X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=09624a80ac779a1cab0f2aef87cf56793575441e;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=6da6cc385caf32f6b639565cf2948367b37d2298;hpb=c3b91c81342d21498ffcb4639c3597a25aa2753c;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 6da6cc3..09624a8 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import java.util.Locale; + import jalview.analysis.AlignSeq; import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; @@ -34,6 +36,7 @@ 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; @@ -135,6 +138,7 @@ public class AnnotationLabels extends JPanel */ public AnnotationLabels(AlignmentPanel ap) { + this.ap = ap; av = ap.av; ToolTipManager.sharedInstance().registerComponent(this); @@ -208,41 +212,33 @@ 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++) { @@ -251,13 +247,12 @@ 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(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) @@ -272,46 +267,53 @@ 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); + annotation.description, name, description); - if (!dialog.accept) + dialog.showDialog(ap.alignFrame, title, new Runnable() { - return false; - } - - annotation.label = dialog.getName(); - - String text = dialog.getDescription(); - if (text != null && text.length() == 0) - { - text = null; - } - annotation.description = text; - - return true; + @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); + } + }); } @Override @@ -352,6 +354,8 @@ 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 +403,8 @@ 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 +412,7 @@ 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 +425,169 @@ 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 @@ -436,8 +599,7 @@ public class AnnotationLabels extends JPanel * @param pop */ static void addConsensusMenuOptions(AlignmentPanel ap, - AlignmentAnnotation ann, - JPopupMenu pop) + AlignmentAnnotation ann, JPopupMenu pop) { pop.addSeparator(); @@ -754,12 +916,12 @@ public class AnnotationLabels extends JPanel // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature // tooltips String desc = aa.getDescription(true).trim(); - if (!desc.toLowerCase().startsWith(HTML_START_TAG)) + if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) { tooltip.append(HTML_START_TAG); desc = desc.replace("<", "<"); } - else if (desc.toLowerCase().endsWith(HTML_END_TAG)) + else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG)) { desc = desc.substring(0, desc.length() - HTML_END_TAG.length()); } @@ -802,12 +964,13 @@ public class AnnotationLabels extends JPanel protected void showOrHideAdjuster(MouseEvent evt) { boolean was = resizePanel; - resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && 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(); } @@ -970,7 +1133,7 @@ public class AnnotationLabels extends JPanel seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(output), Desktop.instance); + .setContents(new StringSelection(output), Desktop.getInstance()); HiddenColumns hiddenColumns = null; @@ -980,20 +1143,12 @@ 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) { @@ -1001,7 +1156,7 @@ public class AnnotationLabels extends JPanel int width = getWidth(); if (width == 0) { - width = ap.calculateIdWidth().width + 4; + width = ap.calculateIdWidth().width; } Graphics2D g2 = (Graphics2D) g;