X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=122afa8664df4b4874db5c4e4f3405ae90626b4f;hb=8546ee20c998cd48567d324027d1885a771e688f;hp=3e919f65c0e2b471d0e3faa4460b0cc099b9090a;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 3e919f6..122afa8 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -20,46 +20,14 @@ */ package jalview.appletgui; -import java.awt.BorderLayout; -import java.awt.Canvas; -import java.awt.CheckboxMenuItem; -import java.awt.Color; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Frame; -import java.awt.Graphics; -import java.awt.Label; -import java.awt.Menu; -import java.awt.MenuBar; -import java.awt.MenuItem; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.FocusEvent; -import java.awt.event.FocusListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyEvent; -import java.awt.event.KeyListener; -import java.awt.event.WindowAdapter; -import java.awt.event.WindowEvent; -import java.io.IOException; -import java.net.URL; -import java.net.URLEncoder; -import java.util.Arrays; -import java.util.Deque; -import java.util.HashMap; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; -import java.util.StringTokenizer; -import java.util.Vector; - import jalview.analysis.AlignmentSorter; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; import jalview.api.FeatureRenderer; +import jalview.api.FeatureSettingsControllerI; import jalview.api.SequenceStructureBinding; import jalview.bin.JalviewLite; import jalview.commands.CommandI; @@ -93,7 +61,6 @@ import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.RNAHelicesColourChooser; -import jalview.schemes.RNAInteractionColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; @@ -103,6 +70,44 @@ import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.Canvas; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.IOException; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Arrays; +import java.util.Deque; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; + +import org.jmol.viewer.Viewer; public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener, AlignViewControllerGuiI @@ -113,9 +118,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public AlignViewport viewport; - int DEFAULT_WIDTH = 700; + // width and height may be overridden by applet parameters + int frameWidth = 700; - int DEFAULT_HEIGHT = 500; + int frameHeight = 500; String jalviewServletURL; @@ -135,8 +141,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * @param title * @param embedded */ - public AlignFrame(AlignmentI al, JalviewLite applet, - String title, boolean embedded) + public AlignFrame(AlignmentI al, JalviewLite applet, String title, + boolean embedded) { this(al, applet, title, embedded, true); } @@ -151,7 +157,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * @param embedded * @param addToDisplay */ - public AlignFrame(AlignmentI al, JalviewLite applet, + public AlignFrame(AlignmentI al, JalviewLite applet, String title, + boolean embedded, boolean addToDisplay) + { + this(al, null, null, applet, title, embedded, addToDisplay); + } + + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection columnSelection, JalviewLite applet, + String title, boolean embedded) + { + this(al, hiddenSeqs, columnSelection, applet, title, embedded, true); + } + + public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs, + ColumnSelection columnSelection, JalviewLite applet, String title, boolean embedded, boolean addToDisplay) { if (applet != null) @@ -176,19 +196,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (param != null) { int width = Integer.parseInt(param); - DEFAULT_WIDTH = width; + frameWidth = width; } param = applet.getParameter("windowHeight"); if (param != null) { int height = Integer.parseInt(param); - DEFAULT_HEIGHT = height; + frameHeight = height; } } catch (Exception ex) { } } viewport = new AlignViewport(al, applet); + + if (hiddenSeqs != null && hiddenSeqs.length > 0) + { + viewport.hideSequence(hiddenSeqs); + } + if (columnSelection != null) + { + viewport.setColumnSelection(columnSelection); + } + viewport.setScaleAboveWrapped(scaleAbove.getState()); + alignPanel = new AlignmentPanel(this, viewport); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); @@ -196,15 +227,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.updateConsensus(alignPanel); displayNonconservedMenuItem.setState(viewport.getShowUnconserved()); - followMouseOverFlag.setState(viewport.getFollowHighlight()); + followMouseOverFlag.setState(viewport.isFollowHighlight()); showGroupConsensus.setState(viewport.isShowGroupConsensus()); showGroupConservation.setState(viewport.isShowGroupConservation()); showConsensusHistogram.setState(viewport.isShowConsensusHistogram()); showSequenceLogo.setState(viewport.isShowSequenceLogo()); normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); - showAlignmentAnnotations.setState(viewport.isShowAnnotation()); - showSequenceAnnotations.setState(viewport.isShowAnnotation()); + annotationPanelMenuItem.setState(viewport.isShowAnnotation()); + showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAlignmentAnnotations.setState(true); + showSequenceAnnotations.setState(false); seqLimits.setState(viewport.getShowJVSuffix()); @@ -273,6 +307,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.annotationSpaceFillerHolder.addKeyListener(this); alignPanel.alabels.addKeyListener(this); + setAnnotationsVisibility(); + if (addToDisplay) { addToDisplay(embedded); @@ -329,18 +365,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay) { - // TODO: test if importing a features file onto an alignment which already - // has features with links overwrites the original links. - - Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; try { - featuresFile = new jalview.io.FeaturesFile(file, type) - .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().getFeatureColours(), featureLinks, - true, viewport.applet.getDefaultParameter( - "relaxedidmatch", false)); + Map colours = alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().getFeatureColours(); + boolean relaxedIdMatching = viewport.applet.getDefaultParameter( + "relaxedidmatch", false); + featuresFile = new FeaturesFile(file, type).parse( + viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { ex.printStackTrace(); @@ -348,10 +381,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (featuresFile) { - if (featureLinks.size() > 0) - { - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; - } if (autoenabledisplay) { viewport.setShowSequenceFeatures(true); @@ -523,8 +552,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; statusBar.setText(MessageManager.formatMessage( - "label.keyboard_editing_mode", new String[] - { (viewport.cursorMode ? "on" : "off") })); + "label.keyboard_editing_mode", + new String[] { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; @@ -673,9 +702,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. - if ((viewport.getColumnSelection() != null - && viewport.getColumnSelection().getSelected() != null && viewport - .getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -703,8 +730,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hide = true; viewport.hideAllSelectedSeqs(); } - else if (!(toggleCols && viewport.getColumnSelection().getSelected() - .size() > 0)) + else if (!(toggleCols && viewport.hasSelectedColumns())) { viewport.showAllHiddenSeqs(); } @@ -712,7 +738,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { viewport.hideSelectedColumns(); if (!toggleSeqs) @@ -724,6 +750,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.showAllHiddenColumns(); } + viewport.sendSelection(); } } @@ -783,8 +810,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (source == annotationPanelMenuItem) { - viewport.setShowAnnotation(annotationPanelMenuItem.getState()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + boolean showAnnotations = annotationPanelMenuItem.getState(); + showAlignmentAnnotations.setEnabled(showAnnotations); + showSequenceAnnotations.setEnabled(showAnnotations); + viewport.setShowAnnotation(showAnnotations); + alignPanel.setAnnotationVisible(showAnnotations); } else if (source == sequenceFeatures) { @@ -884,7 +914,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /** * Set the visibility state of sequence-related and/or alignment-related - * annotations depending on checkbox selections. Repaint after calling. + * annotations depending on checkbox selections, and repaint. * * @param visible */ @@ -892,14 +922,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { boolean showForAlignment = showAlignmentAnnotations.getState(); boolean showForSequences = showSequenceAnnotations.getState(); - for (AlignmentAnnotation aa : alignPanel.getAlignment() - .getAlignmentAnnotation()) + if (alignPanel.getAlignment().getAlignmentAnnotation() != null) { - boolean visible = (aa.sequenceRef == null ? showForAlignment - : showForSequences); + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + boolean visible = (aa.sequenceRef == null ? showForAlignment + : showForSequences); aa.visible = visible; + } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); + validate(); + repaint(); } private void setAnnotationSortOrder(SequenceAnnotationOrder order) @@ -924,7 +959,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, private void mouseOverFlag_stateChanged() { - viewport.followHighlight = followMouseOverFlag.getState(); + viewport.setFollowHighlight(followMouseOverFlag.getState()); // TODO: could kick the scrollTo mechanism to reset view for current // searchresults. } @@ -938,6 +973,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, @Override public void actionPerformed(ActionEvent evt) { + viewport.applet.currentAlignFrame = this; + Object source = evt.getSource(); if (source == inputText) @@ -1035,11 +1072,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, else if (source == invertSequenceMenuItem) { invertSequenceMenuItem_actionPerformed(); + // uncomment to slave sequence selections in split frame + // viewport.sendSelection(); } else if (source == invertColSel) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == remove2LeftMenuItem) { @@ -1073,27 +1113,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.showAllHiddenColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == showSeqs) { viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + // uncomment if we want to slave sequence selections in split frame + // viewport.sendSelection(); } else if (source == hideColumns) { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == hideSequences && viewport.getSelectionGroup() != null) { viewport.hideAllSelectedSeqs(); alignPanel.paintAlignment(true); + // uncomment if we want to slave sequence selections in split frame + // viewport.sendSelection(); } else if (source == hideAllButSelection) { toggleHiddenRegions(false, false); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == hideAllSelection) { @@ -1102,12 +1149,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == showAllHidden) { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } else if (source == showGroupConsensus) { @@ -1146,8 +1195,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new String[] - { getTitle() }), 400, 250); + "label.alignment_properties", new String[] { getTitle() }), + 400, 250); } else if (source == overviewMenuItem) { @@ -1198,10 +1247,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new PurinePyrimidineColourScheme()); } - else if (source == RNAInteractionColour) - { - changeColour(new RNAInteractionColourScheme()); - } + // else if (source == RNAInteractionColour) + // { + // changeColour(new RNAInteractionColourScheme()); + // } else if (source == RNAHelixColour) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -1308,9 +1357,11 @@ 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 Object[] - { e.getActionCommand() }), 600, 500); - cap.setText(new AppletFormatAdapter().formatSequences( + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); + + FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer(); + cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( e.getActionCommand(), viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -1346,13 +1397,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return annotation; } - private Map getDisplayedFeatureCols() + private Map getDisplayedFeatureCols() { if (alignPanel.getFeatureRenderer() != null - && viewport.getFeaturesDisplayed()!= null) + && viewport.getFeaturesDisplayed() != null) { return alignPanel.getFeatureRenderer().getDisplayedFeatureCols(); - + } return null; } @@ -1360,15 +1411,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public String outputFeatures(boolean displayTextbox, String format) { String features; + FeaturesFile formatter = new FeaturesFile(); if (format.equalsIgnoreCase("Jalview")) { - features = new FeaturesFile().printJalviewFormat(viewport - .getAlignment().getSequencesArray(), - getDisplayedFeatureCols()); + features = formatter.printJalviewFormat(viewport.getAlignment() + .getSequencesArray(), getDisplayedFeatureCols()); } else { - features = new FeaturesFile().printGFFFormat(viewport.getAlignment() + features = formatter.printGffFormat(viewport.getAlignment() .getSequencesArray(), getDisplayedFeatureCols()); } @@ -1535,8 +1586,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, undoMenuItem.setEnabled(true); CommandI command = viewport.getHistoryList().peek(); undoMenuItem.setLabel(MessageManager.formatMessage( - "label.undo_command", new Object[] - { command.getDescription() })); + "label.undo_command", + new Object[] { command.getDescription() })); } else { @@ -1550,8 +1601,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CommandI command = viewport.getRedoList().peek(); redoMenuItem.setLabel(MessageManager.formatMessage( - "label.redo_command", new Object[] - { command.getDescription() })); + "label.redo_command", + new Object[] { command.getDescription() })); } else { @@ -1592,7 +1643,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.addToRedoList(command); command.undoCommand(null); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); // JBPNote Test if (originalSource != viewport) { @@ -1624,7 +1675,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.addToHistoryList(command); command.doCommand(null); - AlignViewport originalSource = getOriginatingSource(command); + AlignmentViewport originalSource = getOriginatingSource(command); // JBPNote Test if (originalSource != viewport) { @@ -1640,9 +1691,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getAlignment().getSequences()); } - AlignViewport getOriginatingSource(CommandI command) + AlignmentViewport getOriginatingSource(CommandI command) { - AlignViewport originalSource = null; + AlignmentViewport originalSource = null; // For sequence removal and addition, we need to fire // the property change event FROM the viewport where the // original alignment was altered @@ -1708,9 +1759,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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 + getSplitFrame().getComplement(this).alignPanel.paintAlignment(true); } } @@ -1846,8 +1895,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, int hiddenOffset = viewport.getSelectionGroup().getStartRes(); for (int[] region : viewport.getColumnSelection().getHiddenColumns()) { - copiedHiddenColumns.addElement(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); + copiedHiddenColumns.addElement(new int[] { + region[0] - hiddenOffset, region[1] - hiddenOffset }); } } else @@ -1944,14 +1993,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (newAlignment) { - String newtitle = MessageManager.getString("label.copied_sequences"); - if (getTitle().startsWith(MessageManager.getString("label.copied_sequences"))) + String newtitle = MessageManager + .getString("label.copied_sequences"); + if (getTitle().startsWith( + MessageManager.getString("label.copied_sequences"))) { newtitle = getTitle(); } else { - newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()})); + newtitle = newtitle.concat(MessageManager.formatMessage( + "label.from_msname", new String[] { getTitle() })); } AlignFrame af = new AlignFrame(new Alignment(newSeqs), viewport.applet, newtitle, false); @@ -1964,8 +2016,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } - jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth, + frameHeight); } else { @@ -2021,9 +2073,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, seqs.addElement(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()) { + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport + .getAlignment().getWidth()) ? true : false; + if (isEntireAlignWidth) + { + String title = MessageManager.getString("label.delete_all"); + Panel infoPanel = new Panel(); + infoPanel.setLayout(new FlowLayout()); + infoPanel + .add(new Label(MessageManager.getString("warn.delete_all"))); + + final JVDialog dialog = new JVDialog(this, title, true, 400, 200); + dialog.setMainPanel(infoPanel); + dialog.ok.setLabel(MessageManager.getString("action.ok")); + dialog.cancel.setLabel(MessageManager.getString("action.cancel")); + dialog.setVisible(true); + + if (!dialog.accept) + { + return; + } + } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } @@ -2154,7 +2229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2171,7 +2249,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewport.setSelectionGroup(null); alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.paintAlignment(true); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + alignPanel.paintAlignment(false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2201,7 +2282,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2226,23 +2307,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, TrimRegionCommand trimRegion; if (trimLeft) { - trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Left", true, seqs, + column, viewport.getAlignment()); viewport.setStartRes(0); } else { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.getAlignment(), viewport.getColumnSelection(), - viewport.getSelectionGroup()); + trimRegion = new TrimRegionCommand("Remove Right", false, seqs, + column, viewport.getAlignment()); } statusBar.setText(MessageManager.formatMessage( - "label.removed_columns", new String[] - { Integer.valueOf(trimRegion.getSize()).toString() })); + "label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()) + .toString() })); addHistoryItem(trimRegion); for (SequenceGroup sg : viewport.getAlignment().getGroups()) @@ -2283,8 +2361,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, addHistoryItem(removeGapCols); statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", new String[] - { Integer.valueOf(removeGapCols.getSize()).toString() })); + "label.removed_empty_columns", + new String[] { Integer.valueOf(removeGapCols.getSize()) + .toString() })); // This is to maintain viewport position on first residue // of first sequence @@ -2466,7 +2545,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (alignPanel != null && (fr = alignPanel.getFeatureRenderer()) != null) { - + fr.setGroupVisibility(Arrays.asList(groups), state); alignPanel.seqPanel.seqCanvas.repaint(); if (alignPanel.overviewPanel != null) @@ -2517,8 +2596,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, frame.add(overview); // +50 must allow for applet frame window jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.overview_params", new String[] - { this.getTitle() }), overview.getPreferredSize().width, + "label.overview_params", new String[] { this.getTitle() }), + overview.getPreferredSize().width, overview.getPreferredSize().height + 50); frame.pack(); @@ -2539,9 +2618,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } - void changeColour(ColourSchemeI cs) + @Override + public void changeColour(ColourSchemeI cs) { - int threshold = 0; if (cs != null) { @@ -2564,15 +2643,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } viewport.setGlobalColourScheme(cs); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(viewport.applet) - .sequenceColoursChanged(alignPanel); - alignPanel.paintAlignment(true); } @@ -2804,8 +2874,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // addHistoryItem(new HistoryItem("Sort", viewport.alignment, // HistoryItem.SORT)); addHistoryItem(new OrderCommand(MessageManager.formatMessage( - "label.order_by_params", new String[] - { title }), oldOrder, viewport.getAlignment())); + "label.order_by_params", new String[] { title }), oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -2902,12 +2972,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // lite and application g.setFont(new Font("Helvetica", Font.BOLD, 14)); g.drawString(MessageManager.formatMessage( - "label.jalviewLite_release", new String[] - { version }), x, y += fh); + "label.jalviewLite_release", new String[] { version }), x, + y += fh); g.setFont(new Font("Helvetica", Font.BOLD, 12)); g.drawString(MessageManager.formatMessage( - "label.jaview_build_date", new String[] - { builddate }), x, y += fh); + "label.jaview_build_date", new String[] { builddate }), x, + y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g.drawString(MessageManager.getString("label.jalview_authors_1"), x, y += fh * 1.5); @@ -2968,10 +3038,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MessageManager.getString("label.load_features_annotations")); MenuItem outputFeatures = new MenuItem( - MessageManager.getString("label.export_features").concat("...")); + MessageManager.getString("label.export_features")); MenuItem outputAnnotations = new MenuItem( - MessageManager.getString("label.export_annotations").concat("...")); + MessageManager.getString("label.export_annotations")); MenuItem closeMenuItem = new MenuItem( MessageManager.getString("action.close")); @@ -3037,7 +3107,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem purinePyrimidineColour = new MenuItem(); - MenuItem RNAInteractionColour = new MenuItem(); + // MenuItem RNAInteractionColour = new MenuItem(); MenuItem RNAHelixColour = new MenuItem(); @@ -3220,8 +3290,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, removeAllGapsMenuItem.setLabel(MessageManager .getString("action.remove_all_gaps")); removeAllGapsMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel(MessageManager.getString( - "action.remove_redundancy").concat("...")); + removeRedundancyMenuItem.setLabel(MessageManager + .getString("action.remove_redundancy")); removeRedundancyMenuItem.addActionListener(this); /* @@ -3245,7 +3315,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, grpsFromSelection.addActionListener(this); createGroup.setLabel(MessageManager.getString("action.create_group")); unGroup.setLabel(MessageManager.getString("action.remove_group")); - annotationColumnSelection.setLabel("Select by Annotation"); + annotationColumnSelection.setLabel(MessageManager + .getString("action.select_by_annotation")); annotationColumnSelection.addActionListener(this); /* @@ -3275,7 +3346,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hideAllSelection.addActionListener(this); showAllHidden.addActionListener(this); featureSettings.setLabel(MessageManager - .getString("label.feature_settings")); + .getString("action.feature_settings")); featureSettings.addActionListener(this); sequenceFeatures.setLabel(MessageManager .getString("label.show_sequence_features")); @@ -3326,8 +3397,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MessageManager.getString("label.sort_annotations_by_label")); showAutoFirst = new CheckboxMenuItem( MessageManager.getString("label.show_first")); + showAutoFirst.setState(false); // pending applet parameter + setShowAutoCalculatedAbove(showAutoFirst.getState()); showAutoLast = new CheckboxMenuItem( MessageManager.getString("label.show_last")); + showAutoLast.setState(!showAutoFirst.getState()); showAlignmentAnnotations.addItemListener(this); showSequenceAnnotations.addItemListener(this); sortAnnBySequence.addItemListener(this); @@ -3407,9 +3481,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, purinePyrimidineColour.setLabel(MessageManager .getString("label.purine_pyrimidine")); purinePyrimidineColour.addActionListener(this); - RNAInteractionColour.setLabel(MessageManager - .getString("label.rna_interaction")); - RNAInteractionColour.addActionListener(this); + // RNAInteractionColour.setLabel(MessageManager + // .getString("label.rna_interaction")); + // RNAInteractionColour.addActionListener(this); RNAHelixColour.setLabel(MessageManager .getString("action.by_rna_helixes")); RNAHelixColour.addActionListener(this); @@ -3438,10 +3512,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager - .getString("label.modify_identity_thereshold")); + .getString("label.modify_identity_threshold")); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3596,8 +3670,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /* * Annotations menu */ - // annotationsMenu.add(annotationPanelMenuItem); - // annotationsMenu.addSeparator(); + annotationsMenu.add(annotationPanelMenuItem); + annotationsMenu.addSeparator(); annotationsMenu.add(showAlignmentAnnotations); annotationsMenu.add(showSequenceAnnotations); annotationsMenu.add(sortAnnBySequence); @@ -3695,6 +3769,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.add(statusBar, BorderLayout.SOUTH); } + @Override public void setStatus(String string) { statusBar.setText(string); @@ -3738,6 +3813,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, private CheckboxMenuItem showAutoLast; + private SplitFrame splitFrame; + /** * Attach the alignFrame panels after embedding menus, if necessary. This used * to be called setEmbedded, but is now creates the dropdown menus in a @@ -3770,9 +3847,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, 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, this.getTitle(), - DEFAULT_WIDTH, - DEFAULT_HEIGHT); + jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth, + frameHeight); } } @@ -3838,10 +3914,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public SequenceStructureBinding addStructureViewInstance( Object jmolviewer, String[] sequenceIds) { - org.jmol.api.JmolViewer viewer = null; + Viewer viewer = null; try { - viewer = (org.jmol.api.JmolViewer) jmolviewer; + viewer = (Viewer) jmolviewer; } catch (ClassCastException ex) { System.err.println("Unsupported viewer object :" @@ -3887,8 +3963,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // TODO: search for a jmv that involves viewer if (jmv == null) { // create a new viewer/jalview binding. - jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] - { seqs }); + jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs }); } return jmv; @@ -3914,7 +3989,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, boolean needtoadd = false; if (toaddpdb != null) { - Vector pdbe = toaddpdb.getPDBId(); + Vector pdbe = toaddpdb.getAllPDBEntries(); PDBEntry pdbentry = null; if (pdbe != null && pdbe.size() > 0) { @@ -3948,12 +4023,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (needtoadd) { - // make a note of the access mode and add - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - } - pdbentry.getProperty().put("protocol", protocol); + pdbentry.setProperty("protocol", protocol); toaddpdb.addPDBId(pdbentry); alignPanel.getStructureSelectionManager() .registerPDBEntry(pdbentry); @@ -3971,8 +4041,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (seqs[i] != null) { - sequences.addElement(new Object[] - { seqs[i], (chains != null) ? chains[i] : null }); + sequences.addElement(new Object[] { seqs[i], + (chains != null) ? chains[i] : null }); } } seqs = new SequenceI[sequences.size()]; @@ -3985,8 +4055,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, chains[i] = (String) oj[1]; } } - return new Object[] - { seqs, chains }; + return new Object[] { seqs, chains }; } @@ -4005,7 +4074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (protocol == null || protocol.trim().length() == 0 || protocol.equals("null")) { - protocol = (String) pdb.getProperty().get("protocol"); + protocol = (String) pdb.getProperty("protocol"); if (protocol == null) { System.err.println("Couldn't work out protocol to open structure: " @@ -4164,4 +4233,46 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, return false; } + public SplitFrame getSplitFrame() + { + return this.splitFrame; + } + + public void setSplitFrame(SplitFrame sf) + { + this.splitFrame = sf; + } + + // may not need this + @Override + public void setShowSeqFeatures(boolean b) + { + // showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); + + } + + @Override + public void setMenusForViewport() + { + // setMenusFromViewport(viewport); + + } + + @Override + public void refreshFeatureUI(boolean enableIfNecessary) + { + if (enableIfNecessary) + { + sequenceFeatures.setState(true); + alignPanel.av.setShowSequenceFeatures(true); + } + } + + @Override + public FeatureSettingsControllerI getFeatureSettingsUI() + { + return alignPanel.av.featureSettings; + } + }