X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=ff3b0cddd72c6de52c372992de30cd726c084525;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=87bb7742d22b682b7ac46fe842af145dfb450984;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 87bb774..ff3b0cd 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,543 +1,878 @@ -/* - * 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 - * 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. - * - * 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 - */ -package jalview.gui; - -import jalview.datamodel.*; - -import java.awt.*; -import java.awt.event.*; -import java.awt.image.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -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"; - 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; - - 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); - } - - public AnnotationLabels(AlignViewport av) - { - this.av = av; - } - - /** - * DOCUMENT ME! - * - * @param y DOCUMENT ME! - */ - public void setScrollOffset(int y) - { - scrollOffset = y; - repaint(); - } - - void getSelectedRow(int y) - { - int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - - if(aa!=null) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - - height += aa[i].height; - - if (y < height) - { - selectedRow = i; - - break; - } - } - } - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void actionPerformed(ActionEvent evt) - { - int dif = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - - if (evt.getActionCommand().equals(ADDNEW)) - { - String label = JOptionPane.showInputDialog(this, - "Label for annotation"); - - if (label == null) - { - label = ""; - } - - AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label, - "New description", - new Annotation[ap.av.alignment.getWidth()]); - - ap.av.alignment.addAnnotation(newAnnotation); - ap.av.alignment.setAnnotationIndex(newAnnotation, 0); - if (aa != null) - dif = aa[aa.length - 1].height; - } - else if (evt.getActionCommand().equals(HIDE)) - { - aa[selectedRow].visible = false; - - if (aa[selectedRow].label.equals("Conservation")) - { - ap.av.showConservation = false; - } - - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.showQuality = false; - } - - if (aa[selectedRow].label.equals("Consensus")) - { - ap.av.showIdentity = false; - } - - dif = aa[selectedRow].height * -1; - } - else if (evt.getActionCommand().equals(DELETE)) - { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); - dif = aa[selectedRow].height * -1; - } - else if (evt.getActionCommand().equals(SHOWALL)) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - dif += aa[i].height; - aa[i].visible = true; - } - } - } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) - { - new AnnotationExporter().exportAnnotations( - ap, - new AlignmentAnnotation[] - {aa[selectedRow]} - ); - } - - - ap.annotationPanel.adjustPanelHeight(); - ap.annotationScroller.validate(); - ap.repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mousePressed(MouseEvent evt) - { - getSelectedRow(evt.getY() - scrollOffset); - oldY = evt.getY(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) - { - int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); - int end = selectedRow; - - if(start!=end) - { - //Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start]; - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; - - - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; - } - - resizePanel = false; - dragEvent = null; - repaint(); - ap.annotationPanel.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! - */ - public void mouseExited(MouseEvent evt) - { - if(dragEvent == null) - { - resizePanel = false; - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) - { - dragEvent = evt; - - if (resizePanel) - { - 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(); - } - else - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) - { - resizePanel = evt.getY()<10; - - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseClicked(MouseEvent evt) - { - if(!SwingUtilities.isRightMouseButton(evt)) - return; - - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - - if ((aa == null) || (aa.length == 0)) - { - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - pop.show(this, evt.getX(), evt.getY()); - - 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); - - if (aa[selectedRow].label.equals("Consensus")) - { - 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.repaint(); - } - }); - pop.add(cbmi); - - } - - pop.show(this, evt.getX(), evt.getY()); - } - - /** - * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! - */ - public void paintComponent(Graphics g) - { - - int width = getWidth(); - if(width==0) - width = ap.calculateIdWidth().width + 4; - - Graphics2D g2 = (Graphics2D) g; - if(av.antiAlias) - g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - - drawComponent(g2, width); - - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void drawComponent(Graphics g, 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, scrollOffset); - g.setColor(Color.black); - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int fontHeight = g.getFont().getSize(); - int y = fontHeight; - int x = 0; - int graphExtras = 0; - - - - if (aa != null) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - - x = width - fm.stringWidth(aa[i].label) - 3; - - if (aa[i].graph>0) - { - graphExtras = y; - - y += (aa[i].height / 3); - - if(aa[i].graphGroup<0) - graphExtras = y + fontHeight; - } - - 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; - } - } - } - - if (resizePanel) - { - g.drawImage(image, 2, 0 - scrollOffset, this); - } - else if (dragEvent != null && aa!=null) - { - g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset); - } - - - if ((aa == null) || (aa.length < 1)) - { - g.drawString("Right click", 2, 8); - g.drawString("to add annotation", 2, 18); - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ +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.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AnnotationLabels extends JPanel implements MouseListener, + MouseMotionListener, ActionListener +{ + static String TOGGLE_LABELSCALE = "Scale Label to Column"; + + static String ADDNEW = "Add New Row"; + + static String EDITNAME = "Edit Label/Description"; + + 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); + + private boolean hasHiddenRows; + + /** + * 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); + } + + 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.alignment.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! + */ + public void actionPerformed(ActionEvent evt) + { + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + + if (evt.getActionCommand().equals(ADDNEW)) + { + 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); + } + else if (evt.getActionCommand().equals(EDITNAME)) + { + editLabelDescription(aa[selectedRow]); + repaint(); + } + else if (evt.getActionCommand().equals(HIDE)) + { + aa[selectedRow].visible = false; + } + else if (evt.getActionCommand().equals(DELETE)) + { + ap.av.alignment.deleteAnnotation(aa[selectedRow]); + } + else if (evt.getActionCommand().equals(SHOWALL)) + { + for (int i = 0; i < aa.length; i++) + { + if (!aa[i].visible && aa[i].annotations != null) + { + aa[i].visible = true; + } + } + } + else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + { + new AnnotationExporter().exportAnnotations(ap, + new AlignmentAnnotation[] + { aa[selectedRow] }, null, null); + } + else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + { + 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 (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + { + aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; + } + + ap.validateAnnotationDimensions(false); + ap.addNotify(); + ap.repaint(); + //validate(); + //ap.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + boolean editLabelDescription(AlignmentAnnotation annotation) + { + EditNameDialog dialog = new EditNameDialog(annotation.label, + annotation.description, " Annotation Name ", + "Annotation Description ", "Edit Annotation Name/Description", + ap.alignFrame); + + if (!dialog.accept) + { + return false; + } + + annotation.label = dialog.getName(); + + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + + return true; + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) + { + getSelectedRow(evt.getY() - scrollOffset); + oldY = evt.getY(); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) + { + int start = selectedRow; + getSelectedRow(evt.getY() - scrollOffset); + int end = selectedRow; + + if (start != end) + { + // Swap these annotations + AlignmentAnnotation startAA = ap.av.alignment + .getAlignmentAnnotation()[start]; + if (end == -1) + { + end = ap.av.alignment.getAlignmentAnnotation().length - 1; + } + AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + + ap.av.alignment.getAlignmentAnnotation()[end] = startAA; + ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + } + + resizePanel = false; + dragEvent = null; + repaint(); + ap.annotationPanel.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! + */ + public void mouseExited(MouseEvent evt) + { + if (dragEvent == null) + { + resizePanel = false; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) + { + dragEvent = evt; + + if (resizePanel) + { + 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.paintAlignment(true); + } + + ap.addNotify(); + } + else + { + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) + { + resizePanel = evt.getY() < 10; + + getSelectedRow(evt.getY() - scrollOffset); + + if (selectedRow > -1 + && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) + { + AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow]; + + StringBuffer desc = new StringBuffer(); + 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 + 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()) + { + desc.append("
"); + } + + + } else { + // begin the tooltip's html fragment + desc.append(""); + } + if (aa.hasScore()) + { + // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value). + desc.append(" Score: " + aa.score); + } + + if (desc.length() > 6) + { + desc.append(""); + this.setToolTipText(desc.toString()); + } + else + this.setToolTipText(null); + } + + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + public void mouseClicked(MouseEvent evt) + { + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + if (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.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.av.setSelectionGroup(// new SequenceGroup( + aa[selectedRow].groupRef); // ); + ap.paintAlignment(false); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } + else + { + ap.seqPanel.ap.idPanel + .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); + } + 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) + { + // TODO: pass on reference to ap so the view can be updated. + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + } + }); + 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); + } + } + 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.getSequenceAsString())); + + sq.setDatasetSequence(dseqs[0]); + } + Alignment ds = new Alignment(dseqs); + if (av.hasHiddenColumns) + { + omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, + sq.getLength(), seqs); + } + + String output = new FormatAdapter().formatSequences("Fasta", seqs, + omitHidden); + + 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.addElement(new int[] + { region[0], region[1] }); + } + } + + 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! + */ + public void paintComponent(Graphics g) + { + + int width = getWidth(); + if (width == 0) + { + width = ap.calculateIdWidth().width + 4; + } + + Graphics2D g2 = (Graphics2D) g; + if (av.antiAlias) + { + g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + drawComponent(g2, width); + + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + */ + public void drawComponent(Graphics g, 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, scrollOffset); + g.setColor(Color.black); + + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + int fontHeight = g.getFont().getSize(); + int y = 0; + int x = 0; + int graphExtras = 0; + int offset = 0; + + if (aa != null) + { + hasHiddenRows = false; + for (int i = 0; i < aa.length; i++) + { + g.setColor(Color.black); + + if (!aa[i].visible) + { + hasHiddenRows = true; + continue; + } + + y += aa[i].height; + + 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; + 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; 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].annotations[0] != null) + { + g.setColor(aa[gg].annotations[0].colour); + } + + g.drawLine(x, y - graphExtras - 3, + x + fm.stringWidth(aa[gg].label), y - graphExtras - 3); + + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } + } + } + else + { + g.drawString(aa[i].label, x, y + offset); + } + } + } + + if (resizePanel) + { + g.drawImage(image, 2, 0 - scrollOffset, this); + } + else if (dragEvent != null && aa != null) + { + g.setColor(Color.lightGray); + g.drawString(aa[selectedRow].label, dragEvent.getX(), + dragEvent.getY() - scrollOffset); + } + + if ((aa == null) || (aa.length < 1)) + { + g.drawString("Right click", 2, 8); + g.drawString("to add annotation", 2, 18); + } + } +}