X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;fp=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=6da6cc385caf32f6b639565cf2948367b37d2298;hp=6f8b225a2f208617ebfe152275cdd318a9cd855d;hb=74393b51f368cb9f58589472d432a433d9c4386d;hpb=7a0d503181fe41452120a8a02ca63476392aa08c diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 6f8b225..6da6cc3 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -51,12 +51,9 @@ 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.Iterator; -import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; import javax.swing.JMenuItem; @@ -73,6 +70,10 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { + 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 */ @@ -83,9 +84,6 @@ public class AnnotationLabels extends JPanel */ private static int HEIGHT_ADJUSTER_HEIGHT = 10; - private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern - .compile("<"); - private static final Font font = new Font("Arial", Font.PLAIN, 11); private static final String TOGGLE_LABELSCALE = MessageManager @@ -378,15 +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); } }); @@ -425,174 +414,154 @@ 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() - { - @Override - public void actionPerformed(ActionEvent e) - { - if (aaa.groupRef != null) - { - // TODO: pass on reference to ap so the view can be updated. - aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel() - .paint(ap.getAnnotationPanel().getGraphics()); - } - else - { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); - } - ap.alignmentChanged(); - } - }); - pop.add(cbmi); - // av and sequencegroup need to implement same interface for + addConsensusMenuOptions(ap, aa[selectedRow], pop); + + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + } + pop.show(this, evt.getX(), evt.getY()); + } + + /** + * 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) { - 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) - { - - // 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); + 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()); } /** @@ -705,73 +674,123 @@ 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); + } + } + + /** + * 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; + } - StringBuffer desc = new StringBuffer(); - if (aa.description != null - && !aa.description.equals("New description")) + 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().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; } /**