X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=14bf680152cf531a5830cb72e69725f6b4ac20ac;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=9ce03f467f94df56f012fa9b6492b9d415d93013;hpb=187b75ac779575fa0399f7c3991dcd7bade8ca90;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9ce03f4..14bf680 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -13,37 +13,29 @@ * 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 Software + * 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 jalview.analysis.*; - -import jalview.datamodel.*; - -import jalview.io.*; - -import jalview.jbgui.*; - -import jalview.schemes.*; - -import jalview.ws.*; +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 java.io.*; - -import java.beans.*; - -import java.util.*; - import javax.swing.*; -import javax.swing.event.*; +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! @@ -51,2097 +43,2841 @@ import javax.swing.event.*; * @author $author$ * @version $Revision$ */ -public class AlignFrame extends GAlignFrame +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; - final AlignmentPanel alignPanel; - final 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); - - alignPanel = new AlignmentPanel(this, viewport); - alignPanel.annotationPanel.adjustPanelHeight(); - alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize()); - alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize()); - alignPanel.setAnnotationVisible(viewport.getShowAnnotation()); - - getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); - - addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameActivated(InternalFrameEvent evt) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - alignPanel.requestFocus(); - } - }); - } - }); - } + /** 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! - * - * @param e DOCUMENT ME! - */ - public void parseGroupsFile(String file) - { - try{ - BufferedReader in = new BufferedReader(new FileReader(file)); - SequenceI seq=null; - String line, text, token; - UserColourScheme ucs; - int index, start, end; - StringTokenizer st; - SequenceGroup sg; - while( (line = in.readLine())!=null) - { - st = new StringTokenizer(line, "\t"); - if(st.countTokens()!=6) - { - System.out.println("Groups file "+file+" is invalid. Read help file."); - System.exit(1); - } - - while(st.hasMoreElements()) - { - text = st.nextToken(); - token = st.nextToken(); - if(!token.equals("ID_NOT_SPECIFIED")) - { - index = viewport.alignment.findIndex(viewport.alignment.findName( - token)); - st.nextToken(); - } - else - index = Integer.parseInt( st.nextToken() ); + /** DOCUMENT ME!! */ + public String currentFileFormat = null; + Stack historyList = new Stack(); + Stack redoList = new Stack(); + private int treeCount = 0; - start=Integer.parseInt( st.nextToken() ); - end = Integer.parseInt( st.nextToken() ); - ucs = new UserColourScheme(st.nextToken()); + /** + * new alignment window with hidden columns + * @param al AlignmentI + * @param hiddenColumns ColumnSelection or null + */ + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) { - seq = viewport.alignment.getSequenceAt(index); - start = seq.findIndex(start)-1; - end = seq.findIndex(end)-1; + viewport = new AlignViewport(al, hiddenColumns); - sg = new SequenceGroup(text,ucs,true,true,false,start,end); - sg.addSequence( seq,true); + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - viewport.alignment.addGroup(sg); - } - } - - }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);} - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void saveAlignmentMenu_actionPerformed(ActionEvent e) + if(viewport.vconsensus==null) { - 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); - - chooser.setAcceptAllFileFilterUsed(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(); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); - - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - - saveAlignment(choice, currentFileFormat); - } + //Out of memory calculating consensus. + BLOSUM62Colour.setEnabled(false); + PIDColour.setEnabled(false); + conservationMenuItem.setEnabled(false); + modifyConservation.setEnabled(false); + abovePIDThreshold.setEnabled(false); + modifyPID.setEnabled(false); } - public boolean saveAlignment(String file, String format) - { - if (format.equalsIgnoreCase("Jalview")) - { - String shortName = title; + alignPanel = new AlignmentPanel(this, viewport); - if (shortName.indexOf(java.io.File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); - } + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); - Jalview2XML.SaveAlignment(this, file, shortName); + if(sortby.equals("Id")) + sortIDMenuItem_actionPerformed(null); + else if(sortby.equals("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(null); - // USE Jalview2XML to save this file - return true; - } - else - { - String output = FormatAdapter.formatSequences(format, - viewport.getAlignment(). - getSequences()); - if(output==null) - return false; + // remove(tabbedPane); + getContentPane().add(alignPanel, BorderLayout.CENTER); - try - { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); - out.println(output); - out.close(); - return true; - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - return false; - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void outputText_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - Desktop.addInternalFrame(cap, - "Alignment output - " + e.getActionCommand(), 600, 500); - cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), - viewport.getAlignment().getSequences())); - } + // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void htmlMenuItem_actionPerformed(ActionEvent e) + ///Dataset tab + ///////////////////////// + if(al.getDataset()==null) { - new HTMLOutput(viewport); + 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); + ///////////////////////// - public void createImageMap(File file, String image) - { - alignPanel.makePNGImageMap(file, image); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void createPNG(File f) + viewport.addPropertyChangeListener(new PropertyChangeListener() { - alignPanel.makePNG(f); - } + public void propertyChange(PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + alignmentChanged(); + } + } + }); - /** - * 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) + if (Desktop.desktop != null) { - //Putting in a thread avoids Swing painting problems - PrintThread thread = new PrintThread(); - thread.start(); + addServiceListeners(); + setGUINucleotide(al.isNucleotide()); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void closeMenuItem_actionPerformed(ActionEvent e) + + if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false)) { - try - { - this.setClosed(true); - } - catch (Exception ex) - { - } + wrapMenuItem.setSelected(true); + wrapMenuItem_actionPerformed(null); } - /** - * 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); + /** + * Creates a new AlignFrame object. + * + * @param al DOCUMENT ME! + */ + public AlignFrame(AlignmentI al) + { + this(al, null); + } - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setText("Redo " + hi.getDescription()); - } - else + 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")) { - redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + // System.out.println("Rebuilding web service menu"); + BuildWebServiceMenu(); } - } - - /** - * DOCUMENT ME! - * - * @param hi DOCUMENT ME! - */ - public void addHistoryItem(HistoryItem hi) + } + }); + addInternalFrameListener(new javax.swing.event. + InternalFrameAdapter() { - historyList.push(hi); - updateEditMenuBar(); - } + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + // System.out.println("deregistering discoverer listener"); + Desktop.discoverer.removePropertyChangeListener(thisListener); + closeMenuItem_actionPerformed(null); + } + ; + }); + } - /** - * 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); + 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(); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void redoMenuItem_actionPerformed(ActionEvent e) - { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); - } + 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); - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + layout.setRows(layout.getRows() - 1); + } + else { - if (hi.getType() == HistoryItem.SORT) - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - viewport.alignment.getSequences().setElementAt(hi.getSequences() - .elementAt(i), - i); - } - } - else - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - SequenceI restore = (SequenceI) hi.getSequences().elementAt(i); + progressPanel = new JPanel(new BorderLayout(10, 5)); - if (restore.getLength() == 0) - { - restore.setSequence(hi.getHidden().elementAt(i).toString()); - viewport.alignment.getSequences().insertElementAt(restore, - hi.getAlignIndex(i)); - } - else - { - restore.setSequence(hi.getHidden().elementAt(i).toString()); - } - } + JProgressBar progressBar = new JProgressBar(); + progressBar.setIndeterminate(true); - if (hi.getType() == HistoryItem.PASTE) - { - for (int i = viewport.alignment.getHeight() - 1; - i > (hi.getSequences().size() - 1); i--) - { - viewport.alignment.deleteSequence(i); - } - } - } + progressPanel.add(new JLabel(message), BorderLayout.WEST); + progressPanel.add(progressBar, BorderLayout.CENTER); - updateEditMenuBar(); + layout.setRows(layout.getRows() + 1); + statusPanel.add(progressPanel); - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + progressBars.put(new Long(id), progressPanel); } - /** - * DOCUMENT ME! - * - * @param up DOCUMENT ME! - */ - public void moveSelectedSequences(boolean up) - { - SequenceGroup sg = viewport.getSelectionGroup(); + validate(); + } - if (sg == null) - { - return; - } - if (up) - { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); + /* + Added so Castor Mapping file can obtain Jalview Version + */ + public String getVersion() + { + return jalview.bin.Cache.getProperty("VERSION"); + } - if (!sg.sequences.contains(seq)) - { - continue; - } + public FeatureRenderer getFeatureRenderer() + { + return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); + } - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) - { - continue; - } + public void fetchSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(this); + } - 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); + public void addFromFile_actionPerformed(ActionEvent e) + { + Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); + } - if (!sg.sequences.contains(seq)) - { - continue; - } + public void addFromText_actionPerformed(ActionEvent e) + { + Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); + } - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + public void addFromURL_actionPerformed(ActionEvent e) + { + Desktop.instance.inputURLMenuItem_actionPerformed(viewport); + } - if (sg.sequences.contains(temp)) - { - continue; - } + /** + * 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); - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } - alignPanel.repaint(); - } + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save Alignment to file"); + chooser.setToolTipText("Save"); + + int value = chooser.showSaveDialog(this); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void copy_actionPerformed(ActionEvent e) + if (value == JalviewFileChooser.APPROVE_OPTION) { - if (viewport.getSelectionGroup() == null) + currentFileFormat = chooser.getSelectedFormat(); + + if (currentFileFormat == null) { - return; + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "You must select a file format before saving!", + "File format not specified", + JOptionPane.WARNING_MESSAGE); + value = chooser.showSaveDialog(this); + return; } - SequenceGroup sg = viewport.getSelectionGroup(); + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat); - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - StringBuffer buffer = new StringBuffer(); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - Hashtable orderedSeqs = new Hashtable(); + saveAlignment(choice, currentFileFormat); + } + } - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); - orderedSeqs.put(index + "", seq); - } + public boolean saveAlignment(String file, String format) + { + if (format.equalsIgnoreCase("Jalview")) + { + String shortName = title; - int index = 0; + if (shortName.indexOf(java.io.File.separatorChar) > -1) + { + shortName = shortName.substring(shortName.lastIndexOf( + java.io.File.separatorChar) + 1); + } - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = null; + new Jalview2XML().SaveAlignment(this, file, shortName); - while (seq == null) - { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; + // USE Jalview2XML to save this file + return true; + } + else + { - break; - } - else - { - index++; - } - } + String[] omitHidden = null; - buffer.append(seq.getName() + "\t" + - seq.findPosition(sg.getStartRes()) + "\t" + - seq.findPosition(sg.getEndRes()) + "\t" + - sg.getSequenceAt(i).getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); - } + 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); + } - c.setContents(new StringSelection(buffer.toString()), null); - } + String output = new FormatAdapter().formatSequences( + format, + viewport.alignment.getSequencesArray(), + omitHidden); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void pasteNew_actionPerformed(ActionEvent e) - { - paste(true); - } + if (output == null) + { + return false; + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void pasteThis_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); - paste(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 newAlignment DOCUMENT ME! - */ - void paste(boolean newAlignment) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void outputText_actionPerformed(ActionEvent e) + { + String [] omitHidden = null; + + if(viewport.hasHiddenColumns) { - try - { - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - Transferable contents = c.getContents(this); + 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 (contents == null) - { - return; - } + if(reply==JOptionPane.YES_OPTION) + { + omitHidden = viewport.getViewAsString(false); + } + } - String str = (String) contents.getTransferData(DataFlavor.stringFlavor); - StringTokenizer st = new StringTokenizer(str); - ArrayList seqs = new ArrayList(); + 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); + } - while (st.hasMoreElements()) - { - String name = st.nextToken(); - int start = Integer.parseInt(st.nextToken()); - int end = Integer.parseInt(st.nextToken()); - Sequence sequence = new Sequence(name, st.nextToken(), start, - end); + /** + * 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(); + } - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.add(sequence); - } - } + /** + * 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()); + } - if (newAlignment) - { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - seqs.toArray(newSeqs); + /** + * 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()); + } - AlignFrame af = new AlignFrame(new Alignment(newSeqs)); - String newtitle = new String("Copied sequences"); + // used by undo and redo + void restoreHistoryItem(HistoryItem hi) + { - if (title.startsWith("Copied sequences")) - { - newtitle = title; - } - else - { - newtitle = newtitle.concat("- from " + title); - } + hi.restore(); - Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - } - else - { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } - } - catch (Exception ex) - { - } + updateEditMenuBar(); - // could be anything being pasted in here - } + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + } + + /** + * DOCUMENT ME! + * + * @param up DOCUMENT ME! + */ + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void cut_actionPerformed(ActionEvent e) + if (sg == null) { - copy_actionPerformed(null); - delete_actionPerformed(null); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void delete_actionPerformed(ActionEvent e) + if (up) { - boolean seqsdeleted = false; + for (int i = 1; i < viewport.alignment.getHeight(); i++) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); - if (viewport.getSelectionGroup() == null) + if (!sg.getSequences(false).contains(seq)) { - return; + continue; } - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); + SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) - allSequences = true; - - for (int i = 0; i < sg.sequences.size(); i++) + if (sg.getSequences(false).contains(temp)) { - 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(allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1); - } - - - if (seq.getSequence().length() < 1) - { - seqsdeleted = true; - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } + continue; } - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); + 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 (seqsdeleted) + if (!sg.getSequences(false).contains(seq)) { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + continue; } - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); + SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (viewport.getAlignment().getHeight() < 1) + if (sg.getSequences(false).contains(temp)) { - try - { - this.setClosed(true); - } - catch (Exception ex) - { - } + continue; } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i + 1); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void deleteGroups_actionPerformed(ActionEvent e) - { - viewport.alignment.deleteAllGroups(); - viewport.setSelectionGroup(null); - alignPanel.repaint(); - } + 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()); - viewport.setSelectionGroup(sg); - PaintRefresher.Refresh(null, viewport.alignment); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void copy_actionPerformed(ActionEvent e) + { + if (viewport.getSelectionGroup() == null) + { + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + SequenceI [] seqs = viewport.getSelectionAsNewSequence(); + String[] omitHidden = null; + + if (viewport.hasHiddenColumns) { - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.annotationPanel.activeRes = null; - PaintRefresher.Refresh(null, viewport.alignment); + omitHidden = viewport.getViewAsString(true); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = viewport.getSelectionGroup(); + String output = new FormatAdapter().formatSequences( + "Fasta", + seqs, + omitHidden); - if (sg == null) - { - selectAllSequenceMenuItem_actionPerformed(null); - return; - } + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(output), Desktop.instance); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); - } + Vector hiddenColumns = null; + if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null) + { + hiddenColumns =new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for(int i=0; i 0) - { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); + String str = (String) contents.getTransferData(DataFlavor.stringFlavor); + if(str.length()<1) + return; - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); + String format = new IdentifyFile().Identify(str, "Paste"); + SequenceI[] sequences; - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } - Vector groups = viewport.alignment.getGroups(); + if(Desktop.jalviewClipboard!=null) + { + // The clipboard was filled from within Jalview, we must use the sequences + // And dataset from the copied alignment + sequences = (SequenceI[])Desktop.jalviewClipboard[0]; + } + else + { + sequences = new FormatAdapter().readFile(str, "Paste", format); + } - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.get(i); + AlignmentI alignment = null; - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } + if (newAlignment) + { + alignment = new Alignment(sequences); - alignPanel.repaint(); - } - } + if(Desktop.jalviewClipboard!=null) + alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] ); + else + alignment.setDataset( null ); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void remove2RightMenuItem_actionPerformed(ActionEvent e) - { - ColumnSelection colSel = viewport.getColumnSelection(); + } + else + { + alignment = viewport.getAlignment(); - if (colSel.size() > 0) + //!newAlignment + for (int i = 0; i < sequences.length; i++) { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); + Sequence newseq = new Sequence(sequences[i].getName(), + sequences[i].getSequence(), sequences[i].getStart(), + sequences[i].getEnd()); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); + alignment.addSequence(newseq); + } - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } - Vector groups = viewport.alignment.getGroups(); + viewport.setEndSeq(alignment.getHeight()); + alignment.getWidth(); + viewport.firePropertyChange("alignment", null, alignment.getSequences()); + } - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.get(i); - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } - alignPanel.repaint(); - } - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, HistoryItem.HIDE)); - viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } + // 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++) + { + AlignmentAnnotation newAnnot = + new AlignmentAnnotation( + sequences[i].getAnnotation()[a].label, + sequences[i].getAnnotation()[a].description, + sequences[i].getAnnotation()[a].annotations, + sequences[i].getAnnotation()[a].graphMin, + sequences[i].getAnnotation()[a].graphMax, + sequences[i].getAnnotation()[a].graph); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); + sequences[i].getAnnotation()[a] = newAnnot; + newAnnot.sequenceMapping = sequences[i].getAnnotation()[a]. + sequenceMapping; + newAnnot.sequenceRef = sequences[i]; + newAnnot.adjustForAlignment(); + alignment.addAnnotation(newAnnot); + alignment.setAnnotationIndex(newAnnot, a); + } - SequenceI current; - int jSize; + alignPanel.annotationPanel.adjustPanelHeight(); + } + } - Vector seqs = null; + if(newAlignment) + { + AlignFrame af = new AlignFrame(alignment); + String newtitle = new String("Copied sequences"); - int start = 0; - int end = viewport.alignment.getWidth(); + if(Desktop.jalviewClipboard[2]!=null) + { + Vector hc = (Vector)Desktop.jalviewClipboard[2]; + 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()); - int j = start; - do - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - current.deleteCharAt(j); - j--; - jSize--; - } + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } - j++; - } - while (j < end && j < jSize); - } + Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + + } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void padGapsMenuitem_actionPerformed(ActionEvent e) + } + catch (Exception ex) { - addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment, - HistoryItem.HIDE)); + ex.printStackTrace(); + System.out.println("Exception whilst pasting: "+ex); + // could be anything being pasted in here + } - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) - { - current = viewport.getAlignment().getSequenceAt(i); + } - if (current.getLength() < Width) - { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); - } - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void cut_actionPerformed(ActionEvent e) + { + copy_actionPerformed(null); + delete_actionPerformed(null); + } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void delete_actionPerformed(ActionEvent e) + { - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findMenuItem_actionPerformed(ActionEvent e) + if (viewport.getSelectionGroup() == null) { - JInternalFrame frame = new JInternalFrame(); - Finder finder = new Finder(viewport, alignPanel, frame); - frame.setContentPane(finder); - Desktop.addInternalFrame(frame, "Find", 340, 110); - frame.setLayer(JLayeredPane.PALETTE_LAYER); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void font_actionPerformed(ActionEvent e) - { - FontChooser fc = new FontChooser(alignPanel); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void fullSeqId_actionPerformed(ActionEvent e) - { - viewport.setShowFullId(fullSeqId.isSelected()); + SequenceGroup sg = viewport.getSelectionGroup(); - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.repaint(); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void colourTextMenuItem_actionPerformed(ActionEvent e) - { - viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.repaint(); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void wrapMenuItem_actionPerformed(ActionEvent e) + //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) { - viewport.setWrapAlignment(wrapMenuItem.isSelected()); - alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); - scaleAbove.setVisible(wrapMenuItem.isSelected()); - scaleLeft.setVisible(wrapMenuItem.isSelected()); - scaleRight.setVisible(wrapMenuItem.isSelected()); - alignPanel.repaint(); - } + 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); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void scaleAbove_actionPerformed(ActionEvent e) - { - viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.repaint(); - } + return; + } + j++; + }while(j<=sg.getEndRes()); + } + }*/ - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void scaleLeft_actionPerformed(ActionEvent e) - { - viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.repaint(); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void scaleRight_actionPerformed(ActionEvent e) - { - viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.repaint(); - } + addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, + HistoryItem.HIDE)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void viewBoxesMenuItem_actionPerformed(ActionEvent e) - { - viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); - alignPanel.repaint(); - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void viewTextMenuItem_actionPerformed(ActionEvent e) + for (int i = 0; i < sg.getSize(false); i++) { - viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.repaint(); + 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); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + viewport.setSelectionGroup(null); + viewport.alignment.deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + + + + if (viewport.getAlignment().getHeight() < 1) { - viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.repaint(); + 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); + } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void sequenceFeatures_actionPerformed(ActionEvent evt) - { - viewport.showSequenceFeatures(sequenceFeatures.isSelected()); + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.get(i); - if (viewport.showSequenceFeatures && - !((Alignment) viewport.alignment).featuresAdded) + if (!sg.adjustForRemoveLeft(min)) { - SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, - alignPanel); - ((Alignment) viewport.alignment).featuresAdded = true; + viewport.alignment.deleteGroup(sg); } + } - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void remove2RightMenuItem_actionPerformed(ActionEvent e) + { + ColumnSelection colSel = viewport.getColumnSelection(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void annotationPanelMenuItem_actionPerformed(ActionEvent e) + if (colSel.size() > 0) { - if (annotationPanelMenuItem.isSelected() && - viewport.getWrapAlignment()) - { - annotationPanelMenuItem.setSelected(false); + addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, + HistoryItem.HIDE)); - return; - } + int max = colSel.getMax(); + viewport.getAlignment().trimRight(max); - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); - } + if (viewport.getSelectionGroup() != null) + { + viewport.getSelectionGroup().adjustForRemoveRight(max); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void overviewMenuItem_actionPerformed(ActionEvent e) - { - if (alignPanel.overviewPanel != null) + Vector groups = viewport.alignment.getGroups(); + + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.get(i); + + if (!sg.adjustForRemoveRight(max)) { - return; + viewport.alignment.deleteGroup(sg); } + } - 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); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - changeColour(null); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Remove Gapped Columns", + viewport.alignment, HistoryItem.HIDE)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void clustalColour_actionPerformed(ActionEvent e) - { - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment.getWidth())); - } + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void zappoColour_actionPerformed(ActionEvent e) - { - changeColour(new ZappoColourScheme()); - } + viewport.getAlignment().removeGaps(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void taylorColour_actionPerformed(ActionEvent e) - { - changeColour(new TaylorColourScheme()); - } + viewport.setStartRes(seq.findIndex(startRes)-1); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void hydrophobicityColour_actionPerformed(ActionEvent e) - { - changeColour(new HydrophobicColourScheme()); - } + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void helixColour_actionPerformed(ActionEvent e) - { - changeColour(new HelixColourScheme()); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, + HistoryItem.HIDE)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void strandColour_actionPerformed(ActionEvent e) - { - changeColour(new StrandColourScheme()); - } + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); - /** - * 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()); - } + SequenceI current; + int jSize; + + Vector seqs = null; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void nucleotideColour_actionPerformed(ActionEvent e) + int start = 0; + int end = viewport.alignment.getWidth(); + + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSequences(true) != null + && viewport.getSelectionGroup().getSize(true) > 0) { - changeColour(new NucleotideColourScheme()); + seqs = viewport.getSelectionGroup().getSequences(true); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes()+1; } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void applyToAllGroups_actionPerformed(ActionEvent e) + else { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + seqs = viewport.alignment.getSequences(); } - /** - * DOCUMENT ME! - * - * @param cs DOCUMENT ME! - */ - void changeColour(ColourSchemeI cs) + for (int i = 0; i < seqs.size(); i++) { - int threshold = 0; - - if (viewport.getAbovePIDThreshold()) - { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); + current = (SequenceI) seqs.elementAt(i); + jSize = current.getLength(); - if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(threshold); - } - else if (cs instanceof ScoreColourScheme) - { - ((ScoreColourScheme) cs).setThreshold(threshold); - } + // Removing a range is much quicker than removing gaps + // one by one for long sequences + int j = start; + int rangeStart=-1, rangeEnd=-1; - viewport.setGlobalColourScheme(cs); - } - else if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(0); + do + { + if (jalview.util.Comparison.isGap(current.getCharAt(j))) + { + if(rangeStart==-1) + { + rangeStart = j; + rangeEnd = j+1; + } + else + { + rangeEnd++; + } + j++; } - else if (cs instanceof ScoreColourScheme) + else { - ((ScoreColourScheme) cs).setThreshold(0); + 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); + } + } - if (viewport.getConservationSelected()) - { - ConservationColourScheme ccs = null; + viewport.setStartRes(seq.findIndex(startRes)-1); - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() - 1); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); + public void alignmentChanged() + { + if(viewport.padGaps) + viewport.getAlignment().padGaps(); - ccs = new ConservationColourScheme(c, cs); + if(viewport.vconsensus!=null && viewport.autoCalculateConsensus) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - ccs.setConsensus(viewport.vconsensus); - viewport.setGlobalColourScheme(ccs); + viewport.alignment.adjustSequenceAnnotations(); - ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, - "Background"); - } - else - { - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - if (cs != null) - { - cs.setConsensus(viewport.vconsensus); - } + alignPanel.repaint(); + } - viewport.setGlobalColourScheme(cs); - } + void resetAllColourSchemes() + { + ColourSchemeI cs = viewport.globalColourScheme; + if(cs!=null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). + resetClustalX(viewport.alignment.getSequences(), + viewport.alignment.getWidth()); + } - if (viewport.getColourAppliesToAllGroups()) - { - Vector groups = viewport.alignment.getGroups(); + 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); + } + } - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + int s, sSize = viewport.alignment.getGroups().size(); + for(s=0; s 0)) || - (viewport.getAlignment().getHeight() < 4)) + 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) + { + addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, + HistoryItem.SORT)); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void sortIDMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + HistoryItem.SORT)); + AlignmentSorter.sortByID(viewport.getAlignment()); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void sortGroupMenuItem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + HistoryItem.SORT)); + + AlignmentSorter.sortByGroup(viewport.getAlignment()); + alignPanel.repaint(); + } + + /** + * 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(false) < 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(false) < 4) && + (viewport.getSelectionGroup().getSize(false) > 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.showInternalMessageDialog(this, - "Principal component analysis must take\n" + - "at least 4 input sequences.", - "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE); + 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; + return; } + } - try - { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(pcaPanel); - Desktop.addInternalFrame(frame, "Principal component analysis", - 400, 400); - } - catch (java.lang.OutOfMemoryError ex) - { - JOptionPane.showInternalMessageDialog(this, - "Too many sequences selected\nfor Principal Component Analysis!!", - "Out of memory", JOptionPane.WARNING_MESSAGE); - } + title = title + " on region"; + tp = new TreePanel(viewport, type, pwType); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + else { - NewTreePanel("AV", "PID", "Average distance tree using PID"); + //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); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + 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() { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } + public void actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Sort", viewport.alignment, + HistoryItem.SORT)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + // 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) { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); + sort.add(sortByTreeMenu); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); - } + public void actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Tree Sort", + viewport.alignment, HistoryItem.SORT)); + AlignmentSorter.sortByTree(viewport.getAlignment(), + treePanel.getTree()); + alignPanel.repaint(); + } + }); - /** - * DOCUMENT ME! - * - * @param type DOCUMENT ME! - * @param pwType DOCUMENT ME! - * @param title DOCUMENT ME! - */ - void NewTreePanel(String type, String pwType, String title) + treePanel.addInternalFrameListener(new javax.swing.event. + InternalFrameAdapter() { - final TreePanel tp; + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + treeCount--; + sortByTreeMenu.remove(item); - if ((viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 3)) + if (treeCount == 0) { - int s = 0; - SequenceGroup sg = viewport.getSelectionGroup(); + sort.remove(sortByTreeMenu); + } + } + ; + }); + } + + /** + * Work out whether the whole set of sequences + * or just the selected set will be submitted for multiple alignment. + * + */ + private jalview.datamodel.AlignmentView gatherSequencesForAlignment() + { + // Now, check we have enough sequences + AlignmentView 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); + } */ + msa = viewport.getAlignmentView(true); + } + else + { + /*Vector seqs = viewport.getAlignment().getSequences(); - /* Decide if the selection is a column region */ - while (s < sg.sequences.size()) - { - if (((SequenceI) sg.sequences.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; - } - } + if (seqs.size() > 1) + { + msa = new SequenceI[seqs.size()]; - title = title + " on region"; - tp = new TreePanel(viewport, - viewport.getSelectionGroup().sequences, type, pwType, - sg.getStartRes(), sg.getEndRes()); - } - else + for (int i = 0; i < seqs.size(); i++) { - //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); + msa[i] = (SequenceI) seqs.elementAt(i); + } + }*/ + msa = viewport.getAlignmentView(false); + } + return msa; + } - return; - } + /** + * 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; - tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), type, pwType, 0, - viewport.alignment.getWidth()); - } + 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(); - addTreeMenuItem(tp, title); - viewport.setCurrentTree(tp.getTree()); + if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned()) + { + seq = (SequenceI) seqs.getSequenceAt(0); + } + else + { + int sz; + msa = new SequenceI[sz = seqs.getSize(false)]; - Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500); + 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()]; - /** - * DOCUMENT ME! - * - * @param title DOCUMENT ME! - * @param order DOCUMENT ME! - */ - public void addSortByOrderMenuItem(String title, final AlignmentOrder order) + for (int i = 0; i < seqs.size(); i++) + { + msa[i] = (SequenceI) seqs.elementAt(i); + } + } + } + if (msa != null) + { + return msa; + } + else { - final JMenuItem item = new JMenuItem("by " + title); - sort.add(item); - item.addActionListener(new java.awt.event.ActionListener() + if (seq != null) + { + return new SequenceI[] { - 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(); - } - }); + 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; - /** - * DOCUMENT ME! - * - * @param treePanel DOCUMENT ME! - * @param title DOCUMENT ME! - */ - void addTreeMenuItem(final TreePanel treePanel, String title) + try { - final JMenuItem item = new JMenuItem(title); + nf.parse(); - treeCount++; + if (nf.getTree() != null) + { + tp = new TreePanel(viewport, + "FromFile", + title, + nf); - if (treeCount == 1) - { - sort.add(sortByTreeMenu); - } + tp.setSize(w,h); - 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(); - } - }); + if(x>0 && y>0) + tp.setLocation(x,y); - 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); - } - } - ; - }); - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() - { - public void propertyChange(PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue()); - treePanel.repaint(); - } - } - }); + Desktop.addInternalFrame(tp, title, w, h); + addTreeMenuItem(tp, title); + } + } + catch (Exception ex) + { + ex.printStackTrace(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void clustalAlignMenuItem_actionPerformed(ActionEvent e) + return tp; + } + + class PrintThread + extends Thread + { + public void run() { - // TODO:resolve which menu item was actually selected - // Now, check we have enough sequences - SequenceI[] msa = null; + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + printJob.setPrintable(alignPanel, pf); - if ((viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 1)) + if (printJob.printDialog()) + { + try { - // 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()]; - - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } + printJob.print(); } - else + catch (Exception PrintException) { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) + 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) { - msa = new SequenceI[seqs.size()]; + AlignmentView msa = gatherSequencesForAlignment(); + new jalview.ws.MsaWSClient(sh, title, msa, + false, true, viewport.getAlignment().getDataset(), af); - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } } - } - if (msa != null) - { - jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", - title, msa, false, true); - } - } + }); + 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) + { + AlignmentView msa = gatherSequencesForAlignment(); + new jalview.ws.MsaWSClient(sh, title, msa, + true, true, viewport.getAlignment().getDataset(), af); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void ClustalRealign_actionPerformed(ActionEvent e) - { - // TODO:resolve which menu item was actually selected - // Now, check we have enough sequences - SequenceI[] 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()]; + }); + msawsmenu.add(methodR); - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } + } } - else - { - Vector seqs = viewport.getAlignment().getSequences(); - - if (seqs.size() > 1) + 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) { - msa = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) + SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction(); + if (msa.length == 1) + { + // Single Sequence prediction + new jalview.ws.JPredClient(sh,title, msa[0]); + } + else + { + if (msa.length > 1) { - msa[i] = (SequenceI) seqs.elementAt(i); + // Single Sequence prediction + jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh, + title, msa); } + } } + }); + secstrmenu.add(method); } - - if (msa != null) - { - jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", - title, msa, true, true); - } + wsmenu.add(secstrmenu); + } + this.webService.removeAll(); + for (int i = 0, j = wsmenu.size(); i < j; i++) + { + webService.add( (JMenu) wsmenu.get(i)); + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void jpred_actionPerformed(ActionEvent e) + else { - SequenceI seq = null; - SequenceI[] msa = null; + 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. + } - if ((viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 0)) - { - // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! - SequenceGroup seqs = viewport.getSelectionGroup(); + /* public void vamsasStore_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); - if ((seqs.getSize() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.getSequenceAt(0); - } - else - { - int sz; - msa = new SequenceI[sz = seqs.getSize()]; + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Export to Vamsas file"); + chooser.setToolTipText("Export"); - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); + int value = chooser.showSaveDialog(this); - if ((seqs.size() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.elementAt(0); - } - else - { - msa = new SequenceI[seqs.size()]; + 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); + } + }*/ - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } - if (msa != null) - { - JPredClient ct = new JPredClient(title, msa); - } - else if (seq != null) - { - JPredClient ct = new JPredClient(title, seq); - } - else - { - System.err.print( - "JALVIEW ERROR! - Unexpected JPred selection state!\n"); - } + + +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 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()]; + AlignmentI al = new Alignment(newSeq); + al.setDataset(null); - 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()]; + //////////////////////////////// + // Copy annotations across + jalview.datamodel.AlignmentAnnotation[] annotations + = viewport.alignment.getAlignmentAnnotation(); + int a, aSize; + if(annotations!=null) + { + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i].label.equals("Quality") || + annotations[i].label.equals("Conservation") || + annotations[i].label.equals("Consensus")) + { + continue; + } - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } + aSize = viewport.alignment.getWidth() / 3; + jalview.datamodel.Annotation[] anots = + new jalview.datamodel.Annotation[aSize]; - if (msa != null) - { - MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa, - false, true); - } + for (a = 0; a < viewport.alignment.getWidth(); a++) + { + if (annotations[i].annotations[a] == null + || annotations[i].annotations[a] == null) + continue; + + anots[a / 3] = new Annotation( + annotations[i].annotations[a].displayCharacter, + annotations[i].annotations[a].description, + annotations[i].annotations[a].secondaryStructure, + annotations[i].annotations[a].value, + annotations[i].annotations[a].colour); + } + + jalview.datamodel.AlignmentAnnotation aa + = new jalview.datamodel.AlignmentAnnotation(annotations[i].label, + annotations[i].description, anots); + al.addAnnotation(aa); } + } - /** - * 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"); + AlignFrame af = new AlignFrame(al); + Desktop.addInternalFrame(af, "Translation of "+this.getTitle(), + NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); - int value = chooser.showOpenDialog(null); - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + // AlignViewport newViewport = new AlignViewport(al); + // AlignmentPanel ap = new AlignmentPanel(this, newViewport); + // tabbedPane.add("Protein", ap); + // viewports.add(newViewport); + // alignPanels.add(ap); - 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(); - } - } + ///Dataset tab + ///////////////////////// + + // AlignViewport ds = new AlignViewport(al.getDataset()); + // ds.setDataset(true); + // AlignmentPanel dap = new AlignmentPanel(this, ds); + // tabbedPane.add("Dataset", dap); + // viewports.add(ds); + // alignPanels.add(dap); + ///////////////////////// + + +} + +/*public void tabSelected() + { + int index = tabbedPane.getSelectedIndex(); + viewport = (AlignViewport)viewports.elementAt(index); + alignPanel = (AlignmentPanel)alignPanels.elementAt(index); + }*/ + +/** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ +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); + } + catch(Exception ex) + { + ex.printStackTrace(); } - /** - * DOCUMENT ME! - * - * @param nf DOCUMENT ME! - * @param title DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public TreePanel ShowNewickTree(NewickFile nf, String title) + if(featuresFile) { - TreePanel tp = null; + viewport.showSequenceFeatures = true; + showSeqFeatures.setSelected(true); + alignPanel.repaint(); + } - try - { - nf.parse(); + return featuresFile; +} - if (nf.getTree() != null) - { - tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), nf, "FromFile", - title); - Desktop.addInternalFrame(tp, title, 600, 500); - addTreeMenuItem(tp, title); - } +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); + java.io.File file = new java.io.File(uri); + files.add(file); } - catch (Exception ex) + } + } + catch (Exception e) + { + e.printStackTrace(); + } + if (files != null) + { + try + { + + for (int i = 0; i < files.size(); i++) { - ex.printStackTrace(); + loadJalviewDataFile(files.get(i).toString()); } - - return tp; + } + catch (Exception ex) + { + ex.printStackTrace(); + } } +} - class PrintThread extends Thread - { - public void run() + // This method will attempt to load a "dropped" file first by testing + // whether its and Annotation file, then features file. If both are + // false then the user may have dropped an alignment file onto this + // AlignFrame + public void loadJalviewDataFile(String file) + { + try{ + boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport. + alignment, file); + + if (!isAnnotation) + { + boolean isGroupsFile = parseFeaturesFile(file, + AppletFormatAdapter.FILE); + if (!isGroupsFile) { - 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(); - } - } + String format = new IdentifyFile().Identify(file, FormatAdapter.FILE); + new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format); } + } + else + { + // (isAnnotation) + alignPanel.adjustAnnotationHeight(); + } + + }catch(Exception ex) + { + ex.printStackTrace(); } + } }