X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=a0a0df8cbbcf1c713f17be3615f3e8fb9b239dcb;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=72789016f914bd4e720a4f42ad1cb93fc59aaf47;hpb=aaace4c8c53d4bb08a5bad0ea18ccfedbef90cd9;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 7278901..a0a0df8 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,119 +1,148 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * 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 Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.util.*; -import java.util.regex.Pattern; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; -import java.awt.image.*; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.io.*; +import jalview.analysis.AlignSeq; +import jalview.analysis.AlignmentUtils; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.FileFormat; +import jalview.io.FormatAdapter; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.Platform; + +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.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.util.Arrays; +import java.util.Collections; +import java.util.Iterator; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** - * 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 TOGGLE_LABELSCALE = "Scale Label to Column"; + private static final String HTML_END_TAG = ""; - static String ADDNEW = "Add New Row"; + private static final String HTML_START_TAG = ""; - static String EDITNAME = "Edit Label/Description"; + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; - static String HIDE = "Hide This Row"; + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; - static String DELETE = "Delete This Row"; + private static final Font font = new Font("Arial", Font.PLAIN, 11); - static String SHOWALL = "Show All Hidden Rows"; + private static final String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); - static String OUTPUT_TEXT = "Export Annotation"; + private static final String ADDNEW = MessageManager + .getString("label.add_new_row"); - static String COPYCONS_SEQ = "Copy Consensus Sequence"; + private static final String EDITNAME = MessageManager + .getString("label.edit_label_description"); - boolean resizePanel = false; + private static final String HIDE = MessageManager + .getString("label.hide_row"); - Image image; + private static final String DELETE = MessageManager + .getString("label.delete_row"); - AlignmentPanel ap; + private static final String SHOWALL = MessageManager + .getString("label.show_all_hidden_rows"); - AlignViewport av; + private static final String OUTPUT_TEXT = MessageManager + .getString("label.export_annotation"); + + private static final String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); - boolean resizing = false; + private final boolean debugRedraw = false; - MouseEvent dragEvent; + private AlignmentPanel ap; - int oldY; + AlignViewport av; + + private MouseEvent dragEvent; - int selectedRow; + private int oldY; - int scrollOffset = 0; + private int selectedRow; - Font font = new Font("Arial", Font.PLAIN, 11); + private int scrollOffset = 0; private boolean hasHiddenRows; + private boolean resizePanel = false; + /** - * Creates a new AnnotationLabels object. + * Creates a new AnnotationLabels object * * @param ap - * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { + this.ap = ap; av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); - java.net.URL url = getClass().getResource("/images/idwidth.gif"); - Image temp = null; - - if (url != null) - { - temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); - } - - try - { - MediaTracker mt = new MediaTracker(this); - mt.addImage(temp, 0); - mt.waitForID(0); - } catch (Exception ex) - { - } - - 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); + addMouseWheelListener(ap.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -143,7 +172,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, void getSelectedRow(int y) { int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); selectedRow = -2; if (aa != null) { @@ -173,37 +203,39 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); - if (evt.getActionCommand().equals(ADDNEW)) + String action = evt.getActionCommand(); + if (ADDNEW.equals(action)) { + /* + * non-returning dialog + */ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, - null, new Annotation[ap.av.alignment.getWidth()]); - - if (!editLabelDescription(newAnnotation)) - { - return; - } - - ap.av.alignment.addAnnotation(newAnnotation); - ap.av.alignment.setAnnotationIndex(newAnnotation, 0); + null, new Annotation[ap.av.getAlignment().getWidth()]); + editLabelDescription(newAnnotation, true); } - else if (evt.getActionCommand().equals(EDITNAME)) + else if (EDITNAME.equals(action)) { - editLabelDescription(aa[selectedRow]); - repaint(); + /* + * non-returning dialog + */ + editLabelDescription(aa[selectedRow], false); } - else if (evt.getActionCommand().equals(HIDE)) + else if (HIDE.equals(action)) { aa[selectedRow].visible = false; } - else if (evt.getActionCommand().equals(DELETE)) + else if (DELETE.equals(action)) { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); + ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); } - else if (evt.getActionCommand().equals(SHOWALL)) + else if (SHOWALL.equals(action)) { for (int i = 0; i < aa.length; i++) { @@ -213,13 +245,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + else if (OUTPUT_TEXT.equals(action)) { - new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] - { aa[selectedRow] }, null, null); + new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } - else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + else if (COPYCONS_SEQ.equals(action)) { SequenceI cons = null; if (aa[selectedRow].groupRef != null) @@ -234,119 +264,357 @@ public class AnnotationLabels extends JPanel implements MouseListener, { copy_annotseqtoclipboard(cons); } - } - else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + else if (TOGGLE_LABELSCALE.equals(action)) { aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.validateAnnotationDimensions(false); - ap.addNotify(); - ap.repaint(); - //validate(); - //ap.paintAlignment(true); + ap.refresh(true); } /** - * DOCUMENT ME! + * 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 e - * DOCUMENT ME! + * @param annotation + * @param addNew */ - boolean editLabelDescription(AlignmentAnnotation annotation) + 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, " Annotation Name ", - "Annotation Description ", "Edit Annotation Name/Description", - ap.alignFrame); + annotation.description, name, description); - if (!dialog.accept) + dialog.showDialog(ap.alignFrame, title, + new Runnable() + { + @Override + public void run() + { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + if (addNew) + { + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); + } + ap.refresh(true); + } + }); + } + + @Override + public void mousePressed(MouseEvent evt) + { + getSelectedRow(evt.getY() - getScrollOffset()); + oldY = evt.getY(); + if (evt.isPopupTrigger()) { - return false; + showPopupMenu(evt); } + } - annotation.label = dialog.getName(); + /** + * 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(); - String text = dialog.getDescription(); - if (text != null && text.length() == 0) + 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() + { + @Override + public void actionPerformed(ActionEvent e) + { + AlignmentUtils.showOrHideSequenceAnnotations( + ap.av.getAlignment(), Collections.singleton(label), + null, false, false); + ap.refresh(true); + } + }); + pop.add(hideType); + } + } + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + if (hasHiddenRows) { - text = null; + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); } - annotation.description = text; + 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) + { + 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); - return true; + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + } + pop.show(this, evt.getX(), evt.getY()); } /** - * DOCUMENT ME! + * 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 evt - * DOCUMENT ME! + * @param ap + * @param ann + * @param pop */ - public void mousePressed(MouseEvent evt) + static void addConsensusMenuOptions(AlignmentPanel ap, + AlignmentAnnotation ann, + JPopupMenu pop) { - getSelectedRow(evt.getY() - scrollOffset); - oldY = evt.getY(); + 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); + + 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(); + } + }); + 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) + { + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); + } + }); + 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) + { + 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(); + } + }); + 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) + { + ap.av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + } + }); + 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) + { + ap.av.setShowSequenceLogo(true); + ap.av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + } + }); + pop.add(cprofnorm); + } } /** - * DOCUMENT ME! + * Reorders annotation rows after a drag of a label * * @param evt - * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { + if (evt.isPopupTrigger()) + { + showPopupMenu(evt); + return; + } + int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; + /* + * if dragging to resize instead, start == end + */ if (start != end) { // Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment + AlignmentAnnotation startAA = ap.av.getAlignment() .getAlignmentAnnotation()[start]; if (end == -1) { - end = ap.av.alignment.getAlignmentAnnotation().length - 1; + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; } - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } resizePanel = false; dragEvent = null; repaint(); - ap.annotationPanel.repaint(); + ap.getAnnotationPanel().repaint(); } /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseEntered(MouseEvent evt) - { - if (evt.getY() < 10) - { - resizePanel = true; - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! + * Removes the height adjuster image on leaving the panel, unless currently + * dragging it */ + @Override public void mouseExited(MouseEvent evt) { - if (dragEvent == null) + if (resizePanel && dragEvent == null) { resizePanel = false; repaint(); @@ -354,11 +622,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { dragEvent = evt; @@ -368,17 +638,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, Dimension d = ap.annotationScroller.getPreferredSize(); int dif = evt.getY() - oldY; - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); if ((d.height - dif) > 20) { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + 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); + ap.annotationSpaceFillerHolder + .setPreferredSize(new Dimension(d.width, d.height - dif)); + ap.paintAlignment(true, false); } ap.addNotify(); @@ -390,79 +660,166 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Updates the tooltip as the mouse moves over the labels * * @param evt - * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent evt) { - resizePanel = evt.getY() < 10; + 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; + } - getSelectedRow(evt.getY() - scrollOffset); + StringBuilder msg = new StringBuilder(32); + if (aa.sequenceRef != null) + { + msg.append(aa.sequenceRef.getName()).append(" : "); + } - if (selectedRow > -1 - && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) + if (aa.graphGroup == -1) { - AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow]; - - StringBuffer desc = new StringBuffer(); - if (aa.description != null - && !aa.description.equals("New description")) + msg.append(aa.label); + } + else if (anns != null) + { + boolean first = true; + for (int i = anns.length - 1; i >= 0; i--) { - // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips - desc.append(aa.getDescription(true).trim()); - // check to see if the description is an html fragment. - if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("")<0)) - { - // clean the description ready for embedding in html - desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<")); - desc.insert(0, ""); - } else { - // remove terminating html if any - int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf(""); - if (i>-1) { - desc.setLength(desc.length()-7+i); - } - } - if (aa.hasScore()) + if (anns[i].graphGroup == aa.graphGroup) { - desc.append("
"); + if (!first) + { + msg.append(", "); + } + msg.append(anns[i].label); + first = false; } - - - } else { - // begin the tooltip's html fragment - desc.append(""); } - if (aa.hasScore()) + } + + 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) + { + 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().startsWith(HTML_START_TAG)) { - // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value). - desc.append(" Score: " + aa.score); + tooltip.append(HTML_START_TAG); + desc = desc.replace("<", "<"); } - - if (desc.length() > 6) + else if (desc.toLowerCase().endsWith(HTML_END_TAG)) { - desc.append(""); - System.err.println(desc.toString()); - this.setToolTipText(desc.toString()); + desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); } - else - this.setToolTipText(null); + tooltip.append(desc); + } + else + { + // begin the tooltip's html fragment + tooltip.append(HTML_START_TAG); + } + if (aa.hasScore()) + { + if (tooltip.length() > HTML_START_TAG.length()) + { + tooltip.append("
"); + } + // 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)); + } + + if (tooltip.length() > HTML_START_TAG.length()) + { + return tooltip.append(HTML_END_TAG).toString(); } + /* + * nothing in the tooltip (except "") + */ + return null; } /** - * DOCUMENT ME! + * 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 - * DOCUMENT ME! */ + protected void showOrHideAdjuster(MouseEvent evt) + { + boolean was = resizePanel; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + + if (resizePanel != was) + { + setCursor(Cursor + .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR + : Cursor.DEFAULT_CURSOR)); + repaint(); + } + } + + @Override public void mouseClicked(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - if (SwingUtilities.isLeftMouseButton(evt)) + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) { if (selectedRow > -1 && selectedRow < aa.length) { @@ -470,213 +827,110 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() >= 2) { - // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects - ap.seqPanel.ap.idPanel.highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); - ap.paintAlignment(false); + // 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); + } + } + } + + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } else { - ap.seqPanel.ap.idPanel - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); } return; } else if (aa[selectedRow].sequenceRef != null) { - Vector sr = new Vector(); - sr.addElement(aa[selectedRow].sequenceRef); if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.highlightSearchResults(sr); + ap.getSeqPanel().ap.getIdPanel() + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { - ap.seqPanel.ap.idPanel.highlightSearchResults(null); - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(aa[selectedRow].sequenceRef, false); - ap.av.setSelectionGroup(sg); - ap.av.sendSelection(); - ap.paintAlignment(false); - PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); - } - - } - } - } - if (!SwingUtilities.isRightMouseButton(evt)) - { - return; - } - - JPopupMenu pop = new JPopupMenu("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); - 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) - { - 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 (aa[selectedRow].label.indexOf("Consensus") > -1) - { - pop.addSeparator(); - // av and sequencegroup need to implement same interface for - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .getIgnoreGapsConsensus()); - final AlignmentAnnotation aaa = aa[selectedRow]; - cbmi.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - if (aaa.groupRef != null) + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) { - // TODO: pass on reference to ap so the view can be updated. - aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + // 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 { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + 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.add(cbmi); - // av and sequencegroup need to implement same interface for - if (aaa.groupRef != null) - { - final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "Show Group Histogram", - aa[selectedRow].groupRef.isShowConsensusHistogram()); - chist.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setShowConsensusHistogram(chist.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(chist); - final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - "Show Group Logo", - aa[selectedRow].groupRef.isShowSequenceLogo()); - cprofl.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setshowSequenceLogo(cprofl.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cprofl); - } - else - { - final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "Show Histogram", av.isShowConsensusHistogram()); - chist.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowConsensusHistogram(chist.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(chist); - final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "Show Logo", av.isShowSequenceLogo()); - cprof.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowSequenceLogo(cprof.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cprof); + } - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); } + return; } - pop.show(this, evt.getX(), evt.getY()); } /** @@ -687,48 +941,50 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ protected void copy_annotseqtoclipboard(SequenceI sq) { - SequenceI[] seqs = new SequenceI[] - { sq }; + SequenceI[] seqs = new SequenceI[] { sq }; String[] omitHidden = null; - SequenceI[] dseqs = new SequenceI[] - { sq.getDatasetSequence() }; + 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.getSequenceAsString())); + dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, + sq.getSequenceAsString())); sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); - if (av.hasHiddenColumns) + 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()) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - Vector hiddenColumns = null; - if (av.hasHiddenColumns) - { - hiddenColumns = new Vector(); - for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) - { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(i); + HiddenColumns hiddenColumns = null; - hiddenColumns.addElement(new int[] - { region[0], region[1] }); - } + if (av.hasHiddenColumns()) + { + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } - Desktop.jalviewClipboard = new Object[] - { seqs, ds, // what is the dataset of a consensus sequence ? need to flag + Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset + // of a consensus + // sequence ? need to + // flag // sequence as special. hiddenColumns }; } @@ -739,6 +995,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param g1 * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { @@ -755,18 +1012,39 @@ public class AnnotationLabels extends JPanel implements MouseListener, RenderingHints.VALUE_ANTIALIAS_ON); } - drawComponent(g2, width); + drawComponent(g2, true, width); } /** - * DOCUMENT ME! + * Draw the full set of annotation Labels for the alignment at the given + * cursor * * @param g - * DOCUMENT ME! + * Graphics2D instance (needed for font scaling) + * @param width + * Width for scaling labels + * */ public void drawComponent(Graphics g, int width) { + drawComponent(g, false, width); + } + + /** + * Draw the full set of annotation Labels for the alignment at the given + * cursor + * + * @param g + * Graphics2D instance (needed for font scaling) + * @param clip + * - true indicates that only current visible area needs to be + * rendered + * @param width + * Width for scaling labels + */ + public void drawComponent(Graphics g, boolean clip, int width) + { if (av.getFont().getSize() < 10) { g.setFont(font); @@ -780,30 +1058,75 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - g.translate(0, scrollOffset); + g.translate(0, getScrollOffset()); g.setColor(Color.black); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; int x = 0; int graphExtras = 0; int offset = 0; - + Font baseFont = g.getFont(); + FontMetrics baseMetrics = fm; + int ofontH = fontHeight; + int sOffset = 0; + int visHeight = 0; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) + ? ap.getAnnotationPanel().getVisibleVRange() + : null; + if (clip && visr != null) + { + sOffset = visr[0]; + visHeight = visr[1]; + } + boolean visible = true, before = false, after = false; if (aa != null) { hasHiddenRows = false; + int olY = 0; for (int i = 0; i < aa.length; i++) { - g.setColor(Color.black); - + visible = true; if (!aa[i].visible) { hasHiddenRows = true; continue; } - + olY = y; y += aa[i].height; + if (clip) + { + if (y < sOffset) + { + if (!before) + { + if (debugRedraw) + { + System.out.println("before vis: " + i); + } + before = true; + } + // don't draw what isn't visible + continue; + } + if (olY > visHeight) + { + + 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); offset = -aa[i].height / 2; @@ -813,13 +1136,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, offset -= fm.getDescent(); } else + { offset += fm.getDescent(); + } x = width - fm.stringWidth(aa[i].label) - 3; if (aa[i].graphGroup > -1) { 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) @@ -827,30 +1154,57 @@ public class AnnotationLabels extends JPanel implements MouseListener, groupSize++; } } - if (groupSize * (fontHeight + 8) < aa[i].height) { - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } - - for (int gg = 0; gg < aa.length; gg++) + else { - if (aa[gg].graphGroup == aa[i].graphGroup) + // 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++) { - x = width - fm.stringWidth(aa[gg].label) - 3; - g.drawString(aa[gg].label, x, y - graphExtras); - if (aa[gg].annotations[0] != null) + if (aa[gg].graphGroup == aa[i].graphGroup) { - g.setColor(aa[gg].annotations[0].colour); - } + x = width - fm.stringWidth(aa[gg].label) - 3; + g.drawString(aa[gg].label, x, y - graphExtras); + + if (aa[gg]._linecolour != null) + { - g.drawLine(x, y - graphExtras - 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - 3); + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); + } - g.setColor(Color.black); - graphExtras += fontHeight + 8; + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } } } + g.setFont(baseFont); + fm = baseMetrics; + fontHeight = ofontH; } else { @@ -859,21 +1213,28 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - if (resizePanel) - { - g.drawImage(image, 2, 0 - scrollOffset, this); - } - else if (dragEvent != null && aa != null) + if (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - scrollOffset); + dragEvent.getY() - getScrollOffset()); } - if ((aa == null) || (aa.length < 1)) + if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) { - g.drawString("Right click", 2, 8); - g.drawString("to add annotation", 2, 18); + 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) + { + } }