X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=d459217f11ac3cb994441f97a2b0952eb846bf16;hb=f16c439627f599f52a372704e72ae5464134fa2b;hp=d9039798786fed9ef6ba3c0fe14b272ddf8fe672;hpb=0af574276d914ed4ba6af684c2c6a6c7cb70562c;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index d903979..d459217 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,20 +20,6 @@ */ 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.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; @@ -41,8 +27,6 @@ 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; @@ -52,11 +36,10 @@ 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 java.util.Iterator; +import java.util.Locale; import javax.swing.JCheckBoxMenuItem; import javax.swing.JMenuItem; @@ -65,6 +48,25 @@ import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; +import jalview.analysis.AlignSeq; +import jalview.analysis.AlignmentUtils; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.ContactMatrixI; +import jalview.datamodel.GroupSet; +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; + /** * The panel that holds the labels for alignment annotations, providing * tooltips, context menus, drag to reorder rows, and drag to adjust panel @@ -73,11 +75,19 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - // width in pixels within which height adjuster arrows are shown and active + 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; - private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern - .compile("<"); + /** + * height in pixels for allowing height adjuster to be active + */ + private static int HEIGHT_ADJUSTER_HEIGHT = 10; private static final Font font = new Font("Arial", Font.PLAIN, 11); @@ -105,9 +115,7 @@ public class AnnotationLabels extends JPanel private static final String COPYCONS_SEQ = MessageManager .getString("label.copy_consensus_sequence"); - private static Image adjusterImage; - - private static int adjusterImageHeight; + private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH"; private final boolean debugRedraw = false; @@ -138,11 +146,6 @@ public class AnnotationLabels extends JPanel av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); - if (adjusterImage == null) - { - loadAdjusterImage(); - } - addMouseListener(this); addMouseMotionListener(this); addMouseWheelListener(ap.getAnnotationPanel()); @@ -154,37 +157,6 @@ public class AnnotationLabels extends JPanel } /** - * 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 = 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); - adjusterImage = bi; - adjusterImageHeight = bi.getHeight(); - } - - /** * DOCUMENT ME! * * @param y @@ -243,41 +215,33 @@ public class AnnotationLabels extends JPanel AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - boolean fullRepaint = false; - if (evt.getActionCommand().equals(ADDNEW)) + String action = evt.getActionCommand(); + if (ADDNEW.equals(action)) { + /* + * non-returning dialog + */ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, null, new Annotation[ap.av.getAlignment().getWidth()]); - - if (!editLabelDescription(newAnnotation)) - { - return; - } - - ap.av.getAlignment().addAnnotation(newAnnotation); - ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); - fullRepaint = true; + editLabelDescription(newAnnotation, true); } - else if (evt.getActionCommand().equals(EDITNAME)) + else if (EDITNAME.equals(action)) { - String name = aa[selectedRow].label; - editLabelDescription(aa[selectedRow]); - if (!name.equalsIgnoreCase(aa[selectedRow].label)) - { - fullRepaint = true; - } + /* + * non-returning dialog + */ + editLabelDescription(aa[selectedRow], false); } - else if (evt.getActionCommand().equals(HIDE)) + else if (HIDE.equals(action)) { aa[selectedRow].visible = false; } - else if (evt.getActionCommand().equals(DELETE)) + else if (DELETE.equals(action)) { ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); - fullRepaint = true; } - else if (evt.getActionCommand().equals(SHOWALL)) + else if (SHOWALL.equals(action)) { for (int i = 0; i < aa.length; i++) { @@ -286,15 +250,12 @@ public class AnnotationLabels extends JPanel aa[i].visible = true; } } - fullRepaint = true; } - else if (evt.getActionCommand().equals(OUTPUT_TEXT)) + else if (OUTPUT_TEXT.equals(action)) { - new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] - { aa[selectedRow] }); + new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]); } - else if (evt.getActionCommand().equals(COPYCONS_SEQ)) + else if (COPYCONS_SEQ.equals(action)) { SequenceI cons = null; if (aa[selectedRow].groupRef != null) @@ -309,46 +270,48 @@ public class AnnotationLabels extends JPanel { copy_annotseqtoclipboard(cons); } - } - else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + else if (TOGGLE_LABELSCALE.equals(action)) { aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.refresh(fullRepaint); - + ap.refresh(true); } /** - * DOCUMENT ME! + * Shows a dialog where the annotation name and description may be edited. If + * parameter addNew is true, then on confirmation, a new AlignmentAnnotation + * is added, else an existing annotation is updated. * - * @param e - * DOCUMENT ME! + * @param annotation + * @param addNew */ - boolean editLabelDescription(AlignmentAnnotation annotation) + void editLabelDescription(AlignmentAnnotation annotation, boolean addNew) { - // TODO i18n + String name = MessageManager.getString("label.annotation_name"); + String description = MessageManager + .getString("label.annotation_description"); + String title = MessageManager + .getString("label.edit_annotation_name_description"); EditNameDialog dialog = new EditNameDialog(annotation.label, - annotation.description, " Annotation Name ", - "Annotation Description ", "Edit Annotation Name/Description", - ap.alignFrame); - - if (!dialog.accept) - { - return false; - } - - annotation.label = dialog.getName(); - - String text = dialog.getDescription(); - if (text != null && text.length() == 0) - { - text = null; - } - annotation.description = text; + annotation.description, name, description); - return true; + dialog.showDialog(ap.alignFrame, title, () -> { + annotation.label = dialog.getName(); + String text = dialog.getDescription(); + if (text != null && text.length() == 0) + { + text = null; + } + annotation.description = text; + if (addNew) + { + ap.av.getAlignment().addAnnotation(annotation); + ap.av.getAlignment().setAnnotationIndex(annotation, 0); + } + ap.refresh(true); + }); } @Override @@ -413,15 +376,6 @@ public class AnnotationLabels extends JPanel 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); } }); @@ -460,174 +414,300 @@ public class AnnotationLabels extends JPanel } 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); + } + + addColourOrFilterByOptions(ap, aa[selectedRow], pop); + + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP) + { + addContactMatrixOptions(ap, aa[selectedRow], pop); + // Set/adjust threshold for grouping ? + // colour alignment by this [type] + // select/hide columns by this row + + } + } + + pop.show(this, evt.getX(), evt.getY()); + } + + static void addColourOrFilterByOptions(final AlignmentPanel ap, + final AlignmentAnnotation alignmentAnnotation, + final JPopupMenu pop) + { + JMenuItem item; + item = new JMenuItem( + MessageManager.getString("label.colour_by_annotation")); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, + false); + }; + }); + pop.add(item); + if (alignmentAnnotation.sequenceRef != null) + { + item = new JMenuItem( + MessageManager.getString("label.colour_by_annotation") + " (" + + MessageManager.getString("label.per_seq") + ")"); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { + AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation, + true); + }; + }); + pop.add(item); + } + item = new JMenuItem( + MessageManager.getString("action.select_by_annotation")); + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation); + }; + }); + pop.add(item); + } + + static void addContactMatrixOptions(final AlignmentPanel ap, + final AlignmentAnnotation alignmentAnnotation, + final JPopupMenu pop) + { + + final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation); + JMenuItem item; + if (cm != null) + { + pop.addSeparator(); + + if (cm.hasGroups()) + { + JCheckBoxMenuItem chitem = new JCheckBoxMenuItem( + MessageManager.getString("action.show_groups_on_matrix")); + chitem.setToolTipText(MessageManager + .getString("action.show_groups_on_matrix_tooltip")); + boolean showGroups = alignmentAnnotation + .isShowGroupsForContactMatrix(); + final AlignmentAnnotation sel_row = alignmentAnnotation; + chitem.setState(showGroups); + chitem.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(); + sel_row.setShowGroupsForContactMatrix(chitem.getState()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); } }); - pop.add(cbmi); - // av and sequencegroup need to implement same interface for - if (aaa.groupRef != null) + pop.add(chitem); + } + if (cm.hasTree()) + { + item = new JMenuItem( + MessageManager.getString("action.show_tree_for_matrix")); + item.setToolTipText(MessageManager + .getString("action.show_tree_for_matrix_tooltip")); + item.addActionListener(new ActionListener() { - 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) { - @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() + + ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); + + } + }); + pop.add(item); + } + else + { + item = new JMenuItem( + MessageManager.getString("action.cluster_matrix")); + item.setToolTipText( + MessageManager.getString("action.cluster_matrix_tooltip")); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - @Override - public void actionPerformed(ActionEvent e) + new Thread(new Runnable() { + @Override + public void run() + { + final long progBar; + ap.alignFrame.setProgressBar( + MessageManager.formatMessage( + "action.clustering_matrix_for", + cm.getAnnotDescr(), 5f), + progBar = System.currentTimeMillis()); + cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true)); + ap.alignFrame.showContactMapTree(alignmentAnnotation, cm); + ap.alignFrame.setProgressBar(null, progBar); + } + }).start(); + } + }); + pop.add(item); + } + } + } - // 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()); } /** @@ -740,73 +820,123 @@ public class AnnotationLabels extends JPanel if (selectedRow > -1 && ap.av.getAlignment() .getAlignmentAnnotation().length > selectedRow) { - AlignmentAnnotation aa = ap.av.getAlignment() - .getAlignmentAnnotation()[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); + } + } - StringBuffer desc = new StringBuffer(); - if (aa.description != null - && !aa.description.equals("New description")) + /** + * Constructs suitable text to show in the status bar when over an annotation + * label, containing the associated sequence name (if any), and the annotation + * labels (or all labels for a graph group annotation) + * + * @param aa + * @param anns + * @return + */ + static String getStatusMessage(AlignmentAnnotation aa, + AlignmentAnnotation[] anns) + { + if (aa == null) + { + return null; + } + + StringBuilder msg = new StringBuilder(32); + if (aa.sequenceRef != null) + { + msg.append(aa.sequenceRef.getName()).append(" : "); + } + + if (aa.graphGroup == -1) + { + msg.append(aa.label); + } + else if (anns != null) + { + boolean first = true; + for (int i = anns.length - 1; i >= 0; i--) { - // 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(Locale.ROOT).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(Locale.ROOT).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; } /** @@ -818,12 +948,13 @@ public class AnnotationLabels extends JPanel protected void showOrHideAdjuster(MouseEvent evt) { boolean was = resizePanel; - resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH; + resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT + && evt.getX() < HEIGHT_ADJUSTER_WIDTH; if (resizePanel != was) { - setCursor(Cursor.getPredefinedCursor( - resizePanel ? Cursor.S_RESIZE_CURSOR + setCursor(Cursor + .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); repaint(); } @@ -970,8 +1101,9 @@ public class AnnotationLabels extends JPanel Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getAlignment().getHiddenColumns() - .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 }; @@ -987,12 +1119,12 @@ public class AnnotationLabels extends JPanel Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (av.hasHiddenColumns()) { - hiddenColumns = av.getAlignment().getHiddenColumns() - .getHiddenColumnsCopy(); + hiddenColumns = new HiddenColumns( + av.getAlignment().getHiddenColumns()); } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@ -1016,7 +1148,7 @@ public class AnnotationLabels extends JPanel int width = getWidth(); if (width == 0) { - width = ap.calculateIdWidth().width + 4; + width = ap.calculateIdWidth().width; } Graphics2D g2 = (Graphics2D) g; @@ -1057,8 +1189,58 @@ public class AnnotationLabels extends JPanel * @param width * Width for scaling labels */ - public void drawComponent(Graphics g, boolean clip, int width) + public void drawComponent(Graphics g, boolean clip, int givenWidth) { + int width = givenWidth; + IdwidthAdjuster iwa = ap.idwidthAdjuster; + if ((Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true) + || Jalview.isHeadlessMode()) && !iwa.manuallyAdjusted()) + { + Graphics2D g2d = (Graphics2D) g; + Graphics dummy = g2d.create(); + int annotationIdWidth = drawLabels(dummy, clip, width, false); + Dimension d = ap.calculateDefaultAlignmentIdWidth(); + int alignmentIdWidth = d.width; + if (!iwa.manuallyAdjusted()) + { + // If no manual adjustment to ID column with has been made then adjust + // width match widest of alignment or annotation id widths + width = Math.max(alignmentIdWidth, annotationIdWidth); + } + else if (annotationIdWidth > givenWidth + && annotationIdWidth > alignmentIdWidth) + { + // otherwise if the annotation id width has become larger than the + // current id width, increase + width = annotationIdWidth; + } + // set the width if it's changed + if (width != ap.av.getIdWidth()) + { + iwa.setWidth(width); + ap.validateAnnotationDimensions(false); + } + } + drawLabels(g, clip, width, true); + } + + /** + * Render the full set of annotation Labels for the alignment at the given + * cursor. If actuallyDraw is false then no actual drawing will occur, but the + * widest label width will be returned. + * + * @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 int drawLabels(Graphics g, boolean clip, int width, + boolean actuallyDraw) + { + int actualWidth = 0; if (av.getFont().getSize() < 10) { g.setFont(font); @@ -1069,12 +1251,19 @@ public class AnnotationLabels extends JPanel } FontMetrics fm = g.getFontMetrics(g.getFont()); - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - - g.translate(0, getScrollOffset()); - g.setColor(Color.black); + if (actuallyDraw) + { + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); + } + if (actuallyDraw) + { + g.translate(0, getScrollOffset()); + g.setColor(Color.black); + } + SequenceI lastSeqRef = null; + String lastLabel = null; AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; @@ -1099,6 +1288,7 @@ public class AnnotationLabels extends JPanel { hasHiddenRows = false; int olY = 0; + int nexAA = 0; for (int i = 0; i < aa.length; i++) { visible = true; @@ -1108,6 +1298,10 @@ public class AnnotationLabels extends JPanel continue; } olY = y; + // look ahead to next annotation + for (nexAA = i + 1; nexAA < aa.length + && !aa[nexAA].visible; nexAA++) + ; y += aa[i].height; if (clip) { @@ -1140,8 +1334,10 @@ public class AnnotationLabels extends JPanel continue; } } - g.setColor(Color.black); - + if (actuallyDraw) + { + g.setColor(Color.black); + } offset = -aa[i].height / 2; if (aa[i].hasText) @@ -1153,8 +1349,42 @@ public class AnnotationLabels extends JPanel { offset += fm.getDescent(); } + String label = aa[i].label; + boolean vertBar = false; + if ((lastLabel != null && lastLabel.equals(label))) + { + label = aa[i].description; + } + else + { + if (nexAA < aa.length && label.equals(aa[nexAA].label)) // && + // aa[nexY].sequenceRef==aa[i].sequenceRef) + { + lastLabel = label; + // next label is the same as this label + label = aa[i].description; + } + else + { + lastLabel = label; + } + } + if (aa[i].sequenceRef != null) + { + if (aa[i].sequenceRef != lastSeqRef) + { + label = aa[i].sequenceRef.getName() + " " + label; + // TODO record relationship between sequence and this annotation and + // display it here + } + else + { + vertBar = true; + } + } - x = width - fm.stringWidth(aa[i].label) - 3; + int labelWidth = fm.stringWidth(label) + 3; + x = width - labelWidth; if (aa[i].graphGroup > -1) { @@ -1199,19 +1429,23 @@ public class AnnotationLabels extends JPanel { if (aa[gg].graphGroup == aa[i].graphGroup) { - x = width - fm.stringWidth(aa[gg].label) - 3; - g.drawString(aa[gg].label, x, y - graphExtras); - - if (aa[gg]._linecolour != null) + labelWidth = fm.stringWidth(aa[gg].label) + 3; + x = width - labelWidth; + if (actuallyDraw) { + g.drawString(aa[gg].label, x, y - graphExtras); - g.setColor(aa[gg]._linecolour); - g.drawLine(x, y - graphExtras + 3, - x + fm.stringWidth(aa[gg].label), - y - graphExtras + 3); - } + if (aa[gg]._linecolour != null) + { - g.setColor(Color.black); + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); + } + + g.setColor(Color.black); + } graphExtras += fontHeight + 8; } } @@ -1222,24 +1456,51 @@ public class AnnotationLabels extends JPanel } else { - g.drawString(aa[i].label, x, y + offset); + if (actuallyDraw) + { + if (vertBar) + { + g.drawLine(width - 3, y + offset - fontHeight, width - 3, + (int) (y - 1.5 * aa[i].height - offset - fontHeight)); + // g.drawLine(20, y + offset, x - 20, y + offset); + + } + g.drawString(label, x, y + offset); + } + } + lastSeqRef = aa[i].sequenceRef; + + if (labelWidth > actualWidth) + { + actualWidth = labelWidth; } } } if (!resizePanel && dragEvent != null && aa != null) { - g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - getScrollOffset()); + if (actuallyDraw) + { + g.setColor(Color.lightGray); + g.drawString( + (aa[selectedRow].sequenceRef == null ? "" + : aa[selectedRow].sequenceRef.getName()) + + aa[selectedRow].label, + dragEvent.getX(), dragEvent.getY() - getScrollOffset()); + } } if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) { - g.drawString(MessageManager.getString("label.right_click"), 2, 8); - g.drawString(MessageManager.getString("label.to_add_annotation"), 2, - 18); + if (actuallyDraw) + { + g.drawString(MessageManager.getString("label.right_click"), 2, 8); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); + } } + + return actualWidth; } public int getScrollOffset()