X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=184ffeb58ba6d1c9f0fbcde5ef8bdd73542c1bd5;hb=ef887ebe817cd6595b6275f5f51001677c377214;hp=1bd15410041b0757edbe841a0291726760f5963d;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 1bd1541..184ffeb 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -26,6 +26,7 @@ import jalview.analysis.CrossRef; import jalview.analysis.Dna; import jalview.analysis.ParseProperties; import jalview.analysis.SequenceIdMatcher; +import jalview.analysis.TreeModel; import jalview.api.AlignExportSettingI; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; @@ -34,7 +35,6 @@ import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; -import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.commands.CommandI; @@ -53,6 +53,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; import jalview.datamodel.AlignmentView; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DBRefEntry; import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; @@ -60,6 +61,11 @@ import jalview.datamodel.SeqCigar; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.ext.archaeopteryx.AptxInit; +import jalview.ext.forester.io.SupportedTreeFileFilter; +import jalview.ext.forester.io.TreeParser; +import jalview.ext.treeviewer.ExternalTreeFrame; +import jalview.ext.treeviewer.ExternalTreeViewerBindingI; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; @@ -86,6 +92,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; +import jalview.util.DBRefUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; @@ -98,6 +105,8 @@ import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; import java.awt.Component; +import java.awt.Dimension; +import java.awt.GridLayout; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; @@ -123,6 +132,7 @@ import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; +import java.io.IOException; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; @@ -131,17 +141,26 @@ import java.util.Deque; import java.util.Enumeration; import java.util.Hashtable; import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.StringTokenizer; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; +import javax.swing.JComboBox; 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.JPanel; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; +import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient; +import org.forester.archaeopteryx.webservices.WebservicesManager; + /** * DOCUMENT ME! * @@ -163,8 +182,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; - ViewportRanges vpRanges; - public AlignViewControllerI avc; List alignPanels = new ArrayList<>(); @@ -336,7 +353,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } - vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -654,9 +670,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + ViewportRanges ranges = viewport.getRanges(); + alignPanel.getSeqPanel().seqCanvas.cursorX = ranges .getStartRes(); - alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + alignPanel.getSeqPanel().seqCanvas.cursorY = ranges .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); @@ -689,10 +706,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - vpRanges.pageUp(); + viewport.getRanges().pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - vpRanges.pageDown(); + viewport.getRanges().pageDown(); break; } } @@ -1711,7 +1728,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } synchronized void slideSequences(boolean right, int size) @@ -2147,7 +2164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - vpRanges.setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2397,7 +2414,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -2423,7 +2440,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } @@ -2448,7 +2465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // JAL-2034 - should delegate to // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2479,7 +2496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2488,7 +2505,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); viewport.sendSelection(); } @@ -2548,7 +2565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - vpRanges.setStartRes(0); + viewport.getRanges().setStartRes(0); } else { @@ -2613,13 +2630,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + ViewportRanges ranges = viewport.getRanges(); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + ranges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -2652,12 +2670,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + int startRes = seq.findPosition(viewport.getRanges().getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -2713,8 +2731,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Create a new AlignmentPanel (with its own, new Viewport) */ - AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, - true); + AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel); if (!copyAnnotation) { /* @@ -2868,21 +2885,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getIdPanel().getIdCanvas() .setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.setRightAlignIds(idRightAlign.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -2915,7 +2932,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -2944,7 +2961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3048,7 +3065,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3064,7 +3081,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3072,7 +3089,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3093,7 +3110,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.paintAlignment(true); + // TODO: do we actually need to update overview for scale above change ? + alignPanel.paintAlignment(true, false); } /** @@ -3106,7 +3124,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3119,7 +3137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3132,7 +3150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3145,7 +3163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3158,7 +3176,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } public FeatureSettings featureSettings; @@ -3196,7 +3214,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } /** @@ -3353,7 +3371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setGlobalColourScheme(cs); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } /** @@ -3438,7 +3456,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3454,7 +3472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByID(viewport.getAlignment()); addHistoryItem( new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3470,7 +3488,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3487,7 +3505,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3556,15 +3574,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Constructs a tree panel and adds it to the desktop * - * @param type - * tree type (NJ or AV) - * @param modelName - * name of score model used to compute the tree - * @param options - * parameters for the distance or similarity calculation + * @param params + * @param treeAlgo + * + * @param tree + * + * */ - void newTreePanel(String type, String modelName, - SimilarityParamsI options) + void newTreePanel(TreeModel tree, String treeAlgo, + String substitutionMatrix) { String frameTitle = ""; TreePanel tp; @@ -3576,7 +3594,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ - for (SequenceI _s : sg.getSequences()) + for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx? { if (_s.getLength() < sg.getEndRes()) { @@ -3600,7 +3618,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - tp = new TreePanel(alignPanel, type, modelName, options); + tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix); frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : ""); frameTitle += " from "; @@ -3644,7 +3662,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -3673,7 +3691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -3730,6 +3748,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + /** * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a * TreePanel with an appropriate jalview.analysis.AlignmentSorter @@ -3745,15 +3764,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, List comps = PaintRefresher.components .get(viewport.getSequenceSetId()); List treePanels = new ArrayList<>(); + + Map aptxFrames = AptxInit + .getAllAptxFrames(); + for (Component comp : comps) { + // old treepanels if (comp instanceof TreePanel) { treePanels.add((TreePanel) comp); } + } - if (treePanels.size() < 1) + if (treePanels.isEmpty() && aptxFrames.isEmpty()) { sortByTreeMenu.setVisible(false); return; @@ -3761,6 +3786,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sortByTreeMenu.setVisible(true); + for (Entry aptxFrameWithBinding : aptxFrames + .entrySet()) + { + ExternalTreeFrame aptxFrame = aptxFrameWithBinding.getKey(); + ExternalTreeViewerBindingI binding = aptxFrameWithBinding.getValue(); + + // future support for multiple tabs + // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame + // .getMainPanel().getTreePanels()) + { + final JMenuItem item = new JMenuItem( + aptxFrame.getTree().getTreeName()); + + item.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + binding.sortByTree_actionPerformed(); + addHistoryItem(binding.sortAlignmentIn(alignPanel)); + } + + }); + sortByTreeMenu.add(item); + } + + + + } + + + + + + // old treepanels for (final TreePanel tp : treePanels) { final JMenuItem item = new JMenuItem(tp.getTitle()); @@ -3788,7 +3849,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); return true; } @@ -3878,14 +3939,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void loadTreeMenuItem_actionPerformed(ActionEvent e) { + chooseTreeFile(); + } + + @Override + protected void loadTreeUrlItem_actionPerformed(ActionEvent e) + { + chooseTreeUrl(); + } + + @Override + protected void loadTreeBaseStudy_actionPerformed(ActionEvent e) + { + chooseTreeDb(0, null); + + } + + @Override + protected void loadTreeBase_actionPerformed(ActionEvent e) + { + chooseTreeDb(1, null); + + } + @Override + protected void loadTreePfam_actionPerformed(ActionEvent e) + { + + // only DBRefs of first sequence are checked for matching DB for now, + // iterating through them all seems excessive + SequenceI seq = viewport.getAlignment().getSequenceAt(0); + String dbId = null; + for (DBRefEntry pfamRef : DBRefUtils + .searchRefsForSource(seq.getDBRefs(), "pfam")) + { + if (pfamRef.getAccessionId().startsWith("PF")) + { + dbId = pfamRef.getAccessionId().replaceAll("[A-Za-z]", ""); + } + + } + chooseTreeDb(2, dbId); + + } + @Override + protected void loadTreeFam_actionPerformed(ActionEvent e) + { + chooseTreeDb(3, null); + + } + + @Override + protected void loadTreeOfLife_actionPerformed(ActionEvent e) + { + chooseTreeDb(4, null); + + } + + + + + + public void chooseTreeFile() + { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( - MessageManager.getString("label.select_newick_like_tree_file")); + MessageManager.getString("label.select_tree_file")); // modify chooser.setToolTipText( - MessageManager.getString("label.load_tree_file")); + MessageManager.getString("label.load_tree_for_sequence_set")); + for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter + .values()) + { + chooser.setFileFilter(treeFormat.getTreeFilter()); + } int value = chooser.showOpenDialog(null); @@ -3893,27 +4021,101 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String filePath = chooser.getSelectedFile().getPath(); Cache.setProperty("LAST_DIRECTORY", filePath); - NewickFile fin = null; - try + + + TreeParser treeParser = new TreeParser(filePath); + treeParser.loadTree(viewport); + + } + } + + /** + * Break up and move to TreeParser? + */ + public void chooseTreeUrl() + { + + JLabel label = new JLabel( + MessageManager.getString("label.tree_url_example")); + // add "example" button + final JComboBox history = new JComboBox<>(); + + JPanel panel = new JPanel(new GridLayout(2, 1)); + panel.add(label); + panel.add(history); + history.setPreferredSize(new Dimension(400, 20)); + history.setEditable(true); + history.addItem("http://www."); + + String historyItems = jalview.bin.Cache.getProperty("RECENT_URL"); + + StringTokenizer st; + + if (historyItems != null) { - fin = new NewickFile(filePath, DataSourceType.FILE); - viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); - } catch (Exception ex) + st = new StringTokenizer(historyItems, "\t"); + + while (st.hasMoreTokens()) { - JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - MessageManager.getString("label.problem_reading_tree_file"), - JvOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); + history.addItem(st.nextToken()); + } } - if (fin != null && fin.hasWarningMessage()) + + int reply = JvOptionPane.showInternalConfirmDialog(this, panel, + MessageManager.getString("label.load_tree_url"), + JvOptionPane.OK_CANCEL_OPTION); + + if (reply == JvOptionPane.OK_OPTION) + { + + String urlString = history.getSelectedItem().toString(); + URL treeUrl; + + try { - JvOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), - MessageManager - .getString("label.possible_problem_with_tree_file"), - JvOptionPane.WARNING_MESSAGE); + FileFormatI format = null; + + format = new IdentifyFile().identify(urlString, DataSourceType.URL); + // add actual use for the format identification (jalview .jar files) + treeUrl = new URL(urlString); + AptxInit.createInstancesFromUrl(treeUrl, viewport); + + } catch (IOException | RuntimeException e) + { + JvOptionPane.showMessageDialog(this, MessageManager.formatMessage( + "exception.failed_to_read_data_from_source", new String[] + { urlString }), + MessageManager.getString("label.url_not_found"), + JvOptionPane.ERROR_MESSAGE); + e.printStackTrace(); } } + else + { + + } + } + + /** + * Disgustingly hardcoded atm. + * + * @param databaseIndex + */ + public void chooseTreeDb(int databaseIndex, String defaultIdentifier) + { + final WebservicesManager webservices_manager = WebservicesManager + .getInstance(); + final PhylogeniesWebserviceClient client = webservices_manager + .getAvailablePhylogeniesWebserviceClient(databaseIndex); + String identifier = JvOptionPane + .showInternalInputDialog(Desktop.desktop, + client.getInstructions() + "\n(Reference: " + + client.getReference() + ")", + client.getDescription(), JvOptionPane.QUESTION_MESSAGE, + null, null, defaultIdentifier) + .toString(); + + AptxInit.createInstancesFromDb(client, identifier, viewport); } public TreePanel showNewickTree(NewickFile nf, String treeTitle) @@ -3979,6 +4181,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, private boolean buildingMenu = false; + public void BuildTreeDbMenu() + { + + } /** * Generates menu items and listener event actions for web service clients * @@ -4031,6 +4237,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); + final JMenu phylogenmenu = new JMenu("Phylogenetic inference"); + // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) @@ -4071,6 +4279,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wsmenu.add(secstrmenu); wsmenu.add(dismenu); wsmenu.add(analymenu); + wsmenu.add(phylogenmenu); // No search services yet // wsmenu.add(seqsrchmenu); @@ -4151,7 +4360,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildingMenu = false; } - }).start(); + }, "BuildWebServiceThread").start(); } @@ -4259,7 +4468,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showProductsFor(final SequenceI[] sel, final boolean _odna, final String source) { - new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this)) + new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this), + "CrossReferencesThread") .start(); } @@ -4386,7 +4596,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - List files = new ArrayList<>(); + final AlignFrame thisaf = this; + final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try @@ -4398,133 +4609,146 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (files != null) { - try + new Thread(new Runnable() { - // 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++) + @Override + public void run() { - String file = files.get(i).toString(); - String pdbfn = ""; - DataSourceType protocol = FormatAdapter.checkProtocol(file); - if (protocol == DataSourceType.FILE) - { - File fl = new File(file); - pdbfn = fl.getName(); - } - else if (protocol == DataSourceType.URL) - { - URL url = new URL(file); - pdbfn = url.getFile(); - } - if (pdbfn.length() > 0) + try { - // attempt to find a match in the alignment - SequenceI[] mtch = idm.findAllIdMatches(pdbfn); - int l = 0, c = pdbfn.indexOf("."); - while (mtch == null && c != -1) + // 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++) { - do + String file = files.get(i).toString(); + String pdbfn = ""; + DataSourceType protocol = FormatAdapter.checkProtocol(file); + if (protocol == DataSourceType.FILE) { - l = c; - } while ((c = pdbfn.indexOf(".", l)) > l); - if (l > -1) - { - pdbfn = pdbfn.substring(0, l); + File fl = new File(file); + pdbfn = fl.getName(); } - mtch = idm.findAllIdMatches(pdbfn); - } - if (mtch != null) - { - FileFormatI type = null; - try - { - type = new IdentifyFile().identify(file, protocol); - } catch (Exception ex) + else if (protocol == DataSourceType.URL) { - type = null; + URL url = new URL(file); + pdbfn = url.getFile(); } - if (type != null && type.isStructureFile()) + if (pdbfn.length() > 0) { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; + // 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) + { + FileFormatI type = null; + try + { + type = new IdentifyFile().identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null && type.isStructureFile()) + { + 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); } } - // 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) - || JvOptionPane.showConfirmDialog(this, - MessageManager.formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] - { Integer.valueOf(filesmatched.size()) - .toString() }), - MessageManager.getString( - "label.automatically_associate_structure_files_by_name"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) - - { - for (Object[] fm : filesmatched) + int assocfiles = 0; + if (filesmatched.size() > 0) { - // 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]) + if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) + || JvOptionPane.showConfirmDialog(thisaf, + MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }), + MessageManager.getString( + "label.automatically_associate_structure_files_by_name"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) + { - PDBEntry pe = new AssociatePdbFileWithSeq() - .associatePdbWithSeq((String) fm[0], - (DataSourceType) fm[1], toassoc, false, - Desktop.instance); - if (pe != null) + for (Object[] fm : filesmatched) { - System.err.println("Associated file : " + ((String) fm[0]) - + " with " + toassoc.getDisplayId(true)); - assocfiles++; + // 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], + (DataSourceType) fm[1], toassoc, false, + Desktop.instance); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); } } - alignPanel.paintAlignment(true); } - } - } - if (filesnotmatched.size() > 0) - { - if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) - || JvOptionPane.showConfirmDialog(this, - "" + MessageManager.formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] - { Integer.valueOf(filesnotmatched.size()) - .toString() }) - + "", - MessageManager.getString( - "label.ignore_unmatched_dropped_files"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) - { - return; - } - for (String fn : filesnotmatched) + if (filesnotmatched.size() > 0) + { + if (assocfiles > 0 && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(thisaf, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf( + filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) + { + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); + } + + } + } catch (Exception ex) { - loadJalviewDataFile(fn, null, null, null); + ex.printStackTrace(); } - } - } catch (Exception ex) - { - ex.printStackTrace(); - } + }, "DropFileThread").start(); } } @@ -4638,7 +4862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } else @@ -4653,7 +4877,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } catch (Exception ex) { @@ -4895,7 +5119,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); dbRefFetcher.fetchDBRefs(false); } - }).start(); + }, "BuildFetchDBMenuThread").start(); } @@ -5178,7 +5402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -5267,7 +5491,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5279,7 +5503,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().setSeqrep(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5369,7 +5593,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /**