X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=1e85e55a4035f86a31b57362f992502d51cf7138;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=f719d2762c727a449131d14f9e9f5e5410524092;hpb=ae216fceddd8539d20fa5425cdaef3da73aba8f0;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index f719d27..1e85e55 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -27,6 +27,7 @@ import jalview.jbgui.GUserDefinedColours; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; +import jalview.util.ColorUtils; import jalview.util.MessageManager; import java.awt.Color; @@ -39,9 +40,9 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; +import java.util.ArrayList; import java.util.Hashtable; import java.util.StringTokenizer; -import java.util.Vector; import javax.swing.JButton; import javax.swing.JInternalFrame; @@ -50,19 +51,26 @@ import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; /** - * DOCUMENT ME! + * This panel allows the user to assign colours to Amino Acid residue codes, and + * save the colour scheme. * - * @author $author$ - * @version $Revision$ + * @author Andrew Waterhouse + * @author Mungo Carstairs */ public class UserDefinedColours extends GUserDefinedColours implements ChangeListener { + private static final int MY_FRAME_HEIGHT = 420; + + private static final int MY_FRAME_WIDTH = 810; + + private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970; + AlignmentPanel ap; SequenceGroup seqGroup; - Vector selectedButtons; + ArrayList selectedButtons; ColourSchemeI oldColourScheme; @@ -70,9 +78,9 @@ public class UserDefinedColours extends GUserDefinedColours implements JalviewStructureDisplayI jmol; - Vector upperCaseButtons; + ArrayList upperCaseButtons; - Vector lowerCaseButtons; + ArrayList lowerCaseButtons; /** * Creates a new UserDefinedColours object. @@ -122,7 +130,8 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs) + public UserDefinedColours(JalviewStructureDisplayI jmol, + ColourSchemeI oldcs) { super(); this.jmol = jmol; @@ -148,18 +157,13 @@ public class UserDefinedColours extends GUserDefinedColours implements frame = new JInternalFrame(); frame.setContentPane(this); Desktop.addInternalFrame(frame, - MessageManager.getString("label.user_defined_colours"), 720, - 370, true); + MessageManager.getString("label.user_defined_colours"), + MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true); if (seqGroup != null) { frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")"); } - - if (new jalview.util.Platform().isAMac()) - { - frame.setSize(760, 370); - } } void resetButtonPanel(boolean caseSensitive) @@ -168,7 +172,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (upperCaseButtons == null) { - upperCaseButtons = new Vector(); + upperCaseButtons = new ArrayList(); } JButton button; @@ -209,7 +213,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (lowerCaseButtons == null) { - lowerCaseButtons = new Vector(); + lowerCaseButtons = new ArrayList(); } for (int i = 0; i < 20; i++) @@ -230,6 +234,15 @@ public class UserDefinedColours extends GUserDefinedColours implements buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22)); } + // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA + // codes + if (this.frame != null) + { + int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE + : MY_FRAME_WIDTH; + this.frame.setSize(newWidth, this.frame.getHeight()); + } + buttonPanel.validate(); validate(); } @@ -240,42 +253,55 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param evt * DOCUMENT ME! */ + @Override public void stateChanged(ChangeEvent evt) { if (selectedButtons != null) { JButton button = null; + final Color newColour = colorChooser.getColor(); for (int i = 0; i < selectedButtons.size(); i++) { - button = (JButton) selectedButtons.elementAt(i); - button.setBackground(colorChooser.getColor()); - button.setForeground(button.getBackground().brighter().brighter() - .brighter()); + button = selectedButtons.get(i); + button.setBackground(newColour); + button.setForeground(ColorUtils.brighterThan(newColour)); } if (button == lcaseColour) { for (int i = 0; i < lowerCaseButtons.size(); i++) { - button = (JButton) lowerCaseButtons.elementAt(i); - button.setBackground(colorChooser.getColor()); - button.setForeground(button.getBackground().brighter().brighter() - .brighter()); + button = lowerCaseButtons.get(i); + button.setBackground(newColour); + button.setForeground(ColorUtils.brighterThan(button + .getBackground())); } } } } /** - * DOCUMENT ME! + * Performs actions when a residue button is clicked. This manages the button + * selection set (highlighted by brighter foreground text). + *

+ * On select button(s) with Ctrl/click or Shift/click: set button foreground + * text to brighter than background. + *

+ * On unselect button(s) with Ctrl/click on selected, or click to release + * current selection: reset foreground text to darker than background. + *

+ * Simple click: clear selection (resetting foreground to darker); set clicked + * button foreground to brighter + *

+ * Finally, synchronize the colour chooser to the colour of the first button + * in the selected set. * * @param e - * DOCUMENT ME! */ public void colourButtonPressed(MouseEvent e) { if (selectedButtons == null) { - selectedButtons = new Vector(); + selectedButtons = new ArrayList(); } JButton pressed = (JButton) e.getSource(); @@ -285,8 +311,7 @@ public class UserDefinedColours extends GUserDefinedColours implements JButton start, end = (JButton) e.getSource(); if (selectedButtons.size() > 0) { - start = (JButton) selectedButtons - .elementAt(selectedButtons.size() - 1); + start = selectedButtons.get(selectedButtons.size() - 1); } else { @@ -318,7 +343,8 @@ public class UserDefinedColours extends GUserDefinedColours implements JButton button = (JButton) buttonPanel.getComponent(b); if (!selectedButtons.contains(button)) { - button.setForeground(button.getBackground().brighter().brighter()); + button.setForeground(ColorUtils.brighterThan(button + .getBackground())); selectedButtons.add(button); } } @@ -327,32 +353,32 @@ public class UserDefinedColours extends GUserDefinedColours implements { for (int b = 0; b < selectedButtons.size(); b++) { - JButton button = (JButton) selectedButtons.elementAt(b); - button.setForeground(button.getBackground().darker().darker()); + JButton button = selectedButtons.get(b); + button.setForeground(ColorUtils.darkerThan(button.getBackground())); } selectedButtons.clear(); - pressed.setForeground(pressed.getBackground().brighter().brighter()); - selectedButtons.addElement(pressed); + pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground())); + selectedButtons.add(pressed); } else if (e.isControlDown()) { if (selectedButtons.contains(pressed)) { - pressed.setForeground(pressed.getBackground().darker().darker()); + pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground())); selectedButtons.remove(pressed); } else { - pressed.setForeground(pressed.getBackground().brighter().brighter()); - selectedButtons.addElement(pressed); + pressed.setForeground(ColorUtils.brighterThan(pressed + .getBackground())); + selectedButtons.add(pressed); } } if (selectedButtons.size() > 0) { - colorChooser.setColor(((JButton) selectedButtons.elementAt(0)) - .getBackground()); + colorChooser.setColor((selectedButtons.get(0)).getBackground()); } } @@ -364,15 +390,15 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param aa * DOCUMENT ME! */ - JButton makeButton(String label, String aa, Vector caseSensitiveButtons, - int buttonIndex) + JButton makeButton(String label, String aa, + ArrayList caseSensitiveButtons, int buttonIndex) { final JButton button; Color col; if (buttonIndex < caseSensitiveButtons.size()) { - button = (JButton) caseSensitiveButtons.elementAt(buttonIndex); + button = caseSensitiveButtons.get(buttonIndex); col = button.getBackground(); } else @@ -380,13 +406,14 @@ public class UserDefinedColours extends GUserDefinedColours implements button = new JButton(); button.addMouseListener(new java.awt.event.MouseAdapter() { + @Override public void mouseClicked(MouseEvent e) { colourButtonPressed(e); } }); - caseSensitiveButtons.addElement(button); + caseSensitiveButtons.add(button); col = Color.white; if (oldColourScheme != null) @@ -409,9 +436,10 @@ public class UserDefinedColours extends GUserDefinedColours implements button.setMargin(new java.awt.Insets(2, 14, 2, 14)); } + button.setOpaque(true); // required for the next line to have effect button.setBackground(col); button.setText(label); - button.setForeground(col.darker().darker().darker()); + button.setForeground(ColorUtils.darkerThan(col)); button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10)); return button; @@ -423,26 +451,63 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void okButton_actionPerformed(ActionEvent e) { - applyButton_actionPerformed(null); - - try + if (isNoSelectionMade()) { - frame.setClosed(true); - } catch (Exception ex) + JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + .getString("label.no_colour_selection_in_scheme"), + MessageManager.getString("label.no_colour_selection_warn"), + JOptionPane.WARNING_MESSAGE); + } + else { + applyButton_actionPerformed(null); + + try + { + frame.setClosed(true); + } catch (Exception ex) + { + } } } /** + * Returns true if the user has not made any colour selection (including if + * 'case-sensitive' selected and no lower-case colour chosen). + * + * @return + */ + protected boolean isNoSelectionMade() + { + final boolean noUpperCaseSelected = upperCaseButtons == null + || upperCaseButtons.isEmpty(); + final boolean noLowerCaseSelected = caseSensitive.isSelected() + && (lowerCaseButtons == null || lowerCaseButtons.isEmpty()); + final boolean noSelectionMade = noUpperCaseSelected + || noLowerCaseSelected; + return noSelectionMade; + } + + /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override protected void applyButton_actionPerformed(ActionEvent e) { + if (isNoSelectionMade()) + { + JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + .getString("label.no_colour_selection_in_scheme"), + MessageManager.getString("label.no_colour_selection_warn"), + JOptionPane.WARNING_MESSAGE); + + } UserColourScheme ucs = getSchemeFromButtons(); ucs.setName(schemeName.getText()); @@ -466,10 +531,23 @@ public class UserDefinedColours extends GUserDefinedColours implements Color[] newColours = new Color[24]; - for (int i = 0; i < 24; i++) + int length = upperCaseButtons.size(); + if (length < 24) { - JButton button = (JButton) upperCaseButtons.elementAt(i); - newColours[i] = button.getBackground(); + int i = 0; + for (JButton btn : upperCaseButtons) + { + newColours[i] = btn.getBackground(); + i++; + } + } + else + { + for (int i = 0; i < 24; i++) + { + JButton button = upperCaseButtons.get(i); + newColours[i] = button.getBackground(); + } } UserColourScheme ucs = new UserColourScheme(newColours); @@ -477,17 +555,30 @@ public class UserDefinedColours extends GUserDefinedColours implements if (caseSensitive.isSelected()) { newColours = new Color[23]; - for (int i = 0; i < 23; i++) + length = lowerCaseButtons.size(); + if (length < 23) { - JButton button = (JButton) lowerCaseButtons.elementAt(i); - newColours[i] = button.getBackground(); + int i = 0; + for (JButton btn : lowerCaseButtons) + { + newColours[i] = btn.getBackground(); + i++; + } + } + else + { + for (int i = 0; i < 23; i++) + { + JButton button = lowerCaseButtons.get(i); + newColours[i] = button.getBackground(); + } } ucs.setLowerCaseColours(newColours); } if (ap != null) { - ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } return ucs; @@ -499,15 +590,16 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void loadbutton_actionPerformed(ActionEvent e) { - upperCaseButtons = new Vector(); - lowerCaseButtons = new Vector(); + upperCaseButtons = new ArrayList(); + lowerCaseButtons = new ArrayList(); JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jc" }, new String[] - { "Jalview User Colours" }, "Jalview User Colours"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "jc" }, new String[] { "Jalview User Colours" }, + "Jalview User Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.load_colour_scheme")); @@ -540,7 +632,7 @@ public class UserDefinedColours extends GUserDefinedColours implements resetButtonPanel(true); for (int i = 0; i < lowerCaseButtons.size(); i++) { - JButton button = (JButton) lowerCaseButtons.elementAt(i); + JButton button = lowerCaseButtons.get(i); button.setBackground(ucs.getLowerCaseColours()[i]); } @@ -554,7 +646,7 @@ public class UserDefinedColours extends GUserDefinedColours implements for (int i = 0; i < upperCaseButtons.size(); i++) { - JButton button = (JButton) upperCaseButtons.elementAt(i); + JButton button = upperCaseButtons.get(i); button.setBackground(colors[i]); } @@ -630,8 +722,7 @@ public class UserDefinedColours extends GUserDefinedColours implements name = jucs.getColour(i).getName(); if (ResidueProperties.aa3Hash.containsKey(name)) { - index = ((Integer) ResidueProperties.aa3Hash.get(name)) - .intValue(); + index = ResidueProperties.aa3Hash.get(name).intValue(); } else { @@ -679,7 +770,7 @@ public class UserDefinedColours extends GUserDefinedColours implements jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + jucs = jucs.unmarshal(in); newColours = new Color[jucs.getColourCount()]; @@ -713,6 +804,7 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void savebutton_actionPerformed(ActionEvent e) { if (schemeName.getText().trim().length() < 1) @@ -729,8 +821,8 @@ public class UserDefinedColours extends GUserDefinedColours implements { int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage( - "label.colour_scheme_exists_overwrite", new String[] - { schemeName.getText(), schemeName.getText() }), + "label.colour_scheme_exists_overwrite", new Object[] { + schemeName.getText(), schemeName.getText() }), MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION); if (reply != JOptionPane.YES_OPTION) @@ -741,12 +833,13 @@ public class UserDefinedColours extends GUserDefinedColours implements userColourSchemes.remove(schemeName.getText()); } JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jc" }, new String[] - { "Jalview User Colours" }, "Jalview User Colours"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "jc" }, new String[] { "Jalview User Colours" }, + "Jalview User Colours"); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle("Save colour scheme"); + chooser.setDialogTitle(MessageManager + .getString("label.save_colour_scheme")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -804,6 +897,7 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void cancelButton_actionPerformed(ActionEvent e) { if (ap != null) @@ -933,17 +1027,19 @@ public class UserDefinedColours extends GUserDefinedColours implements } + @Override public void caseSensitive_actionPerformed(ActionEvent e) { resetButtonPanel(caseSensitive.isSelected()); lcaseColour.setEnabled(caseSensitive.isSelected()); } + @Override public void lcaseColour_actionPerformed(ActionEvent e) { if (selectedButtons == null) { - selectedButtons = new Vector(); + selectedButtons = new ArrayList(); } else { @@ -951,5 +1047,4 @@ public class UserDefinedColours extends GUserDefinedColours implements } selectedButtons.add(lcaseColour); } - }