/* * 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. * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.Locale; 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; /** * 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 { 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; private MouseEvent dragEvent; 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) { continue; } height += aa[i].height; if (y < height) { selectedRow = i; break; } } } } /** * 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; } } } else if (OUTPUT_TEXT.equals(action)) { new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } else if (COPYCONS_SEQ.equals(action)) { SequenceI cons = null; if (aa[selectedRow].groupRef != null) { cons = aa[selectedRow].groupRef.getConsensusSeq(); } else { cons = av.getConsensusSeq(); } if (cons != null) { copy_annotseqtoclipboard(cons); } } else if (TOGGLE_LABELSCALE.equals(action)) { aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } 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, 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()) { 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() { @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) { 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) { 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); final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); consclipbrd.addActionListener(this); pop.add(consclipbrd); } } 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); 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); } } /** * Reorders annotation rows after a drag of a label * * @param evt */ @Override public void mouseReleased(MouseEvent evt) { if (evt.isPopupTrigger()) { showPopupMenu(evt); return; } int start = selectedRow; getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; /* * if dragging to resize instead, start == end */ if (start != end) { // 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; } 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) { Dimension d = ap.annotationScroller.getPreferredSize(); int dif = evt.getY() - oldY; 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.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; } StringBuilder msg = new StringBuilder(32); if (aa.sequenceRef != null) { msg.append(aa.sequenceRef.getName()).append(" : "); } if (aa.graphGroup == -1) { msg.append(aa.label); } else if (anns != null) { boolean first = true; for (int i = anns.length - 1; i >= 0; i--) { if (anns[i].graphGroup == aa.graphGroup) { if (!first) { msg.append(", "); } msg.append(anns[i].label); first = false; } } } 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(Locale.ROOT).startsWith(HTML_START_TAG)) { 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); } 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; } /** * 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) { 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) { 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); } } } 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; } else if (aa[selectedRow].sequenceRef != null) { 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(); } } } 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())); 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()); } String output = new FormatAdapter().formatSequences(FileFormat.Fasta, seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); HiddenColumns hiddenColumns = null; 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 // sequence as special. hiddenColumns }; } /** * DOCUMENT ME! * * @param g1 * DOCUMENT ME! */ @Override public void paintComponent(Graphics g) { int width = getWidth(); if (width == 0) { width = ap.calculateIdWidth().width; } Graphics2D g2 = (Graphics2D) g; if (av.antiAlias) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } drawComponent(g2, true, width); } /** * Draw the full set of annotation Labels for the alignment at the given * cursor * * @param g * 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); } else { g.setFont(av.getFont()); } FontMetrics fm = g.getFontMetrics(g.getFont()); g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); g.translate(0, getScrollOffset()); g.setColor(Color.black); 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++) { 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; if (aa[i].hasText) { offset += fm.getHeight() / 2; 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) { 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[gg]._linecolour != null) { 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.setFont(baseFont); fm = baseMetrics; fontHeight = ofontH; } else { g.drawString(aa[i].label, x, y + offset); } } } if (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - getScrollOffset()); } 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) { } }