X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=6df208815fe8f9e1b0d7a08e401f950169c06cb9;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=4268353fb37e3d585a97f778ac9e8ec8c78f3199;hpb=1f705b7d5fb0920573037631b810aac3262ee190;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 4268353..7462bc8 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,591 +1,1316 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * 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. - * - * 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 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 jalview.datamodel.*; -import jalview.io.FormatAdapter; - -import java.awt.*; +import java.awt.Color; +import java.awt.Cursor; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.RenderingHints; +import java.awt.Toolkit; import java.awt.datatransfer.StringSelection; -import java.awt.event.*; -import java.awt.image.*; -import java.util.Vector; - -import javax.swing.*; - +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.geom.AffineTransform; +import java.io.IOException; +import java.util.Arrays; +import java.util.Collections; +import java.util.Iterator; +import java.util.Locale; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; + +import jalview.analysis.AlignSeq; +import jalview.analysis.AlignmentUtils; +import jalview.bin.Console; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.ContactMatrixI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FormatAdapter; +import jalview.io.NewickFile; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel that holds the labels for alignment annotations, providing + * tooltips, context menus, drag to reorder rows, and drag to adjust panel + * height */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel + implements MouseListener, MouseMotionListener, ActionListener { - static String ADDNEW = "Add New Row"; - static String HIDE = "Hide This Row"; - static String DELETE = "Delete This Row"; - static String SHOWALL = "Show All Hidden Rows"; - static String OUTPUT_TEXT = "Export Annotation"; - static String COPYCONS_SEQ = "Copy Consensus Sequence"; - boolean resizePanel = false; - Image image; - AlignmentPanel ap; - AlignViewport av; - boolean resizing = false; - MouseEvent dragEvent; - int oldY; - int selectedRow; - int scrollOffset = 0; - Font font = new Font("Arial", Font.PLAIN, 11); - - - /** - * Creates a new AnnotationLabels object. - * - * @param ap DOCUMENT ME! - */ - public AnnotationLabels(AlignmentPanel ap) - { - this.ap = ap; - av = ap.av; + private static final String HTML_END_TAG = ""; + + private static final String HTML_START_TAG = ""; + + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; + + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; + + private static final Font font = new Font("Arial", Font.PLAIN, 11); + + private static final String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); + + private static final String ADDNEW = MessageManager + .getString("label.add_new_row"); + + private static final String EDITNAME = MessageManager + .getString("label.edit_label_description"); + + private static final String HIDE = MessageManager + .getString("label.hide_row"); + + private static final String DELETE = MessageManager + .getString("label.delete_row"); + + private static final String SHOWALL = MessageManager + .getString("label.show_all_hidden_rows"); + + private static final String OUTPUT_TEXT = MessageManager + .getString("label.export_annotation"); + + private static final String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); + + private final boolean debugRedraw = false; + + private AlignmentPanel ap; + + AlignViewport av; - java.net.URL url = getClass().getResource("/images/idwidth.gif"); - Image temp = null; + private MouseEvent dragEvent; - if (url != null) + private int oldY; + + private int selectedRow; + + private int scrollOffset = 0; + + private boolean hasHiddenRows; + + private boolean resizePanel = false; + + /** + * Creates a new AnnotationLabels object + * + * @param ap + */ + public AnnotationLabels(AlignmentPanel ap) + { + + this.ap = ap; + av = ap.av; + ToolTipManager.sharedInstance().registerComponent(this); + + addMouseListener(this); + addMouseMotionListener(this); + addMouseWheelListener(ap.getAnnotationPanel()); + } + + public AnnotationLabels(AlignViewport av) + { + this.av = av; + } + + /** + * DOCUMENT ME! + * + * @param y + * DOCUMENT ME! + */ + public void setScrollOffset(int y) + { + scrollOffset = y; + repaint(); + } + + /** + * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at + * y + * + * @param y + * coordinate position to search for a row + */ + void getSelectedRow(int y) + { + int height = 0; + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + selectedRow = -2; + if (aa != null) + { + for (int i = 0; i < aa.length; i++) + { + selectedRow = -1; + if (!aa[i].visible) { - temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); + continue; } - try + height += aa[i].height; + + if (y < height) { - MediaTracker mt = new MediaTracker(this); - mt.addImage(temp, 0); - mt.waitForID(0); + selectedRow = i; + + break; } - catch (Exception ex) + } + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void actionPerformed(ActionEvent evt) + { + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + + String action = evt.getActionCommand(); + if (ADDNEW.equals(action)) + { + /* + * non-returning dialog + */ + AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, + null, new Annotation[ap.av.getAlignment().getWidth()]); + editLabelDescription(newAnnotation, true); + } + else if (EDITNAME.equals(action)) + { + /* + * non-returning dialog + */ + editLabelDescription(aa[selectedRow], false); + } + else if (HIDE.equals(action)) + { + aa[selectedRow].visible = false; + } + else if (DELETE.equals(action)) + { + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); + ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); + } + else if (SHOWALL.equals(action)) + { + for (int i = 0; i < aa.length; i++) + { + if (!aa[i].visible && aa[i].annotations != null) { + aa[i].visible = true; } - - BufferedImage bi = new BufferedImage(temp.getHeight(this), - temp.getWidth(this), BufferedImage.TYPE_INT_RGB); - Graphics2D g = (Graphics2D) bi.getGraphics(); - g.rotate(Math.toRadians(90)); - g.drawImage(temp, 0, -bi.getWidth(this), this); - image = (Image) bi; - - addMouseListener(this); - addMouseMotionListener(this); + } } - - public AnnotationLabels(AlignViewport av) + else if (OUTPUT_TEXT.equals(action)) { - this.av = av; + new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } - - /** - * DOCUMENT ME! - * - * @param y DOCUMENT ME! - */ - public void setScrollOffset(int y) + else if (COPYCONS_SEQ.equals(action)) { - scrollOffset = y; - repaint(); + SequenceI cons = null; + if (aa[selectedRow].groupRef != null) + { + cons = aa[selectedRow].groupRef.getConsensusSeq(); + } + else + { + cons = av.getConsensusSeq(); + } + if (cons != null) + { + copy_annotseqtoclipboard(cons); + } } - - void getSelectedRow(int y) + else if (TOGGLE_LABELSCALE.equals(action)) { - int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; + } - if(aa!=null) + ap.refresh(true); + } + + /** + * Shows a dialog where the annotation name and description may be edited. If + * parameter addNew is true, then on confirmation, a new AlignmentAnnotation + * is added, else an existing annotation is updated. + * + * @param annotation + * @param addNew + */ + void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) + { + String name = MessageManager.getString("label.annotation_name"); + String description = MessageManager + .getString("label.annotation_description"); + String title = MessageManager + .getString("label.edit_annotation_name_description"); + EditNameDialog dialog = new EditNameDialog(annotation.label, + annotation.description, name, description); + + dialog.showDialog(ap.alignFrame, title, () -> { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + if (addNew) { - for (int i = 0; i < aa.length; i++) + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); + } + ap.refresh(true); + return null; + }); + } + + @Override + public void mousePressed(MouseEvent evt) + { + getSelectedRow(evt.getY() - getScrollOffset()); + oldY = evt.getY(); + if (evt.isPopupTrigger()) + { + showPopupMenu(evt); + } + } + + /** + * Build and show the Pop-up menu at the right-click mouse position + * + * @param evt + */ + void showPopupMenu(MouseEvent evt) + { + evt.consume(); + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + pop.add(item); + if (selectedRow < 0) + { + if (hasHiddenRows) + { // let the user make everything visible again + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } + pop.show(this, evt.getX(), evt.getY()); + return; + } + item = new JMenuItem(EDITNAME); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(HIDE); + item.addActionListener(this); + pop.add(item); + // JAL-1264 hide all sequence-specific annotations of this type + if (selectedRow < aa.length) + { + if (aa[selectedRow].sequenceRef != null) + { + final String label = aa[selectedRow].label; + JMenuItem hideType = new JMenuItem(); + String text = MessageManager.getString("label.hide_all") + " " + + label; + hideType.setText(text); + hideType.addActionListener(new ActionListener() { - if (!aa[i].visible) + @Override + public void actionPerformed(ActionEvent e) { - continue; - } - - height += aa[i].height; - - if (y < height) - { - selectedRow = i; - - break; + AlignmentUtils.showOrHideSequenceAnnotations( + ap.av.getAlignment(), Collections.singleton(label), + null, false, false); + ap.refresh(true); } - } + }); + pop.add(hideType); } } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void actionPerformed(ActionEvent evt) + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + if (hasHiddenRows) + { + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } + item = new JMenuItem(OUTPUT_TEXT); + item.addActionListener(this); + pop.add(item); + // TODO: annotation object should be typed for autocalculated/derived + // property methods + if (selectedRow < aa.length) { - int dif = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + final String label = aa[selectedRow].label; + if (!aa[selectedRow].autoCalculated) + { + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) + { + // display formatting settings for this row. + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, + aa[selectedRow].scaleColLabel); + item.addActionListener(this); + pop.add(item); + } + } + else if (label.indexOf("Consensus") > -1) + { + addConsensusMenuOptions(ap, aa[selectedRow], pop); - if (evt.getActionCommand().equals(ADDNEW)) + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP + && PAEContactMatrix.PAEMATRIX + .equals(aa[selectedRow].getCalcId())) + { + final PAEContactMatrix cm = (PAEContactMatrix) av + .getContactMatrix(aa[selectedRow]); + if (cm != null && cm.getNewick() != null + && cm.getNewick().length() > 0) { - String label = JOptionPane.showInputDialog(this, - "Label for annotation"); + item = new JMenuItem("Show Tree for Matrix"); + item.addActionListener(new ActionListener() + { - if (label == null) + @Override + public void actionPerformed(ActionEvent e) { - label = ""; - } - AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label, - "New description", - new Annotation[ap.av.alignment.getWidth()]); + ap.alignFrame.showContactMapTree(aa[selectedRow], cm); - ap.av.alignment.addAnnotation(newAnnotation); - ap.av.alignment.setAnnotationIndex(newAnnotation, 0); - if (aa != null) - dif = aa[aa.length - 1].height; + } + }); + pop.addSeparator(); + pop.add(item); } - else if (evt.getActionCommand().equals(HIDE)) - { - aa[selectedRow].visible = false; - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.quality = null; - } + } + } + pop.show(this, evt.getX(), evt.getY()); + } + + /** + * A helper method that adds menu options for calculation and visualisation of + * group and/or alignment consensus annotation to a popup menu. This is + * designed to be reusable for either unwrapped mode (popup menu is shown on + * component AnnotationLabels), or wrapped mode (popup menu is shown on + * IdPanel when the mouse is over an annotation label). + * + * @param ap + * @param ann + * @param pop + */ + static void addConsensusMenuOptions(AlignmentPanel ap, + AlignmentAnnotation ann, JPopupMenu pop) + { + pop.addSeparator(); + + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString("label.ignore_gaps_consensus"), + (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = ann; + cbmi.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (aaa.groupRef != null) + { + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + ap.alignmentChanged(); + } + }); + pop.add(cbmi); - dif = aa[selectedRow].height * -1; + if (aaa.groupRef != null) + { + /* + * group consensus options + */ + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + ann.groupRef.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); } - else if (evt.getActionCommand().equals(DELETE)) + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_logo"), + ann.groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); - dif = aa[selectedRow].height * -1; + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); } - else if (evt.getActionCommand().equals(SHOWALL)) + }); + pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + ann.groupRef.isNormaliseSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - dif += aa[i].height; - aa[i].visible = true; - } - } + aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowSequenceLogo(true); + ap.repaint(); + } + }); + pop.add(cproflnorm); + } + else + { + /* + * alignment consensus options + */ + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + ap.av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ap.av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + ap.av.isShowSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations( - ap, - new AlignmentAnnotation[] - {aa[selectedRow]} - ); + ap.av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); } - else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + ap.av.isNormaliseSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - SequenceI cons=av.getConsensusSeq(); - if (cons!=null) - copy_annotseqtoclipboard(cons); - + ap.av.setShowSequenceLogo(true); + ap.av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); } - - ap.annotationPanel.adjustPanelHeight(); - ap.annotationScroller.validate(); - ap.repaint(); + }); + pop.add(cprofnorm); + } + } + + /** + * Reorders annotation rows after a drag of a label + * + * @param evt + */ + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) + { + showPopupMenu(evt); + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + int start = selectedRow; + getSelectedRow(evt.getY() - getScrollOffset()); + int end = selectedRow; + + /* + * if dragging to resize instead, start == end */ - public void mousePressed(MouseEvent evt) + if (start != end) { - getSelectedRow(evt.getY() - scrollOffset); - oldY = evt.getY(); + // Swap these annotations + AlignmentAnnotation startAA = ap.av.getAlignment() + .getAlignmentAnnotation()[start]; + if (end == -1) + { + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; + } + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; + + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) + resizePanel = false; + dragEvent = null; + repaint(); + ap.getAnnotationPanel().repaint(); + } + + /** + * Removes the height adjuster image on leaving the panel, unless currently + * dragging it + */ + @Override + public void mouseExited(MouseEvent evt) + { + if (resizePanel && dragEvent == null) + { + resizePanel = false; + repaint(); + } + } + + /** + * A mouse drag may be either an adjustment of the panel height (if flag + * resizePanel is set on), or a reordering of the annotation rows. The former + * is dealt with by this method, the latter in mouseReleased. + * + * @param evt + */ + @Override + public void mouseDragged(MouseEvent evt) + { + dragEvent = evt; + + if (resizePanel) { - int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); - int end = selectedRow; + Dimension d = ap.annotationScroller.getPreferredSize(); + int dif = evt.getY() - oldY; - if(start!=end) - { - //Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start]; - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); + if ((d.height - dif) > 20) + { + ap.annotationScroller + .setPreferredSize(new Dimension(d.width, d.height - dif)); + d = ap.annotationSpaceFillerHolder.getPreferredSize(); + ap.annotationSpaceFillerHolder + .setPreferredSize(new Dimension(d.width, d.height - dif)); + ap.paintAlignment(true, false); + } - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; - } + ap.addNotify(); + } + else + { + repaint(); + } + } + + /** + * Updates the tooltip as the mouse moves over the labels + * + * @param evt + */ + @Override + public void mouseMoved(MouseEvent evt) + { + showOrHideAdjuster(evt); + + getSelectedRow(evt.getY() - getScrollOffset()); + + if (selectedRow > -1 && ap.av.getAlignment() + .getAlignmentAnnotation().length > selectedRow) + { + AlignmentAnnotation[] anns = ap.av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation aa = anns[selectedRow]; + + String desc = getTooltip(aa); + this.setToolTipText(desc); + String msg = getStatusMessage(aa, anns); + ap.alignFrame.setStatus(msg); + } + } + + /** + * Constructs suitable text to show in the status bar when over an annotation + * label, containing the associated sequence name (if any), and the annotation + * labels (or all labels for a graph group annotation) + * + * @param aa + * @param anns + * @return + */ + static String getStatusMessage(AlignmentAnnotation aa, + AlignmentAnnotation[] anns) + { + if (aa == null) + { + return null; + } - resizePanel = false; - dragEvent = null; - repaint(); - ap.annotationPanel.repaint(); + StringBuilder msg = new StringBuilder(32); + if (aa.sequenceRef != null) + { + msg.append(aa.sequenceRef.getName()).append(" : "); } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseEntered(MouseEvent evt) + if (aa.graphGroup == -1) + { + msg.append(aa.label); + } + else if (anns != null) { - if(evt.getY()<10) + boolean first = true; + for (int i = anns.length - 1; i >= 0; i--) { - resizePanel = true; - repaint(); + if (anns[i].graphGroup == aa.graphGroup) + { + if (!first) + { + msg.append(", "); + } + msg.append(anns[i].label); + first = false; + } } } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseExited(MouseEvent evt) + return msg.toString(); + } + + /** + * Answers a tooltip, formatted as html, containing the annotation description + * (prefixed by associated sequence id if applicable), and the annotation + * (non-positional) score if it has one. Answers null if neither description + * nor score is found. + * + * @param aa + * @return + */ + static String getTooltip(AlignmentAnnotation aa) + { + if (aa == null) { - if(dragEvent == null) + return null; + } + StringBuilder tooltip = new StringBuilder(); + if (aa.description != null && !aa.description.equals("New description")) + { + // TODO: we could refactor and merge this code with the code in + // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature + // tooltips + String desc = aa.getDescription(true).trim(); + if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) { - resizePanel = false; - repaint(); + tooltip.append(HTML_START_TAG); + desc = desc.replace("<", "<"); } + else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG)) + { + desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); + } + tooltip.append(desc); } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) + else { - dragEvent = evt; - - if (resizePanel) + // begin the tooltip's html fragment + tooltip.append(HTML_START_TAG); + } + if (aa.hasScore()) + { + if (tooltip.length() > HTML_START_TAG.length()) { - Dimension d = ap.annotationScroller.getPreferredSize(); - int dif = evt.getY() - oldY; - - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; - - if ( (d.height - dif) > 20) - { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); - d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.repaint(); - } - - ap.addNotify(); + tooltip.append("
"); } - else - repaint(); + // TODO: limit precision of score to avoid noise from imprecise + // doubles + // (64.7 becomes 64.7+/some tiny value). + tooltip.append(" Score: ").append(String.valueOf(aa.score)); } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) + if (tooltip.length() > HTML_START_TAG.length()) { - resizePanel = evt.getY()<10; - - repaint(); + return tooltip.append(HTML_END_TAG).toString(); } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + /* + * nothing in the tooltip (except "") */ - public void mouseClicked(MouseEvent evt) + return null; + } + + /** + * Shows the height adjuster image if the mouse moves into the top left + * region, or hides it if the mouse leaves the regio + * + * @param evt + */ + protected void showOrHideAdjuster(MouseEvent evt) + { + boolean was = resizePanel; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + + if (resizePanel != was) { - if(!SwingUtilities.isRightMouseButton(evt)) - return; - - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - - if ((aa == null) || (aa.length == 0)) + setCursor(Cursor + .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR + : Cursor.DEFAULT_CURSOR)); + repaint(); + } + } + + @Override + public void mouseClicked(MouseEvent evt) + { + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) + { + if (selectedRow > -1 && selectedRow < aa.length) + { + if (aa[selectedRow].groupRef != null) { - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - pop.show(this, evt.getX(), evt.getY()); + if (evt.getClickCount() >= 2) + { + // todo: make the ap scroll to the selection - not necessary, first + // click highlights/scrolls, second selects + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); + // process modifiers + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg == aa[selectedRow].groupRef + || !(Platform.isControlDown(evt) || evt.isShiftDown())) + { + if (Platform.isControlDown(evt) || evt.isShiftDown()) + { + // clone a new selection group from the associated group + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); + } + else + { + // set selection to the associated group so it can be edited + ap.av.setSelectionGroup(aa[selectedRow].groupRef); + } + } + else + { + // modify current selection with associated group + int remainToAdd = aa[selectedRow].groupRef.getSize(); + for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) + { + if (jalview.util.Platform.isControlDown(evt)) + { + sg.addOrRemove(sgs, --remainToAdd == 0); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(sgs, --remainToAdd == 0); + } + } + } - return; + ap.paintAlignment(false, false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } + else + { + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); + } + return; } - - - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(HIDE); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(DELETE); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(OUTPUT_TEXT); - item.addActionListener(this); - pop.add(item); - // annotation object should be typed - if (aa[selectedRow].label.equals("Consensus")) + else if (aa[selectedRow].sequenceRef != null) { - pop.addSeparator(); - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", - ap.av.getIgnoreGapsConsensus()); - cbmi.addActionListener(new ActionListener() - {public void actionPerformed(ActionEvent e) - { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); - } - }); - pop.add(cbmi); - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); - } + if (evt.getClickCount() == 1) + { + ap.getSeqPanel().ap.getIdPanel() + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); + } + else if (evt.getClickCount() >= 2) + { + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) + { + // we make a copy rather than edit the current selection if no + // modifiers pressed + // see Enhancement JAL-1557 + if (!(Platform.isControlDown(evt) || evt.isShiftDown())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } + else + { + if (Platform.isControlDown(evt)) + { + sg.addOrRemove(aa[selectedRow].sequenceRef, true); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(aa[selectedRow].sequenceRef, true); + } + } + } + else + { + sg = new SequenceGroup(); + sg.setStartRes(0); + sg.setEndRes(ap.av.getAlignment().getWidth() - 1); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } + ap.av.setSelectionGroup(sg); + ap.paintAlignment(false, false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } - pop.show(this, evt.getX(), evt.getY()); - } - /** - * do a single sequence copy to jalview and the system clipboard - * - * @param sq sequence to be copied to clipboard - */ - protected void copy_annotseqtoclipboard(SequenceI sq) - { - SequenceI [] seqs = new SequenceI[] { sq }; - String[] omitHidden = null; - SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()}; - if (dseqs[0]==null) { - dseqs[0] = new Sequence(sq); - dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sq.getSequence())); - sq.setDatasetSequence(dseqs[0]); - } - Alignment ds=new Alignment(dseqs); - if (av.hasHiddenColumns) - { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); + } } + return; + } + } + + /** + * do a single sequence copy to jalview and the system clipboard + * + * @param sq + * sequence to be copied to clipboard + */ + protected void copy_annotseqtoclipboard(SequenceI sq) + { + SequenceI[] seqs = new SequenceI[] { sq }; + String[] omitHidden = null; + SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; + if (dseqs[0] == null) + { + dseqs[0] = new Sequence(sq); + dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, + sq.getSequenceAsString())); - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); + sq.setDatasetSequence(dseqs[0]); + } + Alignment ds = new Alignment(dseqs); + if (av.hasHiddenColumns()) + { + Iterator it = av.getAlignment().getHiddenColumns() + .getVisContigsIterator(0, sq.getLength(), false); + omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; + } + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; + if (av.hasHiddenColumns()) + { + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); + } - Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(output), Desktop.instance); + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); - Vector hiddenColumns = null; - if(av.hasHiddenColumns) - { - hiddenColumns =new Vector(); - for(int i=0; i visHeight) + { - g.translate(0, scrollOffset); + if (!after) + { + if (debugRedraw) + { + System.out.println( + "Scroll offset: " + sOffset + " after vis: " + i); + } + after = true; + } + // don't draw what isn't visible + continue; + } + } g.setColor(Color.black); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int fontHeight = g.getFont().getSize(); - int y = fontHeight; - int x = 0; - int graphExtras = 0; - + offset = -aa[i].height / 2; + if (aa[i].hasText) + { + offset += fm.getHeight() / 2; + offset -= fm.getDescent(); + } + else + { + offset += fm.getDescent(); + } + String label = aa[i].label; + boolean vertBar = false; + if ((lastLabel != null && lastLabel.equals(label))) + { + label = aa[i].description; + } + else + { + if (nexAA < aa.length && label.equals(aa[nexAA].label)) // && + // aa[nexY].sequenceRef==aa[i].sequenceRef) + { + lastLabel = label; + // next label is the same as this label + label = aa[i].description; + } + else + { + lastLabel = label; + } + } + if (aa[i].sequenceRef != null) + { + if (aa[i].sequenceRef != lastSeqRef) + { + label = aa[i].sequenceRef.getName() + " " + label; + // TODO record relationship between sequence and this annotation and + // display it here + } + else + { + vertBar = true; + } + } + x = width - fm.stringWidth(label) - 3; - if (aa != null) + if (aa[i].graphGroup > -1) { - for (int i = 0; i < aa.length; i++) + int groupSize = 0; + // TODO: JAL-1291 revise rendering model so the graphGroup map is + // computed efficiently for all visible labels + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) { - if (!aa[i].visible) - { - continue; - } - - x = width - fm.stringWidth(aa[i].label) - 3; + groupSize++; + } + } + if (groupSize * (fontHeight + 8) < aa[i].height) + { + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; + } + else + { + // scale font to fit + float h = aa[i].height / (float) groupSize, s; + if (h < 9) + { + visible = false; + } + else + { + fontHeight = -8 + (int) h; + s = ((float) fontHeight) / (float) ofontH; + Font f = baseFont + .deriveFont(AffineTransform.getScaleInstance(s, s)); + g.setFont(f); + fm = g.getFontMetrics(); + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; + } + } + if (visible) + { + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) + { + x = width - fm.stringWidth(aa[gg].label) - 3; + g.drawString(aa[gg].label, x, y - graphExtras); - if (aa[i].graph>0 && aa[i].graphHeight>0) + if (aa[gg]._linecolour != null) { - graphExtras = y; - - y += (aa[i].height / 3); - if(aa[i].graphGroup<0) - graphExtras = y + fontHeight; + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); } - if(aa[i].graphGroup>-1) - { - int groupSize = 0; - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup == aa[i].graphGroup) - groupSize++; - } - - if(groupSize * (fontHeight+8) < aa[i].height) - graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2; - - for(int gg=0; gg0) - { - /* if (aa[i].graphLines != null) - { - for (int gl = 0; gl < aa[i].graphLines.size(); gl++) - { - x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3; - g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras); - g.setColor(aa[i].getGraphLine(gl).colour); - Graphics2D g2 = (Graphics2D) g; - g2.setStroke(new BasicStroke(1, - BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, - new float[] - {5f, 3f}, 0f)); - - graphExtras += 3; - - g.drawLine(x, graphExtras, - x+fm.stringWidth(aa[i].label), - graphExtras); - g2.setStroke(new BasicStroke()); - } - }*/ - y += ((2 * aa[i].height) / 3); - } - else - { - y += aa[i].height; - } + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } } + } + g.setFont(baseFont); + fm = baseMetrics; + fontHeight = ofontH; } - - if (resizePanel) - { - g.drawImage(image, 2, 0 - scrollOffset, this); - } - else if (dragEvent != null && aa!=null) + else { - g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset); + if (vertBar) + { + g.drawLine(width - 3, y + offset - fontHeight, width - 3, + (int) (y - 1.5 * aa[i].height - offset - fontHeight)); + // g.drawLine(20, y + offset, x - 20, y + offset); + + } + g.drawString(label, x, y + offset); } + lastSeqRef = aa[i].sequenceRef; + } + } + if (!resizePanel && dragEvent != null && aa != null) + { + g.setColor(Color.lightGray); + g.drawString( + (aa[selectedRow].sequenceRef == null ? "" + : aa[selectedRow].sequenceRef.getName()) + + aa[selectedRow].label, + dragEvent.getX(), dragEvent.getY() - getScrollOffset()); + } - if ((aa == null) || (aa.length < 1)) - { - g.drawString("Right click", 2, 8); - g.drawString("to add annotation", 2, 18); - } + if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) + { + g.drawString(MessageManager.getString("label.right_click"), 2, 8); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); } + } + + public int getScrollOffset() + { + return scrollOffset; + } + + @Override + public void mouseEntered(MouseEvent e) + { + } }