*/
package jalview.gui;
-import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
-import jalview.datamodel.SequenceGroup;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GUserDefinedColours;
import jalview.schemabinding.version2.Colour;
import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import java.awt.Color;
import java.awt.Font;
import java.awt.Insets;
-import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.File;
public class UserDefinedColours extends GUserDefinedColours implements
ChangeListener
{
- private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
+ private static final Font VERDANA_BOLD_10 = new Font("Verdana",
+ Font.BOLD, 10);
public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
- private static final int MY_FRAME_HEIGHT = 420;
+ private static final int MY_FRAME_HEIGHT = 440;
private static final int MY_FRAME_WIDTH = 810;
AlignmentPanel ap;
- SequenceGroup seqGroup;
-
- List<JButton> selectedButtons;
-
ColourSchemeI oldColourScheme;
JInternalFrame frame;
- JalviewStructureDisplayI structureViewer;
-
List<JButton> upperCaseButtons;
List<JButton> lowerCaseButtons;
/**
- * Creates a new UserDefinedColours object.
+ * Creates and displays a new UserDefinedColours panel
*
- * @param ap
- * @param sg
+ * @param alignPanel
*/
- public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+ public UserDefinedColours(AlignmentPanel alignPanel)
{
- super();
+ this();
lcaseColour.setEnabled(false);
- this.ap = ap;
- seqGroup = sg;
+ this.ap = alignPanel;
- if (seqGroup != null)
- {
- oldColourScheme = seqGroup.cs;
- }
- else
- {
- oldColourScheme = ap.av.getGlobalColourScheme();
- }
+ oldColourScheme = alignPanel.av.getGlobalColourScheme();
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
+ schemeName.setText(oldColourScheme.getSchemeName());
if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
showFrame();
}
- public UserDefinedColours(JalviewStructureDisplayI viewer,
- ColourSchemeI oldcs)
+ UserDefinedColours()
{
super();
- this.structureViewer = viewer;
-
- colorChooser.getSelectionModel().addChangeListener(this);
-
- oldColourScheme = oldcs;
-
- if (oldColourScheme instanceof UserColourScheme)
- {
- schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
- }
-
- resetButtonPanel(false);
-
- showFrame();
-
+ selectedButtons = new ArrayList<JButton>();
}
void showFrame()
Desktop.addInternalFrame(frame,
MessageManager.getString("label.user_defined_colours"),
MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
-
- if (seqGroup != null)
- {
- frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
- }
}
- void resetButtonPanel(boolean caseSensitive)
+ /**
+ * Rebuilds the panel with coloured buttons for residues. If not case
+ * sensitive colours, show 3-letter amino acid code as button text. If case
+ * sensitive, just show the single letter code, in order to make space for the
+ * additional buttons.
+ *
+ * @param isCaseSensitive
+ */
+ void resetButtonPanel(boolean isCaseSensitive)
{
buttonPanel.removeAll();
upperCaseButtons = new ArrayList<JButton>();
}
- JButton button;
- String label;
for (int i = 0; i < 20; i++)
{
- if (caseSensitive)
- {
- label = ResidueProperties.aa[i];
- }
- else
- {
- label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
- .toString();
- }
-
- button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
- i);
-
+ String label = isCaseSensitive ? ResidueProperties.aa[i]
+ : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+ .toString();
+ JButton button = makeButton(label, ResidueProperties.aa[i],
+ upperCaseButtons, i);
buttonPanel.add(button);
}
buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
- if (!caseSensitive)
+ if (!isCaseSensitive)
{
gridLayout.setRows(6);
gridLayout.setColumns(4);
{
int row = i / cols + 1;
int index = (row * cols) + i;
- button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
buttonPanel.add(button, index);
}
}
- if (caseSensitive)
+ if (isCaseSensitive)
{
buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
// codes
if (this.frame != null)
{
- int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
: MY_FRAME_WIDTH;
this.frame.setSize(newWidth, this.frame.getHeight());
}
}
/**
- * DOCUMENT ME!
+ * ChangeListener handler for when a colour is picked in the colour chooser.
+ * The action is to apply the colour to all selected buttons as their
+ * background colour. Foreground colour (text) is set to a lighter shade in
+ * order to highlight which buttons are selected. If 'Lower Case Colour' is
+ * active, then the colour is applied to all lower case buttons (as well as
+ * the Lower Case Colour button itself).
*
* @param evt
- * DOCUMENT ME!
*/
@Override
public void stateChanged(ChangeEvent evt)
{
- if (selectedButtons != null)
+ JButton button = null;
+ final Color newColour = colorChooser.getColor();
+ if (lcaseColour.isSelected())
{
- JButton button = null;
- final Color newColour = colorChooser.getColor();
- for (int i = 0; i < selectedButtons.size(); i++)
+ selectedButtons.clear();
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- button = selectedButtons.get(i);
+ button = lowerCaseButtons.get(i);
button.setBackground(newColour);
- button.setForeground(ColorUtils.brighterThan(newColour));
- }
- if (button == lcaseColour)
- {
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- button = lowerCaseButtons.get(i);
- button.setBackground(newColour);
- button.setForeground(ColorUtils.brighterThan(button
- .getBackground()));
- }
+ button.setForeground(ColorUtils.brighterThan(button.getBackground()));
}
}
+ for (int i = 0; i < selectedButtons.size(); i++)
+ {
+ button = selectedButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(newColour));
+ }
}
/**
*/
public void colourButtonPressed(MouseEvent e)
{
- if (selectedButtons == null)
- {
- selectedButtons = new ArrayList<JButton>();
- }
-
JButton pressed = (JButton) e.getSource();
if (e.isShiftDown())
* @param buttonIndex
* the button's position in the list
*/
- JButton makeButton(String label, String residue,
- List<JButton> buttons, int buttonIndex)
+ JButton makeButton(String label, String residue, List<JButton> buttons,
+ int buttonIndex)
{
final JButton button;
Color col;
buttons.add(button);
+ /*
+ * make initial button colour that of the current colour scheme,
+ * if it is a simple per-residue colouring, else white
+ */
col = Color.white;
- if (oldColourScheme != null)
+ if (oldColourScheme != null && oldColourScheme.isSimple())
{
- try
- {
- col = oldColourScheme.findColour(residue.charAt(0), -1, null);
- } catch (Exception ex)
- {
- }
+ col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+ 0f);
}
}
}
/**
- * Applies the current colour scheme to the alignment, sequence group or
- * structure view.
+ * Applies the current colour scheme to the alignment or sequence group
*/
@Override
protected void applyButton_actionPerformed()
}
UserColourScheme ucs = getSchemeFromButtons();
- if (seqGroup != null)
- {
- seqGroup.cs = ucs;
- ap.paintAlignment(true);
- }
- else if (ap != null)
- {
- ap.alignFrame.changeColour(ucs);
- }
- else if (structureViewer != null)
- {
- structureViewer.setJalviewColourScheme(ucs);
- }
+ ap.alignFrame.changeColour(ucs);
}
+ /**
+ * Constructs an instance of UserColourScheme with the residue colours
+ * currently set on the buttons on the panel
+ *
+ * @return
+ */
UserColourScheme getSchemeFromButtons()
{
ucs.setLowerCaseColours(newColours);
}
- if (ap != null)
- {
- ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
- }
-
return ucs;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on clicking Load scheme button.
+ * <ul>
+ * <li>Open a file chooser to browse for files with extension .jc</li>
+ * <li>Load in the colour scheme and transfer it to this panel's buttons</li>
+ * <li>Register the loaded colour scheme</li>
+ * </ul>
*/
@Override
- protected void loadbutton_actionPerformed(ActionEvent e)
+ protected void loadbutton_actionPerformed()
{
upperCaseButtons = new ArrayList<JButton>();
lowerCaseButtons = new ArrayList<JButton>();
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
+ "Jalview User Colours");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.load_colour_scheme"));
File choice = chooser.getSelectedFile();
Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
+ UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
+ .getAbsolutePath());
Color[] colors = ucs.getColours();
schemeName.setText(ucs.getSchemeName());
{
colours = colours.substring(0, colours.indexOf("|"));
}
- ret = ColourSchemes.loadColourScheme(colours);
+ ret = ColourSchemeLoader.loadColourScheme(colours);
}
if (ret == null)
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on pressing the Save button.
+ * <ul>
+ * <li>Check a name has been entered</li>
+ * <li>Warn if the name already exists, remove any existing scheme of the same
+ * name if overwriting</li>
+ * <li>Do the standard file chooser thing to write with extension .jc</li>
+ * <li>If saving changes (possibly not yet applied) to the currently selected
+ * colour scheme, then apply the changes, as it is too late to back out now</li>
+ * <li>Don't apply the changes if the currently selected scheme is different,
+ * to allow a new scheme to be configured and saved but not applied</li>
+ * </ul>
*/
@Override
- protected void savebutton_actionPerformed(ActionEvent e)
+ protected void savebutton_actionPerformed()
{
String name = schemeName.getText().trim();
if (name.length() < 1)
{
return;
}
- ColourSchemes.getInstance().removeColourScheme(name);
}
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty(LAST_DIRECTORY), "jc",
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
- chooser.setFileView(new JalviewFileView());
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
chooser.setDialogTitle(MessageManager
.getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- addNewColourScheme(choice);
- saveToFile(choice);
+ File file = chooser.getSelectedFile();
+ addNewColourScheme(file.getPath());
+ saveToFile(file);
+
+ /*
+ * changes saved - apply to alignment if we are changing
+ * the currently selected colour scheme
+ */
+ if (oldColourScheme != null
+ && name.equals(oldColourScheme.getSchemeName()))
+ {
+ applyButton_actionPerformed();
+ }
}
}
/**
* Saves the colour scheme to file in XML format
*
- * @param filePath
+ * @param path
*/
- protected void saveToFile(String filePath)
+ protected void saveToFile(File toFile)
{
/*
* build a Java model of colour scheme as XML, and
* marshal to file
*/
JalviewUserColours ucs = new JalviewUserColours();
- ucs.setSchemeName(schemeName.getText());
+ String name = schemeName.getText();
+ ucs.setSchemeName(name);
try
{
PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(filePath), "UTF-8"));
+ new FileOutputStream(toFile), "UTF-8"));
for (int i = 0; i < buttonPanel.getComponentCount(); i++)
{
}
/**
- * On cancel, restores the colour scheme before the dialogue was opened
- *
- * @param e
+ * On cancel, restores the colour scheme that was selected before the dialogue
+ * was opened
*/
@Override
- protected void cancelButton_actionPerformed(ActionEvent e)
+ protected void cancelButton_actionPerformed()
{
- if (ap != null)
- {
- if (seqGroup != null)
- {
- seqGroup.cs = oldColourScheme;
- }
- else
- {
- ap.alignFrame.changeColour(oldColourScheme);
- }
- ap.paintAlignment(true);
- }
-
- if (structureViewer != null)
- {
- structureViewer.setJalviewColourScheme(oldColourScheme);
- }
+ ap.alignFrame.changeColour(oldColourScheme);
+ ap.paintAlignment(true);
try
{
}
}
+ /**
+ * Action on selecting or deselecting the Case Sensitive option. When
+ * selected, separate buttons are shown for lower case residues, and the panel
+ * is resized to accommodate them. Also, the checkbox for 'apply colour to all
+ * lower case' is enabled.
+ */
@Override
- public void caseSensitive_actionPerformed(ActionEvent e)
- {
- resetButtonPanel(caseSensitive.isSelected());
- lcaseColour.setEnabled(caseSensitive.isSelected());
- }
-
- @Override
- public void lcaseColour_actionPerformed(ActionEvent e)
+ public void caseSensitive_actionPerformed()
{
- if (selectedButtons == null)
- {
- selectedButtons = new ArrayList<JButton>();
- }
- else
- {
- selectedButtons.clear();
- }
- selectedButtons.add(lcaseColour);
+ boolean selected = caseSensitive.isSelected();
+ resetButtonPanel(selected);
+ lcaseColour.setEnabled(selected);
}
}
git://source.jalview.org / jalview.git / blobdiff