X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=8aac7dcb60a87acc19e2b55dcbb2974b41914426;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=d209be707817c3425b9a03fc04399e4c62430e0c;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index d209be7..8aac7dc 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 2.9.0b2) - * Copyright (C) 2015 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. * @@ -20,24 +20,29 @@ */ package jalview.gui; +import jalview.analysis.AlignSeq; import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; +import jalview.util.Comparison; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.workers.InformationThread; 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; @@ -47,12 +52,9 @@ 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.List; -import java.util.regex.Pattern; +import java.util.Iterator; import javax.swing.JCheckBoxMenuItem; import javax.swing.JMenuItem; @@ -62,63 +64,75 @@ 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 { - private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern - .compile("<"); + private static final String HTML_END_TAG = ""; + + private static final String HTML_START_TAG = ""; + + /** + * width in pixels within which height adjuster arrows are shown and active + */ + private static final int HEIGHT_ADJUSTER_WIDTH = 50; + + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; - String TOGGLE_LABELSCALE = MessageManager + private static final Font font = new Font("Arial", Font.PLAIN, 11); + + private static final String TOGGLE_LABELSCALE = MessageManager .getString("label.scale_label_to_column"); - String ADDNEW = MessageManager.getString("label.add_new_row"); + private static final String ADDNEW = MessageManager + .getString("label.add_new_row"); - String EDITNAME = MessageManager + private static final String EDITNAME = MessageManager .getString("label.edit_label_description"); - String HIDE = MessageManager.getString("label.hide_row"); + private static final String HIDE = MessageManager + .getString("label.hide_row"); - String DELETE = MessageManager.getString("label.delete_row"); + private static final String DELETE = MessageManager + .getString("label.delete_row"); - String SHOWALL = MessageManager.getString("label.show_all_hidden_rows"); + private static final String SHOWALL = MessageManager + .getString("label.show_all_hidden_rows"); - String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); + private static final String OUTPUT_TEXT = MessageManager + .getString("label.export_annotation"); - String COPYCONS_SEQ = MessageManager + private static final String COPYCONS_SEQ = MessageManager .getString("label.copy_consensus_sequence"); - boolean resizePanel = false; - - Image image; + private final boolean debugRedraw = false; - AlignmentPanel ap; + private AlignmentPanel ap; AlignViewport av; - boolean resizing = false; - - MouseEvent dragEvent; + private MouseEvent dragEvent; - int oldY; + private int oldY; - int selectedRow; + private int selectedRow; private int scrollOffset = 0; - Font font = new Font("Arial", Font.PLAIN, 11); - 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) { @@ -126,30 +140,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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 = bi; - addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(ap.getAnnotationPanel()); @@ -266,8 +256,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { - new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] { aa[selectedRow] }); + new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -291,33 +280,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - refresh(fullRepaint); + ap.refresh(fullRepaint); } /** - * Redraw sensibly. - * - * @adjustHeight if true, try to recalculate panel height for visible - * annotations - */ - protected void refresh(boolean adjustHeight) - { - ap.validateAnnotationDimensions(adjustHeight); - ap.addNotify(); - if (adjustHeight) - { - // sort, repaint, update overview - ap.paintAlignment(true); - } - else - { - // lightweight repaint - ap.repaint(); - } - } - - /** * DOCUMENT ME! * * @param e @@ -386,6 +353,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.show(this, evt.getX(), evt.getY()); return; } + + final AlignmentAnnotation ann = aa[selectedRow]; + final boolean isSequenceAnnotation = ann.sequenceRef != null; + item = new JMenuItem(EDITNAME); item.addActionListener(this); pop.add(item); @@ -395,9 +366,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, // JAL-1264 hide all sequence-specific annotations of this type if (selectedRow < aa.length) { - if (aa[selectedRow].sequenceRef != null) + if (isSequenceAnnotation) { - final String label = aa[selectedRow].label; + final String label = ann.label; JMenuItem hideType = new JMenuItem(); String text = MessageManager.getString("label.hide_all") + " " + label; @@ -410,16 +381,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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; - // } - // } - refresh(true); + ap.refresh(true); } }); pop.add(hideType); @@ -441,197 +403,335 @@ public class AnnotationLabels extends JPanel implements MouseListener, // property methods if (selectedRow < aa.length) { - final String label = aa[selectedRow].label; - if (!aa[selectedRow].autoCalculated) + final String label = ann.label; + if (!(ann.autoCalculated) + && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))) { - if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) + if (ann.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); + ann.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() + addConsensusMenuOptions(ap, aa[selectedRow], pop); + + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId())) + { + addHmmerMenu(pop, ann); + } + } + pop.show(this, evt.getX(), evt.getY()); + } + + /** + * Adds context menu options for (alignment or group) Hmmer annotation + * + * @param pop + * @param ann + */ + protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann) + { + final boolean isGroupAnnotation = ann.groupRef != null; + pop.addSeparator(); + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString( + "label.ignore_below_background_frequency"), + isGroupAnnotation + ? ann.groupRef + .isIgnoreBelowBackground() + : ap.av.isIgnoreBelowBackground()); + cbmi.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (isGroupAnnotation) { - @Override - public void actionPerformed(ActionEvent e) + if (!ann.groupRef.isUseInfoLetterHeight()) { - 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(); + ann.groupRef.setIgnoreBelowBackground(cbmi.getState()); + // todo and recompute group annotation } - }); - pop.add(cbmi); - // av and sequencegroup need to implement same interface for - if (aaa.groupRef != null) + } + else if (!ap.av.isInfoLetterHeight()) { - 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) - { + ap.av.setIgnoreBelowBackground(cbmi.getState(), ap); + // todo and recompute annotation + } + ap.alignmentChanged(); // todo not like this + } + }); + pop.add(cbmi); + final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem( + MessageManager.getString("label.use_info_for_height"), + isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight() + : ap.av.isInfoLetterHeight()); + letterHeight.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (isGroupAnnotation) + { + ann.groupRef.setInfoLetterHeight((letterHeight.getState())); + ann.groupRef.setIgnoreBelowBackground(true); + // todo and recompute group annotation + } + else + { + ap.av.setInfoLetterHeight(letterHeight.getState(), ap); + ap.av.setIgnoreBelowBackground(true, ap); + // todo and recompute annotation + } + ap.alignmentChanged(); + } + }); + pop.add(letterHeight); + if (isGroupAnnotation) + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + ann.groupRef.isShowInformationHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ann.groupRef.setShowInformationHistogram(chist.getState()); + ap.repaint(); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_logo"), + ann.groupRef.isShowHMMSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ann.groupRef.setShowHMMSequenceLogo(cprofl.getState()); + ap.repaint(); + } + }); + pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + ann.groupRef.isNormaliseHMMSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ann.groupRef + .setNormaliseHMMSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + ann.groupRef.setShowHMMSequenceLogo(true); + ap.repaint(); + } + }); + pop.add(cproflnorm); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + av.isShowInformationHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + av.setShowInformationHistogram(chist.getState()); + ap.repaint(); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + av.isShowHMMSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + av.setShowHMMSequenceLogo(cprof.getState()); + ap.repaint(); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + av.isNormaliseHMMSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + av.setShowHMMSequenceLogo(true); + av.setNormaliseHMMSequenceLogo(cprofnorm.getState()); + ap.repaint(); + } + }); + pop.add(cprofnorm); + } + } - // 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); + /** + * A helper method that adds menu options for calculation and visualisation of + * group and/or alignment consensus annotation to a popup menu. This is + * designed to be reusable for either unwrapped mode (popup menu is shown on + * component AnnotationLabels), or wrapped mode (popup menu is shown on + * IdPanel when the mouse is over an annotation label). + * + * @param ap + * @param ann + * @param pop + */ + static void addConsensusMenuOptions(AlignmentPanel ap, + AlignmentAnnotation ann, + JPopupMenu pop) + { + pop.addSeparator(); + + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString("label.ignore_gaps_consensus"), + (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = ann; + cbmi.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (aaa.groupRef != null) + { + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); } else { - 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); + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); + ap.alignmentChanged(); } + }); + pop.add(cbmi); + + if (aaa.groupRef != null) + { + /* + * group consensus options + */ + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + ann.groupRef.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_logo"), + ann.groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); + } + }); + pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + ann.groupRef.isNormaliseSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowSequenceLogo(true); + ap.repaint(); + } + }); + pop.add(cproflnorm); + } + else + { + /* + * alignment consensus options + */ + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + ap.av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ap.av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + ap.av.isShowSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ap.av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + ap.av.isNormaliseSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + ap.av.setShowSequenceLogo(true); + ap.av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + } + }); + pop.add(cprofnorm); } - pop.show(this, evt.getX(), evt.getY()); } /** - * DOCUMENT ME! + * Reorders annotation rows after a drag of a label * * @param evt - * DOCUMENT ME! */ @Override public void mouseReleased(MouseEvent evt) @@ -646,6 +746,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; + /* + * if dragging to resize instead, start == end + */ if (start != end) { // Swap these annotations @@ -669,31 +772,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * 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! + * Removes the height adjuster image on leaving the panel, unless currently + * dragging it */ @Override public void mouseExited(MouseEvent evt) { - if (dragEvent == null) + if (resizePanel && dragEvent == null) { resizePanel = false; repaint(); @@ -701,10 +786,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * A mouse drag may be either an adjustment of the panel height (if flag + * resizePanel is set on), or a reordering of the annotation rows. The former + * is dealt with by this method, the latter in mouseReleased. * * @param evt - * DOCUMENT ME! */ @Override public void mouseDragged(MouseEvent evt) @@ -721,12 +807,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, if ((d.height - dif) > 20) { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + ap.annotationScroller + .setPreferredSize(new Dimension(d.width, d.height - dif)); d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.paintAlignment(true); + ap.annotationSpaceFillerHolder + .setPreferredSize(new Dimension(d.width, d.height - dif)); + ap.paintAlignment(true, false); } ap.addNotify(); @@ -738,87 +824,156 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * DOCUMENT ME! + * Updates the tooltip as the mouse moves over the labels * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) { - resizePanel = evt.getY() < 10; + showOrHideAdjuster(evt); getSelectedRow(evt.getY() - getScrollOffset()); - if (selectedRow > -1 - && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + if (selectedRow > -1 && ap.av.getAlignment() + .getAlignmentAnnotation().length > selectedRow) + { + AlignmentAnnotation[] anns = ap.av.getAlignment() + .getAlignmentAnnotation(); + AlignmentAnnotation aa = anns[selectedRow]; + + String desc = getTooltip(aa); + this.setToolTipText(desc); + String msg = getStatusMessage(aa, anns); + ap.alignFrame.setStatus(msg); + } + } + + /** + * Constructs suitable text to show in the status bar when over an annotation + * label, containing the associated sequence name (if any), and the annotation + * labels (or all labels for a graph group annotation) + * + * @param aa + * @param anns + * @return + */ + static String getStatusMessage(AlignmentAnnotation aa, + AlignmentAnnotation[] anns) + { + if (aa == null) + { + return null; + } + + StringBuilder msg = new StringBuilder(32); + if (aa.sequenceRef != null) { - AlignmentAnnotation aa = ap.av.getAlignment() - .getAlignmentAnnotation()[selectedRow]; + msg.append(aa.sequenceRef.getName()).append(" : "); + } - StringBuffer desc = new StringBuffer(); - if (aa.description != null - && !aa.description.equals("New description")) + if (aa.graphGroup == -1) + { + msg.append(aa.label); + } + else if (anns != null) + { + boolean first = true; + for (int i = anns.length - 1; i >= 0; i--) { - // TODO: we could refactor and merge this code with the code in - // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature - // tooltips - desc.append(aa.getDescription(true).trim()); - // check to see if the description is an html fragment. - if (desc.length() < 6 - || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) + if (anns[i].graphGroup == aa.graphGroup) { - // 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) + if (!first) { - desc.setLength(desc.length() - 7 + i); + msg.append(", "); } + msg.append(anns[i].label); + first = false; } - if (aa.hasScore()) - { - desc.append("
"); - } - // if (aa.hasProperties()) - // { - // desc.append(""); - // for (String prop : aa.getProperties()) - // { - // desc.append(""); - // } - // desc.append("
" + prop + "" - // + aa.getProperty(prop) + "
"); - // } } - else + } + + return msg.toString(); + } + + /** + * Answers a tooltip, formatted as html, containing the annotation description + * (prefixed by associated sequence id if applicable), and the annotation + * (non-positional) score if it has one. Answers null if neither description + * nor score is found. + * + * @param aa + * @return + */ + static String getTooltip(AlignmentAnnotation aa) + { + if (aa == null) + { + return null; + } + StringBuilder tooltip = new StringBuilder(); + if (aa.description != null && !aa.description.equals("New description")) + { + // TODO: we could refactor and merge this code with the code in + // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature + // tooltips + String desc = aa.getDescription(true).trim(); + if (!desc.toLowerCase().startsWith(HTML_START_TAG)) { - // 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); - } + tooltip.append(HTML_START_TAG); + desc = desc.replace("<", "<"); } - if (desc.length() > 6) + else if (desc.toLowerCase().endsWith(HTML_END_TAG)) { - desc.append(""); - this.setToolTipText(desc.toString()); + desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); } - else + tooltip.append(desc); + } + else + { + // begin the tooltip's html fragment + tooltip.append(HTML_START_TAG); + } + if (aa.hasScore()) + { + if (tooltip.length() > HTML_START_TAG.length()) { - this.setToolTipText(null); + tooltip.append("
"); } + // TODO: limit precision of score to avoid noise from imprecise + // doubles + // (64.7 becomes 64.7+/some tiny value). + tooltip.append(" Score: ").append(String.valueOf(aa.score)); + } + + if (tooltip.length() > HTML_START_TAG.length()) + { + return tooltip.append(HTML_END_TAG).toString(); + } + + /* + * nothing in the tooltip (except "") + */ + return null; + } + + /** + * Shows the height adjuster image if the mouse moves into the top left + * region, or hides it if the mouse leaves the regio + * + * @param evt + */ + protected void showOrHideAdjuster(MouseEvent evt) + { + boolean was = resizePanel; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + + if (resizePanel != was) + { + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR + : Cursor.DEFAULT_CURSOR)); + repaint(); } } @@ -840,17 +995,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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 (sg == null || sg == aa[selectedRow].groupRef + || !(Platform.isControlDown(evt) || evt.isShiftDown())) { - if (jalview.util.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)); + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); } else { @@ -877,7 +1029,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -892,10 +1044,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.getSeqPanel().ap - .getIdPanel() - .highlightSearchResults( - Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + ap.getSeqPanel().ap.getIdPanel() + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { @@ -906,8 +1057,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // 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())) + if (!(Platform.isControlDown(evt) || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -915,7 +1065,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - if (jalview.util.Platform.isControlDown(evt)) + if (Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); } @@ -935,11 +1085,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } - } } return; @@ -960,39 +1109,38 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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); + Iterator it = av.getAlignment().getHiddenColumns() + .getVisContigsIterator(0, sq.getLength(), false); + omitHidden = new String[] { sq.getSequenceStringFromIterator(it) }; } int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; - List hiddenCols = av.getColumnSelection().getHiddenColumns(); - if (hiddenCols != null) + if (av.hasHiddenColumns()) { - alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex( - hiddenCols); + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden, alignmentStartEnd); + + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; + if (av.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - hiddenColumns.add(new int[] { region[0], region[1] }); - } + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@ -1012,7 +1160,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, @Override public void paintComponent(Graphics g) { - int width = getWidth(); if (width == 0) { @@ -1027,7 +1174,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, } drawComponent(g2, true, width); - } /** @@ -1045,8 +1191,6 @@ 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 @@ -1088,8 +1232,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap - .getAnnotationPanel().getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) + ? ap.getAnnotationPanel().getVisibleVRange() + : null; if (clip && visr != null) { sOffset = visr[0]; @@ -1132,8 +1277,8 @@ 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; } @@ -1171,7 +1316,8 @@ 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 { @@ -1185,11 +1331,12 @@ 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) @@ -1206,8 +1353,8 @@ 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); @@ -1226,11 +1373,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - if (resizePanel) - { - g.drawImage(image, 2, 0 - getScrollOffset(), this); - } - else if (dragEvent != null && aa != null) + if (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), @@ -1249,4 +1392,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, { return scrollOffset; } + + @Override + public void mouseEntered(MouseEvent e) + { + } }