X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=52a6066db16bd0b27de610615574664aa6938374;hb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;hp=294b8db964023849c80b70be9564548496649089;hpb=0eecb83722155f32d5eade88a5e8b4a5caca1a67;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 294b8db..52a6066 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,22 +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.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.util.dialogrunner.RunResponse; - import java.awt.Color; import java.awt.Cursor; import java.awt.Dimension; @@ -52,10 +36,11 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; +import java.io.IOException; import java.util.Arrays; import java.util.Collections; import java.util.Iterator; -import java.util.regex.Pattern; +import java.util.Locale; import javax.swing.JCheckBoxMenuItem; import javax.swing.JMenuItem; @@ -64,6 +49,26 @@ import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; +import jalview.analysis.AlignSeq; +import jalview.analysis.AlignmentUtils; +import jalview.bin.Console; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.ContactMatrixI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FormatAdapter; +import jalview.io.NewickFile; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; + /** * The panel that holds the labels for alignment annotations, providing * tooltips, context menus, drag to reorder rows, and drag to adjust panel @@ -72,6 +77,10 @@ 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 */ @@ -82,9 +91,6 @@ 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 @@ -136,6 +142,7 @@ public class AnnotationLabels extends JPanel */ public AnnotationLabels(AlignmentPanel ap) { + this.ap = ap; av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); @@ -291,27 +298,22 @@ public class AnnotationLabels extends JPanel EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, name, description); - dialog.showDialog(ap.alignFrame, title, - new RunResponse(JvOptionPane.OK_OPTION) - { - @Override - public void run() - { - 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); - } - }); + 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); + return null; + }); } @Override @@ -376,15 +378,6 @@ 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); } }); @@ -423,174 +416,178 @@ 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 - if (aaa.groupRef != null) + addConsensusMenuOptions(ap, aa[selectedRow], pop); + + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP + && PAEContactMatrix.PAEMATRIX + .equals(aa[selectedRow].getCalcId())) + { + final PAEContactMatrix cm = (PAEContactMatrix) av + .getContactMatrix(aa[selectedRow]); + if (cm!=null && cm.getNewick()!=null && cm.getNewick().length()>0) { - 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() + item = new JMenuItem("Show Tree for Matrix"); + item.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()); + ap.alignFrame.showContactMapTree(aa[selectedRow],cm); + } }); - pop.add(cproflnorm); + pop.addSeparator(); + pop.add(item); + } + + } + } + 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) + { + 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()); } /** @@ -703,73 +700,123 @@ 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(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; } /** @@ -981,7 +1028,7 @@ public class AnnotationLabels extends JPanel int width = getWidth(); if (width == 0) { - width = ap.calculateIdWidth().width + 4; + width = ap.calculateIdWidth().width; } Graphics2D g2 = (Graphics2D) g; @@ -1039,7 +1086,8 @@ public class AnnotationLabels extends JPanel 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; @@ -1064,6 +1112,7 @@ public class AnnotationLabels extends JPanel { hasHiddenRows = false; int olY = 0; + int nexAA = 0; for (int i = 0; i < aa.length; i++) { visible = true; @@ -1073,6 +1122,9 @@ public class AnnotationLabels extends JPanel continue; } olY = y; + // look ahead to next annotation + for (nexAA=i+1; nexAA -1) { @@ -1187,16 +1271,26 @@ public class AnnotationLabels extends JPanel } else { - g.drawString(aa[i].label, x, y + offset); + 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 (!resizePanel && dragEvent != null && aa != null) { g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - getScrollOffset()); + 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)))