X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=d07cae270ebb4f259e8a21a7427f889fb8e9695e;hb=6a144c3b2b7f5f04d908c065a017088453bb7fc7;hp=0ea79981081d9f939e35ad4e799ce88ec579f297;hpb=d2642610b86e983bfdde65f7c19c9153206da263;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 0ea7998..d07cae2 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,604 +1,1230 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import jalview.datamodel.*; +import jalview.analysis.AlignmentUtils; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; - -import java.awt.*; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.Image; +import java.awt.MediaTracker; +import java.awt.RenderingHints; +import java.awt.Toolkit; import java.awt.datatransfer.StringSelection; -import java.awt.event.*; -import java.awt.image.*; -import java.util.Vector; - -import javax.swing.*; - +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.awt.geom.AffineTransform; +import java.awt.image.BufferedImage; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.regex.Pattern; + +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 $Revision$ */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel + implements MouseListener, MouseMotionListener, ActionListener { - static String ADDNEW = "Add New Row"; - static String HIDE = "Hide This Row"; - static String DELETE = "Delete This Row"; - static String SHOWALL = "Show All Hidden Rows"; - static String OUTPUT_TEXT = "Export Annotation"; - static String COPYCONS_SEQ = "Copy Consensus Sequence"; - boolean resizePanel = false; - Image image; - AlignmentPanel ap; - AlignViewport av; - boolean resizing = false; - MouseEvent dragEvent; - int oldY; - int selectedRow; - int scrollOffset = 0; - Font font = new Font("Arial", Font.PLAIN, 11); - - - /** - * Creates a new AnnotationLabels object. - * - * @param ap DOCUMENT ME! - */ - public AnnotationLabels(AlignmentPanel ap) - { - this.ap = ap; - av = ap.av; - 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); - } + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern + .compile("<"); - try - { - MediaTracker mt = new MediaTracker(this); - mt.addImage(temp, 0); - mt.waitForID(0); - } - catch (Exception ex) - { - } + String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); - 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; + String ADDNEW = MessageManager.getString("label.add_new_row"); - addMouseListener(this); - addMouseMotionListener(this); - } + String EDITNAME = MessageManager + .getString("label.edit_label_description"); - public AnnotationLabels(AlignViewport av) - { - this.av = av; - } + String HIDE = MessageManager.getString("label.hide_row"); - /** - * DOCUMENT ME! - * - * @param y DOCUMENT ME! - */ - public void setScrollOffset(int y) - { - scrollOffset = y; - repaint(); - } + String DELETE = MessageManager.getString("label.delete_row"); - void getSelectedRow(int y) - { - int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + String SHOWALL = MessageManager.getString("label.show_all_hidden_rows"); - if(aa!=null) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } + String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); - height += aa[i].height; + String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); - if (y < height) - { - selectedRow = i; + boolean resizePanel = false; - break; - } - } - } - } + Image image; - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void actionPerformed(ActionEvent evt) - { - int dif = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentPanel ap; - if (evt.getActionCommand().equals(ADDNEW)) - { - String label = JOptionPane.showInputDialog(this, - "Label for annotation"); + AlignViewport av; - if (label == null) - { - label = ""; - } + boolean resizing = false; - AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label, - "New description", - new Annotation[ap.av.alignment.getWidth()]); + MouseEvent dragEvent; - 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; + int oldY; - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.quality = null; - } + int selectedRow; - 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]} - ); - } - else if (evt.getActionCommand().equals(COPYCONS_SEQ)) - { - SequenceI cons=av.getConsensusSeq(); - if (cons!=null) - copy_annotseqtoclipboard(cons); + private int scrollOffset = 0; - } + Font font = new Font("Arial", Font.PLAIN, 11); - ap.annotationPanel.adjustPanelHeight(); - ap.annotationScroller.validate(); - ap.repaint(); - } + 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); - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mousePressed(MouseEvent evt) + java.net.URL url = getClass().getResource("/images/idwidth.gif"); + Image temp = null; + + if (url != null) { - getSelectedRow(evt.getY() - scrollOffset); - oldY = evt.getY(); + temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) + try + { + MediaTracker mt = new MediaTracker(this); + mt.addImage(temp, 0); + mt.waitForID(0); + } catch (Exception ex) { - int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); - int end = selectedRow; + } - if(start!=end) + 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 = bi; + + 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) { - //Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start]; - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + continue; + } + height += aa[i].height; - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; - } + if (y < height) + { + selectedRow = i; - resizePanel = false; - dragEvent = null; - repaint(); - ap.annotationPanel.repaint(); + break; + } + } } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseEntered(MouseEvent evt) + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void actionPerformed(ActionEvent evt) + { + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + + boolean fullRepaint = false; + if (evt.getActionCommand().equals(ADDNEW)) { - if(evt.getY()<10) + AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, + null, new Annotation[ap.av.getAlignment().getWidth()]); + + if (!editLabelDescription(newAnnotation)) { - resizePanel = true; - repaint(); + return; } - } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseExited(MouseEvent evt) + ap.av.getAlignment().addAnnotation(newAnnotation); + ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); + fullRepaint = true; + } + else if (evt.getActionCommand().equals(EDITNAME)) { - if(dragEvent == null) + String name = aa[selectedRow].label; + editLabelDescription(aa[selectedRow]); + if (!name.equalsIgnoreCase(aa[selectedRow].label)) { - resizePanel = false; - repaint(); + fullRepaint = true; } } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) + else if (evt.getActionCommand().equals(HIDE)) { - dragEvent = evt; - - if (resizePanel) + aa[selectedRow].visible = false; + } + else if (evt.getActionCommand().equals(DELETE)) + { + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); + ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); + fullRepaint = true; + } + else if (evt.getActionCommand().equals(SHOWALL)) + { + for (int i = 0; i < aa.length; i++) { - Dimension d = ap.annotationScroller.getPreferredSize(); - int dif = evt.getY() - oldY; - - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; - - if ( (d.height - dif) > 20) + if (!aa[i].visible && aa[i].annotations != null) { - 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(); + aa[i].visible = true; } - - ap.addNotify(); } - else - repaint(); + fullRepaint = true; } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) + else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { - resizePanel = evt.getY()<10; - - getSelectedRow(evt.getY() - scrollOffset); - - if(selectedRow>-1) + new AnnotationExporter().exportAnnotations(ap, + new AlignmentAnnotation[] + { aa[selectedRow] }); + } + else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + { + SequenceI cons = null; + if (aa[selectedRow].groupRef != null) { - setToolTipText(ap.av.alignment. - getAlignmentAnnotation()[selectedRow].description); - + cons = aa[selectedRow].groupRef.getConsensusSeq(); + } + else + { + cons = av.getConsensusSeq(); + } + if (cons != null) + { + copy_annotseqtoclipboard(cons); } - repaint(); - } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseClicked(MouseEvent evt) + } + else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) { - if(!SwingUtilities.isRightMouseButton(evt)) - return; + aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; + } - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + ap.refresh(fullRepaint); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + boolean editLabelDescription(AlignmentAnnotation annotation) + { + // TODO i18n + EditNameDialog dialog = new EditNameDialog(annotation.label, + annotation.description, " Annotation Name ", + "Annotation Description ", "Edit Annotation Name/Description", + ap.alignFrame); + + if (!dialog.accept) + { + return false; + } - 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()); + annotation.label = dialog.getName(); - return; - } + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + return true; + } - 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); + @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); - item = new JMenuItem(OUTPUT_TEXT); - item.addActionListener(this); - pop.add(item); - // annotation object should be typed - if (aa[selectedRow].label.equals("Consensus")) + } + 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); + // for (AlignmentAnnotation ann : ap.av.getAlignment() + // .getAlignmentAnnotation()) + // { + // if (ann.sequenceRef != null && ann.label != null + // && ann.label.equals(label)) + // { + // ann.visible = 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(); - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", - ap.av.getIgnoreGapsConsensus()); - cbmi.addActionListener(new ActionListener() - {public void actionPerformed(ActionEvent e) - { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); - } - }); - pop.add(cbmi); - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); + // 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) + { + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString("label.ignore_gaps_consensus"), + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef.getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = aa[selectedRow]; + cbmi.addActionListener(new ActionListener() + { + @Override + 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.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + ap.alignmentChanged(); + } + }); + pop.add(cbmi); + // av and sequencegroup need to implement same interface for + if (aaa.groupRef != null) + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + aa[selectedRow].groupRef.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + 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( + MessageManager.getString("label.show_group_logo"), + aa[selectedRow].groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + 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); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + aa[selectedRow].groupRef.isNormaliseSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { - 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]); + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowSequenceLogo(true); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cproflnorm); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + av.isShowSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + av.isNormaliseSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(true); + av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofnorm); + } + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); } - Alignment ds=new Alignment(dseqs); - if (av.hasHiddenColumns) + } + pop.show(this, evt.getX(), evt.getY()); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) + { + showPopupMenu(evt); + return; + } + + int start = selectedRow; + getSelectedRow(evt.getY() - getScrollOffset()); + int end = selectedRow; + + if (start != end) + { + // Swap these annotations + AlignmentAnnotation startAA = ap.av.getAlignment() + .getAlignmentAnnotation()[start]; + if (end == -1) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); + 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(); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseEntered(MouseEvent evt) + { + if (evt.getY() < 10) + { + resizePanel = true; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseExited(MouseEvent evt) + { + if (dragEvent == null) + { + resizePanel = false; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseDragged(MouseEvent evt) + { + dragEvent = evt; + + if (resizePanel) + { + Dimension d = ap.annotationScroller.getPreferredSize(); + int dif = evt.getY() - oldY; - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); + 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); + } - Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(output), Desktop.instance); + ap.addNotify(); + } + else + { + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseMoved(MouseEvent evt) + { + resizePanel = evt.getY() < 10; + + getSelectedRow(evt.getY() - getScrollOffset()); + + if (selectedRow > -1 && ap.av.getAlignment() + .getAlignmentAnnotation().length > selectedRow) + { + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; - Vector hiddenColumns = null; - if(av.hasHiddenColumns) + StringBuffer desc = new StringBuffer(); + if (aa.description != null + && !aa.description.equals("New description")) { - hiddenColumns =new Vector(); - for(int i=0; i") < 0)) { - int[] region = (int[]) - av.getColumnSelection().getHiddenColumns().elementAt(i); + // clean the description ready for embedding in html + desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.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(""); + } + // if (aa.hasProperties()) + // { + // desc.append(""); + // for (String prop : aa.getProperties()) + // { + // desc.append("" + prop + "" + // + aa.getProperty(prop) + ""); + // } + // 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); + } + } + } + + @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 + || !(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) + { + if (jalview.util.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); + 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 (!(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } + else + { + if (jalview.util.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); + PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); + } - hiddenColumns.addElement(new int[]{region[0], - region[1]}); } } + 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(jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, sq.getSequenceAsString())); - Desktop.jalviewClipboard = new Object[]{ seqs, - ds, // what is the dataset of a consensus sequence ? need to flag sequence as special. - hiddenColumns}; + sq.setDatasetSequence(dseqs[0]); } - /** - * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! - */ - public void paintComponent(Graphics g) + Alignment ds = new Alignment(dseqs); + if (av.hasHiddenColumns()) { + omitHidden = av.getAlignment().getHiddenColumns() + .getVisibleSequenceStrings(0, sq.getLength(), seqs); + } - int width = getWidth(); - if(width==0) - width = ap.calculateIdWidth().width + 4; + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; + if (av.hasHiddenColumns()) + { + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); + } - Graphics2D g2 = (Graphics2D) g; - if(av.antiAlias) - g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); - drawComponent(g2, width); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(output), Desktop.instance); + ArrayList hiddenColumns = null; + + if (av.hasHiddenColumns()) + { + hiddenColumns = av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy(); } - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void drawComponent(Graphics g, int width) + 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) { - if(av.getFont().getSize()<10) - g.setFont(font); - else - g.setFont(av.getFont()); + width = ap.calculateIdWidth().width + 4; + } + + Graphics2D g2 = (Graphics2D) g; + if (av.antiAlias) + { + g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } - FontMetrics fm = g.getFontMetrics(g.getFont()); - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + 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); + } + + private final boolean debugRedraw = false; + + /** + * 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) + { - g.translate(0, scrollOffset); + if (!after) + { + if (debugRedraw) + { + System.out.println( + "Scroll offset: " + sOffset + " after vis: " + i); + } + after = true; + } + // don't draw what isn't visible + continue; + } + } g.setColor(Color.black); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int fontHeight = g.getFont().getSize(); - int y = fontHeight; - int x = 0; - int graphExtras = 0; + offset = -aa[i].height / 2; + if (aa[i].hasText) + { + offset += fm.getHeight() / 2; + offset -= fm.getDescent(); + } + else + { + offset += fm.getDescent(); + } + x = width - fm.stringWidth(aa[i].label) - 3; - if (aa != null) + if (aa[i].graphGroup > -1) { - for (int i = 0; i < aa.length; i++) + int groupSize = 0; + // TODO: JAL-1291 revise rendering model so the graphGroup map is + // computed efficiently for all visible labels + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) { - if (!aa[i].visible) - { - continue; - } - - x = width - fm.stringWidth(aa[i].label) - 3; + groupSize++; + } + } + if (groupSize * (fontHeight + 8) < aa[i].height) + { + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; + } + else + { + // scale font to fit + float h = aa[i].height / (float) groupSize, s; + if (h < 9) + { + visible = false; + } + else + { + fontHeight = -8 + (int) h; + s = ((float) fontHeight) / (float) ofontH; + Font f = baseFont + .deriveFont(AffineTransform.getScaleInstance(s, s)); + g.setFont(f); + fm = g.getFontMetrics(); + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; + } + } + if (visible) + { + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) + { + x = width - fm.stringWidth(aa[gg].label) - 3; + g.drawString(aa[gg].label, x, y - graphExtras); - if (aa[i].graph>0 && aa[i].graphHeight>0) + if (aa[gg]._linecolour != null) { - graphExtras = y; - y += (aa[i].height / 3); - - if(aa[i].graphGroup<0) - graphExtras = y + fontHeight; + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); } - if(aa[i].graphGroup>-1) - { - int groupSize = 0; - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup == aa[i].graphGroup) - groupSize++; - } - - if(groupSize * (fontHeight+8) < aa[i].height) - graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2; - - for(int gg=0; gg0) - { - /* if (aa[i].graphLines != null) - { - for (int gl = 0; gl < aa[i].graphLines.size(); gl++) - { - x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3; - g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras); - g.setColor(aa[i].getGraphLine(gl).colour); - Graphics2D g2 = (Graphics2D) g; - g2.setStroke(new BasicStroke(1, - BasicStroke.CAP_SQUARE, - BasicStroke.JOIN_ROUND, 3f, - new float[] - {5f, 3f}, 0f)); - - graphExtras += 3; - - g.drawLine(x, graphExtras, - x+fm.stringWidth(aa[i].label), - graphExtras); - g2.setStroke(new BasicStroke()); - } - }*/ - y += ((2 * aa[i].height) / 3); - } - else - { - y += aa[i].height; - } + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } } + } + g.setFont(baseFont); + fm = baseMetrics; + fontHeight = ofontH; } - - if (resizePanel) - { - g.drawImage(image, 2, 0 - scrollOffset, this); - } - else if (dragEvent != null && aa!=null) + else { - g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset); + g.drawString(aa[i].label, x, y + offset); } + } + } + if (resizePanel) + { + g.drawImage(image, 2, 0 - getScrollOffset(), this); + } + else if (dragEvent != null && aa != null) + { + g.setColor(Color.lightGray); + g.drawString(aa[selectedRow].label, dragEvent.getX(), + dragEvent.getY() - getScrollOffset()); + } - if ((aa == null) || (aa.length < 1)) - { - g.drawString("Right click", 2, 8); - g.drawString("to add annotation", 2, 18); - } + if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) + { + g.drawString(MessageManager.getString("label.right_click"), 2, 8); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); } + } + + public int getScrollOffset() + { + return scrollOffset; + } }