X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=d30f10dfa5ca249bdf946b10bdbe9dd85a24b776;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=0861f2d4250d8fdc07ac7fc623e582aa4dd59596;hpb=c86442e455c858f4a092fbb2e9394faa3e161a89;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 0861f2d..d30f10d 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -25,6 +25,7 @@ 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; @@ -48,7 +49,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.FeaturesFile; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -59,7 +64,7 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.RNAHelicesColour; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; @@ -75,6 +80,7 @@ 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; @@ -83,6 +89,7 @@ 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; @@ -99,7 +106,6 @@ 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; @@ -139,8 +145,8 @@ 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); } @@ -155,8 +161,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * @param embedded * @param addToDisplay */ - public AlignFrame(AlignmentI al, JalviewLite applet, - String title, boolean embedded, boolean addToDisplay) + public AlignFrame(AlignmentI al, JalviewLite applet, String title, + boolean embedded, boolean addToDisplay) { this(al, null, null, applet, title, embedded, addToDisplay); } @@ -216,6 +222,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.setColumnSelection(columnSelection); } + viewport.setScaleAboveWrapped(scaleAbove.getState()); alignPanel = new AlignmentPanel(this, viewport); avc = new jalview.controller.AlignViewController(this, viewport, @@ -232,8 +239,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, normSequenceLogo.setState(viewport.isNormaliseSequenceLogo()); applyToAllGroups.setState(viewport.getColourAppliesToAllGroups()); annotationPanelMenuItem.setState(viewport.isShowAnnotation()); - showAlignmentAnnotations.setState(viewport.isShowAnnotation()); - showSequenceAnnotations.setState(viewport.isShowAnnotation()); + showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState()); + showAlignmentAnnotations.setState(true); + showSequenceAnnotations.setState(false); seqLimits.setState(viewport.getShowJVSuffix()); @@ -289,6 +298,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { RNAHelixColour.setEnabled(false); purinePyrimidineColour.setEnabled(false); + nucleotideColour.setEnabled(false); } // Some JVMS send keyevents to Top frame or lowest panel, // Havent worked out why yet. So add to both this frame and seqCanvas for @@ -302,6 +312,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.annotationSpaceFillerHolder.addKeyListener(this); alignPanel.alabels.addKeyListener(this); + setAnnotationsVisibility(); + if (addToDisplay) { addToDisplay(embedded); @@ -338,7 +350,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * is protocol for accessing data referred to by file */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType type) { return parseFeaturesFile(file, type, true); } @@ -348,28 +360,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, * * @param file * file URL, content, or other resolvable path - * @param type + * @param sourceType * is protocol for accessing data referred to by file * @param autoenabledisplay * when true, display features flag will be automatically enabled if * features are loaded * @return true if data parsed as a features file */ - public boolean parseFeaturesFile(String file, String type, + public boolean parseFeaturesFile(String file, DataSourceType sourceType, 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, sourceType).parse( + viewport.getAlignment(), colours, true, relaxedIdMatching); } catch (Exception ex) { ex.printStackTrace(); @@ -377,10 +386,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (featuresFile) { - if (featureLinks.size() > 0) - { - alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks; - } if (autoenabledisplay) { viewport.setShowSequenceFeatures(true); @@ -552,8 +557,8 @@ 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; @@ -702,9 +707,7 @@ 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())) { @@ -732,8 +735,7 @@ 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(); } @@ -741,7 +743,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (toggleCols) { - if (viewport.getColumnSelection().getSelected().size() > 0) + if (viewport.hasSelectedColumns()) { viewport.hideSelectedColumns(); if (!toggleSeqs) @@ -753,6 +755,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { viewport.showAllHiddenColumns(); } + viewport.sendSelection(); } } @@ -812,8 +815,11 @@ 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) { @@ -913,7 +919,7 @@ 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 */ @@ -921,12 +927,15 @@ 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(true); validate(); @@ -969,6 +978,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, @Override public void actionPerformed(ActionEvent evt) { + viewport.applet.currentAlignFrame = this; + Object source = evt.getSource(); if (source == inputText) @@ -1066,11 +1077,14 @@ 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) { @@ -1104,27 +1118,34 @@ 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) { @@ -1133,12 +1154,14 @@ 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) { @@ -1177,8 +1200,8 @@ 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) { @@ -1235,7 +1258,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // } else if (source == RNAHelixColour) { - new RNAHelicesColourChooser(viewport, alignPanel); + changeColour(new RNAHelicesColour(viewport.getAlignment())); + // new RNAHelicesColourChooser(viewport, alignPanel); } else if (source == modifyPID) { @@ -1338,13 +1362,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] - { e.getActionCommand() }), 600, 500); + JalviewLite.addFrame(frame, MessageManager.formatMessage( + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); - FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer(); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( - e.getActionCommand(), viewport.getAlignment(), + fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -1379,13 +1404,13 @@ 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; } @@ -1393,15 +1418,15 @@ 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()); } @@ -1460,10 +1485,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if (viewport.applet.getParameter("jnetfile") != null) + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) @@ -1568,8 +1596,8 @@ 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 { @@ -1583,8 +1611,8 @@ 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 { @@ -1741,9 +1769,7 @@ 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); } } @@ -1879,8 +1905,8 @@ 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 @@ -1977,14 +2003,17 @@ 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); @@ -2054,9 +2083,32 @@ 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); } @@ -2187,7 +2239,10 @@ 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(); } @@ -2204,7 +2259,10 @@ 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(); } @@ -2234,7 +2292,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, ColumnSelection colSel = viewport.getColumnSelection(); int column; - if (colSel.size() > 0) + if (!colSel.isEmpty()) { if (trimLeft) { @@ -2259,23 +2317,20 @@ 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()) @@ -2316,8 +2371,9 @@ 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 @@ -2499,7 +2555,7 @@ 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) @@ -2550,8 +2606,8 @@ 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(); @@ -2572,28 +2628,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } + @Override public void changeColour(ColourSchemeI cs) { - - if (cs != null) - { - if (viewport.getAbovePIDThreshold()) - { - viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, - cs, "Background")); - } - - if (viewport.getConservationSelected()) - { - cs.setConservationApplied(true); - viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel, - cs, "Background")); - } - else - { - cs.setConservationApplied(false); - } - } viewport.setGlobalColourScheme(cs); alignPanel.paintAlignment(true); @@ -2605,7 +2642,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getViewportColourScheme(), alignPanel.getViewName()); SliderPanel.showPIDSlider(); } } @@ -2616,33 +2653,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.getGlobalColourScheme(), "Background"); + viewport.getViewportColourScheme(), alignPanel.getViewName()); SliderPanel.showConservationSlider(); } } protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.getState()); + boolean selected = conservationMenuItem.getState(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setState(false); + // viewport.setAbovePIDThreshold(false); + // abovePIDThreshold.setState(false); changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } public void abovePIDThreshold_actionPerformed() { - viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); - - conservationMenuItem.setState(false); - viewport.setConservationSelected(false); + boolean selected = abovePIDThreshold.getState(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + // conservationMenuItem.setState(false); + // viewport.setConservationSelected(false); changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } public void sortPairwiseMenuItem_actionPerformed() @@ -2827,8 +2881,8 @@ 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); } @@ -2925,12 +2979,12 @@ 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); @@ -3187,11 +3241,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, inputText.addActionListener(this); Menu outputTextboxMenu = new Menu( MessageManager.getString("label.out_to_textbox")); - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { - - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(ff); item.addActionListener(new java.awt.event.ActionListener() { @@ -3350,8 +3402,11 @@ 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); @@ -3386,7 +3441,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.colour_text")); colourTextMenuItem.addItemListener(this); displayNonconservedMenuItem.setLabel(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconservedMenuItem.addItemListener(this); wrapMenuItem.setLabel(MessageManager.getString("action.wrap")); wrapMenuItem.addItemListener(this); @@ -3409,45 +3464,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); - clustalColour.setLabel(MessageManager.getString("label.clustalx")); + clustalColour.setLabel(MessageManager + .getString("label.colourScheme_clustal")); clustalColour.addActionListener(this); - zappoColour.setLabel(MessageManager.getString("label.zappo")); + zappoColour.setLabel(MessageManager + .getString("label.colourScheme_zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel(MessageManager.getString("label.taylor")); + taylorColour.setLabel(MessageManager + .getString("label.colourScheme_taylor")); taylorColour.addActionListener(this); hydrophobicityColour.setLabel(MessageManager - .getString("label.hydrophobicity")); + .getString("label.colourScheme_hydrophobic")); hydrophobicityColour.addActionListener(this); - helixColour - .setLabel(MessageManager.getString("label.helix_propensity")); + helixColour.setLabel(MessageManager + .getString("label.colourScheme_helix_propensity")); helixColour.addActionListener(this); strandColour.setLabel(MessageManager - .getString("label.strand_propensity")); + .getString("label.colourScheme_strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel(MessageManager.getString("label.turn_propensity")); + turnColour.setLabel(MessageManager + .getString("label.colourScheme_turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel(MessageManager.getString("label.buried_index")); + buriedColour.setLabel(MessageManager + .getString("label.colourScheme_buried_index")); buriedColour.addActionListener(this); purinePyrimidineColour.setLabel(MessageManager - .getString("label.purine_pyrimidine")); + .getString("label.colourScheme_purine/pyrimidine")); purinePyrimidineColour.addActionListener(this); // RNAInteractionColour.setLabel(MessageManager // .getString("label.rna_interaction")); // RNAInteractionColour.addActionListener(this); RNAHelixColour.setLabel(MessageManager - .getString("action.by_rna_helixes")); + .getString("label.colourScheme_rna_helices")); RNAHelixColour.addActionListener(this); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(this); PIDColour.setLabel(MessageManager - .getString("label.percentage_identity")); + .getString("label.colourScheme_%_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel(MessageManager - .getString("label.blosum62_score")); + .getString("label.colourScheme_blosum62")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour - .setLabel(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setLabel(MessageManager + .getString("label.colourScheme_t-coffee_scores")); // it will be enabled only if a score file is provided tcoffeeColour.setEnabled(false); tcoffeeColour.addActionListener(this); @@ -3459,13 +3519,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, abovePIDThreshold.setLabel(MessageManager .getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); + nucleotideColour.setLabel(MessageManager + .getString("label.colourScheme_nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager - .getString("label.modify_identity_thereshold")); + .getString("label.modify_identity_threshold")); + modifyPID.setEnabled(abovePIDThreshold.getState()); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager - .getString("label.modify_conservation_thereshold")); + .getString("label.modify_conservation_threshold")); + modifyConservation.setEnabled(conservationMenuItem.getState()); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3499,7 +3562,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.neighbour_joining_identity")); neighbourTreeMenuItem.addActionListener(this); avDistanceTreeBlosumMenuItem.setLabel(MessageManager - .getString("label.average_distance_bloslum62")); + .getString("label.average_distance_blosum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel(MessageManager .getString("label.neighbour_blosum62")); @@ -3719,6 +3782,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.add(statusBar, BorderLayout.SOUTH); } + @Override public void setStatus(String string) { statusBar.setText(string); @@ -3796,8 +3860,7 @@ 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(), - frameWidth, + jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth, frameHeight); } } @@ -3913,8 +3976,7 @@ 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; @@ -3967,19 +4029,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } // resolve data source // TODO: this code should be a refactored to an io package - String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB"); + DataSourceType protocol = AppletFormatAdapter.resolveProtocol( + pdbFile, FileFormat.PDB); if (protocol == null) { return false; } 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); @@ -3997,8 +4055,8 @@ 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()]; @@ -4011,13 +4069,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, chains[i] = (String) oj[1]; } } - return new Object[] - { seqs, chains }; + return new Object[] { seqs, chains }; } public void newStructureView(JalviewLite applet, PDBEntry pdb, - SequenceI[] seqs, String[] chains, String protocol) + SequenceI[] seqs, String[] chains, DataSourceType protocol) { // Scrub any null sequences from the array Object[] sqch = cleanSeqChainArrays(seqs, chains); @@ -4028,10 +4085,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, System.err .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } - if (protocol == null || protocol.trim().length() == 0 - || protocol.equals("null")) + if (protocol == null) { - protocol = (String) pdb.getProperty().get("protocol"); + String sourceType = (String) pdb.getProperty("protocol"); + try + { + protocol = DataSourceType.valueOf(sourceType); + } catch (IllegalArgumentException e) + { + // ignore + } if (protocol == null) { System.err.println("Couldn't work out protocol to open structure: " @@ -4054,12 +4117,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // can only do alignments with Jmol // find the last jmol window assigned to this alignment - jalview.appletgui.AppletJmol ajm = null, tajm; - Vector jmols = applet - .getAppletWindow(jalview.appletgui.AppletJmol.class); + AppletJmol ajm = null, tajm; + Vector jmols = applet.getAppletWindow(AppletJmol.class); for (int i = 0, iSize = jmols.size(); i < iSize; i++) { - tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + tajm = (AppletJmol) jmols.elementAt(i); if (tajm.ap.alignFrame == this) { ajm = tajm; @@ -4078,7 +4140,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // otherwise, create a new window if (applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, + new AppletJmol(pdb, seqs, chains, alignPanel, protocol); applet.lastFrameX += 40; applet.lastFrameY += 40; @@ -4200,7 +4262,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, this.splitFrame = sf; } - // may not need this + // may not need this @Override public void setShowSeqFeatures(boolean b) { @@ -4215,6 +4277,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // setMenusFromViewport(viewport); } + @Override public void refreshFeatureUI(boolean enableIfNecessary) {