X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b91255f50ba15bc43994c328c9457f6738509c0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=1feffa5677643e39441e223f2492ab3ed3140b7e;hpb=62fbf21f8e9c03bb3dd9bf26dd0981d0bf89ab0f;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 1feffa5..9b91255 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,42 +1,125 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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; -import java.beans.*; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; -import javax.swing.event.MenuEvent; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.Conservation; +import jalview.analysis.CrossRef; +import jalview.analysis.NJTree; +import jalview.analysis.ParseProperties; +import jalview.analysis.SequenceIdMatcher; +import jalview.bin.Cache; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.FeaturesFile; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.HTMLOutput; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.jbgui.GAlignFrame; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.ws.WSMenuEntryProviderI; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.GridLayout; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Vector; + +import javax.swing.JButton; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JProgressBar; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; /** * DOCUMENT ME! @@ -81,51 +164,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { this(al, null, width, height); } + /** - * Creates a new AlignFrame object with specific width, height and sequenceSetId + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * * @param al * @param width * @param height * @param sequenceSetId */ - public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId) + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId) { this(al, null, width, height, sequenceSetId); } + /** - * Creates a new AlignFrame object with specific width, height and sequenceSetId + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * * @param al * @param width * @param height * @param sequenceSetId * @param viewId */ - public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId, String viewId) { this(al, null, width, height, sequenceSetId, viewId); } + /** * new alignment window with hidden columns * * @param al - * AlignmentI + * AlignmentI * @param hiddenColumns - * ColumnSelection or null - * @param width Width of alignment frame - * @param height height of frame. + * ColumnSelection or null + * @param width + * Width of alignment frame + * @param height + * height of frame. */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); } + /** - * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * * @param al * @param hiddenColumns * @param width * @param height - * @param sequenceSetId (may be null) + * @param sequenceSetId + * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId) @@ -134,16 +232,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * * @param al * @param hiddenColumns * @param width * @param height - * @param sequenceSetId (may be null) - * @param viewId (may be null) + * @param sequenceSetId + * (may be null) + * @param viewId + * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, - String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId, String viewId) { setSize(width, height); viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); @@ -163,9 +265,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Make a new AlignFrame from exisiting alignmentPanels * * @param ap - * AlignmentPanel + * AlignmentPanel * @param av - * AlignViewport + * AlignViewport */ public AlignFrame(AlignmentPanel ap) { @@ -174,8 +276,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addAlignmentPanel(ap, false); init(); } + /** - * initalise the alignframe from the underlying viewport data and the configurations + * initalise the alignframe from the underlying viewport data and the + * configurations */ void init() { @@ -229,9 +333,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * button functionality. * * @param file - * valid filename + * valid filename * @param format - * format of file + * format of file */ public void setFileName(String file, String format) { @@ -298,7 +402,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || evt.isShiftDown() || evt.isAltDown()); } break; - + + //case KeyEvent.VK_A: + // if (viewport.cursorMode) + // { + // alignPanel.seqPanel.insertNucAtCursor(false,"A"); + // //System.out.println("A"); + // } + // break; + /* + case KeyEvent.VK_CLOSE_BRACKET: + if (viewport.cursorMode) + { + System.out.println("closing bracket"); + } + break; + */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) @@ -385,39 +504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { boolean toggleSeqs = !evt.isControlDown(); boolean toggleCols = !evt.isShiftDown(); - - boolean hide = false; - - SequenceGroup sg = viewport.getSelectionGroup(); - 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: @@ -503,6 +590,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); } } @@ -525,32 +613,47 @@ 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 + new Thread(new Runnable() + { + public void run() + { + BuildWebServiceMenu(); + } + }).start(); } public void setGUINucleotide(boolean nucleotide) @@ -558,12 +661,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showTranslation.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); - + showGroupConservation.setEnabled(!nucleotide); + rnahelicesColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(nucleotide); // Remember AlignFrame always starts as protein - if (!nucleotide) - { - calculateMenu.remove(calculateMenu.getItemCount() - 2); - } + //if (!nucleotide) + // { + // showTr + // calculateMenu.remove(calculateMenu.getItemCount() - 2); + // } } /** @@ -581,7 +687,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * loading from Jalview2XML.java * * @param av - * AlignViewport + * AlignViewport */ void setMenusFromViewport(AlignViewport av) { @@ -600,7 +706,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, annotationPanelMenuItem.setState(av.showAnnotation); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); - + 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())); @@ -609,7 +719,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, applyToAllGroups.setState(av.colourAppliesToAllGroups); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); showDbRefsMenuitem.setSelected(av.isShowDbRefs()); - + autoCalculate.setSelected(av.autoCalculateConsensus); + sortByTree.setSelected(av.sortByTree); + listenToViewSelections.setSelected(av.followSelection); + rnahelicesColour.setEnabled(av.alignment.hasRNAStructure()); + rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); setShowProductsEnabled(); updateEditMenuBar(); @@ -631,20 +745,21 @@ 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); } @@ -661,35 +776,43 @@ 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(); + // setMenusForViewport(); validate(); } - public void registerHandler(final long id, final IProgressIndicatorHandler handler) + + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) { - if (progressBarHandlers==null || !progressBars.contains(new Long(id))) + if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { - throw new Error("call setProgressBar before registering the progress bar's handler."); + throw new Error( + "call setProgressBar before registering the progress bar's handler."); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { JButton cancel = new JButton("Cancel"); - final IProgressIndicator us=this; - cancel.addActionListener(new ActionListener() { + final IProgressIndicator us = this; + cancel.addActionListener(new ActionListener() + { public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar("Cancelled "+((JLabel)progressPanel.getComponent(0)).getText(), id); + us.setProgressBar( + "Cancelled " + + ((JLabel) progressPanel.getComponent(0)) + .getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); } } + /** * * @return true if any progress bars are still active @@ -730,6 +853,8 @@ 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(); @@ -764,7 +889,23 @@ 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); } } @@ -783,8 +924,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void save_actionPerformed(ActionEvent e) { if (fileName == null - || (currentFileFormat == null - || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true)) + || (currentFileFormat == null || !jalview.io.FormatAdapter + .isValidIOFormat(currentFileFormat, true)) || fileName.startsWith("http")) { saveAs_actionPerformed(null); @@ -799,12 +940,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void saveAs_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY"), + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, currentFileFormat, false); @@ -866,12 +1007,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) { - // JBPNote need to have a raise_gui flag here - JOptionPane.showInternalMessageDialog(this, "Cannot save file " - + fileName + " using format " + format, - "Alignment output format not supported", - JOptionPane.WARNING_MESSAGE); + warningMessage("Cannot save file " + fileName + " using format " + + format, "Alignment output format not supported"); saveAs_actionPerformed(null); + // JBPNote need to have a raise_gui flag here return false; } @@ -932,11 +1071,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return success; } + private void warningMessage(String warning, String title) + { + if (new jalview.util.Platform().isHeadless()) + { + System.err.println("Warning: " + title + "\nWarning: " + warning); + + } + else + { + JOptionPane.showInternalMessageDialog(this, warning, title, + JOptionPane.WARNING_MESSAGE); + } + return; + } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void outputText_actionPerformed(ActionEvent e) { @@ -961,24 +1115,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, "Alignment output - " - + e.getActionCommand(), 600, 500); - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - viewport.alignment, omitHidden, viewport.colSel)); + 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(); + } + } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { - new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas - .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer()); + new HTMLOutput(alignPanel, + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); } public void createImageMap(File file, String image) @@ -990,7 +1152,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void createPNG(File f) { @@ -1001,7 +1163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void createEPS(File f) { @@ -1018,7 +1180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void printMenuItem_actionPerformed(ActionEvent e) { @@ -1034,7 +1196,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel, + new AnnotationExporter().exportAnnotations( + alignPanel, viewport.showAnnotation ? viewport.alignment .getAlignmentAnnotation() : null, viewport.alignment .getGroups(), @@ -1044,8 +1207,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Load Jalview Annotations or Features File"); chooser.setToolTipText("Load Jalview Annotations / Features file"); @@ -1056,16 +1219,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice); + loadJalviewDataFile(choice, null, null, null); } } /** - * Close the current view or all views in the alignment frame. - * If the frame only contains one view then the alignment will be removed from memory. + * Close the current view or all views in the alignment frame. If the frame + * only contains one view then the alignment will be removed from memory. * - * @param closeAllTabs + * @param closeAllTabs */ public void closeMenuItem_actionPerformed(boolean closeAllTabs) { @@ -1080,24 +1243,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (closeAllTabs) { - for (int i = 0; i < alignPanels.size(); i++) + if (this.isClosed()) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); - jalview.structure.StructureSelectionManager ssm = - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(); - ssm.removeStructureViewerListener(ap.seqPanel, null); - ssm.removeSelectionListener(ap.seqPanel); - PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(ap.idPanel.idCanvas); - PaintRefresher.RemoveComponent(ap); - ap.av.alignment = null; + // really close all the windows - otherwise wait till + // setClosed(true) is called + for (int i = 0; i < alignPanels.size(); i++) + { + AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); + ap.closePanel(); + } } } else { closeView(alignPanel); - viewport = null; } } @@ -1111,22 +1270,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + /** + * close alignPanel2 and shuffle tabs appropriately. + * + * @param alignPanel2 + */ public void closeView(AlignmentPanel alignPanel2) { int index = tabbedPane.getSelectedIndex(); int closedindex = tabbedPane.indexOfComponent(alignPanel2); alignPanels.removeElement(alignPanel2); - PaintRefresher.RemoveComponent(alignPanel2.seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(alignPanel2.idPanel.idCanvas); - PaintRefresher.RemoveComponent(alignPanel2); - alignPanel2.av.alignment = null; - - if (viewport == alignPanel2.av) - { - viewport = null; - } + // Unnecessary + // if (viewport == alignPanel2.av) + // { + // viewport = null; + // } + alignPanel2.closePanel(); alignPanel2 = null; - + tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); @@ -1136,7 +1297,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, index--; } - this.tabSelectionChanged(index); + this.tabSelectionChanged(index); } /** @@ -1178,7 +1339,9 @@ 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); } } @@ -1210,7 +1373,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed(ActionEvent e) { @@ -1225,7 +1388,9 @@ 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()); } @@ -1235,7 +1400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed(ActionEvent e) { @@ -1253,7 +1418,9 @@ 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()); } @@ -1305,7 +1472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param up - * DOCUMENT ME! + * DOCUMENT ME! */ public void moveSelectedSequences(boolean up) { @@ -1452,7 +1619,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void copy_actionPerformed(ActionEvent e) { @@ -1481,11 +1648,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.gui.Desktop.internalCopy = true; // Its really worth setting the clipboard contents // to empty before setting the large StringSelection!! - Toolkit.getDefaultToolkit().getSystemClipboard().setContents( - new StringSelection(""), null); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(""), null); - Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(ss, Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -1496,15 +1663,18 @@ 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 }); + } } } @@ -1517,7 +1687,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void pasteNew_actionPerformed(ActionEvent e) { @@ -1528,7 +1698,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void pasteThis_actionPerformed(ActionEvent e) { @@ -1539,7 +1709,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Paste contents of Jalview clipboard * * @param newAlignment - * true to paste to a new alignment, otherwise add to this. + * true to paste to a new alignment, otherwise add to this. */ void paste(boolean newAlignment) { @@ -1745,8 +1915,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, alignment - .getSequences()); + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); } else @@ -1808,7 +1978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void cut_actionPerformed(ActionEvent e) { @@ -1820,7 +1990,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void delete_actionPerformed(ActionEvent evt) { @@ -1880,7 +2050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void deleteGroups_actionPerformed(ActionEvent e) { @@ -1888,6 +2058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.sequenceColours = null; viewport.setSelectionGroup(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); } @@ -1895,7 +2066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -1917,7 +2088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -1933,13 +2104,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -1958,21 +2130,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } alignPanel.paintAlignment(true); - viewport.sendSelection(); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); alignPanel.paintAlignment(true); + viewport.sendSelection(); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -1983,7 +2156,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void remove2RightMenuItem_actionPerformed(ActionEvent e) { @@ -2060,7 +2233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { @@ -2106,7 +2279,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2144,7 +2317,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void padGapsMenuitem_actionPerformed(ActionEvent e) { @@ -2152,21 +2325,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } - - //else + + // else { // if (justifySeqs>0) { // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); } } - //} - + + // } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void findMenuItem_actionPerformed(ActionEvent e) { @@ -2175,8 +2349,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void newView_actionPerformed(ActionEvent e) { + newView(true); + } + + /** + * + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(boolean copyAnnotation) + { + return newView(null, copyAnnotation); + } + + /** + * + * @param viewTitle + * title of newly created view + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle) + { + return newView(viewTitle, true); + } + + /** + * + * @param viewTitle + * title of newly created view + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) + { AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, true); + if (!copyAnnotation) + { + // just remove all the current annotation except for the automatic stuff + newap.av.alignment.deleteAllGroups(); + for (AlignmentAnnotation alan : newap.av.alignment + .getAlignmentAnnotation()) + { + if (!alan.autoCalculated) + { + newap.av.alignment.deleteAnnotation(alan); + } + ; + } + } newap.av.gatherViewsHere = false; @@ -2189,8 +2412,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.redoList = viewport.redoList; int index = Desktop.getViewCount(viewport.getSequenceSetId()); - String newViewName = "View " + index; - + // make sure the new view has a unique name - this is essential for Jalview + // 2 archives + boolean addFirstIndex = false; + if (viewTitle == null || viewTitle.trim().length() == 0) + { + viewTitle = "View"; + addFirstIndex = true; + } + else + { + index = 1;// we count from 1 if given a specific name + } + String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); Vector comps = (Vector) PaintRefresher.components.get(viewport .getSequenceSetId()); Vector existingNames = new Vector(); @@ -2208,7 +2442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, while (existingNames.contains(newViewName)) { - newViewName = "View " + (++index); + newViewName = viewTitle + " " + (++index); } newap.av.viewName = newViewName; @@ -2220,6 +2454,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.gatherViewsHere = true; } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; } public void expandViews_actionPerformed(ActionEvent e) @@ -2236,7 +2471,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void font_actionPerformed(ActionEvent e) { @@ -2247,7 +2482,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void seqLimit_actionPerformed(ActionEvent e) { @@ -2269,14 +2504,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); alignPanel.paintAlignment(true); } - /* (non-Javadoc) + + /* + * (non-Javadoc) + * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { - alignPanel.scrollToPosition(alignPanel.seqPanel.seqCanvas.searchResults, false); + alignPanel.scrollToPosition( + alignPanel.seqPanel.seqCanvas.searchResults, false); } } @@ -2284,7 +2523,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -2296,7 +2535,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -2324,6 +2563,116 @@ 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(); @@ -2340,7 +2689,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -2352,7 +2701,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -2364,7 +2713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void scaleRight_actionPerformed(ActionEvent e) { @@ -2376,7 +2725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -2388,7 +2737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -2400,7 +2749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2417,6 +2766,12 @@ 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); } @@ -2424,7 +2779,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Set or clear 'Show Sequence Features' * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -2435,15 +2790,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getOverviewPanel().updateOverviewImage(); } } + /** * Set or clear 'Show Sequence Features' * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { - viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight.isSelected()); + viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight + .isSelected()); if (viewport.getShowSequenceFeaturesHeight()) { // ensure we're actually displaying features @@ -2461,7 +2818,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { @@ -2473,58 +2830,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); - StringBuffer contents = new StringBuffer(""); - - float avg = 0; - int min = Integer.MAX_VALUE, max = 0; - for (int i = 0; i < viewport.alignment.getHeight(); i++) - { - int size = viewport.alignment.getSequenceAt(i).getEnd() - - viewport.alignment.getSequenceAt(i).getStart(); - avg += size; - if (size > max) - max = size; - if (size < min) - min = size; - } - avg = avg / (float) viewport.alignment.getHeight(); - - contents.append("
Sequences: " + viewport.alignment.getHeight()); - contents.append("
Minimum Sequence Length: " + min); - contents.append("
Maximum Sequence Length: " + max); - contents.append("
Average Length: " + (int) avg); - - if (((Alignment) viewport.alignment).getProperties() != null) - { - Hashtable props = ((Alignment) viewport.alignment).getProperties(); - Enumeration en = props.keys(); - contents.append("

"); - while (en.hasMoreElements()) - { - String key = en.nextElement().toString(); - StringBuffer val = new StringBuffer(); - String vals = props.get(key).toString(); - int pos = 0, npos; - do - { - npos = vals.indexOf("\n", pos); - if (npos == -1) - { - val.append(vals.substring(pos)); - } - else - { - val.append(vals.substring(pos, npos)); - val.append("
"); - } - pos = npos + 1; - } while (npos != -1); - contents - .append(""); - } - contents.append("
" + key + "" + val + "
"); - } - editPane.setText(contents.toString() + ""); + StringBuffer contents = new AlignmentProperties(viewport.alignment) + .formatAsHtml(); + editPane.setText("" + contents.toString() + ""); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); @@ -2536,7 +2844,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -2548,19 +2856,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JInternalFrame frame = new JInternalFrame(); OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame - .getWidth(), frame.getHeight()); + Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), + frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - alignPanel.setOverviewPanel(null); - }; - }); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + alignPanel.setOverviewPanel(null); + }; + }); alignPanel.setOverviewPanel(overview); } @@ -2574,7 +2881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed(ActionEvent e) { @@ -2585,20 +2892,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void clustalColour_actionPerformed(ActionEvent e) { changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment - .getWidth())); + viewport.alignment.getSequences(), + viewport.alignment.getWidth())); } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void zappoColour_actionPerformed(ActionEvent e) { @@ -2609,7 +2916,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void taylorColour_actionPerformed(ActionEvent e) { @@ -2620,7 +2927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void hydrophobicityColour_actionPerformed(ActionEvent e) { @@ -2631,7 +2938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void helixColour_actionPerformed(ActionEvent e) { @@ -2642,7 +2949,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void strandColour_actionPerformed(ActionEvent e) { @@ -2653,7 +2960,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void turnColour_actionPerformed(ActionEvent e) { @@ -2664,7 +2971,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void buriedColour_actionPerformed(ActionEvent e) { @@ -2675,23 +2982,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + /* + public void covariationColour_actionPerformed(ActionEvent e) + { + changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0])); + } + */ public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } + + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void applyToAllGroups_actionPerformed(ActionEvent e) { @@ -2702,7 +3024,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ public void changeColour(ColourSchemeI cs) { @@ -2729,8 +3051,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Alignment al = (Alignment) viewport.alignment; Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, al - .getWidth() - 1); + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -2766,8 +3088,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg - .getSequences(viewport.hiddenRepSequences), sg.getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); } else if (cs instanceof UserColourScheme) { @@ -2789,9 +3112,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(viewport.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1)); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1)); } else { @@ -2801,9 +3124,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(viewport.hiddenRepSequences), sg - .getStartRes(), sg.getEndRes() + 1); + ResidueProperties.propHash, 3, + sg.getSequences(viewport.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); sg.cs.setConservation(c); @@ -2827,15 +3150,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null) { - SliderPanel.setPIDSliderSource(alignPanel, viewport - .getGlobalColourScheme(), "Background"); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } @@ -2844,7 +3167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void modifyConservation_actionPerformed(ActionEvent e) { @@ -2861,7 +3184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed(ActionEvent e) { @@ -2879,7 +3202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void abovePIDThreshold_actionPerformed(ActionEvent e) { @@ -2897,7 +3220,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void userDefinedColour_actionPerformed(ActionEvent e) { @@ -2945,8 +3268,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - radioItem - .removeActionListener(radioItem.getActionListeners()[0]); + radioItem.removeActionListener(radioItem.getActionListeners()[0]); int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, @@ -2990,7 +3312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void PIDColour_actionPerformed(ActionEvent e) { @@ -3001,7 +3323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void BLOSUM62Colour_actionPerformed(ActionEvent e) { @@ -3012,7 +3334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -3028,7 +3350,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortIDMenuItem_actionPerformed(ActionEvent e) { @@ -3037,17 +3359,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortLengthMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.alignment)); alignPanel.paintAlignment(true); } @@ -3055,7 +3379,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortGroupMenuItem_actionPerformed(ActionEvent e) { @@ -3071,7 +3395,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { @@ -3082,7 +3406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { @@ -3105,7 +3429,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void PCAMenuItem_actionPerformed(ActionEvent e) { @@ -3135,12 +3459,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getAlignment().getSequences()); } } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + viewport.sortByTree = sortByTree.isSelected(); + } + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + viewport.followSelection = listenToViewSelections.isSelected(); + } /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { @@ -3151,7 +3484,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { @@ -3162,7 +3495,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { @@ -3173,7 +3506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { @@ -3184,11 +3517,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwType - * DOCUMENT ME! + * DOCUMENT ME! * @param title - * DOCUMENT ME! + * DOCUMENT ME! */ void NewTreePanel(String type, String pwType, String title) { @@ -3233,8 +3566,8 @@ 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( @@ -3272,9 +3605,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param title - * DOCUMENT ME! + * DOCUMENT ME! * @param order - * DOCUMENT ME! + * DOCUMENT ME! */ public void addSortByOrderMenuItem(String title, final AlignmentOrder order) @@ -3303,10 +3636,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Add a new sort by annotation score menu item * * @param sort - * the menu to add the option to + * the menu to add the option to * @param scoreLabel - * the label used to retrieve scores for each sequence on the - * alignment + * the label used to retrieve scores for each sequence on the + * alignment */ public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) @@ -3318,8 +3651,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport - .getAlignment());// ,viewport.getSelectionGroup()); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); @@ -3367,8 +3700,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Enumeration labels = scoreSorts.keys(); while (labels.hasMoreElements()) { - addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels - .nextElement()); + addSortByAnnotScoreMenuItem(sortByAnnotScore, + (String) labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); @@ -3386,9 +3719,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * modified. * * @param treePanel - * Displayed tree window. + * Displayed tree window. * @param title - * SortBy menu item title. + * SortBy menu item title. */ public void buildTreeMenu() { @@ -3418,21 +3751,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (i = 0; i < treePanels.size(); i++) { - TreePanel tp = (TreePanel) treePanels.elementAt(i); + final TreePanel tp = (TreePanel) treePanels.elementAt(i); final JMenuItem item = new JMenuItem(tp.getTitle()); final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - SequenceI[] oldOrder = viewport.getAlignment() - .getSequencesArray(); - AlignmentSorter.sortByTree(viewport.getAlignment(), tree); - - addHistoryItem(new OrderCommand("Tree Sort", oldOrder, - viewport.alignment)); - - alignPanel.paintAlignment(true); + tp.sortByTree_actionPerformed(null); + addHistoryItem(tp.sortAlignmentIn(alignPanel)); + } }); @@ -3440,6 +3768,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.alignment)); + } + alignPanel.paintAlignment(true); + return true; + } + /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. @@ -3503,10 +3844,13 @@ 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; } @@ -3515,13 +3859,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Select a newick-like tree file"); chooser.setToolTipText("Load a tree file"); @@ -3545,8 +3889,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (fin != null && fin.hasWarningMessage()) { - JOptionPane.showMessageDialog(Desktop.desktop, fin - .getWarningMessage(), "Possible problem with tree file", + JOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), "Possible problem with tree file", JOptionPane.WARNING_MESSAGE); } } @@ -3574,19 +3918,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * current alignment view * * @param nf - * the tree + * the tree * @param title - * tree viewer title + * tree viewer title * @param input - * Associated alignment input data (or null) + * Associated alignment input data (or null) * @param w - * width + * width * @param h - * height + * height * @param x - * position + * position * @param y - * position + * position * @return TreePanel handle */ public TreePanel ShowNewickTree(NewickFile nf, String title, @@ -3619,98 +3963,201 @@ 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) - Vector wsmenu = new Vector(); - final IProgressIndicator af = this; - if (msaws != null) + while (buildingMenu) + { + try { - // 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.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(msawsmenu, this); - - } - wsmenu.add(msawsmenu); - } - if (secstrpr != null) + System.err.println("Waiting for building menu to finish."); + Thread.sleep(10); + } catch (Exception e) { - // 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.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(secstrmenu, this); - } - wsmenu.add(secstrmenu); } - if (seqsrch != null) + ; + } + final AlignFrame me = this; + buildingMenu = true; + new Thread(new Runnable() + { + public void run() { - // Add any sequence search services - final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - for (int i = 0, j = seqsrch.size(); i < j; i++) + 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. + final Vector wsmenu = new Vector(); + final IProgressIndicator af = me; + final JMenu msawsmenu = new JMenu("Alignment"); + final JMenu secstrmenu = new JMenu( + "Secondary Structure Prediction"); + final JMenu seqsrchmenu = new JMenu( + "Sequence Database Search"); + final JMenu analymenu = new JMenu( + "Analysis"); + // JAL-940 - only show secondary structure prediction services from the legacy server + if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) + // && + 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 = null; // (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services + .get("SecStrPred"); + Vector seqsrch = null; // (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) + { + // Add any Multiple Sequence Alignment Services + 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, me); + + } + } + if (secstrpr != null) + { + // Add any secondary structure prediction services + 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, me); + } + } + if (seqsrch != null) + { + // Add any sequence search services + 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, me); + } + } + } + + // TODO: move into separate menu builder class. + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) + { + if (jws2servs.hasServices()) + { + jws2servs.attachWSMenuEntry(msawsmenu, me); + } + } + } + // Add all submenus in the order they should appear on the web services menu + wsmenu.add(msawsmenu); + wsmenu.add(secstrmenu); + wsmenu.add(analymenu); + // No search services yet + // wsmenu.add(seqsrchmenu); + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + try + { + webService.removeAll(); + // first, add discovered services onto the webservices menu + if (wsmenu.size() > 0) + { + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add((JMenu) wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); + } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + } catch (Exception e) + { + } + ; + } + }); + } catch (Exception e) { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch - .elementAt(i); - jalview.ws.WSClient impl = jalview.ws.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(seqsrchmenu, this); } - // finally, add the whole shebang onto the webservices menu - wsmenu.add(seqsrchmenu); - } - resetWebServiceMenu(); - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add((JMenu) wsmenu.get(i)); + ; + + buildingMenu = false; } - } - else - { - resetWebServiceMenu(); - this.webService.add(this.webServiceNoServices); - } + }).start(); + } + /** - * empty the web service menu and add any ad-hoc functions not dynamically - * discovered. + * construct any groupURL type service menu entries. * + * @param webService */ - private void resetWebServiceMenu() + private void build_urlServiceMenu(JMenu webService) { - webService.removeAll(); - build_fetchdbmenu(webService); + // TODO: remove this code when 2.7 is released + // DEBUG - alignmentView + /* + * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final + * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { + * + * @Override public void actionPerformed(ActionEvent e) { + * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment, + * af.viewport.colSel, af.viewport.selectionGroup); } + * + * }); webService.add(testAlView); + */ + // TODO: refactor to RestClient discoverer and merge menu entries for + // rest-style services with other types of analysis/calculation service + // SHmmr test client - still being implemented. + // DEBUG - alignmentView + + for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) { + client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this); + } + + if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + { + jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry( + webService, this); + } } /* @@ -3764,8 +4211,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); final Alignment ds = dataset; - String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, - dataset); + String[] ptypes = (selection == null || selection.length == 0) ? null + : CrossRef.findSequenceXrefTypes(dna, selection, dataset); // Object[] prods = // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), // selection, dataset, true); @@ -3795,8 +4242,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception e) { jalview.bin.Cache.log - .warn( - "canTranslate threw an exception - please report to help@jalview.org", + .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } @@ -3886,13 +4332,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // old way try { - return (jalview.analysis.Dna.canTranslate(selection, viewport - .getViewAsVisibleContigs(true))); + return (jalview.analysis.Dna.canTranslate(selection, + viewport.getViewAsVisibleContigs(true))); } catch (Exception e) { jalview.bin.Cache.log - .warn( - "canTranslate threw an exception - please report to help@jalview.org", + .warn("canTranslate threw an exception - please report to help@jalview.org", e); return false; } @@ -3971,9 +4416,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Try to load a features file onto the alignment. * * @param file - * contents or path to retrieve file + * contents or path to retrieve file * @param type - * access mode of file (see jalview.io.AlignFile) + * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed corectly. */ public boolean parseFeaturesFile(String file, String type) @@ -3981,9 +4426,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean featuresFile = false; try { - featuresFile = new FeaturesFile(file, type).parse(viewport.alignment - .getDataset(), alignPanel.seqPanel.seqCanvas - .getFeatureRenderer().featureColours, false); + featuresFile = new FeaturesFile(file, type) + .parse(viewport.alignment.getDataset(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, + false, jalview.bin.Cache.getDefault( + "RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { ex.printStackTrace(); @@ -3993,6 +4440,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showSequenceFeatures = true; showSeqFeatures.setSelected(true); + if (alignPanel.seqPanel.seqCanvas.fr != null) + { + // update the min/max ranges where necessary + alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + } + if (featureSettings != null) + { + featureSettings.setTableData(); + } alignPanel.paintAlignment(true); } @@ -4048,8 +4504,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } java.net.URI uri = new java.net.URI(s); - java.io.File file = new java.io.File(uri); - files.add(file); + // check to see if we can handle this kind of URI + if (uri.getScheme().toLowerCase().startsWith("http")) + { + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + files.add(file.toString()); + } } } } catch (Exception e) @@ -4060,10 +4525,127 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - + // check to see if any of these files have names matching sequences in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher(viewport + .getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList(); + ArrayList filesnotmatched = new ArrayList(); for (int i = 0; i < files.size(); i++) { - loadJalviewDataFile(files.get(i).toString()); + String file = files.get(i).toString(); + String pdbfn = ""; + String protocol = FormatAdapter.checkProtocol(file); + if (protocol == jalview.io.FormatAdapter.FILE) + { + File fl = new File(file); + pdbfn = fl.getName(); + } + else if (protocol == jalview.io.FormatAdapter.URL) + { + URL url = new URL(file); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + String type = null; + try + { + type = new IdentifyFile().Identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null) + { + if (type.equalsIgnoreCase("PDB")) + { + filesmatched.add(new Object[] + { file, protocol, mtch }); + continue; + } + } + } + // File wasn't named like one of the sequences or wasn't a PDB file. + filesnotmatched.add(file); + } + } + int assocfiles = 0; + if (filesmatched.size() > 0) + { + if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) + || JOptionPane + .showConfirmDialog( + this, + "Do you want to automatically associate the " + + filesmatched.size() + + " PDB files with sequences in the alignment that have the same name ?", + "Automatically Associate PDB files by name", + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) + + { + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // associating PDB files which have no IDs. + for (SequenceI toassoc: (SequenceI[])fm[2]) { + PDBEntry pe = new AssociatePdbFileWithSeq() + .associatePdbWithSeq((String) fm[0], (String) fm[1], + toassoc, false); + if (pe != null) + { + System.err + .println("Associated file : " + ((String) fm[0]) + + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + alignPanel.paintAlignment(true); + } + } + } + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 + && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + .showConfirmDialog( + this, + "Do you want to ignore the " + + filesnotmatched.size() + + " files whose names did not match any sequence IDs ?", + "Ignore unmatched dropped files ?", + JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + { + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + } } catch (Exception ex) { @@ -4073,43 +4655,70 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Attempt to load a "dropped" file: First by testing whether it's and - * Annotation file, then a JNet file, and finally a features file. If all are - * false then the user may have dropped an alignment file onto this + * Attempt to load a "dropped" file or URL string: First by testing whether + * it's and Annotation file, then a JNet file, and finally a features file. If + * all are false then the user may have dropped an alignment file onto this * AlignFrame. * * @param file - * either a filename or a URL string. + * either a filename or a URL string. */ - public void loadJalviewDataFile(String file) + public void loadJalviewDataFile(String file, String protocol, + String format, SequenceI assocSeq) { try { - String protocol = "File"; - - if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) + if (protocol == null) { - protocol = "URL"; + protocol = jalview.io.FormatAdapter.checkProtocol(file); } - - boolean isAnnotation = new AnnotationFile().readAnnotationFile( - viewport.alignment, file, protocol); + // if the file isn't identified, or not positively identified as some + // other filetype (PFAM is default unidentified alignment file type) then + // try to parse as annotation. + boolean isAnnotation = (format == null || format + .equalsIgnoreCase("PFAM")) ? new AnnotationFile() + .readAnnotationFile(viewport.alignment, file, protocol) + : false; if (!isAnnotation) { // try to see if its a JNet 'concise' style annotation file *before* we // try to parse it as a features file - String format = new IdentifyFile().Identify(file, protocol); + if (format == null) + { + format = new IdentifyFile().Identify(file, protocol); + } if (format.equalsIgnoreCase("JnetFile")) { jalview.io.JPredFile predictions = new jalview.io.JPredFile(file, protocol); - new JnetAnnotationMaker().add_annotation(predictions, viewport - .getAlignment(), 0, false); + new JnetAnnotationMaker().add_annotation(predictions, + viewport.getAlignment(), 0, false); isAnnotation = true; } else { + /* + * if (format.equalsIgnoreCase("PDB")) { + * + * String pdbfn = ""; // try to match up filename with sequence id try + * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new + * File(file); pdbfn = fl.getName(); } else if (protocol == + * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = + * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null) + * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport + * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { // + * attempt to find a match in the alignment SequenceI mtch = + * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while + * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l) + * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch = + * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate + * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() + * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) { + * System.err.println("Associated file : " + file + " with " + + * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // + * TODO: maybe need to load as normal otherwise return; } } + */ // try to parse it as a features file boolean isGroupsFile = parseFeaturesFile(file, protocol); // if it wasn't a features file then we just treat it as a general @@ -4187,16 +4796,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - /* (non-Javadoc) - * @see jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent) + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent + * ) */ protected void showDbRefs_actionPerformed(ActionEvent e) { viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); } - /* (non-Javadoc) - * @see jalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.ActionEvent) + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) */ protected void showNpFeats_actionPerformed(ActionEvent e) { @@ -4204,7 +4820,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * find the viewport amongst the tabs in this alignment frame and close that tab + * find the viewport amongst the tabs in this alignment frame and close that + * tab + * * @param av */ public boolean closeView(AlignViewport av) @@ -4215,7 +4833,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return true; } Component[] comp = tabbedPane.getComponents(); - for (int i=0;comp!=null && i0) - { - for (int i=0; i 0) + { + for (int i = 0; i < otherdb.length; i++) { - new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, dassource) - .fetchDBRefs(false); + String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); + if (mname == null) + { + mname = "from '" + dbname + "'"; + } + fetchr = new JMenuItem(otherdb[i]); + final String[] dassource = new String[] + { otherdb[i] }; + fetchr.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource) + .fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("Retrieve from " + dbname); + dfetch.add(fetchr); + if (comp++ == mcomp || i == (otherdb.length - 1)) + { + dfetch.setText(mname + " to '" + dbname + "'"); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } } - }).start(); + } } - }); - fetchr.setToolTipText("Retrieve from "+dbname); - dfetch.add(fetchr); - if (comp++==mcomp || i==(otherdb.length-1)) - { - dfetch.setText(mname+" to '"+dbname+"'"); - rfetch.add(dfetch); - dfetch = new JMenu(); - mname = null; - comp=0; - } } - } + }).start(); + } + /** - * Left justify the whole alignment. + * Left justify the whole alignment. */ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { @@ -4318,8 +4959,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al.justify(false); viewport.firePropertyChange("alignment", null, al); } + /** - * Right justify the whole alignment. + * Right justify the whole alignment. */ protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { @@ -4327,11 +4969,142 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al.justify(true); viewport.firePropertyChange("alignment", null, al); } + public void setShowSeqFeatures(boolean b) { showSeqFeatures.setSelected(true); viewport.setShowSequenceFeatures(true); } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. + * awt.event.ActionEvent) + */ + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowUnconserved(showNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event + * .ActionEvent) + */ + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + 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()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + if (viewport.getSelectionGroup() != null) + { + SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + viewport.getSequenceSelection(), + viewport.getAlignmentView(true).getSequenceStrings( + viewport.getGapCharacter()), + viewport.alignment.getGroups()); + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + // set view properties for each group + for (int g = 0; g < gps.length; g++) + { + 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)); + col = col.brighter(); + for (Enumeration sq = gps[g].getSequences(null).elements(); sq + .hasMoreElements(); viewport.setSequenceColour( + (SequenceI) sq.nextElement(), col)) + ; + } + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + /** + * make the given alignmentPanel the currently selected tab + * + * @param alignmentPanel + */ + public void setDisplayedView(AlignmentPanel alignmentPanel) + { + if (!viewport.getSequenceSetId().equals( + alignmentPanel.av.getSequenceSetId())) + { + throw new Error( + "Implementation error: cannot show a view from another alignment in an AlignFrame."); + } + if (tabbedPane != null + & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) + { + tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); + } + } } class PrintThread extends Thread