X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=1e85e55a4035f86a31b57362f992502d51cf7138;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=17682c96cf5f2cf01fdedcb126742639cbfe303e;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 17682c9..1e85e55 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,68 +1,94 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; -import javax.swing.event.*; - -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.datamodel.SequenceGroup; +import jalview.io.JalviewFileChooser; +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; +import java.awt.Font; +import java.awt.event.ActionEvent; +import java.awt.event.MouseEvent; +import java.io.File; +import java.io.FileInputStream; +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 javax.swing.JButton; +import javax.swing.JInternalFrame; +import javax.swing.JOptionPane; +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; JInternalFrame frame; - AppJmol jmol; + JalviewStructureDisplayI jmol; - Vector upperCaseButtons; + ArrayList upperCaseButtons; - Vector lowerCaseButtons; + ArrayList lowerCaseButtons; /** * Creates a new UserDefinedColours object. * * @param ap - * DOCUMENT ME! + * DOCUMENT ME! * @param sg - * DOCUMENT ME! + * DOCUMENT ME! */ public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) { @@ -104,7 +130,8 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs) + public UserDefinedColours(JalviewStructureDisplayI jmol, + ColourSchemeI oldcs) { super(); this.jmol = jmol; @@ -129,17 +156,14 @@ public class UserDefinedColours extends GUserDefinedColours implements colorChooser.getSelectionModel().addChangeListener(this); frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true); + 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() + ")"); } - - if (new jalview.util.Platform().isAMac()) - { - frame.setSize(760, 370); - } } void resetButtonPanel(boolean caseSensitive) @@ -148,7 +172,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (upperCaseButtons == null) { - upperCaseButtons = new Vector(); + upperCaseButtons = new ArrayList(); } JButton button; @@ -189,7 +213,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (lowerCaseButtons == null) { - lowerCaseButtons = new Vector(); + lowerCaseButtons = new ArrayList(); } for (int i = 0; i < 20; i++) @@ -210,6 +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(); } @@ -218,44 +251,57 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * 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(); @@ -265,8 +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 { @@ -298,9 +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); } } @@ -309,34 +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()); } } @@ -344,19 +386,19 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param label - * DOCUMENT ME! + * DOCUMENT ME! * @param aa - * DOCUMENT ME! + * 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 @@ -364,20 +406,21 @@ 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) + if (oldColourScheme != null) { try { - col = oldColourScheme.findColour(aa.charAt(0), -1); + col = oldColourScheme.findColour(aa.charAt(0), -1, null); } catch (Exception ex) { } @@ -393,9 +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; @@ -405,28 +449,65 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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! + * 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()); @@ -450,10 +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); @@ -461,17 +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; @@ -481,20 +588,22 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * 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"); + JalviewFileChooser chooser = new JalviewFileChooser( + 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("Load colour scheme"); - chooser.setToolTipText("Load"); + chooser.setDialogTitle(MessageManager + .getString("label.load_colour_scheme")); + chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); @@ -523,7 +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]); } @@ -537,7 +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]); } @@ -581,7 +690,7 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param file - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -613,8 +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 { @@ -662,7 +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()]; @@ -694,15 +802,17 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void savebutton_actionPerformed(ActionEvent e) { if (schemeName.getText().trim().length() < 1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "User colour scheme must have a name!", - "No name for colour scheme", JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .getString("label.user_colour_scheme_must_have_name"), + MessageManager.getString("label.no_name_colour_scheme"), + JOptionPane.WARNING_MESSAGE); return; } @@ -710,10 +820,11 @@ public class UserDefinedColours extends GUserDefinedColours implements && userColourSchemes.containsKey(schemeName.getText())) { int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "Colour scheme " + schemeName.getText() + " exists." - + "\nContinue saving colour scheme as " - + schemeName.getText() + "?", - "Duplicate scheme name", JOptionPane.YES_NO_OPTION); + MessageManager.formatMessage( + "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) { return; @@ -721,14 +832,15 @@ 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"); + JalviewFileChooser chooser = new JalviewFileChooser( + 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.setToolTipText("Save"); + chooser.setDialogTitle(MessageManager + .getString("label.save_colour_scheme")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -783,8 +895,9 @@ public class UserDefinedColours extends GUserDefinedColours implements * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override protected void cancelButton_actionPerformed(ActionEvent e) { if (ap != null) @@ -857,8 +970,8 @@ public class UserDefinedColours extends GUserDefinedColours implements { if (coloursFound.toString().length() > 1) { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound - .toString()); + jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", + coloursFound.toString()); } else { @@ -877,8 +990,8 @@ public class UserDefinedColours extends GUserDefinedColours implements userColourSchemes = new Hashtable(); StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer(jalview.bin.Cache - .getProperty("USER_DEFINED_COLOURS"), "|"); + StringTokenizer st = new StringTokenizer( + jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); while (st.hasMoreElements()) { @@ -903,8 +1016,8 @@ public class UserDefinedColours extends GUserDefinedColours implements if (coloursFound.toString().length() > 1) { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound - .toString()); + jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", + coloursFound.toString()); } else { @@ -914,17 +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 { @@ -932,5 +1047,4 @@ public class UserDefinedColours extends GUserDefinedColours implements } selectedButtons.add(lcaseColour); } - }