X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=77b4ea933227a5f034915991aa8fa78e752bd3af;hb=c1abd9108f6a78bc4e900746ba2a4f3307a218fc;hp=ec7b46e65af683908772ce4df6100f79d78f44ad;hpb=58afea88095280d807e5c2ac8b9155de5ba3503c;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index ec7b46e..77b4ea9 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,72 +20,117 @@ */ package jalview.gui; -import java.util.*; -import java.util.regex.Pattern; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; +import jalview.analysis.AlignSeq; +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 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.Image; +import java.awt.MediaTracker; +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.awt.image.*; -import javax.swing.*; +import java.awt.image.BufferedImage; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.regex.Pattern; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.util.MessageManager; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ + * The panel that holds the labels for alignment annotations, providing + * tooltips, context menus, drag to reorder rows, and drag to adjust panel + * height */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel + implements MouseListener, MouseMotionListener, ActionListener { - String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column"); + // width in pixels within which height adjuster arrows are shown and active + private static final int HEIGHT_ADJUSTER_WIDTH = 50; - String ADDNEW = MessageManager.getString("label.add_new_row"); + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern + .compile("<"); - String EDITNAME = MessageManager.getString("label.edit_label_description"); + private static final Font font = new Font("Arial", Font.PLAIN, 11); - String HIDE = MessageManager.getString("label.hide_row"); + private static final String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); - String DELETE = MessageManager.getString("label.delete_row"); + private static final String ADDNEW = MessageManager + .getString("label.add_new_row"); - String SHOWALL = MessageManager.getString("label.show_all_hidden_rows"); + private static final String EDITNAME = MessageManager + .getString("label.edit_label_description"); - String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); + private static final String HIDE = MessageManager + .getString("label.hide_row"); - String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence"); + private static final String DELETE = MessageManager + .getString("label.delete_row"); - boolean resizePanel = false; + private static final String SHOWALL = MessageManager + .getString("label.show_all_hidden_rows"); - Image image; + private static final String OUTPUT_TEXT = MessageManager + .getString("label.export_annotation"); - AlignmentPanel ap; + private static final String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); - AlignViewport av; + private static Image adjusterImage; - boolean resizing = false; + private static int adjusterImageHeight; - MouseEvent dragEvent; + private final boolean debugRedraw = false; - int oldY; + private AlignmentPanel ap; - int selectedRow; + AlignViewport av; + + private MouseEvent dragEvent; - int scrollOffset = 0; + private int oldY; - Font font = new Font("Arial", Font.PLAIN, 11); + private int selectedRow; + + private int scrollOffset = 0; private boolean hasHiddenRows; + private boolean resizePanel = false; + /** - * Creates a new AnnotationLabels object. + * Creates a new AnnotationLabels object * * @param ap - * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { @@ -93,12 +138,32 @@ public class AnnotationLabels extends JPanel implements MouseListener, av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); + if (adjusterImage == null) + { + loadAdjusterImage(); + } + + addMouseListener(this); + addMouseMotionListener(this); + addMouseWheelListener(ap.getAnnotationPanel()); + } + + public AnnotationLabels(AlignViewport av) + { + this.av = av; + } + + /** + * Loads the gif for the panel height adjustment + */ + protected void loadAdjusterImage() + { java.net.URL url = getClass().getResource("/images/idwidth.gif"); Image temp = null; if (url != null) { - temp = java.awt.Toolkit.getDefaultToolkit().createImage(url); + temp = Toolkit.getDefaultToolkit().createImage(url); } try @@ -115,16 +180,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, Graphics2D g = (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); g.drawImage(temp, 0, -bi.getWidth(this), this); - image = (Image) bi; - - addMouseListener(this); - addMouseMotionListener(this); - addMouseWheelListener(ap.annotationPanel); - } - - public AnnotationLabels(AlignViewport av) - { - this.av = av; + adjusterImage = bi; + adjusterImageHeight = bi.getHeight(); } /** @@ -180,11 +237,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); + boolean fullRepaint = false; if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, @@ -197,11 +256,16 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.av.getAlignment().addAnnotation(newAnnotation); ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); + fullRepaint = true; } else if (evt.getActionCommand().equals(EDITNAME)) { + String name = aa[selectedRow].label; editLabelDescription(aa[selectedRow]); - repaint(); + if (!name.equalsIgnoreCase(aa[selectedRow].label)) + { + fullRepaint = true; + } } else if (evt.getActionCommand().equals(HIDE)) { @@ -210,6 +274,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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)) { @@ -220,12 +286,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[i].visible = true; } } + fullRepaint = true; } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { new AnnotationExporter().exportAnnotations(ap, new AlignmentAnnotation[] - { aa[selectedRow] }, null, null); + { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -249,11 +316,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.validateAnnotationDimensions(false); - ap.addNotify(); - ap.repaint(); - // validate(); - // ap.paintAlignment(true); + ap.refresh(fullRepaint); + } /** @@ -264,6 +328,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ boolean editLabelDescription(AlignmentAnnotation annotation) { + // TODO i18n EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Name ", "Annotation Description ", "Edit Annotation Name/Description", @@ -286,253 +351,27 @@ public class AnnotationLabels extends JPanel implements MouseListener, return true; } - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ + @Override public void mousePressed(MouseEvent evt) { - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); 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.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.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.getAlignment().getAlignmentAnnotation().length > selectedRow) + if (evt.isPopupTrigger()) { - AlignmentAnnotation aa = ap.av.getAlignment() - .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); + showPopupMenu(evt); } - } /** - * DOCUMENT ME! + * Build and show the Pop-up menu at the right-click mouse position * * @param evt - * DOCUMENT ME! */ - public void mouseClicked(MouseEvent evt) + void showPopupMenu(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.getAlignment() + evt.consume(); + final AlignmentAnnotation[] aa = ap.av.getAlignment() .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( MessageManager.getString("label.annotations")); @@ -556,6 +395,39 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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); @@ -572,6 +444,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // property methods if (selectedRow < aa.length) { + final String label = aa[selectedRow].label; if (!aa[selectedRow].autoCalculated) { if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) @@ -585,30 +458,33 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.add(item); } } - else if (aa[selectedRow].label.indexOf("Consensus") > -1) + else if (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()); + 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.annotationPanel.paint(ap.annotationPanel.getGraphics()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); } else { ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } + ap.alignmentChanged(); } }); pop.add(cbmi); @@ -616,10 +492,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "Show Group Histogram", + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -635,10 +512,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - "Show Group Logo", + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -654,10 +532,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprofl); final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - "Normalise Group Logo", + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cproflnorm.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -679,9 +558,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, else { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "Show Histogram", av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), + av.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -698,9 +579,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "Show Logo", av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), + av.isShowSequenceLogo()); cprof.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -717,9 +600,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - "Normalise Logo", av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), + av.isNormaliseSequenceLogo()); cprofnorm.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -746,6 +631,324 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** + * 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 aa = ap.av.getAlignment() + .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(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(""); + // } + // desc.append("
" + prop + "" + // + aa.getProperty(prop) + "
"); + // } + } + 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); + } + } + } + + /** + * 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() < adjusterImageHeight && 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 @@ -753,48 +956,49 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ protected void copy_annotseqtoclipboard(SequenceI sq) { - SequenceI[] seqs = new SequenceI[] - { sq }; + SequenceI[] seqs = new SequenceI[] { sq }; String[] omitHidden = null; - SequenceI[] dseqs = new SequenceI[] - { sq.getDatasetSequence() }; + SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); - dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, sq.getSequenceAsString())); + dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars, + sq.getSequenceAsString())); sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + omitHidden = av.getAlignment().getHiddenColumns() + .getVisibleSequenceStrings(0, sq.getLength(), seqs); + } + + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; + if (av.hasHiddenColumns()) + { + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - Vector hiddenColumns = null; + ArrayList 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] }); - } + hiddenColumns = av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy(); } - Desktop.jalviewClipboard = new Object[] - { seqs, ds, // what is the dataset of a consensus sequence ? need to flag + Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset + // of a consensus + // sequence ? need to + // flag // sequence as special. hiddenColumns }; } @@ -805,6 +1009,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param g1 * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { @@ -840,8 +1045,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, drawComponent(g, false, width); } - private final boolean debugRedraw = false; - /** * Draw the full set of annotation Labels for the alignment at the given * cursor @@ -869,7 +1072,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - g.translate(0, scrollOffset); + g.translate(0, getScrollOffset()); g.setColor(Color.black); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -883,8 +1086,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel - .getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) + ? ap.getAnnotationPanel().getVisibleVRange() + : null; if (clip && visr != null) { sOffset = visr[0]; @@ -927,8 +1131,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (debugRedraw) { - System.out.println("Scroll offset: " + sOffset - + " after vis: " + i); + System.out.println( + "Scroll offset: " + sOffset + " after vis: " + i); } after = true; } @@ -946,7 +1150,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, offset -= fm.getDescent(); } else + { offset += fm.getDescent(); + } x = width - fm.stringWidth(aa[i].label) - 3; @@ -964,7 +1170,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, } if (groupSize * (fontHeight + 8) < aa[i].height) { - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } else { @@ -978,11 +1185,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, { fontHeight = -8 + (int) h; s = ((float) fontHeight) / (float) ofontH; - Font f = baseFont.deriveFont(AffineTransform - .getScaleInstance(s, s)); + Font f = baseFont + .deriveFont(AffineTransform.getScaleInstance(s, s)); g.setFont(f); fm = g.getFontMetrics(); - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } } if (visible) @@ -999,8 +1207,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(aa[gg]._linecolour); g.drawLine(x, y - graphExtras + 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - + 3); + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); } g.setColor(Color.black); @@ -1021,20 +1229,30 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (resizePanel) { - g.drawImage(image, 2, 0 - scrollOffset, this); + // g.drawImage(adjusterImage, 2, 0 - getScrollOffset(), this); } else if (dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - scrollOffset); + dragEvent.getY() - getScrollOffset()); } - if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) + 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) + { + } }