X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b571f2c3868f140483401b8e935b3b4eecf6f3e;hb=92f7b5ee3bbdb5456d498f1c2780d90420491342;hp=6ee243eedff1a43cf9d21c61d6b150d396e70a6e;hpb=d25930a1576379cd45940caa9c1f0e4cf01fbc2c;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 6ee243e..9b571f2 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * @@ -17,28 +17,111 @@ */ 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.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.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; +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.RNAHelicesColourChooser; +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.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; +import jalview.ws.seqfetcher.DbSourceProxy; + +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.List; +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! @@ -202,7 +285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { - if (viewport.conservation == null) + if (viewport.getAlignmentConservationAnnotation() == null) { BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); @@ -228,7 +311,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); addServiceListeners(); - setGUINucleotide(viewport.alignment.isNucleotide()); + setGUINucleotide(viewport.getAlignment().isNucleotide()); } setMenusFromViewport(viewport); @@ -322,6 +405,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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) @@ -488,12 +582,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (newPanel) { - if (ap.av.padGaps) + if (ap.av.isPadGaps()) { - ap.av.alignment.padGaps(); + ap.av.getAlignment().padGaps(); } ap.av.updateConservation(ap); ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); } } @@ -516,10 +611,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; - // Do this once to get current state - BuildWebServiceMenu(); Desktop.instance.addJalviewPropertyChangeListener("services", - thisListener=new java.beans.PropertyChangeListener() + thisListener = new java.beans.PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { @@ -529,7 +622,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SwingUtilities.invokeLater(new Runnable() { - @Override public void run() { System.err @@ -547,10 +639,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, javax.swing.event.InternalFrameEvent evt) { System.out.println("deregistering discoverer listener"); - Desktop.instance.removeJalviewPropertyChangeListener("services",thisListener); + 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) @@ -559,11 +660,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + // } } /** @@ -585,7 +689,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void setMenusFromViewport(AlignViewport av) { - padGapsMenuitem.setSelected(av.padGaps); + padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.showColourText); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); conservationMenuItem.setSelected(av.getConservationSelected()); @@ -600,11 +704,13 @@ 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); + showNonconservedMenuItem.setSelected(av.getShowUnconserved()); + showGroupConsensus.setSelected(av.isShowGroupConsensus()); + showGroupConservation.setSelected(av.isShowGroupConservation()); + showConsensusHistogram.setSelected(av.isShowConsensusHistogram()); + showSequenceLogo.setSelected(av.isShowSequenceLogo()); + normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo()); + setColourSelected(ColourSchemeProperty.getColourName(av .getGlobalColourScheme())); @@ -613,7 +719,12 @@ 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.getAlignment().hasRNAStructure()); + rnahelicesColour + .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); setShowProductsEnabled(); updateEditMenuBar(); @@ -669,7 +780,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBars.put(lId, progressPanel); } // update GUI - setMenusForViewport(); + // setMenusForViewport(); validate(); } @@ -693,8 +804,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -832,8 +945,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ 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); @@ -904,7 +1017,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { int reply = JOptionPane .showInternalConfirmDialog( @@ -921,10 +1034,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } FormatAdapter f = new FormatAdapter(); - String output = f.formatSequences(format, - (Alignment) viewport.alignment, // class cast exceptions will + String output = f.formatSequences( + format, + (Alignment) viewport.getAlignment(), // class cast exceptions will // occur in the distant future - omitHidden, f.getCacheSuffixDefault(format), viewport.colSel); + omitHidden, f.getCacheSuffixDefault(format), + viewport.getColumnSelection()); if (output == null) { @@ -984,7 +1099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { int reply = JOptionPane .showInternalConfirmDialog( @@ -1003,11 +1118,20 @@ 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.getAlignment(), omitHidden, + viewport.getColumnSelection())); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); + cap.dispose(); + } + } /** @@ -1018,9 +1142,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ 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) @@ -1077,17 +1201,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter().exportAnnotations(alignPanel, - viewport.showAnnotation ? viewport.alignment - .getAlignmentAnnotation() : null, viewport.alignment - .getGroups(), - ((Alignment) viewport.alignment).alignmentProperties); + viewport.showAnnotation ? viewport.getAlignment() + .getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), ((Alignment) viewport + .getAlignment()).alignmentProperties); } 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"); @@ -1098,7 +1222,7 @@ 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); } } @@ -1218,9 +1342,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.historyList.push(command); viewport.redoList.clear(); updateEditMenuBar(); - viewport.hasHiddenColumns = (viewport.colSel != null - && viewport.colSel.getHiddenColumns() != null && viewport.colSel - .getHiddenColumns().size() > 0); + viewport.updateHiddenColumns(); + // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); } } @@ -1243,7 +1369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport != null) { return new AlignmentI[] - { viewport.alignment }; + { viewport.getAlignment() }; } return null; } @@ -1267,11 +1393,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != null) { - originalSource.hasHiddenColumns = (viewport.colSel != null - && viewport.colSel.getHiddenColumns() != null && viewport.colSel - .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + if (originalSource != viewport) + { + Cache.log + .warn("Implementation worry: mismatch of viewport origin for undo"); + } + originalSource.updateHiddenColumns(); + // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != + // null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } } @@ -1297,11 +1431,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != null) { - originalSource.hasHiddenColumns = (viewport.colSel != null - && viewport.colSel.getHiddenColumns() != null && viewport.colSel - .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, - originalSource.alignment.getSequences()); + + if (originalSource != viewport) + { + Cache.log + .warn("Implementation worry: mismatch of viewport origin for redo"); + } + originalSource.updateHiddenColumns(); + // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != + // null + // && viewport.getColumnSelection().getHiddenColumns() != null && + // viewport.getColumnSelection() + // .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, originalSource + .getAlignment().getSequences()); } } @@ -1323,7 +1466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (comps.elementAt(i) instanceof AlignmentPanel) { - if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) + if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment()) { originalSource = ((AlignmentPanel) comps.elementAt(i)).av; break; @@ -1338,7 +1481,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // the current view against the closed view first if (al != null) { - PaintRefresher.validateSequences(al, viewport.alignment); + PaintRefresher.validateSequences(al, viewport.getAlignment()); } originalSource = viewport; @@ -1364,46 +1507,46 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (up) { - for (int i = 1; i < viewport.alignment.getHeight(); i++) + for (int i = 1; i < viewport.getAlignment().getHeight(); i++) { - SequenceI seq = viewport.alignment.getSequenceAt(i); + SequenceI seq = viewport.getAlignment().getSequenceAt(i); if (!sg.getSequences(null).contains(seq)) { continue; } - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1); if (sg.getSequences(null).contains(temp)) { continue; } - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); + viewport.getAlignment().getSequences().setElementAt(temp, i); + viewport.getAlignment().getSequences().setElementAt(seq, i - 1); } } else { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--) { - SequenceI seq = viewport.alignment.getSequenceAt(i); + SequenceI seq = viewport.getAlignment().getSequenceAt(i); if (!sg.getSequences(null).contains(seq)) { continue; } - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1); if (sg.getSequences(null).contains(temp)) { continue; } - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); + viewport.getAlignment().getSequences().setElementAt(temp, i); + viewport.getAlignment().getSequences().setElementAt(seq, i + 1); } } @@ -1415,15 +1558,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Vector sg = new Vector(); if (viewport.cursorMode) { - sg.addElement(viewport.alignment - .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + sg.addElement(viewport.getAlignment().getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport.alignment - .getHeight()) + && viewport.getSelectionGroup().getSize() != viewport + .getAlignment().getHeight()) { sg = viewport.getSelectionGroup().getSequences( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } if (sg.size() < 1) @@ -1433,10 +1576,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Vector invertGroup = new Vector(); - for (int i = 0; i < viewport.alignment.getHeight(); i++) + for (int i = 0; i < viewport.getAlignment().getHeight(); i++) { - if (!sg.contains(viewport.alignment.getSequenceAt(i))) - invertGroup.add(viewport.alignment.getSequenceAt(i)); + if (!sg.contains(viewport.getAlignment().getSequenceAt(i))) + invertGroup.add(viewport.getAlignment().getSequenceAt(i)); } SequenceI[] seqs1 = new SequenceI[sg.size()]; @@ -1512,7 +1655,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs = viewport.getSelectionAsNewSequence(); String[] omitHidden = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { omitHidden = viewport.getViewAsString(true); } @@ -1527,11 +1670,11 @@ 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); @@ -1539,7 +1682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } Vector hiddenColumns = null; - if (viewport.hasHiddenColumns) + if (viewport.hasHiddenColumns()) { hiddenColumns = new Vector(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport @@ -1558,7 +1701,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } Desktop.jalviewClipboard = new Object[] - { seqs, viewport.alignment.getDataset(), hiddenColumns }; + { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; statusBar.setText("Copied " + seqs.length + " sequences to clipboard."); } @@ -1794,8 +1937,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } buildSortByAnnotationScoresMenu(); } - viewport.firePropertyChange("alignment", null, alignment - .getSequences()); + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); } else @@ -1889,7 +2032,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // If the cut affects all sequences, remove highlighted columns - if (sg.getSize() == viewport.alignment.getHeight()) + if (sg.getSize() == viewport.getAlignment().getHeight()) { viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); @@ -1906,11 +2049,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, - viewport.alignment)); + viewport.getAlignment())); viewport.setSelectionGroup(null); viewport.sendSelection(); - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); @@ -1933,7 +2076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ protected void deleteGroups_actionPerformed(ActionEvent e) { - viewport.alignment.deleteAllGroups(); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); @@ -1956,7 +2099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth() - 1); + sg.setEndRes(viewport.getAlignment().getWidth() - 1); viewport.setSelectionGroup(sg); viewport.sendSelection(); alignPanel.paintAlignment(true); @@ -1983,6 +2126,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.paintAlignment(true); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); } /** @@ -2008,14 +2152,15 @@ 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(); } /** @@ -2060,11 +2205,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } TrimRegionCommand trimRegion; @@ -2072,23 +2217,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", TrimRegionCommand.TRIM_LEFT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); viewport.setStartRes(0); } else { trimRegion = new TrimRegionCommand("Remove Right", TrimRegionCommand.TRIM_RIGHT, seqs, column, - viewport.alignment, viewport.colSel, - viewport.selectionGroup); + viewport.getAlignment(), viewport.getColumnSelection(), + viewport.getSelectionGroup()); } statusBar.setText("Removed " + trimRegion.getSize() + " columns."); addHistoryItem(trimRegion); - Vector groups = viewport.alignment.getGroups(); + Vector groups = viewport.getAlignment().getGroups(); for (int i = 0; i < groups.size(); i++) { @@ -2097,7 +2242,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { - viewport.alignment.deleteGroup(sg); + viewport.getAlignment().deleteGroup(sg); } } @@ -2114,23 +2259,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } RemoveGapColCommand removeGapCols = new RemoveGapColCommand( - "Remove Gapped Columns", seqs, start, end, viewport.alignment); + "Remove Gapped Columns", seqs, start, end, + viewport.getAlignment()); addHistoryItem(removeGapCols); @@ -2139,7 +2285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); @@ -2160,28 +2306,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { - int start = 0, end = viewport.alignment.getWidth() - 1; + int start = 0, end = viewport.getAlignment().getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.hiddenRepSequences); + viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else { - seqs = viewport.alignment.getSequencesArray(); + seqs = viewport.getAlignment().getSequencesArray(); } // This is to maintain viewport position on first residue // of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); + SequenceI seq = viewport.getAlignment().getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, - viewport.alignment)); + viewport.getAlignment())); viewport.setStartRes(seq.findIndex(startRes) - 1); @@ -2198,7 +2344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void padGapsMenuitem_actionPerformed(ActionEvent e) { - viewport.padGaps = padGapsMenuitem.isSelected(); + viewport.setPadGaps(padGapsMenuitem.isSelected()); viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } @@ -2226,8 +2372,57 @@ 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.getAlignment().deleteAllGroups(); + for (AlignmentAnnotation alan : newap.av.getAlignment() + .getAlignmentAnnotation()) + { + if (!alan.autoCalculated) + { + newap.av.getAlignment().deleteAnnotation(alan); + } + ; + } + } newap.av.gatherViewsHere = false; @@ -2240,8 +2435,19 @@ 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(); @@ -2259,7 +2465,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, while (existingNames.contains(newViewName)) { - newViewName = "View " + (++index); + newViewName = viewTitle + " " + (++index); } newap.av.viewName = newViewName; @@ -2271,6 +2477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.gatherViewsHere = true; } tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; } public void expandViews_actionPerformed(ActionEvent e) @@ -2395,8 +2602,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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) + if ((viewport.getColumnSelection() != null + && viewport.getColumnSelection().getSelected() != null && viewport + .getColumnSelection().getSelected().size() > 0) || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg .getEndRes())) { @@ -2419,12 +2627,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (toggleSeqs) { - if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + if (sg != null && sg.getSize() != viewport.getAlignment().getHeight()) { hideSelSequences_actionPerformed(null); hide = true; } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + else if (!(toggleCols && viewport.getColumnSelection().getSelected() + .size() > 0)) { showAllSeqs_actionPerformed(null); } @@ -2432,12 +2641,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (toggleCols) { - if (viewport.colSel.getSelected().size() > 0) + if (viewport.getColumnSelection().getSelected().size() > 0) { hideSelColumns_actionPerformed(null); if (!toggleSeqs) { - viewport.selectionGroup = sg; + viewport.setSelectionGroup(sg); } } else if (!hide) @@ -2646,58 +2855,9 @@ 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.getAlignment()) + .formatAsHtml(); + editPane.setText("" + contents.toString() + ""); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); @@ -2721,19 +2881,18 @@ 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); } @@ -2762,9 +2921,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void clustalColour_actionPerformed(ActionEvent e) { - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment - .getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment() + .getSequences(), viewport.getAlignment().getWidth())); } /** @@ -2855,11 +3013,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour(new NucleotideColourScheme()); } + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + + /* + * public void covariationColour_actionPerformed(ActionEvent e) { + * changeColour(new + * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation + * ()[0])); } + */ public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } + /** * DOCUMENT ME! * @@ -2900,13 +3074,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getConservationSelected()) { - Alignment al = (Alignment) viewport.alignment; + Alignment al = (Alignment) viewport.getAlignment(); 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); + c.verdict(false, viewport.getConsPercGaps()); cs.setConservation(c); @@ -2918,14 +3092,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cs.setConservation(null); } - cs.setConsensus(viewport.hconsensus); + cs.setConsensus(viewport.getSequenceConsensusHash()); } viewport.setGlobalColourScheme(cs); if (viewport.getColourAppliesToAllGroups()) { - Vector groups = viewport.alignment.getGroups(); + Vector groups = viewport.getAlignment().getGroups(); for (int i = 0; i < groups.size(); i++) { @@ -2939,8 +3113,8 @@ 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 + .getHiddenRepSequences()), sg.getWidth()); } else if (cs instanceof UserColourScheme) { @@ -2962,9 +3136,9 @@ 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.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); } else { @@ -2974,11 +3148,11 @@ 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 + .getHiddenRepSequences()), sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + c.verdict(false, viewport.getConsPercGaps()); sg.cs.setConservation(c); } else @@ -3005,10 +3179,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { - SliderPanel.setPIDSliderSource(alignPanel, viewport - .getGlobalColourScheme(), "Background"); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showPIDSlider(); } } @@ -3022,10 +3196,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void modifyConservation_actionPerformed(ActionEvent e) { if (viewport.getConservationSelected() - && viewport.globalColourScheme != null) + && viewport.getGlobalColourScheme() != null) { SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); + viewport.getGlobalColourScheme(), "Background"); SliderPanel.showConservationSlider(); } } @@ -3118,8 +3292,7 @@ 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, @@ -3193,7 +3366,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByPID(viewport.getAlignment(), viewport .getAlignment().getSequenceAt(0), null); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3207,7 +3380,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3222,7 +3396,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3237,7 +3411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByGroup(viewport.getAlignment()); addHistoryItem(new OrderCommand("Group Sort", oldOrder, - viewport.alignment)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } @@ -3311,6 +3485,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + viewport.sortByTree = sortByTree.isSelected(); + } + + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + viewport.followSelection = listenToViewSelections.isSelected(); + } + /** * DOCUMENT ME! * @@ -3409,7 +3594,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // are the visible sequences aligned? - if (!viewport.alignment.isAligned(false)) + if (!viewport.getAlignment().isAligned(false)) { JOptionPane .showMessageDialog( @@ -3423,7 +3608,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - if (viewport.alignment.getHeight() < 2) + if (viewport.getAlignment().getHeight() < 2) { return; } @@ -3466,8 +3651,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); - addHistoryItem(new OrderCommand(order.getName(), oldOrder, - viewport.alignment)); + addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport + .getAlignment())); alignPanel.paintAlignment(true); } @@ -3493,10 +3678,10 @@ 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)); + viewport.getAlignment())); alignPanel.paintAlignment(true); } }); @@ -3516,18 +3701,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void buildSortByAnnotationScoresMenu() { - if (viewport.alignment.getAlignmentAnnotation() == null) + if (viewport.getAlignment().getAlignmentAnnotation() == null) { return; } - if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) + if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple Hashtable scoreSorts = new Hashtable(); AlignmentAnnotation aann[]; - Enumeration sq = viewport.alignment.getSequences().elements(); + Enumeration sq = viewport.getAlignment().getSequences().elements(); while (sq.hasMoreElements()) { aann = ((SequenceI) sq.nextElement()).getAnnotation(); @@ -3542,13 +3727,13 @@ 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(); - _annotationScoreVectorHash = viewport.alignment + _annotationScoreVectorHash = viewport.getAlignment() .getAlignmentAnnotation().hashCode(); } } @@ -3593,21 +3778,16 @@ 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); + tp.sortByTree_actionPerformed(null); + addHistoryItem(tp.sortAlignmentIn(alignPanel)); - addHistoryItem(new OrderCommand("Tree Sort", oldOrder, - viewport.alignment)); - - alignPanel.paintAlignment(true); } }); @@ -3615,6 +3795,19 @@ 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.getAlignment())); + } + alignPanel.paintAlignment(true); + return true; + } + /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. @@ -3676,9 +3869,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // limit sequences - JBPNote in future - could spawn multiple prediction // jobs - // TODO: viewport.alignment.isAligned is a global state - the local + // TODO: viewport.getAlignment().isAligned is a global state - the local // selection may well be aligned - we preserve 2.0.8 behaviour for moment. - if (!viewport.alignment.isAligned(false)) + if (!viewport.getAlignment().isAligned(false)) { seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] }); @@ -3698,8 +3891,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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"); @@ -3723,8 +3916,8 @@ 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); } } @@ -3816,124 +4009,173 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } ; } + final AlignFrame me = this; buildingMenu = true; - try + new Thread(new Runnable() { - System.err - .println("Building ws menu again " + Thread.currentThread()); - // TODO: add support for context dependent disabling of services based on - // alignment and current selection - // TODO: add additional serviceHandle parameter to specify abstract - // handler - // class independently of AbstractName - // TODO: add in rediscovery GUI function to restart discoverer - // TODO: group services by location as well as function and/or introduce - // object broker mechanism. - Vector wsmenu = new Vector(); - final IProgressIndicator af = this; - if (Cache.getDefault("SHOW_JWS1_SERVICES", true) - && Discoverer.services != null - && (Discoverer.services.size() > 0)) + public void run() { - // TODO: refactor to allow list of AbstractName/Handler bindings to be - // stored or retrieved from elsewhere - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch"); - // TODO: move GUI generation code onto service implementation - so a - // client instance attaches itself to the GUI with method call like - // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, - // alignframe) - if (msaws != null) + try { - // Add any Multiple Sequence Alignment Services + 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"); - for (int i = 0, j = msaws.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(msawsmenu, this); - - } - wsmenu.add(msawsmenu); - } - if (secstrpr != null) - { - // Add any secondary structure prediction services final JMenu secstrmenu = new JMenu( "Secondary Structure Prediction"); - for (int i = 0, j = secstrpr.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr - .get(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(secstrmenu, this); - } - wsmenu.add(secstrmenu); - } - if (seqsrch != null) - { - // Add any sequence search services final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); - for (int i = 0, j = seqsrch.size(); i < j; i++) + final JMenu analymenu = new JMenu("Analysis"); + final JMenu dismenu = new JMenu("Disorder"); + // 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)) { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch - .elementAt(i); - jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer - .getServiceClient(sh); - impl.attachWSMenuEntry(seqsrchmenu, this); + // 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); + } + } } - wsmenu.add(seqsrchmenu); - } - } - // TODO: move into separate menu builder class. - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) - { - Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); - if (jws2servs != null) - { - if (jws2servs.hasServices()) + // Add all submenus in the order they should appear on the web + // services menu + wsmenu.add(msawsmenu); + wsmenu.add(secstrmenu); + wsmenu.add(dismenu); + wsmenu.add(analymenu); + // final ArrayList submens=new ArrayList(); + // submens.add(msawsmenu); + // submens.add(secstrmenu); + // submens.add(dismenu); + // submens.add(analymenu); + + // No search services yet + // wsmenu.add(seqsrchmenu); + + javax.swing.SwingUtilities.invokeLater(new Runnable() { - JMenu jws2men = new JMenu("Jalview 2 Services"); - jws2servs.attachWSMenuEntry(jws2men, this); - wsmenu.add(jws2men); - } - } - } - resetWebServiceMenu(); - // finally, add the whole shebang onto the webservices menu - if (wsmenu.size() > 0) - { - for (int i = 0, j = wsmenu.size(); i < j; i++) + 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); + } + // 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(webService, me); + } + if (jws2servs.isRunning()) + { + JMenuItem tm = new JMenuItem( + "Still discovering JABA Services"); + tm.setEnabled(false); + webService.add(tm); + } + } + } + + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + for (JMenu item : wsmenu) + { + if (item.getItemCount() == 0) + { + item.setEnabled(false); + } + else + { + item.setEnabled(true); + } + } + } catch (Exception e) + { + } + ; + } + }); + } catch (Exception e) { - webService.add((JMenu) wsmenu.get(i)); } + ; + + buildingMenu = false; } - else - { - this.webService.add(this.webServiceNoServices); - } - } catch (Exception e) - { - } - ; - buildingMenu = false; - } + }).start(); - /** - * empty the web service menu and add any ad-hoc functions not dynamically - * discovered. - * - */ - private void resetWebServiceMenu() - { - webService.removeAll(); - build_fetchdbmenu(webService); - build_urlServiceMenu(webService); } /** @@ -3943,6 +4185,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ private void build_urlServiceMenu(JMenu 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.getAlignment(), + * af.viewport.getColumnSelection(), 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( @@ -4032,8 +4300,7 @@ 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; } @@ -4057,7 +4324,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ths.setProgressBar("Searching for sequences from " + fsrc, sttime); try { - Alignment ds = ths.getViewport().alignment.getDataset(); // update + Alignment ds = ths.getViewport().getAlignment().getDataset(); // update // our local // dataset // reference @@ -4123,13 +4390,12 @@ 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; } @@ -4180,8 +4446,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true), viewport - .getGapCharacter(), viewport.alignment - .getAlignmentAnnotation(), viewport.alignment + .getGapCharacter(), viewport.getAlignment() + .getAlignmentAnnotation(), viewport.getAlignment() .getWidth(), viewport.getAlignment().getDataset()); } catch (Exception ex) { @@ -4218,9 +4484,10 @@ 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 + .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureColours, false, + jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } catch (Exception ex) { ex.printStackTrace(); @@ -4315,10 +4582,127 @@ 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) { @@ -4336,36 +4720,62 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * 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 = jalview.io.FormatAdapter.FILE; - String f = file.toLowerCase(); - if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0 - || f.indexOf("file:") == 0) + if (protocol == null) { - protocol = jalview.io.FormatAdapter.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.getAlignment(), 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 @@ -4431,7 +4841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void extractScores_actionPerformed(ActionEvent e) { ParseProperties pp = new jalview.analysis.ParseProperties( - viewport.alignment); + viewport.getAlignment()); // TODO: verify regex and introduce GUI dialog for version 2.5 // if (pp.getScoresFromDescription("col", "score column ", // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", @@ -4501,14 +4911,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // TODO We probably want to store a sequence database checklist in // preferences and have checkboxes.. rather than individual sources selected // here - JMenu rfetch = new JMenu("Fetch DB References"); - rfetch - .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences"); + final JMenu rfetch = new JMenu("Fetch DB References"); + rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences"); webService.add(rfetch); JMenuItem fetchr = new JMenuItem("Standard Databases"); - fetchr - .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources"); + fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources"); fetchr.addActionListener(new ActionListener() { @@ -4529,57 +4937,179 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); rfetch.add(fetchr); - JMenu dfetch = new JMenu(); - rfetch.add(dfetch); - jalview.ws.SequenceFetcher sf = SequenceFetcher - .getSequenceFetcherSingleton(this); - String[] otherdb = sf.getOrderedSupportedSources(); - // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); - // jalview.util.QuickSort.sort(otherdb, otherdb); - int comp = 0, mcomp = 15; - String mname = null; - if (otherdb != null && otherdb.length > 0) - { - for (int i = 0; i < otherdb.length; i++) + final AlignFrame me = this; + new Thread(new Runnable() + { + public void run() { - String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); - if (mname == null) + final jalview.ws.SequenceFetcher sf = SequenceFetcher + .getSequenceFetcherSingleton(me); + javax.swing.SwingUtilities.invokeLater(new Runnable() { - mname = "from '" + dbname + "'"; - } - fetchr = new JMenuItem(otherdb[i]); - final String[] dassource = new String[] - { otherdb[i] }; - fetchr.addActionListener(new ActionListener() - { - - public void actionPerformed(ActionEvent e) + public void run() { - new Thread(new Runnable() + String[] dbclasses = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + List otherdb; + JMenu dfetch = new JMenu(); + JMenu ifetch = new JMenu(); + JMenuItem fetchr = null; + int comp = 0, icomp = 0, mcomp = 15; + String mname = null; + int dbi = 0; + for (String dbclass : dbclasses) { + otherdb = sf.getSourceProxy(dbclass); + // add a single entry for this class, or submenu allowing 'fetch + // all' or pick one + if (otherdb == null || otherdb.size() < 1) + { + continue; + } + // List dbs=otherdb; + // otherdb=new ArrayList(); + // for (DbSourceProxy db:dbs) + // { + // if (!db.isA(DBRefSource.ALIGNMENTDB) + // } + if (mname == null) + { + mname = "From " + dbclass; + } + if (otherdb.size() == 1) + { + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem(src.getDbSource()); + 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(); + } - public void run() + }); + fetchr.setToolTipText("" + + JvSwingUtils.wrapTooltip("Retrieve from " + + src.getDbName()) + ""); + dfetch.add(fetchr); + comp++; + } + else { - new jalview.ws.DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, - dassource).fetchDBRefs(false); + final DbSourceProxy[] dassource = otherdb + .toArray(new DbSourceProxy[0]); + // fetch all entry + DbSourceProxy src = otherdb.get(0); + fetchr = new JMenuItem("Fetch All '" + src.getDbSource() + + "'"); + 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("" + + JvSwingUtils.wrapTooltip("Retrieve from all " + + otherdb.size() + " sources in " + + src.getDbSource() + "
First is :" + + src.getDbName()) + ""); + dfetch.add(fetchr); + comp++; + // and then build the rest of the individual menus + ifetch = new JMenu("Sources from " + src.getDbSource()); + icomp = 0; + String imname = null; + int i = 0; + for (DbSourceProxy sproxy : otherdb) + { + String dbname = sproxy.getDbName(); + String sname = dbname.length() > 5 ? dbname.substring(0, + 5) + "..." : dbname; + String msname = dbname.length() > 10 ? dbname.substring( + 0, 10) + "..." : dbname; + if (imname == null) + { + imname = "from '" + sname + "'"; + } + fetchr = new JMenuItem(msname); + final DbSourceProxy[] dassrc = + { sproxy }; + 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, dassrc) + .fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("" + + JvSwingUtils.wrapTooltip("Retrieve from " + + dbname) + ""); + ifetch.add(fetchr); + ++i; + if (++icomp >= mcomp || i == (otherdb.size())) + { + ifetch.setText(imname + " to '" + sname + "'"); + dfetch.add(ifetch); + ifetch = new JMenu(); + imname = null; + icomp = 0; + comp++; + } + } } - }).start(); + ++dbi; + if (comp >= mcomp || dbi >= (dbclasses.length)) + { + dfetch.setText(mname + " to '" + dbclass + "'"); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } + } } - }); - 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(); + } /** @@ -4674,6 +5204,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); @@ -4691,10 +5227,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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.getSequenceSelection(), + viewport.getAlignmentView(true).getSequenceStrings( + viewport.getGapCharacter()), viewport.getAlignment() + .getGroups()); + viewport.getAlignment().deleteAllGroups(); viewport.sequenceColours = null; viewport.setSelectionGroup(null); // set view properties for each group @@ -4702,9 +5239,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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)); + viewport.getAlignment().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( @@ -4716,6 +5253,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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