X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b91255f50ba15bc43994c328c9457f6738509c0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=2127cd5843004ea3c68d3ca73df37c23c54b5fa7;hpb=2be01e6b8c55c542272c8e7d50b20829cdf10d6c;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2127cd5..9b91255 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,2872 +1,5145 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Softwarechang - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import java.beans.*; -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.ws.*; -import java.awt.dnd.*; -import org.biojava.dasobert.eventmodel.*; - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class AlignFrame - extends GAlignFrame implements DropTargetListener, FeatureListener -{ - /** DOCUMENT ME!! */ - public static final int NEW_WINDOW_WIDTH = 700; - - /** DOCUMENT ME!! */ - public static final int NEW_WINDOW_HEIGHT = 500; - AlignmentPanel alignPanel; - AlignViewport viewport; - - /** DOCUMENT ME!! */ - public String currentFileFormat = null; - Stack historyList = new Stack(); - Stack redoList = new Stack(); - private int treeCount = 0; - - - /** - * Creates a new AlignFrame object. - * - * @param al DOCUMENT ME! - */ - public AlignFrame(AlignmentI al) - { - - viewport = new AlignViewport(al); - - this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - - if(viewport.vconsensus==null) - { - //Out of memory calculating consensus. - BLOSUM62Colour.setEnabled(false); - PIDColour.setEnabled(false); - conservationMenuItem.setEnabled(false); - modifyConservation.setEnabled(false); - abovePIDThreshold.setEnabled(false); - modifyPID.setEnabled(false); - } - - alignPanel = new AlignmentPanel(this, viewport); - - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); - - if(sortby.equals("Id")) - sortIDMenuItem_actionPerformed(null); - else if(sortby.equals("Pairwise Identity")) - sortPairwiseMenuItem_actionPerformed(null); - - // remove(tabbedPane); - getContentPane().add(alignPanel, BorderLayout.CENTER); - - - - // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); - - ///Dataset tab - ///////////////////////// - if(al.getDataset()==null) - { - al.setDataset(null); - } - // AlignViewport ds = new AlignViewport(al.getDataset(), true); - // AlignmentPanel dap = new AlignmentPanel(this, ds); - // tabbedPane.add("Dataset", dap); - // viewports.add(ds); - // alignPanels.add(dap); - ///////////////////////// - - - viewport.addPropertyChangeListener(new PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - - - if (Desktop.desktop != null) - { - addServiceListeners(); - setGUINucleotide(al.isNucleotide()); - } - - - if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false)) - { - wrapMenuItem.setSelected(true); - wrapMenuItem_actionPerformed(null); - } - - } - - public AlignViewport getViewport() - { - return viewport; - } - - /* Set up intrinsic listeners for dynamically generated GUI bits. */ - private void addServiceListeners() - { - final java.beans.PropertyChangeListener thisListener; - // Do this once to get current state - BuildWebServiceMenu(); - Desktop.discoverer.addPropertyChangeListener( - thisListener = new java.beans.PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - // System.out.println("Discoverer property change."); - if (evt.getPropertyName().equals("services")) - { - // System.out.println("Rebuilding web service menu"); - BuildWebServiceMenu(); - } - } - }); - addInternalFrameListener(new javax.swing.event. - InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - // System.out.println("deregistering discoverer listener"); - Desktop.discoverer.removePropertyChangeListener(thisListener); - closeMenuItem_actionPerformed(null); - } - ; - }); - } - - public void setGUINucleotide(boolean nucleotide) - { - showTranslation.setVisible( nucleotide ); - //sequenceFeatures.setVisible(!nucleotide ); - //featureSettings.setVisible( !nucleotide ); - conservationMenuItem.setVisible( !nucleotide ); - modifyConservation.setVisible( !nucleotide ); - - //Remember AlignFrame always starts as protein - if(!nucleotide) - { - calculateMenu.remove(calculateMenu.getItemCount()-2); - } - } - - public void comeBackLater(FeatureEvent evt) - {} - - public void newFeatures(FeatureEvent evt) - { - if (evt.getFeatures().length > 0) - { - alignPanel.seqPanel.seqCanvas.fr.featuresAdded(); - alignPanel.repaint(); - if(featureSettings!=null) - featureSettings.setTableData(); - } - } - - Hashtable progressBars; - public void setProgressBar(String message, long id) - { - if(progressBars == null) - progressBars = new Hashtable(); - - JPanel progressPanel; - GridLayout layout = (GridLayout) statusPanel.getLayout(); - if(progressBars.get( new Long(id) )!=null) - { - progressPanel = (JPanel)progressBars.get( new Long(id) ); - statusPanel.remove(progressPanel); - progressBars.remove( progressPanel ); - progressPanel = null; - if(message!=null) - statusBar.setText(message); - - layout.setRows(layout.getRows() - 1); - } - else - { - progressPanel = new JPanel(new BorderLayout(10, 5)); - - JProgressBar progressBar = new JProgressBar(); - progressBar.setIndeterminate(true); - - progressPanel.add(new JLabel(message), BorderLayout.WEST); - progressPanel.add(progressBar, BorderLayout.CENTER); - - layout.setRows(layout.getRows() + 1); - statusPanel.add(progressPanel); - - progressBars.put(new Long(id), progressPanel); - } - - validate(); - } - - - /* - Added so Castor Mapping file can obtain Jalview Version - */ - public String getVersion() - { - return jalview.bin.Cache.getProperty("VERSION"); - } - - public FeatureRenderer getFeatureRenderer() - { - return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); - } - - - public void fetchSequence_actionPerformed(ActionEvent e) - { - new SequenceFetcher(this); - } - - public void addFromFile_actionPerformed(ActionEvent e) - { - Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); - } - - public void addFromText_actionPerformed(ActionEvent e) - { - Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); - } - - public void addFromURL_actionPerformed(ActionEvent e) - { - Desktop.instance.inputURLMenuItem_actionPerformed(viewport); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void saveAlignmentMenu_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty( "LAST_DIRECTORY"), - new String[] - { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" }, - new String[] - { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" }, - currentFileFormat, - false); - - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - currentFileFormat = chooser.getSelectedFormat(); - - if (currentFileFormat == null) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "You must select a file format before saving!", - "File format not specified", - JOptionPane.WARNING_MESSAGE); - value = chooser.showSaveDialog(this); - return; - } - - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); - - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - - saveAlignment(choice, currentFileFormat); - } - } - - public boolean saveAlignment(String file, String format) - { - if (format.equalsIgnoreCase("Jalview")) - { - String shortName = title; - - if (shortName.indexOf(java.io.File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); - } - - new Jalview2XML().SaveAlignment(this, file, shortName); - - // USE Jalview2XML to save this file - return true; - } - else - { - - String[] omitHidden = null; - - if (viewport.hasHiddenColumns) - { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to save only the visible alignment?", - "Save / Omit Hidden Columns", - JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); - - if (reply == JOptionPane.YES_OPTION) - omitHidden = viewport.getViewAsString(false); - } - - String output = new FormatAdapter().formatSequences( - format, - viewport.alignment.getSequencesArray(), - omitHidden); - - if (output == null) - { - return false; - } - - try - { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); - - out.print(output); - out.close(); - this.setTitle(file); - return true; - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - return false; - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void outputText_actionPerformed(ActionEvent e) - { - String [] omitHidden = null; - - if(viewport.hasHiddenColumns) - { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "The Alignment contains hidden columns." - +"\nDo you want to output only the visible alignment?", - "Save / Omit Hidden Columns", - JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); - - if(reply==JOptionPane.YES_OPTION) - { - omitHidden = viewport.getViewAsString(false); - } - } - - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, - 500); - - - cap.setText(new FormatAdapter().formatSequences( - e.getActionCommand(), - viewport.alignment.getSequencesArray(), - omitHidden)); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void htmlMenuItem_actionPerformed(ActionEvent e) - { - new HTMLOutput(viewport, - alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); - } - - public void createImageMap(File file, String image) - { - alignPanel.makePNGImageMap(file, image); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createPNG(File f) - { - alignPanel.makePNG(f); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createEPS(File f) - { - alignPanel.makeEPS(f); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void printMenuItem_actionPerformed(ActionEvent e) - { - //Putting in a thread avoids Swing painting problems - PrintThread thread = new PrintThread(); - thread.start(); - } - - public void exportFeatures_actionPerformed(ActionEvent e) - { - new AnnotationExporter().exportFeatures(alignPanel); - } - - - public void exportAnnotations_actionPerformed(ActionEvent e) - { - new AnnotationExporter().exportAnnotations( - alignPanel, - viewport.alignment.getAlignmentAnnotation() - ); - } - - - public void associatedData_actionPerformed(ActionEvent e) - { - // Pick the tree file - 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"); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(choice); - } - - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void closeMenuItem_actionPerformed(ActionEvent e) - { - try - { - PaintRefresher.components.remove(viewport.alignment); - this.setClosed(true); - } - catch (Exception ex) - { - } - } - - /** - * DOCUMENT ME! - */ - void updateEditMenuBar() - { - if (historyList.size() > 0) - { - undoMenuItem.setEnabled(true); - - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setText("Undo " + hi.getDescription()); - } - else - { - undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); - } - - if (redoList.size() > 0) - { - redoMenuItem.setEnabled(true); - - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setText("Redo " + hi.getDescription()); - } - else - { - redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); - } - } - - /** - * DOCUMENT ME! - * - * @param hi DOCUMENT ME! - */ - public void addHistoryItem(HistoryItem hi) - { - historyList.push(hi); - updateEditMenuBar(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void undoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) - { - - hi.restore(); - - updateEditMenuBar(); - - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - } - - /** - * DOCUMENT ME! - * - * @param up DOCUMENT ME! - */ - public void moveSelectedSequences(boolean up) - { - SequenceGroup sg = viewport.getSelectionGroup(); - - if (sg == null) - { - return; - } - - if (up) - { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - - if (!sg.getSequences(false).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - - if (sg.getSequences(false).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i - 1); - } - } - else - { - for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); - - if (!sg.getSequences(false).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - - if (sg.getSequences(false).contains(temp)) - { - continue; - } - - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - - alignPanel.repaint(); - } - - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void copy_actionPerformed(ActionEvent e) - { - if (viewport.getSelectionGroup() == null) - { - return; - } - - SequenceI [] seqs = viewport.getSelectionAsNewSequence(); - String[] omitHidden = null; - - if (viewport.hasHiddenColumns) - { - omitHidden = viewport.getViewAsString(true); - } - - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); - - - Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(output), Desktop.instance); - - Vector hiddenColumns = null; - if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null) - { - hiddenColumns =new Vector(); - int hiddenOffset = viewport.getSelectionGroup().getStartRes(); - for(int i=0; i>>This is a fix for the moment, until a better solution is found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); - - - if (title.startsWith("Copied sequences")) - { - newtitle = title; - } - else - { - newtitle = newtitle.concat("- from " + title); - } - - Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - - } - - - } - catch (Exception ex) - { - ex.printStackTrace(); - System.out.println("Exception whilst pasting: "+ex); - // could be anything being pasted in here - } - - - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void cut_actionPerformed(ActionEvent e) - { - copy_actionPerformed(null); - delete_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void delete_actionPerformed(ActionEvent e) - { - - if (viewport.getSelectionGroup() == null) - { - return; - } - - - SequenceGroup sg = viewport.getSelectionGroup(); - - - - //Jalview no longer allows deletion of residues. - //Check here whether any residues are in selection area - /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1) - { - for (int i = 0; i < sg.sequences.size(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int j = sg.getStartRes(); - do - { - if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) - { - JOptionPane.showInternalMessageDialog( - Desktop.desktop, "Cannot delete residues from alignment!\n" - + "Try hiding columns instead.", - "Deletion of residues not permitted", - JOptionPane.WARNING_MESSAGE); - - return; - } - j++; - }while(j<=sg.getEndRes()); - } - }*/ - - - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - - - for (int i = 0; i < sg.getSize(false); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize(false) == viewport.alignment.getHeight()) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - - if (seq.getSequence().length() < 1) - { - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } - } - - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); - - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - - - - if (viewport.getAlignment().getHeight() < 1) - { - try - { - this.setClosed(true); - } - catch (Exception ex) - { - } - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void deleteGroups_actionPerformed(ActionEvent e) - { - viewport.alignment.deleteAllGroups(); - viewport.setSelectionGroup(null); - alignPanel.repaint(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = new SequenceGroup(); - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); - } - - sg.setEndRes(viewport.alignment.getWidth() - 1); - viewport.setSelectionGroup(sg); - PaintRefresher.Refresh(null, viewport.alignment); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) - { - if(viewport.cursorMode) - { - alignPanel.seqPanel.keyboardNo1 = null; - alignPanel.seqPanel.keyboardNo2 = null; - } - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); - alignPanel.idPanel.idCanvas.searchResults = null; - alignPanel.repaint(); - PaintRefresher.Refresh(null, viewport.alignment); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = viewport.getSelectionGroup(); - - if (sg == null) - { - selectAllSequenceMenuItem_actionPerformed(null); - - return; - } - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); - } - - PaintRefresher.Refresh(null, viewport.alignment); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void remove2LeftMenuItem_actionPerformed(ActionEvent e) - { - ColumnSelection colSel = viewport.getColumnSelection(); - - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); - - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } - - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.get(i); - - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void remove2RightMenuItem_actionPerformed(ActionEvent e) - { - ColumnSelection colSel = viewport.getColumnSelection(); - - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } - - Vector groups = viewport.alignment.getGroups(); - - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.get(i); - - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, HistoryItem.HIDE)); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - viewport.getAlignment().removeGaps(); - - viewport.setStartRes(seq.findIndex(startRes)-1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - - SequenceI current; - int jSize; - - Vector seqs = null; - - int start = 0; - int end = viewport.alignment.getWidth(); - - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSequences(true) != null - && viewport.getSelectionGroup().getSize(true) > 0) - { - seqs = viewport.getSelectionGroup().getSequences(true); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes()+1; - } - else - { - seqs = viewport.alignment.getSequences(); - } - - for (int i = 0; i < seqs.size(); i++) - { - current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); - - // Removing a range is much quicker than removing gaps - // one by one for long sequences - int j = start; - int rangeStart=-1, rangeEnd=-1; - - do - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - if(rangeStart==-1) - { - rangeStart = j; - rangeEnd = j+1; - } - else - { - rangeEnd++; - } - j++; - } - else - { - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - j-=rangeEnd-rangeStart; - jSize-=rangeEnd-rangeStart; - rangeStart = -1; - rangeEnd = -1; - } - else - j++; - } - } - while (j < end && j < jSize); - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - } - } - - viewport.setStartRes(seq.findIndex(startRes)-1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - - public void alignmentChanged() - { - if(viewport.padGaps) - viewport.getAlignment().padGaps(); - - if(viewport.vconsensus!=null && viewport.autoCalculateConsensus) - { - viewport.updateConsensus(); - viewport.updateConservation(); - } - resetAllColourSchemes(); - if(alignPanel.overviewPanel!=null) - alignPanel.overviewPanel.updateOverviewImage(); - - viewport.alignment.adjustSequenceAnnotations(); - - alignPanel.repaint(); - } - - void resetAllColourSchemes() - { - ColourSchemeI cs = viewport.globalColourScheme; - if(cs!=null) - { - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). - resetClustalX(viewport.alignment.getSequences(), - viewport.alignment.getWidth()); - } - - cs.setConsensus(viewport.vconsensus); - if (cs.conservationApplied()) - { - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - - cs.setConservation(c); - } - } - - int s, sSize = viewport.alignment.getGroups().size(); - for(s=0; s 0)) || - (viewport.getAlignment().getHeight() < 4)) - { - JOptionPane.showInternalMessageDialog(this, - "Principal component analysis must take\n" + - "at least 4 input sequences.", - "Sequence selection insufficient", - JOptionPane.WARNING_MESSAGE); - - return; - } - - new PCAPanel(viewport); - } - - - public void autoCalculate_actionPerformed(ActionEvent e) - { - viewport.autoCalculateConsensus = autoCalculate.isSelected(); - if(viewport.autoCalculateConsensus) - { - alignmentChanged(); - } - } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "PID", "Average distance tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); - } - - /** - * DOCUMENT ME! - * - * @param type DOCUMENT ME! - * @param pwType DOCUMENT ME! - * @param title DOCUMENT ME! - */ - void NewTreePanel(String type, String pwType, String title) - { - TreePanel tp; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize(false) > 3)) - { - int s = 0; - SequenceGroup sg = viewport.getSelectionGroup(); - - /* Decide if the selection is a column region */ - while (s < sg.getSize(false)) - { - if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() < - sg.getEndRes()) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "The selected region to create a tree may\nonly contain residues or gaps.\n" + - "Try using the Pad function in the edit menu,\n" + - "or one of the multiple sequence alignment web services.", - "Sequences in selection are not aligned", - JOptionPane.WARNING_MESSAGE); - - return; - } - } - - title = title + " on region"; - tp = new TreePanel(viewport, type, pwType); - } - else - { - //are the sequences aligned? - if (!viewport.alignment.isAligned()) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "The sequences must be aligned before creating a tree.\n" + - "Try using the Pad function in the edit menu,\n" + - "or one of the multiple sequence alignment web services.", - "Sequences not aligned", - JOptionPane.WARNING_MESSAGE); - - return; - } - - if(viewport.alignment.getHeight()<2) - return; - - tp = new TreePanel(viewport, type, pwType); - } - - addTreeMenuItem(tp, title); - - Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500); - } - - /** - * DOCUMENT ME! - * - * @param title DOCUMENT ME! - * @param order DOCUMENT ME! - */ - public void addSortByOrderMenuItem(String title, final AlignmentOrder order) - { - final JMenuItem item = new JMenuItem("by " + title); - sort.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); - - // TODO: JBPNote - have to map order entries to curent SequenceI pointers - AlignmentSorter.sortBy(viewport.getAlignment(), order); - alignPanel.repaint(); - } - }); - } - - /** - * Maintain the Order by->Displayed Tree menu. - * Creates a new menu item for a TreePanel with an appropriate - * jalview.analysis.AlignmentSorter call. Listeners are added - * to remove the menu item when the treePanel is closed, and adjust - * the tree leaf to sequence mapping when the alignment is modified. - * @param treePanel Displayed tree window. - * @param title SortBy menu item title. - */ - void addTreeMenuItem(final TreePanel treePanel, String title) - { - final JMenuItem item = new JMenuItem(title); - - treeCount++; - - if (treeCount == 1) - { - sort.add(sortByTreeMenu); - } - - sortByTreeMenu.add(item); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Tree Sort", - viewport.alignment, HistoryItem.SORT)); - AlignmentSorter.sortByTree(viewport.getAlignment(), - treePanel.getTree()); - alignPanel.repaint(); - } - }); - - treePanel.addInternalFrameListener(new javax.swing.event. - InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - treeCount--; - sortByTreeMenu.remove(item); - - if (treeCount == 0) - { - sort.remove(sortByTreeMenu); - } - } - ; - }); - } - - /** - * Work out whether the whole set of sequences - * or just the selected set will be submitted for multiple alignment. - * - */ - private SequenceI[] gatherSequencesForAlignment() - { - // Now, check we have enough sequences - SequenceI[] msa = null; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize(false) > 1)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); - int sz; - msa = new SequenceI[sz = seqs.getSize(false)]; - - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) - { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - return msa; - } - - /** - * Decides what is submitted to a secondary structure prediction service, - * the currently selected sequence, or the currently selected alignment - * (where the first sequence in the set is the one that the prediction - * will be for). - */ - SequenceI[] gatherSeqOrMsaForSecStrPrediction() - { - SequenceI seq = null; - SequenceI[] msa = null; - - if ( (viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize(false) > 0)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); - - if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.getSequenceAt(0); - } - else - { - int sz; - msa = new SequenceI[sz = seqs.getSize(false)]; - - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if ( (seqs.size() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.elementAt(0); - } - else - { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - if (msa != null) - { - return msa; - } - else - { - if (seq != null) - { - return new SequenceI[] - { - seq}; - } - } - return null; - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) - { - // Pick the tree file - 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"); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, - "File"); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); - } - catch (Exception ex) - { - JOptionPane.showMessageDialog(Desktop.desktop, - "Problem reading tree file", - ex.getMessage(), - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - } - } - - - public TreePanel ShowNewickTree(NewickFile nf, String title) - { - return ShowNewickTree(nf,title,600,500,4,5); - } - /** - * DOCUMENT ME! - * - * @param nf DOCUMENT ME! - * @param title DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) - { - TreePanel tp = null; - - try - { - nf.parse(); - - if (nf.getTree() != null) - { - tp = new TreePanel(viewport, - "FromFile", - title, - nf); - - tp.setSize(w,h); - - if(x>0 && y>0) - tp.setLocation(x,y); - - - Desktop.addInternalFrame(tp, title, w, h); - addTreeMenuItem(tp, title); - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - return tp; - } - - class PrintThread - extends Thread - { - public void run() - { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - printJob.setPrintable(alignPanel, pf); - - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } - } - } - - /** - * Generates menu items and listener event actions for web service clients - * - */ - public void BuildWebServiceMenu() - { - if ( (Discoverer.services != null) - && (Discoverer.services.size() > 0)) - { - Vector msaws = (Vector) Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred"); - Vector wsmenu = new Vector(); - if (msaws != null) - { - // Add any Multiple Sequence Alignment Services - final JMenu msawsmenu = new JMenu("Alignment"); - final AlignFrame af = this; - for (int i = 0, j = msaws.size(); i < j; i++) - { - final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws. - get(i); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - SequenceI[] msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - false, true, viewport.getAlignment().getDataset(), af); - - } - - }); - msawsmenu.add(method); - // Deal with services that we know accept partial alignments. - if (sh.getName().indexOf("lustal") > -1) - { - // We know that ClustalWS can accept partial alignments for refinement. - final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign"); - methodR.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - SequenceI[] msa = gatherSequencesForAlignment(); - new jalview.ws.MsaWSClient(sh, title, msa, - true, true, viewport.getAlignment().getDataset(), af); - - } - - }); - msawsmenu.add(methodR); - - } - } - 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); - final JMenuItem method = new JMenuItem(sh.getName()); - method.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction(); - if (msa.length == 1) - { - // Single Sequence prediction - new jalview.ws.JPredClient(sh,title, msa[0]); - } - else - { - if (msa.length > 1) - { - // Single Sequence prediction - jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, - title, msa); - } - } - } - }); - secstrmenu.add(method); - } - wsmenu.add(secstrmenu); - } - this.webService.removeAll(); - for (int i = 0, j = wsmenu.size(); i < j; i++) - { - webService.add( (JMenu) wsmenu.get(i)); - } - } - else - { - this.webService.removeAll(); - this.webService.add(this.webServiceNoServices); - } - // TODO: add in rediscovery function - // TODO: reduce code redundancy. - // TODO: group services by location as well as function. - } - - /* public void vamsasStore_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Export to Vamsas file"); - chooser.setToolTipText("Export"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); - //vs.store(chooser.getSelectedFile().getAbsolutePath() ); - vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); - } - }*/ - - - - -public void showTranslation_actionPerformed(ActionEvent e) -{ - SequenceI [] selection = viewport.getSelectionAsNewSequence(); - String [] seqstring = viewport.getViewAsString(true); - - int s, sSize = selection.length; - SequenceI [] newSeq = new SequenceI[sSize]; - - int res, resSize; - StringBuffer protein; - String seq; - for(s=0; s. + */ +package jalview.gui; + +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentSorter; +import jalview.analysis.Conservation; +import jalview.analysis.CrossRef; +import jalview.analysis.NJTree; +import jalview.analysis.ParseProperties; +import jalview.analysis.SequenceIdMatcher; +import jalview.bin.Cache; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.commands.RemoveGapColCommand; +import jalview.commands.RemoveGapsCommand; +import jalview.commands.SlideSequencesCommand; +import jalview.commands.TrimRegionCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SeqCigar; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.AlignmentProperties; +import jalview.io.AnnotationFile; +import jalview.io.FeaturesFile; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; +import jalview.io.HTMLOutput; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.jbgui.GAlignFrame; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.ws.WSMenuEntryProviderI; +import jalview.ws.jws1.Discoverer; +import jalview.ws.jws2.Jws2Discoverer; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.GridLayout; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Vector; + +import javax.swing.JButton; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JProgressBar; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AlignFrame extends GAlignFrame implements DropTargetListener, + IProgressIndicator +{ + + /** DOCUMENT ME!! */ + public static final int DEFAULT_WIDTH = 700; + + /** DOCUMENT ME!! */ + public static final int DEFAULT_HEIGHT = 500; + + public AlignmentPanel alignPanel; + + AlignViewport viewport; + + Vector alignPanels = new Vector(); + + /** + * Last format used to load or save alignments in this window + */ + String currentFileFormat = null; + + /** + * Current filename for this alignment + */ + String fileName = null; + + /** + * Creates a new AlignFrame object with specific width and height. + * + * @param al + * @param width + * @param height + */ + public AlignFrame(AlignmentI al, int width, int height) + { + this(al, null, width, height); + } + + /** + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * + * @param al + * @param width + * @param height + * @param sequenceSetId + */ + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId) + { + this(al, null, width, height, sequenceSetId); + } + + /** + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * + * @param al + * @param width + * @param height + * @param sequenceSetId + * @param viewId + */ + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId, String viewId) + { + this(al, null, width, height, sequenceSetId, viewId); + } + + /** + * new alignment window with hidden columns + * + * @param al + * AlignmentI + * @param hiddenColumns + * ColumnSelection or null + * @param width + * Width of alignment frame + * @param height + * height of frame. + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height) + { + this(al, hiddenColumns, width, height, null); + } + + /** + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * + * @param al + * @param hiddenColumns + * @param width + * @param height + * @param sequenceSetId + * (may be null) + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId) + { + this(al, hiddenColumns, width, height, sequenceSetId, null); + } + + /** + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * + * @param al + * @param hiddenColumns + * @param width + * @param height + * @param sequenceSetId + * (may be null) + * @param viewId + * (may be null) + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId, String viewId) + { + setSize(width, height); + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); + + alignPanel = new AlignmentPanel(this, viewport); + + if (al.getDataset() == null) + { + al.setDataset(null); + } + + addAlignmentPanel(alignPanel, true); + init(); + } + + /** + * Make a new AlignFrame from exisiting alignmentPanels + * + * @param ap + * AlignmentPanel + * @param av + * AlignViewport + */ + public AlignFrame(AlignmentPanel ap) + { + viewport = ap.av; + alignPanel = ap; + addAlignmentPanel(ap, false); + init(); + } + + /** + * initalise the alignframe from the underlying viewport data and the + * configurations + */ + void init() + { + if (viewport.conservation == null) + { + BLOSUM62Colour.setEnabled(false); + conservationMenuItem.setEnabled(false); + modifyConservation.setEnabled(false); + // PIDColour.setEnabled(false); + // abovePIDThreshold.setEnabled(false); + // modifyPID.setEnabled(false); + } + + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + "No sort"); + + if (sortby.equals("Id")) + { + sortIDMenuItem_actionPerformed(null); + } + else if (sortby.equals("Pairwise Identity")) + { + sortPairwiseMenuItem_actionPerformed(null); + } + + if (Desktop.desktop != null) + { + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); + addServiceListeners(); + setGUINucleotide(viewport.alignment.isNucleotide()); + } + + setMenusFromViewport(viewport); + buildSortByAnnotationScoresMenu(); + if (viewport.wrapAlignment) + { + wrapMenuItem_actionPerformed(null); + } + + if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + { + this.overviewMenuItem_actionPerformed(null); + } + + addKeyListener(); + + } + + /** + * Change the filename and format for the alignment, and enable the 'reload' + * button functionality. + * + * @param file + * valid filename + * @param format + * format of file + */ + public void setFileName(String file, String format) + { + fileName = file; + currentFileFormat = format; + reload.setEnabled(true); + } + + void addKeyListener() + { + addKeyListener(new KeyAdapter() + { + public void keyPressed(KeyEvent evt) + { + if (viewport.cursorMode + && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt + .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt + .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && Character.isDigit(evt.getKeyChar())) + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + + switch (evt.getKeyCode()) + { + + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(null); + + break; + + case KeyEvent.VK_DOWN: + if (evt.isAltDown() || !viewport.cursorMode) + moveSelectedSequences(false); + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(0, 1); + break; + + case KeyEvent.VK_UP: + if (evt.isAltDown() || !viewport.cursorMode) + moveSelectedSequences(true); + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(0, -1); + + break; + + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(-1, 0); + + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor(1, 0); + break; + + case KeyEvent.VK_SPACE: + if (viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + break; + + //case KeyEvent.VK_A: + // if (viewport.cursorMode) + // { + // alignPanel.seqPanel.insertNucAtCursor(false,"A"); + // //System.out.println("A"); + // } + // break; + /* + case KeyEvent.VK_CLOSE_BRACKET: + if (viewport.cursorMode) + { + System.out.println("closing bracket"); + } + break; + */ + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if (!viewport.cursorMode) + { + cut_actionPerformed(null); + } + else + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); + } + + break; + + case KeyEvent.VK_S: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } + break; + case KeyEvent.VK_P: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + alignPanel.seqPanel.seqCanvas.repaint(); + break; + + case KeyEvent.VK_F1: + try + { + ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); + java.net.URL url = javax.help.HelpSet.findHelpSet(cl, + "help/help"); + javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); + + javax.help.HelpBroker hb = hs.createHelpBroker(); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } catch (Exception ex) + { + ex.printStackTrace(); + } + break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + toggleHiddenRegions(toggleSeqs, toggleCols); + break; + } + case KeyEvent.VK_PAGE_UP: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(true); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + - viewport.endSeq + viewport.startSeq); + } + break; + case KeyEvent.VK_PAGE_DOWN: + if (viewport.wrapAlignment) + { + alignPanel.scrollUp(false); + } + else + { + alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + + viewport.endSeq - viewport.startSeq); + } + break; + } + } + + public void keyReleased(KeyEvent evt) + { + switch (evt.getKeyCode()) + { + case KeyEvent.VK_LEFT: + if (evt.isAltDown() || !viewport.cursorMode) + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + break; + + case KeyEvent.VK_RIGHT: + if (evt.isAltDown() || !viewport.cursorMode) + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + break; + } + } + }); + } + + public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) + { + ap.alignFrame = this; + + alignPanels.addElement(ap); + + PaintRefresher.Register(ap, ap.av.getSequenceSetId()); + + int aSize = alignPanels.size(); + + tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null); + + if (aSize == 1 && ap.av.viewName == null) + { + this.getContentPane().add(ap, BorderLayout.CENTER); + } + else + { + if (aSize == 2) + { + setInitialTabVisible(); + } + + expandViews.setEnabled(true); + gatherViews.setEnabled(true); + tabbedPane.addTab(ap.av.viewName, ap); + + ap.setVisible(false); + } + + if (newPanel) + { + if (ap.av.padGaps) + { + ap.av.alignment.padGaps(); + } + ap.av.updateConservation(ap); + ap.av.updateConsensus(ap); + ap.av.updateStrucConsensus(ap); + } + } + + public void setInitialTabVisible() + { + expandViews.setEnabled(true); + gatherViews.setEnabled(true); + tabbedPane.setVisible(true); + AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement(); + tabbedPane.addTab(first.av.viewName, first); + this.getContentPane().add(tabbedPane, BorderLayout.CENTER); + } + + public AlignViewport getViewport() + { + return viewport; + } + + /* Set up intrinsic listeners for dynamically generated GUI bits. */ + private void addServiceListeners() + { + final java.beans.PropertyChangeListener thisListener; + Desktop.instance.addJalviewPropertyChangeListener("services", + thisListener = new java.beans.PropertyChangeListener() + { + public void propertyChange(PropertyChangeEvent evt) + { + // // System.out.println("Discoverer property change."); + // if (evt.getPropertyName().equals("services")) + { + SwingUtilities.invokeLater(new Runnable() + { + + public void run() + { + System.err + .println("Rebuild WS Menu for service change"); + BuildWebServiceMenu(); + } + + }); + } + } + }); + addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + System.out.println("deregistering discoverer listener"); + Desktop.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) + { + showTranslation.setVisible(nucleotide); + conservationMenuItem.setEnabled(!nucleotide); + modifyConservation.setEnabled(!nucleotide); + showGroupConservation.setEnabled(!nucleotide); + rnahelicesColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(nucleotide); + // Remember AlignFrame always starts as protein + //if (!nucleotide) + // { + // showTr + // calculateMenu.remove(calculateMenu.getItemCount() - 2); + // } + } + + /** + * set up menus for the currently viewport. This may be called after any + * operation that affects the data in the current view (selection changed, + * etc) to update the menus to reflect the new state. + */ + public void setMenusForViewport() + { + setMenusFromViewport(viewport); + } + + /** + * Need to call this method when tabs are selected for multiple views, or when + * loading from Jalview2XML.java + * + * @param av + * AlignViewport + */ + void setMenusFromViewport(AlignViewport av) + { + padGapsMenuitem.setSelected(av.padGaps); + colourTextMenuItem.setSelected(av.showColourText); + abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + conservationMenuItem.setSelected(av.getConservationSelected()); + seqLimits.setSelected(av.getShowJVSuffix()); + idRightAlign.setSelected(av.rightAlignIds); + centreColumnLabelsMenuItem.setState(av.centreColumnLabels); + renderGapsMenuItem.setSelected(av.renderGaps); + wrapMenuItem.setSelected(av.wrapAlignment); + scaleAbove.setVisible(av.wrapAlignment); + scaleLeft.setVisible(av.wrapAlignment); + scaleRight.setVisible(av.wrapAlignment); + annotationPanelMenuItem.setState(av.showAnnotation); + viewBoxesMenuItem.setSelected(av.showBoxes); + viewTextMenuItem.setSelected(av.showText); + showNonconservedMenuItem.setSelected(av.showUnconserved); + showGroupConsensus.setSelected(av.showGroupConsensus); + showGroupConservation.setSelected(av.showGroupConservation); + showConsensusHistogram.setSelected(av.showConsensusHistogram); + showSequenceLogo.setSelected(av.showSequenceLogo); + setColourSelected(ColourSchemeProperty.getColourName(av + .getGlobalColourScheme())); + + showSeqFeatures.setSelected(av.showSequenceFeatures); + hiddenMarkers.setState(av.showHiddenMarkers); + applyToAllGroups.setState(av.colourAppliesToAllGroups); + showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); + showDbRefsMenuitem.setSelected(av.isShowDbRefs()); + autoCalculate.setSelected(av.autoCalculateConsensus); + sortByTree.setSelected(av.sortByTree); + listenToViewSelections.setSelected(av.followSelection); + rnahelicesColour.setEnabled(av.alignment.hasRNAStructure()); + rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); + setShowProductsEnabled(); + + updateEditMenuBar(); + } + + Hashtable progressBars, progressBarHandlers; + + /* + * (non-Javadoc) + * + * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) + */ + public void setProgressBar(String message, long id) + { + if (progressBars == null) + { + progressBars = new Hashtable(); + progressBarHandlers = new Hashtable(); + } + + JPanel progressPanel; + Long lId = new Long(id); + GridLayout layout = (GridLayout) statusPanel.getLayout(); + if (progressBars.get(lId) != null) + { + progressPanel = (JPanel) progressBars.get(new Long(id)); + statusPanel.remove(progressPanel); + progressBars.remove(lId); + progressPanel = null; + if (message != null) + { + statusBar.setText(message); + } + if (progressBarHandlers.contains(lId)) + { + progressBarHandlers.remove(lId); + } + layout.setRows(layout.getRows() - 1); + } + else + { + progressPanel = new JPanel(new BorderLayout(10, 5)); + + JProgressBar progressBar = new JProgressBar(); + progressBar.setIndeterminate(true); + + progressPanel.add(new JLabel(message), BorderLayout.WEST); + progressPanel.add(progressBar, BorderLayout.CENTER); + + layout.setRows(layout.getRows() + 1); + statusPanel.add(progressPanel); + + progressBars.put(lId, progressPanel); + } + // update GUI + // setMenusForViewport(); + validate(); + } + + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) + { + if (progressBarHandlers == null || !progressBars.contains(new Long(id))) + { + throw new Error( + "call setProgressBar before registering the progress bar's handler."); + } + progressBarHandlers.put(new Long(id), handler); + final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); + if (handler.canCancel()) + { + JButton cancel = new JButton("Cancel"); + final IProgressIndicator us = this; + cancel.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + handler.cancelActivity(id); + us.setProgressBar( + "Cancelled " + + ((JLabel) progressPanel.getComponent(0)) + .getText(), id); + } + }); + progressPanel.add(cancel, BorderLayout.EAST); + } + } + + /** + * + * @return true if any progress bars are still active + */ + public boolean operationInProgress() + { + if (progressBars != null && progressBars.size() > 0) + { + return true; + } + return false; + } + + /* + * Added so Castor Mapping file can obtain Jalview Version + */ + public String getVersion() + { + return jalview.bin.Cache.getProperty("VERSION"); + } + + public FeatureRenderer getFeatureRenderer() + { + return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + } + + public void fetchSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(this); + } + + public void addFromFile_actionPerformed(ActionEvent e) + { + Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); + } + + public void reload_actionPerformed(ActionEvent e) + { + if (fileName != null) + { + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (currentFileFormat.equals("Jalview")) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + for (int i = 0; i < frames.length; i++) + { + if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName.equals(fileName)) + { + try + { + frames[i].setSelected(true); + Desktop.instance.closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) + { + } + } + + } + Desktop.instance.closeAssociatedWindows(); + + FileLoader loader = new FileLoader(); + String protocol = fileName.startsWith("http:") ? "URL" : "File"; + loader.LoadFile(viewport, fileName, protocol, currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); + + FileLoader loader = new FileLoader(); + String protocol = fileName.startsWith("http:") ? "URL" : "File"; + AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, + protocol, currentFileFormat); + + newframe.setBounds(bounds); + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; + } + this.closeMenuItem_actionPerformed(true); + } + } + } + + public void addFromText_actionPerformed(ActionEvent e) + { + Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); + } + + public void addFromURL_actionPerformed(ActionEvent e) + { + Desktop.instance.inputURLMenuItem_actionPerformed(viewport); + } + + public void save_actionPerformed(ActionEvent e) + { + if (fileName == null + || (currentFileFormat == null || !jalview.io.FormatAdapter + .isValidIOFormat(currentFileFormat, true)) + || fileName.startsWith("http")) + { + saveAs_actionPerformed(null); + } + else + { + saveAlignment(fileName, currentFileFormat); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void saveAs_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, + jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, + currentFileFormat, false); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save Alignment to file"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + currentFileFormat = chooser.getSelectedFormat(); + if (currentFileFormat == null) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "You must select a file format before saving!", + "File format not specified", JOptionPane.WARNING_MESSAGE); + value = chooser.showSaveDialog(this); + return; + } + + fileName = chooser.getSelectedFile().getPath(); + + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat); + + jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); + if (currentFileFormat.indexOf(" ") > -1) + { + currentFileFormat = currentFileFormat.substring(0, + currentFileFormat.indexOf(" ")); + } + saveAlignment(fileName, currentFileFormat); + } + } + + public boolean saveAlignment(String file, String format) + { + boolean success = true; + + if (format.equalsIgnoreCase("Jalview")) + { + String shortName = title; + + if (shortName.indexOf(java.io.File.separatorChar) > -1) + { + shortName = shortName.substring(shortName + .lastIndexOf(java.io.File.separatorChar) + 1); + } + + success = new Jalview2XML().SaveAlignment(this, file, shortName); + + statusBar.setText("Successfully saved to file: " + fileName + " in " + + format + " format."); + + } + else + { + if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) + { + warningMessage("Cannot save file " + fileName + " using format " + + format, "Alignment output format not supported"); + saveAs_actionPerformed(null); + // JBPNote need to have a raise_gui flag here + return false; + } + + String[] omitHidden = null; + + if (viewport.hasHiddenColumns) + { + int reply = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + "The Alignment contains hidden columns." + + "\nDo you want to save only the visible alignment?", + "Save / Omit Hidden Columns", + JOptionPane.YES_NO_OPTION, + JOptionPane.QUESTION_MESSAGE); + + if (reply == JOptionPane.YES_OPTION) + { + omitHidden = viewport.getViewAsString(false); + } + } + FormatAdapter f = new FormatAdapter(); + String output = f.formatSequences(format, + (Alignment) viewport.alignment, // class cast exceptions will + // occur in the distant future + omitHidden, f.getCacheSuffixDefault(format), viewport.colSel); + + if (output == null) + { + success = false; + } + else + { + try + { + java.io.PrintWriter out = new java.io.PrintWriter( + new java.io.FileWriter(file)); + + out.print(output); + out.close(); + this.setTitle(file); + statusBar.setText("Successfully saved to file: " + fileName + + " in " + format + " format."); + } catch (Exception ex) + { + success = false; + ex.printStackTrace(); + } + } + } + + if (!success) + { + JOptionPane.showInternalMessageDialog(this, "Couldn't save file: " + + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE); + } + + return success; + } + + private void warningMessage(String warning, String title) + { + if (new jalview.util.Platform().isHeadless()) + { + System.err.println("Warning: " + title + "\nWarning: " + warning); + + } + else + { + JOptionPane.showInternalMessageDialog(this, warning, title, + JOptionPane.WARNING_MESSAGE); + } + return; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void outputText_actionPerformed(ActionEvent e) + { + String[] omitHidden = null; + + if (viewport.hasHiddenColumns) + { + int reply = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + "The Alignment contains hidden columns." + + "\nDo you want to output only the visible alignment?", + "Save / Omit Hidden Columns", + JOptionPane.YES_NO_OPTION, + JOptionPane.QUESTION_MESSAGE); + + if (reply == JOptionPane.YES_OPTION) + { + omitHidden = viewport.getViewAsString(false); + } + } + + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + + try + { + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + viewport.alignment, omitHidden, viewport.colSel)); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); + cap.dispose(); + } + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void htmlMenuItem_actionPerformed(ActionEvent e) + { + new HTMLOutput(alignPanel, + alignPanel.seqPanel.seqCanvas.getSequenceRenderer(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + } + + public void createImageMap(File file, String image) + { + alignPanel.makePNGImageMap(file, image); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void createPNG(File f) + { + alignPanel.makePNG(f); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void createEPS(File f) + { + alignPanel.makeEPS(f); + } + + public void pageSetup_actionPerformed(ActionEvent e) + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PrintThread.pf = printJob.pageDialog(printJob.defaultPage()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void printMenuItem_actionPerformed(ActionEvent e) + { + // Putting in a thread avoids Swing painting problems + PrintThread thread = new PrintThread(alignPanel); + thread.start(); + } + + public void exportFeatures_actionPerformed(ActionEvent e) + { + new AnnotationExporter().exportFeatures(alignPanel); + } + + public void exportAnnotations_actionPerformed(ActionEvent e) + { + new AnnotationExporter().exportAnnotations( + alignPanel, + viewport.showAnnotation ? viewport.alignment + .getAlignmentAnnotation() : null, viewport.alignment + .getGroups(), + ((Alignment) viewport.alignment).alignmentProperties); + } + + public void associatedData_actionPerformed(ActionEvent e) + { + // Pick the tree file + 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"); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(choice, null, null, null); + } + + } + + /** + * Close the current view or all views in the alignment frame. If the frame + * only contains one view then the alignment will be removed from memory. + * + * @param closeAllTabs + */ + public void closeMenuItem_actionPerformed(boolean closeAllTabs) + { + if (alignPanels != null && alignPanels.size() < 2) + { + closeAllTabs = true; + } + + try + { + if (alignPanels != null) + { + if (closeAllTabs) + { + if (this.isClosed()) + { + // really close all the windows - otherwise wait till + // setClosed(true) is called + for (int i = 0; i < alignPanels.size(); i++) + { + AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); + ap.closePanel(); + } + } + } + else + { + closeView(alignPanel); + } + } + + if (closeAllTabs) + { + this.setClosed(true); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + /** + * close alignPanel2 and shuffle tabs appropriately. + * + * @param alignPanel2 + */ + public void closeView(AlignmentPanel alignPanel2) + { + int index = tabbedPane.getSelectedIndex(); + int closedindex = tabbedPane.indexOfComponent(alignPanel2); + alignPanels.removeElement(alignPanel2); + // Unnecessary + // if (viewport == alignPanel2.av) + // { + // viewport = null; + // } + alignPanel2.closePanel(); + alignPanel2 = null; + + tabbedPane.removeTabAt(closedindex); + tabbedPane.validate(); + + if (index > closedindex || index == tabbedPane.getTabCount()) + { + // modify currently selected tab index if necessary. + index--; + } + + this.tabSelectionChanged(index); + } + + /** + * DOCUMENT ME! + */ + void updateEditMenuBar() + { + + if (viewport.historyList.size() > 0) + { + undoMenuItem.setEnabled(true); + CommandI command = (CommandI) viewport.historyList.peek(); + undoMenuItem.setText("Undo " + command.getDescription()); + } + else + { + undoMenuItem.setEnabled(false); + undoMenuItem.setText("Undo"); + } + + if (viewport.redoList.size() > 0) + { + redoMenuItem.setEnabled(true); + + CommandI command = (CommandI) viewport.redoList.peek(); + redoMenuItem.setText("Redo " + command.getDescription()); + } + else + { + redoMenuItem.setEnabled(false); + redoMenuItem.setText("Redo"); + } + } + + public void addHistoryItem(CommandI command) + { + if (command.getSize() > 0) + { + viewport.historyList.push(command); + viewport.redoList.clear(); + updateEditMenuBar(); + viewport.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); + } + } + + /** + * + * @return alignment objects for all views + */ + AlignmentI[] getViewAlignments() + { + if (alignPanels != null) + { + Enumeration e = alignPanels.elements(); + AlignmentI[] als = new AlignmentI[alignPanels.size()]; + for (int i = 0; e.hasMoreElements(); i++) + { + als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment(); + } + return als; + } + if (viewport != null) + { + return new AlignmentI[] + { viewport.alignment }; + } + return null; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void undoMenuItem_actionPerformed(ActionEvent e) + { + if (viewport.historyList.empty()) + return; + CommandI command = (CommandI) viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(getViewAlignments()); + + AlignViewport originalSource = getOriginatingSource(command); + updateEditMenuBar(); + + if (originalSource != null) + { + originalSource.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void redoMenuItem_actionPerformed(ActionEvent e) + { + if (viewport.redoList.size() < 1) + { + return; + } + + CommandI command = (CommandI) viewport.redoList.pop(); + viewport.historyList.push(command); + command.doCommand(getViewAlignments()); + + AlignViewport originalSource = getOriginatingSource(command); + updateEditMenuBar(); + + if (originalSource != null) + { + originalSource.hasHiddenColumns = (viewport.colSel != null + && viewport.colSel.getHiddenColumns() != null && viewport.colSel + .getHiddenColumns().size() > 0); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); + } + } + + AlignViewport getOriginatingSource(CommandI command) + { + AlignViewport originalSource = null; + // For sequence removal and addition, we need to fire + // the property change event FROM the viewport where the + // original alignment was altered + AlignmentI al = null; + if (command instanceof EditCommand) + { + EditCommand editCommand = (EditCommand) command; + al = editCommand.getAlignment(); + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); + + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment) + { + originalSource = ((AlignmentPanel) comps.elementAt(i)).av; + break; + } + } + } + } + + if (originalSource == null) + { + // The original view is closed, we must validate + // the current view against the closed view first + if (al != null) + { + PaintRefresher.validateSequences(al, viewport.alignment); + } + + originalSource = viewport; + } + + return originalSource; + } + + /** + * DOCUMENT ME! + * + * @param up + * DOCUMENT ME! + */ + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); + + if (sg == null) + { + return; + } + + if (up) + { + for (int i = 1; i < viewport.alignment.getHeight(); i++) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + + if (!sg.getSequences(null).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + + if (sg.getSequences(null).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i - 1); + } + } + else + { + for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + + if (!sg.getSequences(null).contains(seq)) + { + continue; + } + + SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + + if (sg.getSequences(null).contains(temp)) + { + continue; + } + + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i + 1); + } + } + + alignPanel.paintAlignment(true); + } + + synchronized void slideSequences(boolean right, int size) + { + Vector sg = new Vector(); + if (viewport.cursorMode) + { + sg.addElement(viewport.alignment + .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() != viewport.alignment + .getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.hiddenRepSequences); + } + + if (sg.size() < 1) + { + return; + } + + Vector invertGroup = new Vector(); + + for (int i = 0; i < viewport.alignment.getHeight(); i++) + { + if (!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.add(viewport.alignment.getSequenceAt(i)); + } + + SequenceI[] seqs1 = new SequenceI[sg.size()]; + for (int i = 0; i < sg.size(); i++) + seqs1[i] = (SequenceI) sg.elementAt(i); + + SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + for (int i = 0; i < invertGroup.size(); i++) + seqs2[i] = (SequenceI) invertGroup.elementAt(i); + + SlideSequencesCommand ssc; + if (right) + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, + size, viewport.getGapCharacter()); + else + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, + size, viewport.getGapCharacter()); + + int groupAdjustment = 0; + if (ssc.getGapsInsertedBegin() && right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(size, 0); + else + groupAdjustment = size; + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(-size, 0); + else + groupAdjustment = -size; + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + boolean appendHistoryItem = false; + if (viewport.historyList != null && viewport.historyList.size() > 0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc + .appendSlideCommand((SlideSequencesCommand) viewport.historyList + .peek()); + } + + if (!appendHistoryItem) + addHistoryItem(ssc); + + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void copy_actionPerformed(ActionEvent e) + { + System.gc(); + if (viewport.getSelectionGroup() == null) + { + return; + } + // TODO: preserve the ordering of displayed alignment annotation in any + // internal paste (particularly sequence associated annotation) + SequenceI[] seqs = viewport.getSelectionAsNewSequence(); + String[] omitHidden = null; + + if (viewport.hasHiddenColumns) + { + omitHidden = viewport.getViewAsString(true); + } + + String output = new FormatAdapter().formatSequences("Fasta", seqs, + omitHidden); + + StringSelection ss = new StringSelection(output); + + try + { + 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(ss, Desktop.instance); + } catch (OutOfMemoryError er) + { + new OOMWarning("copying region", er); + return; + } + + Vector hiddenColumns = null; + if (viewport.hasHiddenColumns) + { + hiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport + .getSelectionGroup().getEndRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns() + .size(); i++) + { + int[] region = (int[]) viewport.getColumnSelection() + .getHiddenColumns().elementAt(i); + if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) + { + hiddenColumns.addElement(new int[] + { region[0] - hiddenOffset, region[1] - hiddenOffset }); + } + } + } + + Desktop.jalviewClipboard = new Object[] + { seqs, viewport.alignment.getDataset(), hiddenColumns }; + statusBar.setText("Copied " + seqs.length + " sequences to clipboard."); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void pasteNew_actionPerformed(ActionEvent e) + { + paste(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void pasteThis_actionPerformed(ActionEvent e) + { + paste(false); + } + + /** + * Paste contents of Jalview clipboard + * + * @param newAlignment + * true to paste to a new alignment, otherwise add to this. + */ + void paste(boolean newAlignment) + { + boolean externalPaste = true; + try + { + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); + + if (contents == null) + { + return; + } + + String str, format; + try + { + str = (String) contents.getTransferData(DataFlavor.stringFlavor); + if (str.length() < 1) + { + return; + } + + format = new IdentifyFile().Identify(str, "Paste"); + + } catch (OutOfMemoryError er) + { + new OOMWarning("Out of memory pasting sequences!!", er); + return; + } + + SequenceI[] sequences; + boolean annotationAdded = false; + AlignmentI alignment = null; + + if (Desktop.jalviewClipboard != null) + { + // The clipboard was filled from within Jalview, we must use the + // sequences + // And dataset from the copied alignment + SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0]; + // be doubly sure that we create *new* sequence objects. + sequences = new SequenceI[newseq.length]; + for (int i = 0; i < newseq.length; i++) + { + sequences[i] = new Sequence(newseq[i]); + } + alignment = new Alignment(sequences); + externalPaste = false; + } + else + { + // parse the clipboard as an alignment. + alignment = new FormatAdapter().readFile(str, "Paste", format); + sequences = alignment.getSequencesArray(); + } + + int alwidth = 0; + + if (newAlignment) + { + + if (Desktop.jalviewClipboard != null) + { + // dataset is inherited + alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]); + } + else + { + // new dataset is constructed + alignment.setDataset(null); + } + alwidth = alignment.getWidth() + 1; + } + else + { + AlignmentI pastedal = alignment; // preserve pasted alignment object + // Add pasted sequences and dataset into existing alignment. + alignment = viewport.getAlignment(); + alwidth = alignment.getWidth() + 1; + // decide if we need to import sequences from an existing dataset + boolean importDs = Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[1] != alignment.getDataset(); + // importDs==true instructs us to copy over new dataset sequences from + // an existing alignment + Vector newDs = (importDs) ? new Vector() : null; // used to create + // minimum dataset set + + for (int i = 0; i < sequences.length; i++) + { + if (importDs) + { + newDs.addElement(null); + } + SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple + // paste + if (importDs && ds != null) + { + if (!newDs.contains(ds)) + { + newDs.setElementAt(ds, i); + ds = new Sequence(ds); + // update with new dataset sequence + sequences[i].setDatasetSequence(ds); + } + else + { + ds = sequences[newDs.indexOf(ds)].getDatasetSequence(); + } + } + else + { + // copy and derive new dataset sequence + sequences[i] = sequences[i].deriveSequence(); + alignment.getDataset().addSequence( + sequences[i].getDatasetSequence()); + // TODO: avoid creation of duplicate dataset sequences with a + // 'contains' method using SequenceI.equals()/SequenceI.contains() + } + alignment.addSequence(sequences[i]); // merges dataset + } + if (newDs != null) + { + newDs.clear(); // tidy up + } + if (pastedal.getAlignmentAnnotation() != null) + { + // Add any annotation attached to alignment. + AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation(); + for (int i = 0; i < alann.length; i++) + { + annotationAdded = true; + if (alann[i].sequenceRef == null && !alann[i].autoCalculated) + { + AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + newann.padAnnotation(alwidth); + alignment.addAnnotation(newann); + } + } + } + } + if (!newAlignment) + { + // ///// + // ADD HISTORY ITEM + // + addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + sequences, 0, alignment.getWidth(), alignment)); + } + // Add any annotations attached to sequences + for (int i = 0; i < sequences.length; i++) + { + if (sequences[i].getAnnotation() != null) + { + for (int a = 0; a < sequences[i].getAnnotation().length; a++) + { + annotationAdded = true; + sequences[i].getAnnotation()[a].adjustForAlignment(); + sequences[i].getAnnotation()[a].padAnnotation(alwidth); + alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation + // was + // duplicated + // earlier + alignment + .setAnnotationIndex(sequences[i].getAnnotation()[a], a); + } + } + } + if (!newAlignment) + { + + // propagate alignment changed. + viewport.setEndSeq(alignment.getHeight()); + if (annotationAdded) + { + // Duplicate sequence annotation in all views. + AlignmentI[] alview = this.getViewAlignments(); + for (int i = 0; i < sequences.length; i++) + { + AlignmentAnnotation sann[] = sequences[i].getAnnotation(); + if (sann == null) + continue; + for (int avnum = 0; avnum < alview.length; avnum++) + { + if (alview[avnum] != alignment) + { + // duplicate in a view other than the one with input focus + int avwidth = alview[avnum].getWidth() + 1; + // this relies on sann being preserved after we + // modify the sequence's annotation array for each duplication + for (int a = 0; a < sann.length; a++) + { + AlignmentAnnotation newann = new AlignmentAnnotation( + sann[a]); + sequences[i].addAlignmentAnnotation(newann); + newann.padAnnotation(avwidth); + alview[avnum].addAnnotation(newann); // annotation was + // duplicated earlier + alview[avnum].setAnnotationIndex(newann, a); + } + } + } + } + buildSortByAnnotationScoresMenu(); + } + viewport.firePropertyChange("alignment", null, + alignment.getSequences()); + + } + else + { + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Copied sequences"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) + { + Vector hc = (Vector) Desktop.jalviewClipboard[2]; + for (int i = 0; i < hc.size(); i++) + { + int[] region = (int[]) hc.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + .transferSettings( + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. + if (!externalPaste) + { + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } + } + else + { + newtitle = new String("Pasted sequences"); + } + + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + + } + + } catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Exception whilst pasting: " + ex); + // could be anything being pasted in here + } + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void cut_actionPerformed(ActionEvent e) + { + copy_actionPerformed(null); + delete_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void delete_actionPerformed(ActionEvent evt) + { + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) + { + return; + } + + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + seqs.addElement(seq); + } + + // If the cut affects all sequences, remove highlighted columns + if (sg.getSize() == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } + + SequenceI[] cut = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + cut[i] = (SequenceI) seqs.elementAt(i); + } + + /* + * //ADD HISTORY ITEM + */ + addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, + sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.alignment)); + + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.alignment.deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + this.setClosed(true); + } catch (Exception ex) + { + } + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void deleteGroups_actionPerformed(ActionEvent e) + { + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = new SequenceGroup(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + } + + sg.setEndRes(viewport.alignment.getWidth() - 1); + viewport.setSelectionGroup(sg); + viewport.sendSelection(); + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + { + if (viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1 = null; + alignPanel.seqPanel.keyboardNo2 = null; + } + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.idPanel.idCanvas.searchResults = null; + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void invertSequenceMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + + if (sg == null) + { + selectAllSequenceMenuItem_actionPerformed(null); + + return; + } + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) + { + sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + } + + alignPanel.paintAlignment(true); + PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); + viewport.sendSelection(); + } + + public void invertColSel_actionPerformed(ActionEvent e) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + viewport.sendSelection(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + { + trimAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void remove2RightMenuItem_actionPerformed(ActionEvent e) + { + trimAlignment(false); + } + + void trimAlignment(boolean trimLeft) + { + ColumnSelection colSel = viewport.getColumnSelection(); + int column; + + if (colSel.size() > 0) + { + if (trimLeft) + { + column = colSel.getMin(); + } + else + { + column = colSel.getMax(); + } + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + TrimRegionCommand trimRegion; + if (trimLeft) + { + trimRegion = new TrimRegionCommand("Remove Left", + TrimRegionCommand.TRIM_LEFT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); + viewport.setStartRes(0); + } + else + { + trimRegion = new TrimRegionCommand("Remove Right", + TrimRegionCommand.TRIM_RIGHT, seqs, column, + viewport.alignment, viewport.colSel, + viewport.selectionGroup); + } + + statusBar.setText("Removed " + trimRegion.getSize() + " columns."); + + addHistoryItem(trimRegion); + + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.get(i); + + if ((trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) + { + viewport.alignment.deleteGroup(sg); + } + } + + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + RemoveGapColCommand removeGapCols = new RemoveGapColCommand( + "Remove Gapped Columns", seqs, start, end, viewport.alignment); + + addHistoryItem(removeGapCols); + + statusBar.setText("Removed " + removeGapCols.getSize() + + " empty columns."); + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + viewport.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + { + int start = 0, end = viewport.alignment.getWidth() - 1; + + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray( + viewport.hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + { + seqs = viewport.alignment.getSequencesArray(); + } + + // This is to maintain viewport position on first residue + // of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + + addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, + viewport.alignment)); + + viewport.setStartRes(seq.findIndex(startRes) - 1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void padGapsMenuitem_actionPerformed(ActionEvent e) + { + viewport.padGaps = padGapsMenuitem.isSelected(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment() + .getSequences()); + } + + // else + { + // if (justifySeqs>0) + { + // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); + } + } + + // } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void findMenuItem_actionPerformed(ActionEvent e) + { + new Finder(); + } + + public void newView_actionPerformed(ActionEvent e) + { + newView(true); + } + + /** + * + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(boolean copyAnnotation) + { + return newView(null, copyAnnotation); + } + + /** + * + * @param viewTitle + * title of newly created view + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle) + { + return newView(viewTitle, true); + } + + /** + * + * @param viewTitle + * title of newly created view + * @param copyAnnotation + * if true then duplicate all annnotation, groups and settings + * @return new alignment panel, already displayed. + */ + public AlignmentPanel newView(String viewTitle, boolean copyAnnotation) + { + AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, + true); + if (!copyAnnotation) + { + // just remove all the current annotation except for the automatic stuff + newap.av.alignment.deleteAllGroups(); + for (AlignmentAnnotation alan : newap.av.alignment + .getAlignmentAnnotation()) + { + if (!alan.autoCalculated) + { + newap.av.alignment.deleteAnnotation(alan); + } + ; + } + } + + newap.av.gatherViewsHere = false; + + if (viewport.viewName == null) + { + viewport.viewName = "Original"; + } + + newap.av.historyList = viewport.historyList; + newap.av.redoList = viewport.redoList; + + int index = Desktop.getViewCount(viewport.getSequenceSetId()); + // 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(); + for (int i = 0; i < comps.size(); i++) + { + if (comps.elementAt(i) instanceof AlignmentPanel) + { + AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i); + if (!existingNames.contains(ap.av.viewName)) + { + existingNames.addElement(ap.av.viewName); + } + } + } + + while (existingNames.contains(newViewName)) + { + newViewName = viewTitle + " " + (++index); + } + + newap.av.viewName = newViewName; + + addAlignmentPanel(newap, true); + + if (alignPanels.size() == 2) + { + viewport.gatherViewsHere = true; + } + tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1); + return newap; + } + + public void expandViews_actionPerformed(ActionEvent e) + { + Desktop.instance.explodeViews(this); + } + + public void gatherViews_actionPerformed(ActionEvent e) + { + Desktop.instance.gatherViews(this); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void font_actionPerformed(ActionEvent e) + { + new FontChooser(alignPanel); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void seqLimit_actionPerformed(ActionEvent e) + { + viewport.setShowJVSuffix(seqLimits.isSelected()); + + alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel + .calculateIdWidth()); + alignPanel.paintAlignment(true); + } + + public void idRightAlign_actionPerformed(ActionEvent e) + { + viewport.rightAlignIds = idRightAlign.isSelected(); + alignPanel.paintAlignment(true); + } + + public void centreColumnLabels_actionPerformed(ActionEvent e) + { + viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() + */ + protected void followHighlight_actionPerformed() + { + if (viewport.followHighlight = this.followHighlightMenuItem.getState()) + { + alignPanel.scrollToPosition( + alignPanel.seqPanel.seqCanvas.searchResults, false); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void colourTextMenuItem_actionPerformed(ActionEvent e) + { + viewport.setColourText(colourTextMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void wrapMenuItem_actionPerformed(ActionEvent e) + { + scaleAbove.setVisible(wrapMenuItem.isSelected()); + scaleLeft.setVisible(wrapMenuItem.isSelected()); + scaleRight.setVisible(wrapMenuItem.isSelected()); + viewport.setWrapAlignment(wrapMenuItem.isSelected()); + alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); + } + + public void showAllSeqs_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenSeqs(); + } + + public void showAllColumns_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + repaint(); + } + + public void hideSelSequences_actionPerformed(ActionEvent e) + { + viewport.hideAllSelectedSeqs(); + alignPanel.paintAlignment(true); + } + + /** + * called by key handler and the hide all/show all menu items + * + * @param toggleSeqs + * @param toggleCols + */ + private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + { + + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + if (!toggleSeqs && !toggleCols) + { + // Hide everything by the current selection - this is a hack - we do the + // invert and then hide + // first check that there will be visible columns after the invert. + if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel + .getSelected().size() > 0) + || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg + .getEndRes())) + { + // now invert the sequence set, if required - empty selection implies + // that no hiding is required. + if (sg != null) + { + invertSequenceMenuItem_actionPerformed(null); + sg = viewport.getSelectionGroup(); + toggleSeqs = true; + + } + viewport.expandColSelection(sg, true); + // finally invert the column selection and get the new sequence + // selection. + invertColSel_actionPerformed(null); + toggleCols = true; + } + } + + if (toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + { + hideSelSequences_actionPerformed(null); + hide = true; + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + { + showAllSeqs_actionPerformed(null); + } + } + + if (toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + hideSelColumns_actionPerformed(null); + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } + } + else if (!hide) + { + showAllColumns_actionPerformed(null); + } + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. + * event.ActionEvent) + */ + public void hideAllButSelection_actionPerformed(ActionEvent e) + { + toggleHiddenRegions(false, false); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event + * .ActionEvent) + */ + public void hideAllSelection_actionPerformed(ActionEvent e) + { + SequenceGroup sg = viewport.getSelectionGroup(); + viewport.expandColSelection(sg, false); + viewport.hideAllSelectedSeqs(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. + * ActionEvent) + */ + public void showAllhidden_actionPerformed(ActionEvent e) + { + viewport.showAllHiddenColumns(); + viewport.showAllHiddenSeqs(); + alignPanel.paintAlignment(true); + } + + public void hideSelColumns_actionPerformed(ActionEvent e) + { + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); + } + + public void hiddenMarkers_actionPerformed(ActionEvent e) + { + viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void scaleAbove_actionPerformed(ActionEvent e) + { + viewport.setScaleAboveWrapped(scaleAbove.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void scaleLeft_actionPerformed(ActionEvent e) + { + viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void scaleRight_actionPerformed(ActionEvent e) + { + viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void viewBoxesMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void viewTextMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowText(viewTextMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { + viewport.setRenderGaps(renderGapsMenuItem.isSelected()); + alignPanel.paintAlignment(true); + } + + public FeatureSettings featureSettings; + + public void featureSettings_actionPerformed(ActionEvent e) + { + if (featureSettings != null) + { + featureSettings.close(); + featureSettings = null; + } + if (!showSeqFeatures.isSelected()) + { + // make sure features are actually displayed + showSeqFeatures.setSelected(true); + showSeqFeatures_actionPerformed(null); + } + featureSettings = new FeatureSettings(this); + } + + /** + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! + */ + public void showSeqFeatures_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); + alignPanel.paintAlignment(true); + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + } + + /** + * Set or clear 'Show Sequence Features' + * + * @param evt + * DOCUMENT ME! + */ + public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight + .isSelected()); + if (viewport.getShowSequenceFeaturesHeight()) + { + // ensure we're actually displaying features + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); + } + alignPanel.paintAlignment(true); + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void annotationPanelMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); + } + + public void alignmentProperties() + { + JEditorPane editPane = new JEditorPane("text/html", ""); + editPane.setEditable(false); + StringBuffer contents = new AlignmentProperties(viewport.alignment) + .formatAsHtml(); + editPane.setText("" + contents.toString() + ""); + JInternalFrame frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(editPane)); + + Desktop.instance.addInternalFrame(frame, "Alignment Properties: " + + getTitle(), 500, 400); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void overviewMenuItem_actionPerformed(ActionEvent e) + { + if (alignPanel.overviewPanel != null) + { + return; + } + + JInternalFrame frame = new JInternalFrame(); + OverviewPanel overview = new OverviewPanel(alignPanel); + frame.setContentPane(overview); + 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); + }; + }); + + alignPanel.setOverviewPanel(overview); + } + + public void textColour_actionPerformed(ActionEvent e) + { + new TextColourChooser().chooseColour(alignPanel, null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { + changeColour(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void clustalColour_actionPerformed(ActionEvent e) + { + changeColour(new ClustalxColourScheme( + viewport.alignment.getSequences(), + viewport.alignment.getWidth())); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void zappoColour_actionPerformed(ActionEvent e) + { + changeColour(new ZappoColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void taylorColour_actionPerformed(ActionEvent e) + { + changeColour(new TaylorColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void hydrophobicityColour_actionPerformed(ActionEvent e) + { + changeColour(new HydrophobicColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void helixColour_actionPerformed(ActionEvent e) + { + changeColour(new HelixColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void strandColour_actionPerformed(ActionEvent e) + { + changeColour(new StrandColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void turnColour_actionPerformed(ActionEvent e) + { + changeColour(new TurnColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void buriedColour_actionPerformed(ActionEvent e) + { + changeColour(new BuriedColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void nucleotideColour_actionPerformed(ActionEvent e) + { + changeColour(new NucleotideColourScheme()); + } + + public void purinePyrimidineColour_actionPerformed(ActionEvent e) + { + changeColour(new PurinePyrimidineColourScheme()); + } + /* + public void covariationColour_actionPerformed(ActionEvent e) + { + changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0])); + } + */ + public void annotationColour_actionPerformed(ActionEvent e) + { + new AnnotationColourChooser(viewport, alignPanel); + } + + public void rnahelicesColour_actionPerformed(ActionEvent e) + { + new RNAHelicesColourChooser(viewport, alignPanel); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void applyToAllGroups_actionPerformed(ActionEvent e) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + } + + /** + * DOCUMENT ME! + * + * @param cs + * DOCUMENT ME! + */ + public void changeColour(ColourSchemeI cs) + { + int threshold = 0; + + if (cs != null) + { + if (viewport.getAbovePIDThreshold()) + { + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); + + cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + + viewport.setGlobalColourScheme(cs); + } + else + { + cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + if (viewport.getConservationSelected()) + { + + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, al.getSequences(), 0, + al.getWidth() - 1); + + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + + cs.setConservation(c); + + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, + cs, "Background")); + } + else + { + cs.setConservation(null); + } + + cs.setConsensus(viewport.hconsensus); + } + + viewport.setGlobalColourScheme(cs); + + if (viewport.getColourAppliesToAllGroups()) + { + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + + if (cs == null) + { + sg.cs = null; + continue; + } + + if (cs instanceof ClustalxColourScheme) + { + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); + } + else if (cs instanceof UserColourScheme) + { + sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours()); + } + else + { + try + { + sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + } catch (Exception ex) + { + } + } + + if (viewport.getAbovePIDThreshold() + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) + { + sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); + + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1)); + } + else + { + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } + + if (viewport.getConservationSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(viewport.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + sg.cs.setConservation(c); + } + else + { + sg.cs.setConservation(null); + } + } + } + + if (alignPanel.getOverviewPanel() != null) + { + alignPanel.getOverviewPanel().updateOverviewImage(); + } + + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void modifyPID_actionPerformed(ActionEvent e) + { + if (viewport.getAbovePIDThreshold() + && viewport.globalColourScheme != null) + { + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), "Background"); + SliderPanel.showPIDSlider(); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void modifyConservation_actionPerformed(ActionEvent e) + { + if (viewport.getConservationSelected() + && viewport.globalColourScheme != null) + { + SliderPanel.setConservationSlider(alignPanel, + viewport.globalColourScheme, "Background"); + SliderPanel.showConservationSlider(); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { + viewport.setConservationSelected(conservationMenuItem.isSelected()); + + viewport.setAbovePIDThreshold(false); + abovePIDThreshold.setSelected(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyConservation_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void abovePIDThreshold_actionPerformed(ActionEvent e) + { + viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); + + conservationMenuItem.setSelected(false); + viewport.setConservationSelected(false); + + changeColour(viewport.getGlobalColourScheme()); + + modifyPID_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void userDefinedColour_actionPerformed(ActionEvent e) + { + if (e.getActionCommand().equals("User Defined...")) + { + new UserDefinedColours(alignPanel, null); + } + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); + + changeColour(udc); + } + } + + public void updateUserColourMenu() + { + + Component[] menuItems = colourMenu.getMenuComponents(); + int i, iSize = menuItems.length; + for (i = 0; i < iSize; i++) + { + if (menuItems[i].getName() != null + && menuItems[i].getName().equals("USER_DEFINED")) + { + colourMenu.remove(menuItems[i]); + iSize--; + } + } + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( + userColours.nextElement().toString()); + radioItem.setName("USER_DEFINED"); + radioItem.addMouseListener(new MouseAdapter() + { + public void mousePressed(MouseEvent evt) + { + if (evt.isControlDown() + || SwingUtilities.isRightMouseButton(evt)) + { + radioItem.removeActionListener(radioItem.getActionListeners()[0]); + + int option = JOptionPane.showInternalConfirmDialog( + jalview.gui.Desktop.desktop, + "Remove from default list?", + "Remove user defined colour", + JOptionPane.YES_NO_OPTION); + if (option == JOptionPane.YES_OPTION) + { + jalview.gui.UserDefinedColours + .removeColourFromDefaults(radioItem.getText()); + colourMenu.remove(radioItem); + } + else + { + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + } + } + } + }); + radioItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + + colourMenu.insert(radioItem, 15); + colours.add(radioItem); + } + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void PIDColour_actionPerformed(ActionEvent e) + { + changeColour(new PIDColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + changeColour(new Blosum62ColourScheme()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByPID(viewport.getAlignment(), viewport + .getAlignment().getSequenceAt(0), null); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void sortIDMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByID(viewport.getAlignment()); + addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void sortLengthMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByLength(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void sortGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByGroup(viewport.getAlignment()); + addHistoryItem(new OrderCommand("Group Sort", oldOrder, + viewport.alignment)); + + alignPanel.paintAlignment(true); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + { + new RedundancyPanel(alignPanel, this); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) + { + if ((viewport.getSelectionGroup() == null) + || (viewport.getSelectionGroup().getSize() < 2)) + { + JOptionPane.showInternalMessageDialog(this, + "You must select at least 2 sequences.", "Invalid Selection", + JOptionPane.WARNING_MESSAGE); + } + else + { + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(new PairwiseAlignPanel(viewport)); + Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); + } + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void PCAMenuItem_actionPerformed(ActionEvent e) + { + if (((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() < 4) && (viewport + .getSelectionGroup().getSize() > 0)) + || (viewport.getAlignment().getHeight() < 4)) + { + JOptionPane.showInternalMessageDialog(this, + "Principal component analysis must take\n" + + "at least 4 input sequences.", + "Sequence selection insufficient", + JOptionPane.WARNING_MESSAGE); + + return; + } + + new PCAPanel(alignPanel); + } + + public void autoCalculate_actionPerformed(ActionEvent e) + { + viewport.autoCalculateConsensus = autoCalculate.isSelected(); + if (viewport.autoCalculateConsensus) + { + viewport.firePropertyChange("alignment", null, viewport + .getAlignment().getSequences()); + } + } + public void sortByTreeOption_actionPerformed(ActionEvent e) + { + viewport.sortByTree = sortByTree.isSelected(); + } + + @Override + protected void listenToViewSelections_actionPerformed(ActionEvent e) + { + viewport.followSelection = listenToViewSelections.isSelected(); + } + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + { + NewTreePanel("AV", "PID", "Average distance tree using PID"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + { + NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + { + NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + { + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + } + + /** + * DOCUMENT ME! + * + * @param type + * DOCUMENT ME! + * @param pwType + * DOCUMENT ME! + * @param title + * DOCUMENT ME! + */ + void NewTreePanel(String type, String pwType, String title) + { + TreePanel tp; + + if (viewport.getSelectionGroup() != null) + { + if (viewport.getSelectionGroup().getSize() < 3) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + "You need to have more than two sequences selected to build a tree!", + "Not enough sequences", JOptionPane.WARNING_MESSAGE); + return; + } + + int s = 0; + SequenceGroup sg = viewport.getSelectionGroup(); + + /* Decide if the selection is a column region */ + while (s < sg.getSize()) + { + if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg + .getEndRes()) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + "The selected region to create a tree may\nonly contain residues or gaps.\n" + + "Try using the Pad function in the edit menu,\n" + + "or one of the multiple sequence alignment web services.", + "Sequences in selection are not aligned", + JOptionPane.WARNING_MESSAGE); + + return; + } + } + + title = title + " on region"; + tp = new TreePanel(alignPanel, type, pwType); + } + else + { + // are the visible sequences aligned? + if (!viewport.alignment.isAligned(false)) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + "The sequences must be aligned before creating a tree.\n" + + "Try using the Pad function in the edit menu,\n" + + "or one of the multiple sequence alignment web services.", + "Sequences not aligned", + JOptionPane.WARNING_MESSAGE); + + return; + } + + if (viewport.alignment.getHeight() < 2) + { + return; + } + + tp = new TreePanel(alignPanel, type, pwType); + } + + title += " from "; + + if (viewport.viewName != null) + { + title += viewport.viewName + " of "; + } + + title += this.title; + + Desktop.addInternalFrame(tp, title, 600, 500); + } + + /** + * DOCUMENT ME! + * + * @param title + * DOCUMENT ME! + * @param order + * DOCUMENT ME! + */ + public void addSortByOrderMenuItem(String title, + final AlignmentOrder order) + { + final JMenuItem item = new JMenuItem("by " + title); + sort.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + + // TODO: JBPNote - have to map order entries to curent SequenceI + // pointers + AlignmentSorter.sortBy(viewport.getAlignment(), order); + + addHistoryItem(new OrderCommand(order.getName(), oldOrder, + viewport.alignment)); + + alignPanel.paintAlignment(true); + } + }); + } + + /** + * Add a new sort by annotation score menu item + * + * @param sort + * the menu to add the option to + * @param scoreLabel + * the label used to retrieve scores for each sequence on the + * alignment + */ + public void addSortByAnnotScoreMenuItem(JMenu sort, + final String scoreLabel) + { + final JMenuItem item = new JMenuItem(scoreLabel); + sort.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortByAnnotationScore(scoreLabel, + viewport.getAlignment());// ,viewport.getSelectionGroup()); + addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); + } + }); + } + + /** + * last hash for alignment's annotation array - used to minimise cost of + * rebuild. + */ + protected int _annotationScoreVectorHash; + + /** + * search the alignment and rebuild the sort by annotation score submenu the + * last alignment annotation vector hash is stored to minimize cost of + * rebuilding in subsequence calls. + * + */ + public void buildSortByAnnotationScoresMenu() + { + if (viewport.alignment.getAlignmentAnnotation() == null) + { + return; + } + + if (viewport.alignment.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(); + while (sq.hasMoreElements()) + { + aann = ((SequenceI) sq.nextElement()).getAnnotation(); + for (int i = 0; aann != null && i < aann.length; i++) + { + if (aann[i].hasScore() && aann[i].sequenceRef != null) + { + scoreSorts.put(aann[i].label, aann[i].label); + } + } + } + Enumeration labels = scoreSorts.keys(); + while (labels.hasMoreElements()) + { + addSortByAnnotScoreMenuItem(sortByAnnotScore, + (String) labels.nextElement()); + } + sortByAnnotScore.setVisible(scoreSorts.size() > 0); + scoreSorts.clear(); + + _annotationScoreVectorHash = viewport.alignment + .getAlignmentAnnotation().hashCode(); + } + } + + /** + * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a + * TreePanel with an appropriate jalview.analysis.AlignmentSorter + * call. Listeners are added to remove the menu item when the treePanel is + * closed, and adjust the tree leaf to sequence mapping when the alignment is + * modified. + * + * @param treePanel + * Displayed tree window. + * @param title + * SortBy menu item title. + */ + public void buildTreeMenu() + { + sortByTreeMenu.removeAll(); + + Vector comps = (Vector) PaintRefresher.components.get(viewport + .getSequenceSetId()); + Vector treePanels = new Vector(); + int i, iSize = comps.size(); + for (i = 0; i < iSize; i++) + { + if (comps.elementAt(i) instanceof TreePanel) + { + treePanels.add(comps.elementAt(i)); + } + } + + iSize = treePanels.size(); + + if (iSize < 1) + { + sortByTreeMenu.setVisible(false); + return; + } + + sortByTreeMenu.setVisible(true); + + for (i = 0; i < treePanels.size(); 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) + { + tp.sortByTree_actionPerformed(null); + addHistoryItem(tp.sortAlignmentIn(alignPanel)); + + } + }); + + sortByTreeMenu.add(item); + } + } + + public boolean sortBy(AlignmentOrder alorder, String undoname) + { + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); + AlignmentSorter.sortBy(viewport.getAlignment(), alorder); + if (undoname != null) + { + addHistoryItem(new OrderCommand(undoname, oldOrder, + viewport.alignment)); + } + alignPanel.paintAlignment(true); + return true; + } + + /** + * Work out whether the whole set of sequences or just the selected set will + * be submitted for multiple alignment. + * + */ + public jalview.datamodel.AlignmentView gatherSequencesForAlignment() + { + // Now, check we have enough sequences + AlignmentView msa = null; + + if ((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() > 1)) + { + // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to + // some common interface! + /* + * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new + * SequenceI[sz = seqs.getSize(false)]; + * + * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) + * seqs.getSequenceAt(i); } + */ + msa = viewport.getAlignmentView(true); + } + else + { + /* + * Vector seqs = viewport.getAlignment().getSequences(); + * + * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; + * + * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) + * seqs.elementAt(i); } } + */ + msa = viewport.getAlignmentView(false); + } + return msa; + } + + /** + * Decides what is submitted to a secondary structure prediction service: the + * first sequence in the alignment, or in the current selection, or, if the + * alignment is 'aligned' (ie padded with gaps), then the currently selected + * region or the whole alignment. (where the first sequence in the set is the + * one that the prediction will be for). + */ + public AlignmentView gatherSeqOrMsaForSecStrPrediction() + { + AlignmentView seqs = null; + + if ((viewport.getSelectionGroup() != null) + && (viewport.getSelectionGroup().getSize() > 0)) + { + seqs = viewport.getAlignmentView(true); + } + else + { + seqs = viewport.getAlignmentView(false); + } + // limit sequences - JBPNote in future - could spawn multiple prediction + // jobs + // TODO: viewport.alignment.isAligned is a global state - the local + // selection may well be aligned - we preserve 2.0.8 behaviour for moment. + if (!viewport.alignment.isAligned(false)) + { + seqs.setSequences(new SeqCigar[] + { seqs.getSequences()[0] }); + // TODO: if seqs.getSequences().length>1 then should really have warned + // user! + + } + return seqs; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + { + // Pick the tree file + 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"); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + jalview.io.NewickFile fin = null; + try + { + fin = new jalview.io.NewickFile(choice, "File"); + viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); + } catch (Exception ex) + { + JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + "Problem reading tree file", JOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + if (fin != null && fin.hasWarningMessage()) + { + JOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), "Possible problem with tree file", + JOptionPane.WARNING_MESSAGE); + } + } + } + + public TreePanel ShowNewickTree(NewickFile nf, String title) + { + return ShowNewickTree(nf, title, 600, 500, 4, 5); + } + + public TreePanel ShowNewickTree(NewickFile nf, String title, + AlignmentView input) + { + return ShowNewickTree(nf, title, input, 600, 500, 4, 5); + } + + public TreePanel ShowNewickTree(NewickFile nf, String title, int w, + int h, int x, int y) + { + return ShowNewickTree(nf, title, null, w, h, x, y); + } + + /** + * Add a treeviewer for the tree extracted from a newick file object to the + * current alignment view + * + * @param nf + * the tree + * @param title + * tree viewer title + * @param input + * Associated alignment input data (or null) + * @param w + * width + * @param h + * height + * @param x + * position + * @param y + * position + * @return TreePanel handle + */ + public TreePanel ShowNewickTree(NewickFile nf, String title, + AlignmentView input, int w, int h, int x, int y) + { + TreePanel tp = null; + + try + { + nf.parse(); + + if (nf.getTree() != null) + { + tp = new TreePanel(alignPanel, "FromFile", title, nf, input); + + tp.setSize(w, h); + + if (x > 0 && y > 0) + { + tp.setLocation(x, y); + } + + Desktop.addInternalFrame(tp, title, w, h); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + + return tp; + } + + private boolean buildingMenu = false; + + /** + * Generates menu items and listener event actions for web service clients + * + */ + public void BuildWebServiceMenu() + { + while (buildingMenu) + { + try + { + System.err.println("Waiting for building menu to finish."); + Thread.sleep(10); + } catch (Exception e) + { + } + ; + } + final AlignFrame me = this; + buildingMenu = true; + new Thread(new Runnable() + { + public void run() + { + try + { + System.err.println("Building ws menu again " + + Thread.currentThread()); + // TODO: add support for context dependent disabling of services based + // on + // alignment and current selection + // TODO: add additional serviceHandle parameter to specify abstract + // handler + // class independently of AbstractName + // TODO: add in rediscovery GUI function to restart discoverer + // TODO: group services by location as well as function and/or + // introduce + // object broker mechanism. + final Vector wsmenu = new Vector(); + final IProgressIndicator af = me; + final JMenu msawsmenu = new JMenu("Alignment"); + final JMenu secstrmenu = new JMenu( + "Secondary Structure Prediction"); + final JMenu seqsrchmenu = new JMenu( + "Sequence Database Search"); + final JMenu analymenu = new JMenu( + "Analysis"); + // JAL-940 - only show secondary structure prediction services from the legacy server + if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) + // && + Discoverer.services != null + && (Discoverer.services.size() > 0)) + { + // TODO: refactor to allow list of AbstractName/Handler bindings to + // be + // stored or retrieved from elsewhere + Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS"); + Vector secstrpr = (Vector) Discoverer.services + .get("SecStrPred"); + Vector seqsrch = null; // (Vector) Discoverer.services.get("SeqSearch"); + // TODO: move GUI generation code onto service implementation - so a + // client instance attaches itself to the GUI with method call like + // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, + // alignframe) + if (msaws != null) + { + // Add any Multiple Sequence Alignment Services + for (int i = 0, j = msaws.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(msawsmenu, me); + + } + } + if (secstrpr != null) + { + // Add any secondary structure prediction services + for (int i = 0, j = secstrpr.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr + .get(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(secstrmenu, me); + } + } + if (seqsrch != null) + { + // Add any sequence search services + for (int i = 0, j = seqsrch.size(); i < j; i++) + { + final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch + .elementAt(i); + jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer + .getServiceClient(sh); + impl.attachWSMenuEntry(seqsrchmenu, me); + } + } + } + + // TODO: move into separate menu builder class. + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer(); + if (jws2servs != null) + { + if (jws2servs.hasServices()) + { + jws2servs.attachWSMenuEntry(msawsmenu, me); + } + } + } + // Add all submenus in the order they should appear on the web services menu + wsmenu.add(msawsmenu); + wsmenu.add(secstrmenu); + wsmenu.add(analymenu); + // No search services yet + // wsmenu.add(seqsrchmenu); + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + try + { + webService.removeAll(); + // first, add discovered services onto the webservices menu + if (wsmenu.size() > 0) + { + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add((JMenu) wsmenu.get(i)); + } + } + else + { + webService.add(me.webServiceNoServices); + } + build_urlServiceMenu(me.webService); + build_fetchdbmenu(webService); + } catch (Exception e) + { + } + ; + } + }); + } catch (Exception e) + { + } + ; + + buildingMenu = false; + } + }).start(); + + } + + + /** + * construct any groupURL type service menu entries. + * + * @param webService + */ + 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.alignment, + * af.viewport.colSel, af.viewport.selectionGroup); } + * + * }); webService.add(testAlView); + */ + // TODO: refactor to RestClient discoverer and merge menu entries for + // rest-style services with other types of analysis/calculation service + // SHmmr test client - still being implemented. + // DEBUG - alignmentView + + for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) { + client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this); + } + + if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) + { + jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry( + webService, this); + } + } + + /* + * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser + * chooser = new JalviewFileChooser(jalview.bin.Cache. + * getProperty("LAST_DIRECTORY")); + * + * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export + * to Vamsas file"); chooser.setToolTipText("Export"); + * + * int value = chooser.showSaveDialog(this); + * + * if (value == JalviewFileChooser.APPROVE_OPTION) { + * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); + * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( + * chooser.getSelectedFile().getAbsolutePath(), this); } } + */ + /** + * prototype of an automatically enabled/disabled analysis function + * + */ + protected void setShowProductsEnabled() + { + SequenceI[] selection = viewport.getSequenceSelection(); + if (canShowProducts(selection, viewport.getSelectionGroup() != null, + viewport.getAlignment().getDataset())) + { + showProducts.setEnabled(true); + + } + else + { + showProducts.setEnabled(false); + } + } + + /** + * search selection for sequence xRef products and build the show products + * menu. + * + * @param selection + * @param dataset + * @return true if showProducts menu should be enabled. + */ + public boolean canShowProducts(SequenceI[] selection, + boolean isRegionSelection, Alignment dataset) + { + boolean showp = false; + try + { + showProducts.removeAll(); + final boolean dna = viewport.getAlignment().isNucleotide(); + final Alignment ds = dataset; + String[] ptypes = (selection == null || selection.length == 0) ? null + : CrossRef.findSequenceXrefTypes(dna, selection, dataset); + // Object[] prods = + // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), + // selection, dataset, true); + final SequenceI[] sel = selection; + for (int t = 0; ptypes != null && t < ptypes.length; t++) + { + showp = true; + final boolean isRegSel = isRegionSelection; + final AlignFrame af = this; + final String source = ptypes[t]; + JMenuItem xtype = new JMenuItem(ptypes[t]); + xtype.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + // TODO: new thread for this call with vis-delay + af.showProductsFor(af.viewport.getSequenceSelection(), ds, + isRegSel, dna, source); + } + + }); + showProducts.add(xtype); + } + showProducts.setVisible(showp); + showProducts.setEnabled(showp); + } catch (Exception e) + { + jalview.bin.Cache.log + .warn("canTranslate threw an exception - please report to help@jalview.org", + e); + return false; + } + return showp; + } + + protected void showProductsFor(SequenceI[] sel, Alignment ds, + boolean isRegSel, boolean dna, String source) + { + final boolean fisRegSel = isRegSel; + final boolean fdna = dna; + final String fsrc = source; + final AlignFrame ths = this; + final SequenceI[] fsel = sel; + Runnable foo = new Runnable() + { + + public void run() + { + final long sttime = System.currentTimeMillis(); + ths.setProgressBar("Searching for sequences from " + fsrc, sttime); + try + { + Alignment ds = ths.getViewport().alignment.getDataset(); // update + // our local + // dataset + // reference + Alignment prods = CrossRef + .findXrefSequences(fsel, fdna, fsrc, ds); + if (prods != null) + { + SequenceI[] sprods = new SequenceI[prods.getHeight()]; + for (int s = 0; s < sprods.length; s++) + { + sprods[s] = (prods.getSequenceAt(s)).deriveSequence(); + if (ds.getSequences() == null + || !ds.getSequences().contains( + sprods[s].getDatasetSequence())) + ds.addSequence(sprods[s].getDatasetSequence()); + sprods[s].updatePDBIds(); + } + Alignment al = new Alignment(sprods); + AlignedCodonFrame[] cf = prods.getCodonFrames(); + al.setDataset(ds); + for (int s = 0; cf != null && s < cf.length; s++) + { + al.addCodonFrame(cf[s]); + cf[s] = null; + } + AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ") + + " for " + ((fisRegSel) ? "selected region of " : "") + + getTitle(); + Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + else + { + System.err.println("No Sequences generated for xRef type " + + fsrc); + } + } catch (Exception e) + { + jalview.bin.Cache.log.error( + "Exception when finding crossreferences", e); + } catch (OutOfMemoryError e) + { + new OOMWarning("whilst fetching crossreferences", e); + } catch (Error e) + { + jalview.bin.Cache.log.error("Error when finding crossreferences", + e); + } + ths.setProgressBar("Finished searching for sequences from " + fsrc, + sttime); + } + + }; + Thread frunner = new Thread(foo); + frunner.start(); + } + + public boolean canShowTranslationProducts(SequenceI[] selection, + AlignmentI alignment) + { + // old way + try + { + 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", + e); + return false; + } + } + + public void showProducts_actionPerformed(ActionEvent e) + { + // ///////////////////////////// + // Collect Data to be translated/transferred + + SequenceI[] selection = viewport.getSequenceSelection(); + AlignmentI al = null; + try + { + al = jalview.analysis.Dna.CdnaTranslate(selection, viewport + .getViewAsVisibleContigs(true), viewport.getGapCharacter(), + viewport.getAlignment().getDataset()); + } catch (Exception ex) + { + al = null; + jalview.bin.Cache.log.debug("Exception during translation.", ex); + } + if (al == null) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", + "Translation Failed", JOptionPane.WARNING_MESSAGE); + } + else + { + AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), + DEFAULT_WIDTH, DEFAULT_HEIGHT); + } + } + + public void showTranslation_actionPerformed(ActionEvent e) + { + // ///////////////////////////// + // Collect Data to be translated/transferred + + SequenceI[] selection = viewport.getSequenceSelection(); + String[] seqstring = viewport.getViewAsString(true); + AlignmentI al = null; + try + { + al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, + viewport.getViewAsVisibleContigs(true), viewport + .getGapCharacter(), viewport.alignment + .getAlignmentAnnotation(), viewport.alignment + .getWidth(), viewport.getAlignment().getDataset()); + } catch (Exception ex) + { + al = null; + jalview.bin.Cache.log.debug("Exception during translation.", ex); + } + if (al == null) + { + JOptionPane + .showMessageDialog( + Desktop.desktop, + "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", + "Translation Failed", JOptionPane.WARNING_MESSAGE); + } + else + { + AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, "Translation of " + this.getTitle(), + DEFAULT_WIDTH, DEFAULT_HEIGHT); + } + } + + /** + * Try to load a features file onto the alignment. + * + * @param file + * contents or path to retrieve file + * @param type + * access mode of file (see jalview.io.AlignFile) + * @return true if features file was parsed corectly. + */ + public boolean parseFeaturesFile(String file, String type) + { + boolean featuresFile = false; + try + { + featuresFile = new FeaturesFile(file, type) + .parse(viewport.alignment.getDataset(), + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours, + false, jalview.bin.Cache.getDefault( + "RELAXEDSEQIDMATCHING", false)); + } catch (Exception ex) + { + ex.printStackTrace(); + } + + if (featuresFile) + { + viewport.showSequenceFeatures = true; + showSeqFeatures.setSelected(true); + if (alignPanel.seqPanel.seqCanvas.fr != null) + { + // update the min/max ranges where necessary + alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); + } + if (featureSettings != null) + { + featureSettings.setTableData(); + } + alignPanel.paintAlignment(true); + } + + return featuresFile; + } + + public void dragEnter(DropTargetDragEvent evt) + { + } + + public void dragExit(DropTargetEvent evt) + { + } + + public void dragOver(DropTargetDragEvent evt) + { + } + + public void dropActionChanged(DropTargetDragEvent evt) + { + } + + public void drop(DropTargetDropEvent evt) + { + Transferable t = evt.getTransferable(); + java.util.List files = null; + + try + { + DataFlavor uriListFlavor = new DataFlavor( + "text/uri-list;class=java.lang.String"); + if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { + // Works on Windows and MacOSX + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + files = (java.util.List) t + .getTransferData(DataFlavor.javaFileListFlavor); + } + else if (t.isDataFlavorSupported(uriListFlavor)) + { + // This is used by Unix drag system + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + String data = (String) t.getTransferData(uriListFlavor); + files = new java.util.ArrayList(1); + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, "\r\n"); st.hasMoreTokens();) + { + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + + java.net.URI uri = new java.net.URI(s); + // check to see if we can handle this kind of URI + if (uri.getScheme().toLowerCase().startsWith("http")) + { + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + files.add(file.toString()); + } + } + } + } catch (Exception e) + { + e.printStackTrace(); + } + if (files != null) + { + 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++) + { + 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) + { + ex.printStackTrace(); + } + } + } + + /** + * Attempt to load a "dropped" file or URL string: First by testing whether + * it's and Annotation file, then a JNet file, and finally a features file. If + * all are false then the user may have dropped an alignment file onto this + * AlignFrame. + * + * @param file + * either a filename or a URL string. + */ + public void loadJalviewDataFile(String file, String protocol, + String format, SequenceI assocSeq) + { + try + { + if (protocol == null) + { + protocol = jalview.io.FormatAdapter.checkProtocol(file); + } + // if the file isn't identified, or not positively identified as some + // other filetype (PFAM is default unidentified alignment file type) then + // try to parse as annotation. + boolean isAnnotation = (format == null || format + .equalsIgnoreCase("PFAM")) ? new AnnotationFile() + .readAnnotationFile(viewport.alignment, file, protocol) + : false; + + if (!isAnnotation) + { + // try to see if its a JNet 'concise' style annotation file *before* we + // try to parse it as a features file + 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); + 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 + // alignment file to load into the current view. + if (!isGroupsFile) + { + new FileLoader().LoadFile(viewport, file, protocol, format); + } + else + { + alignPanel.paintAlignment(true); + } + } + } + if (isAnnotation) + { + + alignPanel.adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + buildSortByAnnotationScoresMenu(); + alignPanel.paintAlignment(true); + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + public void tabSelectionChanged(int index) + { + if (index > -1) + { + alignPanel = (AlignmentPanel) alignPanels.elementAt(index); + viewport = alignPanel.av; + setMenusFromViewport(viewport); + } + } + + public void tabbedPane_mousePressed(MouseEvent e) + { + if (SwingUtilities.isRightMouseButton(e)) + { + String reply = JOptionPane.showInternalInputDialog(this, + "Enter View Name", "Edit View Name", + JOptionPane.QUESTION_MESSAGE); + + if (reply != null) + { + viewport.viewName = reply; + tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); + } + } + } + + public AlignViewport getCurrentView() + { + return viewport; + } + + /** + * Open the dialog for regex description parsing. + */ + protected void extractScores_actionPerformed(ActionEvent e) + { + ParseProperties pp = new jalview.analysis.ParseProperties( + viewport.alignment); + // 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*)", + // true)>0) + if (pp.getScoresFromDescription("description column", + "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0) + { + buildSortByAnnotationScoresMenu(); + } + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent + * ) + */ + protected void showDbRefs_actionPerformed(ActionEvent e) + { + viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); + } + + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) + */ + protected void showNpFeats_actionPerformed(ActionEvent e) + { + viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); + } + + /** + * find the viewport amongst the tabs in this alignment frame and close that + * tab + * + * @param av + */ + public boolean closeView(AlignViewport av) + { + if (viewport == av) + { + this.closeMenuItem_actionPerformed(false); + return true; + } + Component[] comp = tabbedPane.getComponents(); + for (int i = 0; comp != null && i < comp.length; i++) + { + if (comp[i] instanceof AlignmentPanel) + { + if (((AlignmentPanel) comp[i]).av == av) + { + // close the view. + closeView((AlignmentPanel) comp[i]); + return true; + } + } + } + return false; + } + + protected void build_fetchdbmenu(JMenu webService) + { + // Temporary hack - DBRef Fetcher always top level ws entry. + // TODO We probably want to store a sequence database checklist in + // preferences and have checkboxes.. rather than individual sources selected + // here + 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.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), alignPanel.alignFrame) + .fetchDBRefs(false); + } + }).start(); + + } + + }); + rfetch.add(fetchr); + final AlignFrame me = this; + new Thread(new Runnable() + { + public void run() + { + final jalview.ws.SequenceFetcher sf = SequenceFetcher + .getSequenceFetcherSingleton(me); + final String[] otherdb = sf.getOrderedSupportedSources(); + // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + // jalview.util.QuickSort.sort(otherdb, otherdb); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + + JMenu dfetch = new JMenu(); + JMenuItem fetchr; + rfetch.add(dfetch); + int comp = 0, mcomp = 15; + String mname = null; + if (otherdb != null && otherdb.length > 0) + { + for (int i = 0; i < otherdb.length; i++) + { + String dbname = sf.getSourceProxy(otherdb[i]).getDbName(); + if (mname == null) + { + mname = "from '" + dbname + "'"; + } + fetchr = new JMenuItem(otherdb[i]); + final String[] dassource = new String[] + { otherdb[i] }; + fetchr.addActionListener(new ActionListener() + { + + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + new jalview.ws.DBRefFetcher(alignPanel.av + .getSequenceSelection(), + alignPanel.alignFrame, dassource) + .fetchDBRefs(false); + } + }).start(); + } + + }); + fetchr.setToolTipText("Retrieve from " + dbname); + dfetch.add(fetchr); + if (comp++ == mcomp || i == (otherdb.length - 1)) + { + dfetch.setText(mname + " to '" + dbname + "'"); + rfetch.add(dfetch); + dfetch = new JMenu(); + mname = null; + comp = 0; + } + } + } + } + }); + } + }).start(); + + } + + /** + * Left justify the whole alignment. + */ + protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(false); + viewport.firePropertyChange("alignment", null, al); + } + + /** + * Right justify the whole alignment. + */ + protected void justifyRightMenuItem_actionPerformed(ActionEvent e) + { + AlignmentI al = viewport.getAlignment(); + al.justify(true); + viewport.firePropertyChange("alignment", null, al); + } + + public void setShowSeqFeatures(boolean b) + { + showSeqFeatures.setSelected(true); + viewport.setShowSequenceFeatures(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. + * awt.event.ActionEvent) + */ + protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) + { + viewport.setShowUnconserved(showNonconservedMenuItem.getState()); + alignPanel.paintAlignment(true); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event + * .ActionEvent) + */ + protected void showGroupConsensus_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConsensus(showGroupConsensus.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showGroupConservation_actionPerformed(ActionEvent e) + { + viewport.setShowGroupConservation(showGroupConservation.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showConsensusHistogram_actionPerformed(ActionEvent e) + { + viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void showSequenceLogo_actionPerformed(ActionEvent e) + { + viewport.setShowSequenceLogo(showSequenceLogo.getState()); + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) + { + alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt + * .event.ActionEvent) + */ + protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) + { + if (viewport.getSelectionGroup() != null) + { + SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom( + viewport.getSequenceSelection(), + viewport.getAlignmentView(true).getSequenceStrings( + viewport.getGapCharacter()), + viewport.alignment.getGroups()); + viewport.alignment.deleteAllGroups(); + viewport.sequenceColours = null; + viewport.setSelectionGroup(null); + // set view properties for each group + for (int g = 0; g < gps.length; g++) + { + gps[g].setShowNonconserved(viewport.getShowUnconserved()); + gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo()); + viewport.alignment.addGroup(gps[g]); + Color col = new Color((int) (Math.random() * 255), + (int) (Math.random() * 255), (int) (Math.random() * 255)); + col = col.brighter(); + for (Enumeration sq = gps[g].getSequences(null).elements(); sq + .hasMoreElements(); viewport.setSequenceColour( + (SequenceI) sq.nextElement(), col)) + ; + } + PaintRefresher.Refresh(this, viewport.getSequenceSetId()); + alignPanel.updateAnnotation(); + alignPanel.paintAlignment(true); + } + } + + /** + * make the given alignmentPanel the currently selected tab + * + * @param alignmentPanel + */ + public void setDisplayedView(AlignmentPanel alignmentPanel) + { + if (!viewport.getSequenceSetId().equals( + alignmentPanel.av.getSequenceSetId())) + { + throw new Error( + "Implementation error: cannot show a view from another alignment in an AlignFrame."); + } + if (tabbedPane != null + & alignPanels.indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) + { + tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); + } + } +} + +class PrintThread extends Thread +{ + AlignmentPanel ap; + + public PrintThread(AlignmentPanel ap) + { + this.ap = ap; + } + + static PageFormat pf; + + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + + if (pf != null) + { + printJob.setPrintable(ap, pf); + } + else + { + printJob.setPrintable(ap); + } + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } +}