From: Renia Correya Date: Thu, 7 Nov 2024 10:09:50 +0000 (+0000) Subject: JAL-4435 Menu option and colouring for sec struct providers X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeature%2FJAL-4386_JAL-4435_reformat_node_labels;p=jalview.git JAL-4435 Menu option and colouring for sec struct providers Added menu option in tree panel for the users to choose between coloured lines or labels or none for secondary structure providers in tree panel. Code changes for using jcolorbrewer colouring palette --- diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index e52f3f6..f41a5f9 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -35,6 +35,7 @@ intervalstore-v1.1.jar jabaws-min-client-NO_LOG4J-2.2.1.jar Apache license - pre-release of JABAWS 2.2.1 client built from https://source.jalview.org/crucible/changelog/jabaws?cs=586260b9f877e0954513fcffb0aa27eaddc5d0ff java-json.jar jaxrpc.jar +jcolorbrewer-5.2.jar GNU LGPL v2 - http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html @@ -112,6 +113,7 @@ javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.co jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1 jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md +jcolorbrewer-5.2.jar GNU LGPL v2 - http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php diff --git a/j11lib/jcolorbrewer-5.2.jar b/j11lib/jcolorbrewer-5.2.jar new file mode 100644 index 0000000..5a6e59c Binary files /dev/null and b/j11lib/jcolorbrewer-5.2.jar differ diff --git a/j8lib/jcolorbrewer-5.2.jar b/j8lib/jcolorbrewer-5.2.jar new file mode 100644 index 0000000..5a6e59c Binary files /dev/null and b/j8lib/jcolorbrewer-5.2.jar differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index b9738a0..27e9404 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -335,6 +335,9 @@ label.protein_matrix = Protein matrix label.show_bootstrap_values = Show Bootstrap Values label.show_distances = Show distances label.show_secondary_structure_provider = Show Secondary Structure Providers +label.hide_structure_provider = None +label.show_structure_provider_as_labels = As Labels +label.show_structure_provider_as_coloured_lines = As Coloured Lines label.mark_unassociated_leaves = Mark Unassociated Leaves label.fit_to_window = Fit To Window label.newick_format = Newick Format diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 7b632d8..a7d03c4 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -40,6 +40,8 @@ import java.util.TreeMap; import java.util.Vector; import java.util.stream.Collectors; +import org.jcolorbrewer.ColorBrewer; + import jalview.api.AlignCalcWorkerI; import jalview.bin.Console; import jalview.commands.RemoveGapColCommand; @@ -3238,4 +3240,27 @@ public class AlignmentUtils c = Color.BLACK; return c; } + + + public static void assignSecondaryStructureProviderColor(Map secondaryStructureProviderColorMap, + List labels) { + + // Use a Set to track unique labels + Set uniqueLabels = new HashSet<>(labels); + + Color[] palette = ColorBrewer.Paired.getColorPalette(uniqueLabels.size()); + + + List colorList = new ArrayList<>(); + Collections.addAll(colorList, palette); + Collections.shuffle(colorList); + int i = 0; + + // Loop through each unique label and add it to the map with a color. + for (String label : uniqueLabels) { + // Generate or retrieve a color for the label. + secondaryStructureProviderColorMap.put(label.toUpperCase().trim(), colorList.get(i)); + i++; + } + } } \ No newline at end of file diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java index 156657a..f388051 100644 --- a/src/jalview/analysis/TreeBuilder.java +++ b/src/jalview/analysis/TreeBuilder.java @@ -31,6 +31,7 @@ import jalview.datamodel.SequenceNode; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; + import java.util.ArrayList; import java.util.BitSet; import java.util.List; @@ -45,7 +46,7 @@ public abstract class TreeBuilder extends TreeEngine protected SequenceI[] sequences; protected List labels; - + public AlignmentView seqData; private AlignmentView seqStrings; @@ -110,6 +111,10 @@ public abstract class TreeBuilder extends TreeEngine { return true; } + + public List getLabels(){ + return this.labels; + } /** * Calculates the tree using the given score model and parameters, and the diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 4efedc3..494360f 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -30,6 +30,7 @@ import java.awt.Graphics2D; import java.awt.Point; import java.awt.Rectangle; import java.awt.RenderingHints; +import java.awt.Stroke; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; @@ -39,6 +40,7 @@ import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import java.util.ArrayList; import java.util.BitSet; +import java.util.Collections; import java.util.HashMap; import java.util.Hashtable; import java.util.LinkedHashSet; @@ -46,6 +48,7 @@ import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Vector; +import org.jcolorbrewer.ColorBrewer; import javax.swing.JPanel; import javax.swing.JScrollPane; @@ -87,7 +90,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, /** DOCUMENT ME!! */ public static final String PLACEHOLDER = " * "; - private static final int DASHED_LINE_Y_OFFSET = 5; + private static final int DASHED_LINE_Y_OFFSET = 6; TreeModel tree; @@ -106,8 +109,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, boolean fitToWindow = true; boolean showDistances = false; - - boolean showSecondaryStructureProvider = false; + + boolean showStructureProviderLabels = false; + + boolean showStructureProviderColouredLines = false; boolean showBootstrap = false; @@ -302,8 +307,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, return; } + Vector leaves = tree.findLeaves(node); + gatherLabelsTo(node, leaves); + if ((node.left() == null) && (node.right() == null)) { + Color originalColor, translucentColor = Color.WHITE; // Drawing leaf node double height = node.height; double dist = node.dist; @@ -323,7 +332,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - g.setColor(av.getSequenceColour(seq).darker()); + originalColor = av.getSequenceColour(seq); + translucentColor = new Color(originalColor.getRed(), originalColor.getGreen(), originalColor.getBlue(), 128); // 128 for 50% transparency + g.setColor(Color.black); } } else @@ -331,7 +342,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.setColor(Color.black); } - // Draw horizontal line + // horizontal line g.drawLine(xstart, ypos, xend, ypos); String nodeLabel = ""; @@ -350,8 +361,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, nodeLabel = nodeLabel + String.valueOf(node.bootstrap); } + if(node.hasLabel() && showStructureProviderColouredLines) { - if (!nodeLabel.equals("")) + drawLinesAndLabelsForSecondaryStructureProvider(g, node, xstart, xend, ypos, nodeLabel); + + Rectangle labelBounds = new Rectangle(xstart, ypos, xend, ypos + DASHED_LINE_Y_OFFSET); + + // Add the bounding box to the map for this node + labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); + + } + else if (!nodeLabel.equals("")) { g.drawString(nodeLabel, xstart + 2, ypos - 2); } @@ -368,7 +388,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, charWidth, charHeight); nameHash.put(node, rect); - + + g.setColor(translucentColor); + g.fillRect(xend + 10, ypos - charHeight / 2, charWidth, charHeight); + //g.fillRect(xstart - 2, ypos - 10, (xend + 20 + charWidth) - xstart, 20); + + g.setColor(Color.black); + // Colour selected leaves differently boolean isSelected = false; if (tp.isColumnWise()) @@ -410,8 +436,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; - g.setColor(node.color.darker()); + //g.setColor(node.color.darker()); + + g.setColor(Color.black); + // Draw horizontal line g.drawLine(xstart, ypos, xend, ypos); if (node == highlightNode) @@ -452,66 +481,65 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } - boolean showColouredLinesForSSProviders = true; - - //Display secondary structure providers as labels only if: + //Display secondary structure providers only if: // ~ node has Label assigned (Secondary structure providers) - // ~ node count is greater than 3 - // ~ showSecondaryStructureProvider option is set to true by the user - if ( node.hasLabel() && showSecondaryStructureProvider && showColouredLinesForSSProviders) - { - - drawLinesAndLabelsForSecondaryStructureProvider(g, node, xstart, xend, ypos, nodeLabel); - - int labelWidth = 20; - int labelHeight = fm.getHeight(); - - // Calculate the bounding box of the string - int xLabelPos = xstart + 2; - int yLabelPos = ypos - 2; - Rectangle labelBounds = new Rectangle(xLabelPos, yLabelPos - labelHeight, labelWidth, labelHeight); - - // Add the bounding box to the map for this node (list allows multiple bounding boxes) - labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); - - } - else if ( node.hasLabel() && showSecondaryStructureProvider && node.count > 3) - { - - String label = node.getLabel(); + // ~ either label or coloured lines option is selected by the user + boolean labelHandled = false; + if(node.hasLabel()) { - if(label.length() > labelLengthThreshold) { + if (showStructureProviderColouredLines) + { + drawLinesAndLabelsForSecondaryStructureProvider(g, node, xstart, xend, ypos, nodeLabel); + + Rectangle labelBounds = new Rectangle(xstart, ypos, xend, ypos + DASHED_LINE_Y_OFFSET); + + // Add the bounding box to the map for this node (list allows multiple bounding boxes) + labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); + labelHandled = true; - //label = AlignmentUtils.reduceLabelLength(label); } - nodeLabel = label + " | " + nodeLabel; - - // Split the nodeLabel by "|" - String[] lines = nodeLabel.split("\\|"); - - // Iterate over the lines and draw each string separately - String longestLabelString = ""; - int i = 0; - for (i = 0; i < lines.length; i++) { - g.drawString(lines[i].trim(), xstart + 2, ypos - 2 - (i * fm.getHeight())); - if(longestLabelString.length() < lines[i].trim().length()) { - longestLabelString = lines[i].trim(); - } + if (showStructureProviderLabels && node.count > 3) + { + + String label = node.getLabel(); + + if(label.length() > labelLengthThreshold) { + + //label = AlignmentUtils.reduceLabelLength(label); + } + + nodeLabel = label + " | " + nodeLabel; + + // Split the nodeLabel by "|" + String[] lines = nodeLabel.split("\\|"); + + // Draw each string separately + String longestLabelString = ""; + int i = 0; + for (i = 0; i < lines.length; i++) { + g.drawString(lines[i].trim(), xstart + 2, ypos - 2 - (i * fm.getHeight())); + if(longestLabelString.length() < lines[i].trim().length()) { + longestLabelString = lines[i].trim(); + } + } + + int labelWidth = fm.stringWidth(longestLabelString); + int labelHeight = fm.getHeight() * (i-1); + + // Bounding box of the string + int xLabelPos = xstart + 2; + int yLabelPos = ypos - 2; + Rectangle labelBounds = new Rectangle(xLabelPos, yLabelPos - labelHeight, labelWidth, labelHeight); + + // Add the bounding box to the map for the node + labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); + + labelHandled = true; } - - int labelWidth = fm.stringWidth(longestLabelString); - int labelHeight = fm.getHeight() * (i-1); - - // Calculate the bounding box of the string - int xLabelPos = xstart + 2; - int yLabelPos = ypos - 2; - Rectangle labelBounds = new Rectangle(xLabelPos, yLabelPos - labelHeight, labelWidth, labelHeight); - - // Add the bounding box to the map for this node (list allows multiple bounding boxes) - labelBoundsMap.computeIfAbsent(node, k -> new ArrayList<>()).add(labelBounds); } - else if (!nodeLabel.equals("")) + + if (!nodeLabel.equals("") && !labelHandled) { g.drawString(nodeLabel, xstart + 2, ypos - 2); } @@ -521,18 +549,24 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, private void drawLinesAndLabelsForSecondaryStructureProvider(Graphics g, BinaryNode node, int xstart, int xend, int ypos, String nodeLabel) { - // Cast the Graphics object to Graphics2D + Graphics2D g2d = (Graphics2D) g.create(); // Set dash pattern - float[] dashPattern = {2, 3}; +// float[] dashPattern = {2, 2}; +// g2d.setStroke(new BasicStroke( +// 2.5f, +// BasicStroke.CAP_BUTT, +// BasicStroke.JOIN_ROUND, +// 0.0f, +// dashPattern, +// 0.0f)); + g2d.setStroke(new BasicStroke( - 1.5f, - BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, - 0.0f, - dashPattern, - 0.0f)); + 4.0f, + BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND + )); String label = node.getLabel(); String[] lines = label.split("\\|"); @@ -552,7 +586,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int secondHalfLinesCount = lines.length - mid; drawSecondaryStructureProviderLinesSection(g2d, lines, mid, lines.length, xstart, xend, - ypos + DASHED_LINE_Y_OFFSET, + ypos, false); drawVerticalLineAndLabel(g, xstart, ypos, secondHalfLinesCount, false, nodeLabel); @@ -560,26 +594,36 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } private void drawSecondaryStructureProviderLinesSection(Graphics2D g2d, String[] lines, int start, int end, int xstart, int xend, int baseY, boolean above) { - for (int i = start; i < end; i++) { + + for (int i = start, j=0; i < end; i++, j++) { int adjustedY = above ? baseY - ((i - start) * DASHED_LINE_Y_OFFSET) : baseY +((i - start) * DASHED_LINE_Y_OFFSET); - Color providerColor = AlignmentUtils.getSecondaryStructureProviderColor(lines[i]); + //Color providerColor = AlignmentUtils.getSecondaryStructureProviderColor(lines[i]); + + Map secondaryStructureProviderColorMap = tp.getSecondaryStructureProviderColorMap(); + Color providerColor = secondaryStructureProviderColorMap.getOrDefault(lines[i].toUpperCase().trim(), Color.BLACK); g2d.setColor(providerColor); - g2d.drawLine(xstart, adjustedY, xend, adjustedY); + if(i==start && !above) { + g2d.drawLine(xstart, adjustedY, xend-3, adjustedY); + } + else + { + g2d.drawLine(xstart, adjustedY, xend, adjustedY); + } } } private void drawVerticalLineAndLabel(Graphics g, int xstart, int ypos, - int linesCount, boolean above, String nodeLabel) { - int adjustedY = above - ? ypos - (linesCount) * DASHED_LINE_Y_OFFSET - : ypos + (linesCount) * DASHED_LINE_Y_OFFSET; + int linesCount, boolean above, String nodeLabel) { + + int adjustment = (linesCount * DASHED_LINE_Y_OFFSET) + (DASHED_LINE_Y_OFFSET / 3); + int adjustedY = ypos + (above ? -adjustment : adjustment - DASHED_LINE_Y_OFFSET); - // Draw vertical line + // draw vertical line g.drawLine(xstart, ypos, xstart, adjustedY); - // Draw label + // draw label if(above && !nodeLabel.equals("")) g.drawString(nodeLabel, xstart + 2, adjustedY - 2); } @@ -1232,7 +1276,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); - gatherLabelsTo(groups.get(i), l); + //gatherLabelsTo(groups.get(i), l); if (!tp.isColumnWise()) { createSeqGroupFor(aps, l, col, groups.get(i).getLabel()); @@ -1574,15 +1618,30 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, repaint(); } - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowSecondaryStructureProvider(boolean state) + public void hideStructureProviders(boolean state) + { + if(state) { + this.showStructureProviderColouredLines = false; + this.showStructureProviderLabels = false; + repaint(); + } + } + + public void setShowStructureProviderColouredLines(boolean state) { - this.showSecondaryStructureProvider = state; + this.showStructureProviderColouredLines = state; + if(state) { + this.showStructureProviderLabels = false; + } + repaint(); + } + + public void setShowStructureProviderLabels(boolean state) + { + this.showStructureProviderLabels = state; + if(state) { + this.showStructureProviderColouredLines = false; + } repaint(); } diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 6a1b381..0fae337 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -21,8 +21,12 @@ package jalview.gui; import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; import java.awt.Font; import java.awt.Graphics; +import java.awt.GridLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.KeyAdapter; @@ -32,14 +36,17 @@ import java.beans.PropertyChangeListener; import java.io.File; import java.io.FileOutputStream; import java.util.ArrayList; +import java.util.HashMap; import java.util.List; import java.util.Locale; +import java.util.Map; import javax.swing.ButtonGroup; import javax.swing.JLabel; import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; import javax.swing.SwingConstants; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; @@ -47,6 +54,7 @@ import javax.swing.event.InternalFrameEvent; import org.jibble.epsgraphics.EpsGraphics2D; import jalview.analysis.AlignmentSorter; +import jalview.analysis.AlignmentUtils; import jalview.analysis.AverageDistanceTree; import jalview.analysis.NJTree; import jalview.analysis.TreeBuilder; @@ -103,6 +111,8 @@ public class TreePanel extends GTreePanel // New JLabel for subtitle private JLabel subtitleLabel; + + private Map secondaryStructureProviderColorMap; /** * Creates a new TreePanel object. @@ -191,6 +201,12 @@ public class TreePanel extends GTreePanel // @Mungo - Why don't we return our own viewport ??? return getTreeCanvas().getViewport(); } + + + public Map getSecondaryStructureProviderColorMap() + { + return secondaryStructureProviderColorMap; + } private void addSubtitlePanel(String subTitle) { @@ -446,6 +462,11 @@ public class TreePanel extends GTreePanel TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(av, sm, similarityParams) : new AverageDistanceTree(av, sm, similarityParams); + List labels = njtree.getLabels(); + if(labels != null && labels.size()>0) { + secondaryStructureProviderColorMap = new HashMap(); + AlignmentUtils.assignSecondaryStructureProviderColor(secondaryStructureProviderColorMap, labels); + } tree = new TreeModel(njtree); // don't display distances for columnwise trees } @@ -769,16 +790,22 @@ public class TreePanel extends GTreePanel treeCanvas.setShowDistances(distanceMenu.isSelected()); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ @Override - public void showSecondaryStructureProviderMenu_actionPerformed(ActionEvent e) + public void hideStructureProviders_actionPerformed(ActionEvent e) + { + treeCanvas.hideStructureProviders(hideStructureProviders.isSelected()); + } + + @Override + public void showStructureProviderColouredLines_actionPerformed(ActionEvent e) + { + treeCanvas.setShowStructureProviderColouredLines(showStructureProviderColouredLines.isSelected()); + } + + @Override + public void showStructureProviderLabels_actionPerformed(ActionEvent e) { - treeCanvas.setShowSecondaryStructureProvider(showSecondaryStructureProviderMenu.isSelected()); + treeCanvas.setShowStructureProviderLabels(showStructureProviderLabels.isSelected()); } /** diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java index 884f3eb..9120b15 100755 --- a/src/jalview/jbgui/GTreePanel.java +++ b/src/jalview/jbgui/GTreePanel.java @@ -24,12 +24,16 @@ import java.awt.BorderLayout; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; +import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; @@ -65,7 +69,16 @@ public class GTreePanel extends JInternalFrame //Menu option for the user to select their preference in //displaying secondary structure providers as labels. //Visible only for secondary structure similarity. - public JCheckBoxMenuItem showSecondaryStructureProviderMenu = new JCheckBoxMenuItem(); + + public JMenu showSecondaryStructureProviderMenu = new JMenu(); + + ButtonGroup showSecondaryStructureProviderButtonGroup = new ButtonGroup(); + + public JRadioButtonMenuItem hideStructureProviders = new JRadioButtonMenuItem(); + + public JRadioButtonMenuItem showStructureProviderLabels = new JRadioButtonMenuItem(); + + public JRadioButtonMenuItem showStructureProviderColouredLines = new JRadioButtonMenuItem(); public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem(); @@ -179,15 +192,43 @@ public class GTreePanel extends JInternalFrame distanceMenu_actionPerformed(e); } }); + + showSecondaryStructureProviderButtonGroup.add(hideStructureProviders); + showSecondaryStructureProviderButtonGroup.add(showStructureProviderLabels); + showSecondaryStructureProviderButtonGroup.add(showStructureProviderColouredLines); showSecondaryStructureProviderMenu.setText(MessageManager.getString("label.show_secondary_structure_provider")); - showSecondaryStructureProviderMenu.addActionListener(new java.awt.event.ActionListener() + hideStructureProviders.setText(MessageManager.getString("label.hide_structure_provider")); + hideStructureProviders.setSelected(true); + hideStructureProviders.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showSecondaryStructureProviderMenu_actionPerformed(e); + hideStructureProviders_actionPerformed(e); } }); + + showStructureProviderLabels.setText(MessageManager.getString("label.show_structure_provider_as_labels")); + showStructureProviderLabels.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showStructureProviderLabels_actionPerformed(e); + } + }); + + showStructureProviderColouredLines.setText(MessageManager.getString("label.show_structure_provider_as_coloured_lines")); + showStructureProviderColouredLines.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showStructureProviderColouredLines_actionPerformed(e); + } + + }); + fitToWindow.setSelected(true); fitToWindow.setText(MessageManager.getString("label.fit_to_window")); fitToWindow.addActionListener(new java.awt.event.ActionListener() @@ -259,7 +300,7 @@ public class GTreePanel extends JInternalFrame viewMenu.add(fitToWindow); viewMenu.add(font); viewMenu.add(distanceMenu); - viewMenu.add(showSecondaryStructureProviderMenu); + viewMenu.add(showSecondaryStructureProviderMenu); viewMenu.add(bootstrapMenu); viewMenu.add(placeholdersMenu); viewMenu.add(sortAssocViews); @@ -267,6 +308,10 @@ public class GTreePanel extends JInternalFrame saveAsMenu.add(saveAsNewick); saveAsMenu.add(epsTree); saveAsMenu.add(pngTree); + showSecondaryStructureProviderMenu.add(hideStructureProviders); + showSecondaryStructureProviderMenu.add(showStructureProviderLabels); + showSecondaryStructureProviderMenu.add(showStructureProviderColouredLines); + } public void printMenu_actionPerformed(ActionEvent e) @@ -284,6 +329,18 @@ public class GTreePanel extends JInternalFrame public void showSecondaryStructureProviderMenu_actionPerformed(ActionEvent e) { } + + public void hideStructureProviders_actionPerformed(ActionEvent e) + { + } + + public void showStructureProviderColouredLines_actionPerformed(ActionEvent e) + { + } + + public void showStructureProviderLabels_actionPerformed(ActionEvent e) + { + } public void bootstrapMenu_actionPerformed(ActionEvent e) {