X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ba90075826c895ef2b0b2802963fd3fd9680c577;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=8449a530716e9b24bdddcc903a7759a1b1aaada9;hpb=3325395b33ef3b52b4a62327621c5bddf12ee4e0;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 8449a53..ba90075 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/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. * @@ -23,10 +23,13 @@ package jalview.appletgui; import jalview.analysis.AlignmentSorter; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; +import jalview.api.AlignViewportI; +import jalview.api.FeatureRenderer; import jalview.api.SequenceStructureBinding; import jalview.bin.JalviewLite; 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; @@ -61,6 +64,8 @@ import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.MappingUtils; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -88,9 +93,11 @@ import java.awt.event.WindowEvent; import java.io.IOException; import java.net.URL; import java.net.URLEncoder; -import java.util.Enumeration; +import java.util.Arrays; +import java.util.Deque; import java.util.Hashtable; import java.util.List; +import java.util.Map; import java.util.StringTokenizer; import java.util.Vector; @@ -109,9 +116,33 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, String jalviewServletURL; - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, + /** + * Constructor that creates the frame and adds it to the display. + * + * @param al + * @param applet + * @param title + * @param embedded + */ + public AlignFrame(AlignmentI al, JalviewLite applet, String title, boolean embedded) { + this(al, applet, title, embedded, true); + } + + /** + * Constructor that optionally allows the frame to be displayed or only + * created. + * + * @param al + * @param applet + * @param title + * @param embedded + * @param addToDisplay + */ + public AlignFrame(AlignmentI al, JalviewLite applet, + String title, boolean embedded, boolean addToDisplay) + { if (applet != null) { jalviewServletURL = applet.getParameter("APPLICATION_URL"); @@ -153,7 +184,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.updateConservation(alignPanel); viewport.updateConsensus(alignPanel); - annotationPanelMenuItem.setState(viewport.showAnnotation); + annotationPanelMenuItem.setState(viewport.isShowAnnotation()); displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); followMouseOverFlag.setState(viewport.getFollowHighlight()); showGroupConsensus.setState(viewport.isShowGroupConsensus()); @@ -163,7 +194,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); - seqLimits.setState(viewport.showJVSuffix); + seqLimits.setState(viewport.getShowJVSuffix()); if (applet != null) { @@ -229,8 +260,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.annotationPanelHolder.addKeyListener(this); alignPanel.annotationSpaceFillerHolder.addKeyListener(this); alignPanel.alabels.addKeyListener(this); - createAlignFrameWindow(embedded, title); + if (addToDisplay) + { + addToDisplay(embedded); + } + } + + /** + * @param embedded + */ + public void addToDisplay(boolean embedded) + { + createAlignFrameWindow(embedded); validate(); alignPanel.adjustAnnotationHeight(); alignPanel.paintAlignment(true); @@ -284,7 +326,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { featuresFile = new jalview.io.FeaturesFile(file, type) .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, featureLinks, + .getFeatureRenderer().getFeatureColours(), featureLinks, true, viewport.applet.getDefaultParameter( "relaxedidmatch", false)); } catch (Exception ex) @@ -300,9 +342,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (autoenabledisplay) { - viewport.showSequenceFeatures = true; + viewport.setShowSequenceFeatures(true); sequenceFeatures.setState(true); } + if (alignPanel.seqPanel.seqCanvas.fr != null) + { + // update the min/max ranges where necessary + alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + } if (viewport.featureSettings != null) { viewport.featureSettings.refreshTable(); @@ -489,7 +536,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } case KeyEvent.VK_PAGE_UP: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(true); } @@ -501,7 +548,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, break; case KeyEvent.VK_PAGE_DOWN: - if (viewport.wrapAlignment) + if (viewport.getWrapAlignment()) { alignPanel.scrollUp(false); } @@ -728,7 +775,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (evt.getSource() == sequenceFeatures) { - viewport.showSequenceFeatures(sequenceFeatures.getState()); + viewport.setShowSequenceFeatures(sequenceFeatures.getState()); alignPanel.seqPanel.seqCanvas.repaint(); } else if (evt.getSource() == conservationMenuItem) @@ -1098,6 +1145,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { new AnnotationColourChooser(viewport, alignPanel); } + else if (source == annotationColumnSelection) + { + new AnnotationColumnChooser(viewport, alignPanel); + } else if (source == sortPairwiseMenuItem) { sortPairwiseMenuItem_actionPerformed(); @@ -1168,11 +1219,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); cap.setText(new AppletFormatAdapter().formatSequences( e.getActionCommand(), viewport.getAlignment(), - viewport.showJVSuffix)); + viewport.getShowJVSuffix())); } public void loadAnnotations() @@ -1190,11 +1241,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public String outputAnnotations(boolean displayTextbox) { - String annotation = new AnnotationFile().printAnnotations( - viewport.showAnnotation ? viewport.getAlignment() - .getAlignmentAnnotation() : null, viewport - .getAlignment().getGroups(), ((Alignment) viewport - .getAlignment()).alignmentProperties); + String annotation = new AnnotationFile() + .printAnnotationsForView(viewport); if (displayTextbox) { @@ -1209,20 +1257,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return annotation; } - private Hashtable getDisplayedFeatureCols() + private Map getDisplayedFeatureCols() { if (alignPanel.getFeatureRenderer() != null - && viewport.featuresDisplayed != null) + && viewport.getFeaturesDisplayed()!= null) { - FeatureRenderer fr = alignPanel.getFeatureRenderer(); - Hashtable fcols = new Hashtable(); - Enumeration en = viewport.featuresDisplayed.keys(); - while (en.hasMoreElements()) - { - Object col = en.nextElement(); - fcols.put(col, fr.featureColours.get(col)); - } - return fcols; + return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); + } return null; } @@ -1277,7 +1318,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { StringBuffer url = new StringBuffer(jalviewServletURL); - url.append("?open=" + // allow servlet parameters to be passed in applet parameter + String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&" + : "?"; + url.append(firstSep); + + url.append("open=" + appendProtocol(viewport.applet.getParameter("file"))); if (viewport.applet.getParameter("features") != null) @@ -1395,12 +1441,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, void updateEditMenuBar() { - if (viewport.historyList.size() > 0) + if (viewport.getHistoryList().size() > 0) { undoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.historyList.peek(); + CommandI command = viewport.getHistoryList().peek(); undoMenuItem.setLabel(MessageManager.formatMessage( - "label.undo_command", new String[] + "label.undo_command", new Object[] { command.getDescription() })); } else @@ -1409,13 +1455,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, undoMenuItem.setLabel(MessageManager.getString("action.undo")); } - if (viewport.redoList.size() > 0) + if (viewport.getRedoList().size() > 0) { redoMenuItem.setEnabled(true); - CommandI command = (CommandI) viewport.redoList.peek(); + CommandI command = viewport.getRedoList().peek(); redoMenuItem.setLabel(MessageManager.formatMessage( - "label.redo_command", new String[] + "label.redo_command", new Object[] { command.getDescription() })); } else @@ -1428,12 +1474,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /** * TODO: JAL-1104 */ + @Override public void addHistoryItem(CommandI command) { if (command.getSize() > 0) { - viewport.historyList.push(command); - viewport.redoList.removeAllElements(); + viewport.addToHistoryList(command); + viewport.clearRedoList(); updateEditMenuBar(); viewport.updateHiddenColumns(); } @@ -1447,13 +1494,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, */ protected void undoMenuItem_actionPerformed() { - if (viewport.historyList.size() < 1) + if (viewport.getHistoryList().isEmpty()) { return; } - CommandI command = (CommandI) viewport.historyList.pop(); - viewport.redoList.push(command); + CommandI command = viewport.getHistoryList().pop(); + viewport.addToRedoList(command); command.undoCommand(null); AlignViewport originalSource = getOriginatingSource(command); @@ -1479,13 +1526,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, */ protected void redoMenuItem_actionPerformed() { - if (viewport.redoList.size() < 1) + if (viewport.getRedoList().isEmpty()) { return; } - CommandI command = (CommandI) viewport.redoList.pop(); - viewport.historyList.push(command); + CommandI command = viewport.getRedoList().pop(); + viewport.addToHistoryList(command); command.doCommand(null); AlignViewport originalSource = getOriginatingSource(command); @@ -1545,6 +1592,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return originalSource; } + /** + * Move the currently selected sequences up or down one position in the + * alignment + * + * @param up + */ public void moveSelectedSequences(boolean up) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -1555,6 +1608,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true); + + /* + * Also move cDNA/protein complement sequences + */ + AlignViewportI complement = viewport.getCodingComplement(); + if (complement != null) + { + SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg, + viewport, complement); + complement.getAlignment().moveSelectedSequencesByOne(mappedSelection, + up ? null : complement.getHiddenRepSequences(), up); + // TODO need to trigger a repaint of the complementary panel - how? + // would prefer to handle in SplitFrame but it is not overriding key + // listener chiz + } } synchronized void slideSequences(boolean right, int size) @@ -1642,11 +1710,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } boolean appendHistoryItem = false; - if (viewport.historyList != null && viewport.historyList.size() > 0 - && viewport.historyList.peek() instanceof SlideSequencesCommand) + Deque historyList = viewport.getHistoryList(); + if (historyList != null && historyList.size() > 0 + && historyList.peek() instanceof SlideSequencesCommand) { appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .appendSlideCommand((SlideSequencesCommand) historyList .peek()); } @@ -1686,12 +1755,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { copiedHiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() - .size(); i++) + for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) viewport.getColumnSelection() - .getHiddenColumns().elementAt(i); - copiedHiddenColumns.addElement(new int[] { region[0] - hiddenOffset, region[1] - hiddenOffset }); } @@ -1833,7 +1898,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // !newAlignment - addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE, + addHistoryItem(new EditCommand( + MessageManager.getString("label.add_sequences"), Action.PASTE, seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment())); @@ -1883,8 +1949,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /* * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand(MessageManager.getString("label.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); @@ -2253,8 +2320,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, newaf.setTitle(title.toString()); - newaf.viewport.historyList = viewport.historyList; - newaf.viewport.redoList = viewport.redoList; + newaf.viewport.setHistoryList(viewport.getHistoryList()); + newaf.viewport.setRedoList(viewport.getRedoList()); return newaf; } @@ -2268,7 +2335,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - return fr.getGroups(); + List gps = fr.getFeatureGroups(); + int p=0; + String[] _gps = new String[gps.size()]; + for (Object gp:gps) + { + _gps[p++] = gp.toString(); + } + return _gps; } return null; } @@ -2286,7 +2360,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - return fr.getGroups(visible); + List gps = fr.getGroups(visible); + int p=0; + String[] _gps = new String[gps.size()]; + for (Object gp:gps) + { + _gps[p++] = gp.toString(); + } + return _gps; } return null; } @@ -2303,11 +2384,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { FeatureRenderer fr = null; this.sequenceFeatures.setState(true); - viewport.showSequenceFeatures(true); + viewport.setShowSequenceFeatures(true); if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - fr.setGroupState(groups, state); + + fr.setGroupVisibility(Arrays.asList(groups), state); alignPanel.seqPanel.seqCanvas.repaint(); if (alignPanel.overviewPanel != null) { @@ -2331,7 +2413,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void displayNonconservedMenuItem_actionPerformed() { - viewport.setShowunconserved(displayNonconservedMenuItem.getState()); + viewport.setShowUnconserved(displayNonconservedMenuItem.getState()); alignPanel.paintAlignment(true); } @@ -3254,6 +3336,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, annotationColour.setLabel(MessageManager .getString("action.by_annotation")); annotationColour.addActionListener(this); + + annotationColumnSelection.setLabel("Select by Annotation"); + annotationColumnSelection.addActionListener(this); + invertSequenceMenuItem.setLabel(MessageManager .getString("action.invert_sequence_selection")); invertColSel.setLabel(MessageManager @@ -3442,6 +3528,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, selectMenu.add(unGroup); selectMenu.add(grpsFromSelection); selectMenu.add(deleteGroups); + selectMenu.add(annotationColumnSelection); } @@ -3456,6 +3543,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem annotationColour = new MenuItem(); + MenuItem annotationColumnSelection = new MenuItem(); + MenuItem invertColSel = new MenuItem(); Menu menu1 = new Menu(); @@ -3491,46 +3580,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * true to attach the view to the applet area on the page rather than * in a new window */ - public void createAlignFrameWindow(boolean reallyEmbedded, String title) + public void createAlignFrameWindow(boolean reallyEmbedded) { if (reallyEmbedded) { - // //// - // Explicly build the embedded menu panel for the on-page applet - // - // view cannot be closed if its actually on the page - fileMenu.remove(closeMenuItem); - fileMenu.remove(3); // Remove Seperator - embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", - Font.PLAIN, 11, false); // use our own fonts. - // and actually add the components to the applet area - viewport.applet.setLayout(new BorderLayout()); - viewport.applet.add(embeddedMenu, BorderLayout.NORTH); - viewport.applet.add(statusBar, BorderLayout.SOUTH); - alignPanel.setSize(viewport.applet.getSize().width, - viewport.applet.getSize().height - embeddedMenu.HEIGHT - - statusBar.HEIGHT); - viewport.applet.add(alignPanel, BorderLayout.CENTER); - final AlignFrame me = this; - viewport.applet.addFocusListener(new FocusListener() - { - - @Override - public void focusLost(FocusEvent e) - { - if (me.viewport.applet.currentAlignFrame == me) - { - me.viewport.applet.currentAlignFrame = null; - } - } - - @Override - public void focusGained(FocusEvent e) - { - me.viewport.applet.currentAlignFrame = me; - } - }); - viewport.applet.validate(); + embedAlignFrameInApplet(viewport.applet); } else { @@ -3539,19 +3593,69 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // if (embedMenuIfNeeded(alignPanel)) { - // adjust for status bar height too - alignPanel.setSize(getSize().width, getSize().height - - statusBar.HEIGHT); + /* + * adjust for status bar height too. ? pointless as overridden by layout + * manager + */ + alignPanel.setSize(getSize().width, + getSize().height - statusBar.getHeight()); } add(statusBar, BorderLayout.SOUTH); add(alignPanel, BorderLayout.CENTER); // and register with the applet so it can pass external API calls to us - jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + jalview.bin.JalviewLite.addFrame(this, this.getTitle(), + DEFAULT_WIDTH, DEFAULT_HEIGHT); } } /** + * Add the components of this AlignFrame to the applet container. + * + * @param theApplet + */ + public void embedAlignFrameInApplet(final JalviewLite theApplet) + { + // //// + // Explicitly build the embedded menu panel for the on-page applet + // + // view cannot be closed if its actually on the page + fileMenu.remove(closeMenuItem); + fileMenu.remove(3); // Remove Separator + // construct embedded menu, using default font + embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false); + // and actually add the components to the applet area + theApplet.setLayout(new BorderLayout()); + theApplet.add(embeddedMenu, BorderLayout.NORTH); + theApplet.add(statusBar, BorderLayout.SOUTH); + // TODO should size be left to the layout manager? + alignPanel.setSize(theApplet.getSize().width, + theApplet.getSize().height - embeddedMenu.getHeight() + - statusBar.getHeight()); + theApplet.add(alignPanel, BorderLayout.CENTER); + final AlignFrame me = this; + theApplet.addFocusListener(new FocusListener() + { + + @Override + public void focusLost(FocusEvent e) + { + if (theApplet.currentAlignFrame == me) + { + theApplet.currentAlignFrame = null; + } + } + + @Override + public void focusGained(FocusEvent e) + { + theApplet.currentAlignFrame = me; + } + }); + theApplet.validate(); + } + + /** * create a new binding between structures in an existing jmol viewer instance * and an alignpanel with sequences that have existing PDBFile entries. Note, * this does not open a new Jmol window, or modify the display of the @@ -3612,7 +3716,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return null; } } - ExtJmol jmv = null; + AAStructureBindingModel jmv = null; // TODO: search for a jmv that involves viewer if (jmv == null) { // create a new viewer/jalview binding. @@ -3684,6 +3788,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } pdbentry.getProperty().put("protocol", protocol); toaddpdb.addPDBId(pdbentry); + alignPanel.getStructureSelectionManager() + .registerPDBEntry(pdbentry); } } return true;