme must have a name!",\r
+ "No name for colour scheme",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void savebutton_actionPerformed(ActionEvent e)\r
+ if (userColourSchemes != null &&\r
+ userColourSchemes.containsKey(schemeName.getText()))\r
{\r
- if(schemeName.getText().trim().length()<1)\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "Colour scheme " + schemeName.getText() + " exists."\r
+ + "\nContinue saving colour scheme as " + schemeName.getText() + "?",\r
+ "Duplicate scheme name", JOptionPane.YES_NO_OPTION);\r
+ if (reply != JOptionPane.YES_OPTION)\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "User colour scheme must have a name!",\r
- "No name for colour scheme",\r
- JOptionPane.WARNING_MESSAGE);\r
return;\r
}\r
\r
- if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )\r
- {\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."\r
- +"\nContinue saving colour scheme as "+schemeName.getText()+"?",\r
- "Duplicate scheme name", JOptionPane.YES_NO_OPTION);\r
- if(reply != JOptionPane.YES_OPTION)\r
- return;\r
-\r
- userColourSchemes.remove(schemeName.getText());\r
- }\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[] { "jc" },\r
- new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Save colour scheme");\r
- chooser.setToolTipText("Save");\r
+ userColourSchemes.remove(schemeName.getText());\r
+ }\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jc"},\r
+ new String[]\r
+ {"Jalview User Colours"}, "Jalview User Colours");\r
\r
- int value = chooser.showSaveDialog(this);\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Save colour scheme");\r
+ chooser.setToolTipText("Save");\r
\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);\r
- if(defaultColours.indexOf(choice)==-1)\r
- {\r
- if(defaultColours.length()>0)\r
- defaultColours = defaultColours.concat("|");\r
- defaultColours = defaultColours.concat(choice);\r
- }\r
-\r
- userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());\r
-\r
- ap.alignFrame.updateUserColourMenu();\r
-\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
-\r
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
- ucs.setSchemeName(schemeName.getText());\r
- try\r
- {\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
- new FileOutputStream(choice), "UTF-8"));\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\r
- JButton button = (JButton) buttonPanel.getComponent(i);\r
- jalview.binding.Colour col = new jalview.binding.Colour();\r
- col.setName(button.getText());\r
- col.setRGB(jalview.util.Format.getHexString(\r
- button.getBackground()));\r
- ucs.addColour(col);\r
- }\r
-\r
- ucs.marshal(out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
+ int value = chooser.showSaveDialog(this);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void cancelButton_actionPerformed(ActionEvent e)\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- if (seqGroup != null)\r
- {\r
- seqGroup.cs = oldColourScheme;\r
- }\r
- else\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ String defaultColours = jalview.bin.Cache.getDefault(\r
+ "USER_DEFINED_COLOURS", choice);\r
+ if (defaultColours.indexOf(choice) == -1)\r
+ {\r
+ if (defaultColours.length() > 0)\r
{\r
- ap.av.setGlobalColourScheme(oldColourScheme);\r
+ defaultColours = defaultColours.concat("|");\r
}\r
+ defaultColours = defaultColours.concat(choice);\r
+ }\r
\r
- ap.repaint();\r
+ userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());\r
\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
+ ap.alignFrame.updateUserColourMenu();\r
+\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
+\r
+ jalview.schemabinding.version2.JalviewUserColours ucs\r
+ = new jalview.schemabinding.version2.JalviewUserColours();\r
+\r
+ ucs.setSchemeName(schemeName.getText());\r
+ try\r
+ {\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
+ new FileOutputStream(choice), "UTF-8"));\r
+\r
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)\r
{\r
+ JButton button = (JButton) buttonPanel.getComponent(i);\r
+ jalview.schemabinding.version2.Colour col\r
+ = new jalview.schemabinding.version2.Colour();\r
+ col.setName(button.getText());\r
+ col.setRGB(jalview.util.Format.getHexString(\r
+ button.getBackground()));\r
+ ucs.addColour(col);\r
}\r
- }\r
\r
+ ucs.marshal(out);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void cancelButton_actionPerformed(ActionEvent e)\r
+ {\r
+ if (ap != null)\r
+ {\r
+ if (seqGroup != null)\r
+ {\r
+ seqGroup.cs = oldColourScheme;\r
+ }\r
+ else if (ap != null)\r
+ {\r
+ ap.av.setGlobalColourScheme(oldColourScheme);\r
+ }\r
+ ap.repaint();\r
+ }\r
\r
- static Hashtable userColourSchemes;\r
-\r
- public static Hashtable getUserColourSchemes()\r
+ if (pdbcanvas != null)\r
{\r
- return userColourSchemes;\r
+ pdbcanvas.pdb.setColours(oldColourScheme);\r
}\r
\r
- public static void initUserColourSchemes(String files)\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
{\r
- userColourSchemes = new Hashtable();\r
+ }\r
+ }\r
\r
- if(files==null || files.length()==0)\r
- return;\r
+ static Hashtable userColourSchemes;\r
\r
+ public static Hashtable getUserColourSchemes()\r
+ {\r
+ return userColourSchemes;\r
+ }\r
+\r
+ public static void initUserColourSchemes(String files)\r
+ {\r
+ userColourSchemes = new Hashtable();\r
+\r
+ if (files == null || files.length() == 0)\r
+ {\r
+ return;\r
+ }\r
\r
- // In case colours can't be loaded, we'll remove them\r
- // from the default list here.\r
- StringBuffer coloursFound = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(files, "|");\r
- while (st.hasMoreElements())\r
+ // In case colours can't be loaded, we'll remove them\r
+ // from the default list here.\r
+ StringBuffer coloursFound = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(files, "|");\r
+ while (st.hasMoreElements())\r
+ {\r
+ String file = st.nextToken();\r
+ try\r
{\r
- String file = st.nextToken();\r
- try\r
+ UserColourScheme ucs = loadColours(file);\r
+ if (ucs != null)\r
{\r
- UserColourScheme ucs = loadColours(file);\r
- if (ucs != null)\r
+ if (coloursFound.length() > 0)\r
{\r
- if (coloursFound.length() > 0)\r
- coloursFound.append("|");\r
- coloursFound.append(file);\r
- userColourSchemes.put(ucs.getName(), ucs);\r
+ coloursFound.append("|");\r
}\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error loading User ColourFile\n" + ex);\r
+ coloursFound.append(file);\r
+ userColourSchemes.put(ucs.getName(), ucs);\r
}\r
}\r
- if (!files.equals(coloursFound.toString()))\r
+ catch (Exception ex)\r
{\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\r
+ System.out.println("Error loading User ColourFile\n" + ex);\r
}\r
}\r
-\r
- public static void removeColourFromDefaults(String target)\r
+ if (!files.equals(coloursFound.toString()))\r
{\r
- // The only way to find colours by name is to load them in\r
- // In case colours can't be loaded, we'll remove them\r
- // from the default list here.\r
+ if (coloursFound.toString().length() > 1)\r
+ {\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
+ coloursFound.toString());\r
+ }\r
+ else\r
+ {\r
+ jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
+ }\r
+ }\r
+ }\r
\r
- userColourSchemes = new Hashtable();\r
+ public static void removeColourFromDefaults(String target)\r
+ {\r
+ // The only way to find colours by name is to load them in\r
+ // In case colours can't be loaded, we'll remove them\r
+ // from the default list here.\r
\r
- StringBuffer coloursFound = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(\r
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");\r
+ userColourSchemes = new Hashtable();\r
\r
- while (st.hasMoreElements())\r
+ StringBuffer coloursFound = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(\r
+ jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ String file = st.nextToken();\r
+ try\r
{\r
- String file = st.nextToken();\r
- try\r
+ UserColourScheme ucs = loadColours(file);\r
+ if (ucs != null && !ucs.getName().equals(target))\r
{\r
- UserColourScheme ucs = loadColours(file);\r
- if (ucs != null && !ucs.getName().equals(target))\r
+ if (coloursFound.length() > 0)\r
{\r
- if (coloursFound.length() > 0)\r
- coloursFound.append("|");\r
- coloursFound.append(file);\r
- userColourSchemes.put(ucs.getName(), ucs);\r
+ coloursFound.append("|");\r
}\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error loading User ColourFile\n" + ex);\r
+ coloursFound.append(file);\r
+ userColourSchemes.put(ucs.getName(), ucs);\r
}\r
}\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error loading User ColourFile\n" + ex);\r
+ }\r
+ }\r
\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\r
+ if (coloursFound.toString().length() > 1)\r
+ {\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
+ coloursFound.toString());\r
+ }\r
+ else\r
+ {\r
+ jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
+ }\r
+\r
+ }\r
+\r
+ public void caseSensitive_actionPerformed(ActionEvent e)\r
+ {\r
+ resetButtonPanel(caseSensitive.isSelected());\r
+ lcaseColour.setEnabled(caseSensitive.isSelected());\r
+ }\r
\r
+ public void lcaseColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if (selectedButtons == null)\r
+ {\r
+ selectedButtons = new Vector();\r
+ }\r
+ else\r
+ {\r
+ selectedButtons.clear();\r
}\r
+ selectedButtons.add(lcaseColour);\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff