X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2133f50cb755cbc33ea0307e3093d3a99b6a8377;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=e6b7af495fa3cf0d4bb278e0e2706f12cdd81dc4;hpb=25bf7406cdf030f4b5d87d3e93d0fd769d956b19;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e6b7af4..2133f50 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -30,10 +30,12 @@ import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; +import jalview.api.AlignmentViewPanel; import jalview.api.analysis.ScoreModelI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; import jalview.commands.OrderCommand; import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; @@ -53,10 +55,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; +import jalview.io.BioJsHTMLOutput; import jalview.io.FeaturesFile; import jalview.io.FileLoader; import jalview.io.FormatAdapter; -import jalview.io.HTMLOutput; +import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -114,6 +117,7 @@ import java.beans.PropertyChangeEvent; import java.io.File; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; @@ -279,7 +283,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Make a new AlignFrame from exisiting alignmentPanels + * Make a new AlignFrame from existing alignmentPanels * * @param ap * AlignmentPanel @@ -334,6 +338,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); + if (viewport.wrapAlignment) { wrapMenuItem_actionPerformed(null); @@ -376,7 +381,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt .getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + { + alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); + } switch (evt.getKeyCode()) { @@ -388,38 +395,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_DOWN: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(false); + } if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(0, 1); + { + alignPanel.getSeqPanel().moveCursor(0, 1); + } break; case KeyEvent.VK_UP: if (evt.isAltDown() || !viewport.cursorMode) + { moveSelectedSequences(true); + } if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(0, -1); + { + alignPanel.getSeqPanel().moveCursor(0, -1); + } break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + { + slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); + } else - alignPanel.seqPanel.moveCursor(-1, 0); + { + alignPanel.getSeqPanel().moveCursor(-1, 0); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) - slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + { + slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1()); + } else - alignPanel.seqPanel.moveCursor(1, 0); + { + alignPanel.getSeqPanel().moveCursor(1, 0); + } break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } break; @@ -443,7 +466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } @@ -452,19 +475,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_S: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRow(); + alignPanel.getSeqPanel().setCursorRow(); } break; case KeyEvent.VK_C: if (viewport.cursorMode && !evt.isControlDown()) { - alignPanel.seqPanel.setCursorColumn(); + alignPanel.getSeqPanel().setCursorColumn(); } break; case KeyEvent.VK_P: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorPosition(); + alignPanel.getSeqPanel().setCursorPosition(); } break; @@ -472,20 +495,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_COMMA: if (viewport.cursorMode) { - alignPanel.seqPanel.setCursorRowAndColumn(); + alignPanel.getSeqPanel().setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(true); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: if (viewport.cursorMode) { - alignPanel.seqPanel.setSelectionAreaAtCursor(false); + alignPanel.getSeqPanel().setSelectionAreaAtCursor(false); } break; @@ -496,23 +519,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes; + alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq; } - alignPanel.seqPanel.seqCanvas.repaint(); + alignPanel.getSeqPanel().seqCanvas.repaint(); break; case KeyEvent.VK_F1: try { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, - "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); - - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setCurrentID("home"); - hb.setDisplayed(true); + Help.showHelpWindow(); } catch (Exception ex) { ex.printStackTrace(); @@ -557,14 +573,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) + { viewport.firePropertyChange("alignment", null, viewport .getAlignment().getSequences()); + } break; } } @@ -721,14 +741,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); seqLimits.setSelected(av.getShowJVSuffix()); - idRightAlign.setSelected(av.rightAlignIds); + idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.centreColumnLabels); renderGapsMenuItem.setSelected(av.renderGaps); wrapMenuItem.setSelected(av.wrapAlignment); scaleAbove.setVisible(av.wrapAlignment); scaleLeft.setVisible(av.wrapAlignment); scaleRight.setVisible(av.wrapAlignment); - annotationPanelMenuItem.setState(av.showAnnotation); + annotationPanelMenuItem.setState(av.isShowAnnotation()); + /* + * Show/hide annotations only enabled if annotation panel is shown + */ + showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState()); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); @@ -741,7 +768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); - showSeqFeatures.setSelected(av.showSequenceFeatures); + showSeqFeatures.setSelected(av.isShowSequenceFeatures()); hiddenMarkers.setState(av.showHiddenMarkers); applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); @@ -819,8 +846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { - throw new Error( - "call setProgressBar before registering the progress bar's handler."); + throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); @@ -836,10 +862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar( - "Cancelled " - + ((JLabel) progressPanel.getComponent(0)) - .getText(), id); + us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -876,7 +899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureRenderer getFeatureRenderer() { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer(); } @Override @@ -1002,7 +1025,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); + chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -1053,10 +1076,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().SaveAlignment(this, file, shortName); + /* + * First save any linked Chimera session. + */ + Desktop.instance.saveChimeraSessions(file); + + success = new Jalview2XML().saveAlignment(this, file, shortName); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new String[] + "label.successfully_saved_to_file_in_format", new Object[] { fileName, format })); } @@ -1207,11 +1235,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, - alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + // new HTMLOutput(alignPanel, + // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(), + // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + new HtmlSvgOutput(null, alignPanel); } + @Override + public void bioJSMenuItem_actionPerformed(ActionEvent e) + { + new BioJsHTMLOutput(alignPanel, + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); + } public void createImageMap(File file, String image) { alignPanel.makePNGImageMap(file, image); @@ -1241,6 +1276,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.makeEPS(f); } + public void createSVG(File f) + { + alignPanel.makeSVG(f); + } @Override public void pageSetup_actionPerformed(ActionEvent e) { @@ -1271,11 +1310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel, - viewport.showAnnotation ? viewport.getAlignment() - .getAlignmentAnnotation() : null, viewport - .getAlignment().getGroups(), ((Alignment) viewport - .getAlignment()).alignmentProperties); + new AnnotationExporter().exportAnnotations(alignPanel); } @Override @@ -1387,7 +1422,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.historyList.peek(); + CommandI command = viewport.historyList.peek(); undoMenuItem.setText(MessageManager.formatMessage( "label.undo_command", new String[] { command.getDescription() })); @@ -1402,7 +1437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { redoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.redoList.peek(); + CommandI command = viewport.redoList.peek(); redoMenuItem.setText(MessageManager.formatMessage( "label.redo_command", new String[] { command.getDescription() })); @@ -1463,8 +1498,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) + { return; - CommandI command = (CommandI) viewport.historyList.pop(); + } + CommandI command = viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(getViewAlignments()); @@ -1503,7 +1540,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - CommandI command = (CommandI) viewport.redoList.pop(); + CommandI command = viewport.redoList.pop(); viewport.historyList.push(command); command.doCommand(getViewAlignments()); @@ -1596,7 +1633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.cursorMode) { sg.add(viewport.getAlignment().getSequenceAt( - alignPanel.seqPanel.seqCanvas.cursorY)); + alignPanel.getSeqPanel().seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() != viewport @@ -1616,37 +1653,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + { invertGroup.add(viewport.getAlignment().getSequenceAt(i)); + } } SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) + { seqs2[i] = (SequenceI) invertGroup.elementAt(i); + } SlideSequencesCommand ssc; if (right) + { ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, viewport.getGapCharacter()); + } else + { ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, viewport.getGapCharacter()); + } int groupAdjustment = 0; if (ssc.getGapsInsertedBegin() && right) { if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(size, 0); + { + alignPanel.getSeqPanel().moveCursor(size, 0); + } else + { groupAdjustment = size; + } } else if (!ssc.getGapsInsertedBegin() && !right) { if (viewport.cursorMode) - alignPanel.seqPanel.moveCursor(-size, 0); + { + alignPanel.getSeqPanel().moveCursor(-size, 0); + } else + { groupAdjustment = -size; + } } if (groupAdjustment != 0) @@ -1667,7 +1720,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (!appendHistoryItem) + { addHistoryItem(ssc); + } repaint(); } @@ -1717,20 +1772,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector hiddenColumns = null; + ArrayList hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new Vector(); + hiddenColumns = new ArrayList(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport .getSelectionGroup().getEndRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) { - hiddenColumns.addElement(new int[] + hiddenColumns.add(new int[] { region[0] - hiddenOffset, region[1] - hiddenOffset }); } } @@ -1947,7 +1999,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // ///// // ADD HISTORY ITEM // - addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), + Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences @@ -2002,7 +2056,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignmentAnnotation sann[] = sequences[i].getAnnotation(); if (sann == null) + { continue; + } for (int avnum = 0; avnum < alview.length; avnum++) { if (alview[avnum] != alignment) @@ -2053,19 +2109,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int[] region : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2113,19 +2168,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + List hc = (List) Desktop.jalviewClipboard[2]; + for (int region[] : hc) { - int[] region = (int[]) hc.elementAt(i); af.viewport.hideColumns(region[0], region[1]); } } // >>>This is a fix for the moment, until a better solution is // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2182,17 +2236,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector seqs = new Vector(); + List seqs = new ArrayList(sg.getSize()); SequenceI seq; for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); - seqs.addElement(seq); + seqs.add(seq); } - // If the cut affects all sequences, remove highlighted columns + // If the cut affects all sequences, warn, remove highlighted columns if (sg.getSize() == viewport.getAlignment().getHeight()) { + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); + + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } @@ -2200,14 +2264,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] cut = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { - cut[i] = (SequenceI) seqs.elementAt(i); + cut[i] = seqs.get(i); } /* * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, - sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.getAlignment())); viewport.setSelectionGroup(null); @@ -2278,14 +2343,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.cursorMode) { - alignPanel.seqPanel.keyboardNo1 = null; - alignPanel.seqPanel.keyboardNo2 = null; + alignPanel.getSeqPanel().keyboardNo1 = null; + alignPanel.getSeqPanel().keyboardNo2 = null; } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null); + alignPanel.getIdPanel().getIdCanvas().searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); @@ -2610,7 +2675,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { - viewTitle = "View"; + viewTitle = MessageManager.getString("action.view"); addFirstIndex = true; } else @@ -2686,7 +2751,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowJVSuffix(seqLimits.isSelected()); - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel + alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel .calculateIdWidth()); alignPanel.paintAlignment(true); } @@ -2694,7 +2759,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void idRightAlign_actionPerformed(ActionEvent e) { - viewport.rightAlignIds = idRightAlign.isSelected(); + viewport.setRightAlignIds(idRightAlign.isSelected()); alignPanel.paintAlignment(true); } @@ -2716,7 +2781,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { alignPanel.scrollToPosition( - alignPanel.seqPanel.seqCanvas.searchResults, false); + alignPanel.getSeqPanel().seqCanvas.searchResults, false); } } @@ -3023,7 +3088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight .isSelected()); - if (viewport.getShowSequenceFeaturesHeight()) + if (viewport.isShowSequenceFeaturesHeight()) { // ensure we're actually displaying features viewport.setShowSequenceFeatures(true); @@ -3037,16 +3102,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Action on toggle of the 'Show annotations' menu item. This shows or hides + * the annotations panel as a whole. + * + * The options to show/hide all annotations should be enabled when the panel + * is shown, and disabled when the panel is hidden. * * @param e - * DOCUMENT ME! */ @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); + final boolean setVisible = annotationPanelMenuItem.isSelected(); + viewport.setShowAnnotation(setVisible); + alignPanel.setAnnotationVisible(setVisible); + this.showAllSeqAnnotations.setEnabled(setVisible); + this.hideAllSeqAnnotations.setEnabled(setVisible); + this.showAllAlAnnotations.setEnabled(setVisible); + this.hideAllAlAnnotations.setEnabled(setVisible); } @Override @@ -3248,6 +3321,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override + public void annotationColumn_actionPerformed(ActionEvent e) + { + new AnnotationColumnChooser(viewport, alignPanel); + } + + @Override public void rnahelicesColour_actionPerformed(ActionEvent e) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -3888,7 +3967,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem("by " + title); + final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title})); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @@ -4025,6 +4104,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tm.setText(title);// tm.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { NewTreePanel(type, (String) pwtype, title); @@ -4116,16 +4196,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ msa = viewport.getAlignmentView(true); } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() == 1) + { + int option = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.oneseq_msainput_selection"), + MessageManager.getString("label.invalid_selection"), + JOptionPane.OK_CANCEL_OPTION); + if (option == JOptionPane.OK_OPTION) + { + msa = viewport.getAlignmentView(false); + } + } else { - /* - * Vector seqs = viewport.getAlignment().getSequences(); - * - * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * - * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) - * seqs.elementAt(i); } } - */ msa = viewport.getAlignmentView(false); } return msa; @@ -4337,6 +4421,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); + // final JMenu msawsmenu = new + // JMenu(MessageManager.getString("label.alignment")); + // final JMenu secstrmenu = new + // JMenu(MessageManager.getString("label.secondary_structure_prediction")); + // final JMenu seqsrchmenu = new + // JMenu(MessageManager.getString("label.sequence_database_search")); + // final JMenu analymenu = new + // JMenu(MessageManager.getString("label.analysis")); + // final JMenu dismenu = new + // JMenu(MessageManager.getString("label.protein_disorder")); // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) @@ -4603,7 +4697,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void run() { final long sttime = System.currentTimeMillis(); - ths.setProgressBar("Searching for sequences from " + fsrc, sttime); + ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime); try { Alignment ds = ths.getViewport().getAlignment().getDataset(); // update @@ -4621,7 +4715,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (ds.getSequences() == null || !ds.getSequences().contains( sprods[s].getDatasetSequence())) + { ds.addSequence(sprods[s].getDatasetSequence()); + } sprods[s].updatePDBIds(); } Alignment al = new Alignment(sprods); @@ -4657,7 +4753,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.bin.Cache.log.error("Error when finding crossreferences", e); } - ths.setProgressBar("Finished searching for sequences from " + fsrc, + ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}), sttime); } @@ -4787,8 +4883,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, try { featuresFile = new FeaturesFile(file, type).parse(viewport - .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, false, + .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer().getFeatureColours(), false, jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { @@ -4797,12 +4893,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (featuresFile) { - viewport.showSequenceFeatures = true; + viewport.setShowSequenceFeatures(true); showSeqFeatures.setSelected(true); - if (alignPanel.seqPanel.seqCanvas.fr != null) + if (alignPanel.getSeqPanel().seqCanvas.fr != null) { // update the min/max ranges where necessary - alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true); } if (featureSettings != null) { @@ -4983,7 +5079,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq((String) fm[0], - (String) fm[1], toassoc, false); + (String) fm[1], toassoc, false, + Desktop.instance); if (pe != null) { System.err.println("Associated file : " @@ -5003,14 +5100,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane .showConfirmDialog( this, - MessageManager + ""+MessageManager .formatMessage( "label.ignore_unmatched_dropped_files_info", new String[] { Integer.valueOf( filesnotmatched .size()) - .toString() }), + .toString() })+"", MessageManager .getString("label.ignore_unmatched_dropped_files"), JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) @@ -5053,7 +5150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse as annotation. boolean isAnnotation = (format == null || format .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .readAnnotationFile(viewport.getAlignment(), file, protocol) + .annotateAlignmentView(viewport, file, protocol) : false; if (!isAnnotation) @@ -5313,6 +5410,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); trimrs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); @@ -5416,9 +5514,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText("" - + JvSwingUtils.wrapTooltip("Retrieve from " - + src.getDbName()) + ""); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()}))); dfetch.add(fetchr); comp++; } @@ -5451,15 +5547,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText("" - + JvSwingUtils.wrapTooltip("Retrieve from all " - + otherdb.size() + " sources in " - + src.getDbSource() + "
First is :" - + src.getDbName()) + ""); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()}))); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus - ifetch = new JMenu("Sources from " + src.getDbSource()); + ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()})); icomp = 0; String imname = null; int i = 0; @@ -5472,7 +5564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 0, 10) + "..." : dbname; if (imname == null) { - imname = "from '" + sname + "'"; + imname = MessageManager.formatMessage("label.from_msname", new String[]{sname}); } fetchr = new JMenuItem(msname); final DbSourceProxy[] dassrc = @@ -5499,8 +5591,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText("" - + JvSwingUtils.wrapTooltip("Retrieve from " - + dbname) + ""); + + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname})); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) @@ -5664,6 +5755,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } } + public void clearAlignmentSeqRep() + { + // TODO refactor alignmentseqrep to controller + if (viewport.getAlignment().hasSeqrep()) { + viewport.getAlignment().setSeqrep(null); + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } @Override protected void createGroup_actionPerformed(ActionEvent e) @@ -5693,8 +5794,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!viewport.getSequenceSetId().equals( alignmentPanel.av.getSequenceSetId())) { - throw new Error( - "Implementation error: cannot show a view from another alignment in an AlignFrame."); + throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame")); } if (tabbedPane != null & alignPanels.indexOf(alignmentPanel) != tabbedPane @@ -5703,6 +5803,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } } + + /** + * Action on selection of menu options to Show or Hide annotations. + * + * @param visible + * @param forSequences + * update sequence-related annotations + * @param forAlignment + * update non-sequence-related annotations + */ + @Override + protected void setAnnotationsVisibility(boolean visible, + boolean forSequences, boolean forAlignment) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + boolean apply = (aa.sequenceRef == null && forAlignment) + || (aa.sequenceRef != null && forSequences); + if (apply) + { + aa.visible = visible; + } + } + alignPanel.validateAnnotationDimensions(false); + alignPanel.alignmentChanged(); + } + + /** + * Store selected annotation sort order for the view and repaint. + */ + @Override + protected void sortAnnotations_actionPerformed() + { + this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); + this.alignPanel.av + .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); + alignPanel.paintAlignment(true); + } + + /** + * + * @return alignment panels in this alignemnt frame + */ + public List getAlignPanels() + { + return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + } } class PrintThread extends Thread