X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=673f04dd2ca672bd6a21e1a05011318969315b03;hb=0751c58086542f9e0466201b624f84d1efd547bb;hp=27dcebfe7db9b9b218785d9b898c8bf23c15454b;hpb=e82c0bb610425c3829037bec88b6c03509d07e36;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 27dcebf..673f04d 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,21 +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 java.awt.Color; import java.awt.Cursor; import java.awt.Dimension; @@ -62,6 +47,22 @@ import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; +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; + /** * The panel that holds the labels for alignment annotations, providing * tooltips, context menus, drag to reorder rows, and drag to adjust panel @@ -352,6 +353,10 @@ public class AnnotationLabels extends JPanel 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); @@ -399,7 +404,8 @@ public class AnnotationLabels extends JPanel if (selectedRow < aa.length) { final String label = aa[selectedRow].label; - if (!aa[selectedRow].autoCalculated) + if (!(aa[selectedRow].autoCalculated) + && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))) { if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) { @@ -407,7 +413,7 @@ public class AnnotationLabels extends JPanel pop.addSeparator(); // av and sequencegroup need to implement same interface for item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, - aa[selectedRow].scaleColLabel); + aa[selectedRow].scaleColLabel); item.addActionListener(this); pop.add(item); } @@ -420,11 +426,169 @@ public class AnnotationLabels extends JPanel 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) + { + if (!ann.groupRef.isUseInfoLetterHeight()) + { + ann.groupRef.setIgnoreBelowBackground(cbmi.getState()); + // todo and recompute group annotation + } + } + else if (!ap.av.isInfoLetterHeight()) + { + 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); + } + } + + /** * 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 @@ -926,7 +1090,6 @@ public class AnnotationLabels extends JPanel PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } - } } return; @@ -981,24 +1144,15 @@ public class AnnotationLabels extends JPanel av.getAlignment().getHiddenColumns()); } - Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset - // of a consensus - // sequence ? need to - // flag - // sequence as special. + // what is the dataset of a consensus sequence? + // need to flag sequence as special. + Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds, hiddenColumns }; } - /** - * DOCUMENT ME! - * - * @param g1 - * DOCUMENT ME! - */ @Override public void paintComponent(Graphics g) { - int width = getWidth(); if (width == 0) { @@ -1013,7 +1167,6 @@ public class AnnotationLabels extends JPanel } drawComponent(g2, true, width); - } /**