X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b0d30a28da9df4794050df0601c0588a08364701;hb=1b85d0acd9a09b646ac2dd6f1ea6db5db6f3731d;hp=45a0c856f812c828ed6bb9f34be7738e5e8e09ae;hpb=98897348951ee59ce6c6ff7e0e2789a5f115030f;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 45a0c85..b0d30a2 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -31,12 +30,15 @@ import javax.swing.*; import javax.swing.event.MenuEvent; import jalview.analysis.*; +import jalview.bin.Cache; import jalview.commands.*; import jalview.datamodel.*; import jalview.io.*; import jalview.jbgui.*; import jalview.schemes.*; import jalview.ws.*; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; /** * DOCUMENT ME! @@ -406,70 +408,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { boolean toggleSeqs = !evt.isControlDown(); boolean toggleCols = !evt.isShiftDown(); - - boolean hide = false; - SequenceGroup sg = viewport.getSelectionGroup(); - // TODO: document ctrl-shift-h for show visible selected area and fix hack so columns for the current selected region get transferred. - if (!toggleSeqs && !toggleCols) - { - // 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.colSel!=null && viewport.colSel.getSelected()!=null && viewport.colSel.getSelected().size()>0) || (sg!=null && sg.getSize()>0 && sg.getStartRes()<=sg.getEndRes())) - { - // now invert the sequence set, if required - empty selection implies that no hiding is required. - if (sg!=null) { - invertSequenceMenuItem_actionPerformed(null); - sg = viewport.getSelectionGroup(); - toggleSeqs = true; - - } - - if (sg!=null && sg.getStartRes()>=0 && sg.getStartRes()<=sg.getEndRes()&& (viewport.colSel==null || viewport.colSel.getSelected()==null || viewport.colSel.getSelected().size()==0)) - { - // synthesize a column selection if none exists. this happens if a single region has been selected rather than whole columns. - if (viewport.colSel==null) - { - viewport.colSel = new ColumnSelection(); - } - for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) { - viewport.colSel.addElement(cspos); - } - } - // finally invert the column selection and get the new sequence selection. - invertColSel_actionPerformed(null); - toggleCols = true; - } - } - - if (toggleSeqs) - { - if (sg != null - && sg.getSize() != viewport.alignment.getHeight()) - { - hideSelSequences_actionPerformed(null); - hide = true; - } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) - { - showAllSeqs_actionPerformed(null); - } - } - - if (toggleCols) - { - if (viewport.colSel.getSelected().size() > 0) - { - hideSelColumns_actionPerformed(null); - if (!toggleSeqs) - { - viewport.selectionGroup = sg; - } - } - else if (!hide) - { - showAllColumns_actionPerformed(null); - } - } + toggleHiddenRegions(toggleSeqs, toggleCols); break; } case KeyEvent.VK_PAGE_UP: @@ -577,32 +516,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; - // Do this once to get current state - BuildWebServiceMenu(); - Desktop.discoverer - .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener() + Desktop.instance.addJalviewPropertyChangeListener("services", + thisListener = new java.beans.PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { - // System.out.println("Discoverer property change."); - if (evt.getPropertyName().equals("services")) + // // System.out.println("Discoverer property change."); + // if (evt.getPropertyName().equals("services")) { - // System.out.println("Rebuilding web service menu"); - BuildWebServiceMenu(); + SwingUtilities.invokeLater(new Runnable() + { + + public void run() + { + System.err + .println("Rebuild WS Menu for service change"); + BuildWebServiceMenu(); + } + + }); } } }); - addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { - // System.out.println("deregistering discoverer listener"); - Desktop.discoverer.removePropertyChangeListener(thisListener); + System.out.println("deregistering discoverer listener"); + Desktop.instance.removeJalviewPropertyChangeListener("services", + thisListener); closeMenuItem_actionPerformed(true); }; }); + // Finally, build the menu once to get current service state + javax.swing.SwingUtilities.invokeLater(new Runnable() { + public void run() { BuildWebServiceMenu();} + }); } public void setGUINucleotide(boolean nucleotide) @@ -610,7 +560,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showTranslation.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); - + showGroupConservation.setEnabled(!nucleotide); // Remember AlignFrame always starts as protein if (!nucleotide) { @@ -652,9 +602,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); - showUnconservedMenuItem.setSelected(av.showUnconserved); + showNonconservedMenuItem.setSelected(av.showUnconserved); showGroupConsensus.setSelected(av.showGroupConsensus); showGroupConservation.setSelected(av.showGroupConservation); + showConsensusHistogram.setSelected(av.showConsensusHistogram); + showSequenceLogo.setSelected(av.showSequenceLogo); setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); @@ -685,20 +637,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JPanel progressPanel; + Long lId = new Long(id); GridLayout layout = (GridLayout) statusPanel.getLayout(); - if (progressBars.get(new Long(id)) != null) + if (progressBars.get(lId) != null) { progressPanel = (JPanel) progressBars.get(new Long(id)); statusPanel.remove(progressPanel); - progressBars.remove(progressPanel); + progressBars.remove(lId); progressPanel = null; if (message != null) { statusBar.setText(message); } - if (progressBarHandlers.contains(new Long(id))) + if (progressBarHandlers.contains(lId)) { - progressBarHandlers.remove(new Long(id)); + progressBarHandlers.remove(lId); } layout.setRows(layout.getRows() - 1); } @@ -715,7 +668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, layout.setRows(layout.getRows() + 1); statusPanel.add(progressPanel); - progressBars.put(new Long(id), progressPanel); + progressBars.put(lId, progressPanel); } // update GUI setMenusForViewport(); @@ -790,6 +743,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (fileName != null) { + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. if (currentFileFormat.equals("Jalview")) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -824,7 +779,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protocol, currentFileFormat); newframe.setBounds(bounds); - + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; + } this.closeMenuItem_actionPerformed(true); } } @@ -1034,11 +1005,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); + + try { + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + viewport.alignment, omitHidden, viewport.colSel)); Desktop.addInternalFrame(cap, "Alignment output - " + e.getActionCommand(), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as "+e.getActionCommand(),oom); + cap.dispose(); + } - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.alignment, omitHidden, viewport.colSel)); } /** @@ -1249,7 +1227,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.historyList.push(command); viewport.redoList.clear(); updateEditMenuBar(); - viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + viewport.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); } } @@ -1296,7 +1276,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != null) { - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + originalSource.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences()); } @@ -1324,7 +1306,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != null) { - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + originalSource.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences()); } @@ -1567,15 +1551,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.hasHiddenColumns) { hiddenColumns = new Vector(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport + .getSelectionGroup().getEndRes(); for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() .size(); i++) { int[] region = (int[]) viewport.getColumnSelection() .getHiddenColumns().elementAt(i); - - hiddenColumns.addElement(new int[] - { region[0] - hiddenOffset, region[1] - hiddenOffset }); + if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) + { + hiddenColumns.addElement(new int[] + { region[0] - hiddenOffset, region[1] - hiddenOffset }); + } } } @@ -2401,6 +2388,116 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // 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.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel + .getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(null); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection. + invertColSel_actionPerformed(null); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + { + hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + { + showAllSeqs_actionPerformed(null); + } + } + + if (toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + hideSelColumns_actionPerformed(null); + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } + } + else if (!hide) + { + showAllColumns_actionPerformed(null); + } + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. + * event.ActionEvent) + */ + public void hideAllButSelection_actionPerformed(ActionEvent e) + { + toggleHiddenRegions(false, false); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event + * .ActionEvent) + */ + public void hideAllSelection_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. + * ActionEvent) + */ + public void showAllhidden_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); @@ -2494,6 +2591,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, featureSettings.close(); featureSettings = null; } + if (!showSeqFeatures.isSelected()) + { + // make sure features are actually displayed + showSeqFeatures.setSelected(true); + showSeqFeatures_actionPerformed(null); + } featureSettings = new FeatureSettings(this); } @@ -3314,8 +3417,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - // are the sequences aligned? - if (!viewport.alignment.isAligned()) + // are the visible sequences aligned? + if (!viewport.alignment.isAligned(false)) { JOptionPane .showMessageDialog( @@ -3584,10 +3687,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // jobs // TODO: viewport.alignment.isAligned is a global state - the local // selection may well be aligned - we preserve 2.0.8 behaviour for moment. - if (!viewport.alignment.isAligned()) + if (!viewport.alignment.isAligned(false)) { seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); + // TODO: if seqs.getSequences().length>1 then should really have warned + // user! + } return seqs; } @@ -3700,87 +3806,134 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } + private boolean buildingMenu = false; + /** * Generates menu items and listener event actions for web service clients * */ public void BuildWebServiceMenu() { - // TODO: add support for context dependent disabling of services based on - // alignment and current selection - // TODO: add additional serviceHandle parameter to specify abstract handler - // class independently of AbstractName - // TODO: add in rediscovery GUI function to restart discoverer - // TODO: group services by location as well as function and/or introduce - // object broker mechanism. - if ((Discoverer.services != null) && (Discoverer.services.size() > 0)) - { - // TODO: refactor to allow list of AbstractName/Handler bindings to be - // stored or retrieved from elsewhere - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch"); - // TODO: move GUI generation code onto service implementation - so a - // client instance attaches itself to the GUI with method call like - // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, - // alignframe) + while (buildingMenu) + { + try + { + System.err.println("Waiting for building menu to finish."); + Thread.sleep(10); + } catch (Exception e) + { + } + ; + } + buildingMenu = true; + try + { + System.err + .println("Building ws menu again " + Thread.currentThread()); + // TODO: add support for context dependent disabling of services based on + // alignment and current selection + // TODO: add additional serviceHandle parameter to specify abstract + // handler + // class independently of AbstractName + // TODO: add in rediscovery GUI function to restart discoverer + // TODO: group services by location as well as function and/or introduce + // object broker mechanism. Vector wsmenu = new Vector(); final IProgressIndicator af = this; - if (msaws != null) + if (Cache.getDefault("SHOW_JWS1_SERVICES", true) + && Discoverer.services != null + && (Discoverer.services.size() > 0)) { - // Add any Multiple Sequence Alignment Services - final JMenu msawsmenu = new JMenu("Alignment"); - for (int i = 0, j = msaws.size(); i < j; i++) + // TODO: refactor to allow list of AbstractName/Handler bindings to be + // stored or retrieved from elsewhere + Vector msaws = (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); + Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch"); + // TODO: move GUI generation code onto service implementation - so a + // client instance attaches itself to the GUI with method call like + // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, + // alignframe) + if (msaws != null) { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws - .get(i); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(msawsmenu, this); + // Add any Multiple Sequence Alignment Services + final JMenu msawsmenu = new JMenu("Alignment"); + for (int i = 0, j = msaws.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(msawsmenu, this); + } + wsmenu.add(msawsmenu); + } + if (secstrpr != null) + { + // Add any secondary structure prediction services + final JMenu secstrmenu = new JMenu( + "Secondary Structure Prediction"); + for (int i = 0, j = secstrpr.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(secstrmenu, this); + } + wsmenu.add(secstrmenu); + } + if (seqsrch != null) + { + // Add any sequence search services + final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); + for (int i = 0, j = seqsrch.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch + .elementAt(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(seqsrchmenu, this); + } + wsmenu.add(seqsrchmenu); } - wsmenu.add(msawsmenu); } - if (secstrpr != null) + + // TODO: move into separate menu builder class. + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - // Add any secondary structure prediction services - final JMenu secstrmenu = new JMenu("Secondary Structure Prediction"); - for (int i = 0, j = secstrpr.size(); i < j; i++) + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr - .get(i); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(secstrmenu, this); + if (jws2servs.hasServices()) + { + JMenu jws2men = new JMenu("Jalview 2 Services"); + jws2servs.attachWSMenuEntry(jws2men, this); + for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++) + { + wsmenu.add(jws2men.getMenuComponent(i)); + } + } } - wsmenu.add(secstrmenu); } - if (seqsrch != null) + resetWebServiceMenu(); + // finally, add the whole shebang onto the webservices menu + if (wsmenu.size() > 0) { - // Add any sequence search services - final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - for (int i = 0, j = seqsrch.size(); i < j; i++) + for (int i = 0, j = wsmenu.size(); i < j; i++) { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch - .elementAt(i); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(seqsrchmenu, this); + webService.add((JMenu) wsmenu.get(i)); } - // finally, add the whole shebang onto the webservices menu - wsmenu.add(seqsrchmenu); } - resetWebServiceMenu(); - for (int i = 0, j = wsmenu.size(); i < j; i++) + else { - webService.add((JMenu) wsmenu.get(i)); + this.webService.add(this.webServiceNoServices); } - } - else + } catch (Exception e) { - resetWebServiceMenu(); - this.webService.add(this.webServiceNoServices); } + ; + buildingMenu = false; } /** @@ -3792,6 +3945,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { webService.removeAll(); build_fetchdbmenu(webService); + build_urlServiceMenu(webService); + } + + /** + * construct any groupURL type service menu entries. + * + * @param webService + */ + private void build_urlServiceMenu(JMenu webService) + { + if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + { + jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry( + webService, this); + } } /* @@ -4079,6 +4247,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // update the min/max ranges where necessary alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); } + if (featureSettings != null) + { + featureSettings.setTableData(); + } alignPanel.paintAlignment(true); } @@ -4457,7 +4629,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowUnconserved(showUnconservedMenuItem.getState()); + viewport.setShowUnconserved(showNonconservedMenuItem.getState()); alignPanel.paintAlignment(true); } @@ -4471,7 +4643,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showGroupConsensus_actionPerformed(ActionEvent e) { viewport.setShowGroupConsensus(showGroupConsensus.getState()); - alignPanel.updateAnnotation(); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } @@ -4485,7 +4657,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showGroupConservation_actionPerformed(ActionEvent e) { viewport.setShowGroupConservation(showGroupConservation.getState()); - alignPanel.updateAnnotation(); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } /* @@ -4509,8 +4712,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // set view properties for each group for (int g = 0; g < gps.length; g++) { - gps[g].setShowunconserved(viewport.getShowUnconserved()); - gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols()); + gps[g].setShowNonconserved(viewport.getShowUnconserved()); + gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); viewport.alignment.addGroup(gps[g]); Color col = new Color((int) (Math.random() * 255), (int) (Math .random() * 255), (int) (Math.random() * 255));