X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b714aea53cabf9b96dea336328ca497d1ca28d14;hb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;hp=727e1c6e2cd31da3f9c00a63d9ed7f4f15ec8f8e;hpb=11cfcb7281e45c5958b839e55da66cfbb9582fa7;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 727e1c6..b714aea 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -13,36 +13,28 @@ * 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.*; /** @@ -51,2122 +43,2729 @@ import javax.swing.event.*; * @author $author$ * @version $Revision$ */ -public class AlignFrame extends GAlignFrame +public class AlignFrame + extends GAlignFrame implements ClipboardOwner, DropTargetListener { - /** 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! - * - * @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); - } + /** DOCUMENT ME!! */ + public static final int NEW_WINDOW_HEIGHT = 500; + AlignmentPanel alignPanel; + AlignViewport viewport; - 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() ); + Vector viewports = new Vector(); + Vector alignPanels = new Vector(); - start=Integer.parseInt( st.nextToken() ); - end = Integer.parseInt( st.nextToken() ); - ucs = new UserColourScheme(st.nextToken()); + /** DOCUMENT ME!! */ + public String currentFileFormat = null; + Stack historyList = new Stack(); + Stack redoList = new Stack(); + private int treeCount = 0; - seq = viewport.alignment.getSequenceAt(index); - start = seq.findIndex(start)-1; - end = seq.findIndex(end)-1; - sg = new SequenceGroup(text,ucs,true,true,false,start,end); - sg.addSequence( seq,true); + /** + * Creates a new AlignFrame object. + * + * @param al DOCUMENT ME! + */ + public AlignFrame(AlignmentI al) + { + viewport = new AlignViewport(al); + viewports.add(viewport); - viewport.alignment.addGroup(sg); - } - } + this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);} + 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); } - /** - * 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); + alignPanel = new AlignmentPanel(this, viewport); + alignPanels.add(alignPanel); - chooser.setAcceptAllFileFilterUsed(false); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); - chooser.setToolTipText("Save"); + String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort"); - int value = chooser.showSaveDialog(this); + if(sortby.equals("Id")) + sortIDMenuItem_actionPerformed(null); + else if(sortby.equals("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(null); - if (value == JalviewFileChooser.APPROVE_OPTION) - { - currentFileFormat = chooser.getSelectedFormat(); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); + // remove(tabbedPane); + getContentPane().add(alignPanel, BorderLayout.CENTER); - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - saveAlignment(choice, currentFileFormat); - } + + // 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); + ///////////////////////// - public boolean saveAlignment(String file, String format) + + viewport.addPropertyChangeListener(new PropertyChangeListener() { - if (format.equalsIgnoreCase("Jalview")) - { - String shortName = title; + public void propertyChange(PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + alignmentChanged(); + } + } + }); - if (shortName.indexOf(java.io.File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - java.io.File.separatorChar) + 1); - } - Jalview2XML.SaveAlignment(this, file, shortName); + if (Desktop.desktop != null) + { + addServiceListeners(); + setGUINucleotide(al.isNucleotide()); + } + } - // USE Jalview2XML to save this file - return true; - } - else + /* 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) { - String output = FormatAdapter.formatSequences(format, - viewport.getAlignment(). - getSequences()); - if(output==null) - return false; - - try - { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(file)); - out.println(output); - out.close(); - return true; - } - catch (Exception ex) + // System.out.println("Discoverer property change."); + if (evt.getPropertyName().equals("services")) { - ex.printStackTrace(); + // System.out.println("Rebuilding web service menu"); + BuildWebServiceMenu(); } } - return false; - } + }); + 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); + } + ; + }); + } - /** - * 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())); - } + public void setGUINucleotide(boolean nucleotide) + { + showTranslation.setVisible( nucleotide ); + //sequenceFeatures.setVisible(!nucleotide ); + //featureSettings.setVisible( !nucleotide ); + conservationMenuItem.setVisible( !nucleotide ); + modifyConservation.setVisible( !nucleotide ); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void htmlMenuItem_actionPerformed(ActionEvent e) + //Remember AlignFrame always starts as protein + if(!nucleotide) { - new HTMLOutput(viewport); + calculateMenu.remove(calculateMenu.getItemCount()-2); } + } - 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); - } + /* + Added so Castor Mapping file can obtain Jalview Version + */ + public String getVersion() + { + return jalview.bin.Cache.getProperty("VERSION"); + } - /** - * 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 fetchSequence_actionPerformed(ActionEvent e) + { + new SequenceFetcher(this); + } + /** + * 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); + + chooser.setAcceptAllFileFilterUsed(false); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save Alignment to file"); + chooser.setToolTipText("Save"); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void closeMenuItem_actionPerformed(ActionEvent e) + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) { - try - { - this.setClosed(true); - } - catch (Exception ex) + 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); } + } - /** - * DOCUMENT ME! - */ - void updateEditMenuBar() + public boolean saveAlignment(String file, String format) + { + if (format.equalsIgnoreCase("Jalview")) { - if (historyList.size() > 0) - { - undoMenuItem.setEnabled(true); + String shortName = title; + + if (shortName.indexOf(java.io.File.separatorChar) > -1) + { + shortName = shortName.substring(shortName.lastIndexOf( + java.io.File.separatorChar) + 1); + } + + Jalview2XML.SaveAlignment(this, file, shortName); + + // USE Jalview2XML to save this file + return true; + } + else + { + String output = new FormatAdapter().formatSequences(format, + viewport.getAlignment(). + getSequences()); + if (output == null) + { + return false; + } + + try + { + java.io.PrintWriter out = new java.io.PrintWriter( + new java.io.FileWriter(file)); + + out.print(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(new FormatAdapter().formatSequences(e.getActionCommand(), + viewport.getAlignment(). + getSequences())); + } + + /** + * 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(); + } + + /** + * 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) + { + 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); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setText("Undo " + hi.getDescription()); + if (restore.getLength() == 0) + { + restore.setSequence(hi.getHidden().elementAt(i).toString()); + viewport.alignment.getSequences().insertElementAt(restore, + hi.getAlignIndex(i)); } else { - undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); + restore.setSequence(hi.getHidden().elementAt(i).toString()); } + } - if (redoList.size() > 0) - { - redoMenuItem.setEnabled(true); - - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setText("Redo " + hi.getDescription()); - } - else + if (hi.getType() == HistoryItem.PASTE) + { + for (int i = viewport.alignment.getHeight() - 1; + i > (hi.getSequences().size() - 1); i--) { - redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + viewport.alignment.deleteSequence(i); } + } } - /** - * DOCUMENT ME! - * - * @param hi DOCUMENT ME! - */ - public void addHistoryItem(HistoryItem hi) - { - historyList.push(hi); - updateEditMenuBar(); - } + 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 up DOCUMENT ME! + */ + public void moveSelectedSequences(boolean up) + { + SequenceGroup sg = viewport.getSelectionGroup(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void redoMenuItem_actionPerformed(ActionEvent e) + if (sg == null) { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + return; } - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + if (up) { - if (hi.getType() == HistoryItem.SORT) + for (int i = 1; i < viewport.alignment.getHeight(); i++) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); + + if (!sg.sequences.contains(seq)) { - for (int i = 0; i < hi.getSequences().size(); i++) - { - viewport.alignment.getSequences().setElementAt(hi.getSequences() - .elementAt(i), - i); - } + continue; } - else - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - SequenceI restore = (SequenceI) hi.getSequences().elementAt(i); - 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()); - } - } + SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (hi.getType() == HistoryItem.PASTE) - { - for (int i = viewport.alignment.getHeight() - 1; - i > (hi.getSequences().size() - 1); i--) - { - viewport.alignment.deleteSequence(i); - } - } + if (sg.sequences.contains(temp)) + { + continue; } - updateEditMenuBar(); - - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i - 1); + } } - - /** - * DOCUMENT ME! - * - * @param up DOCUMENT ME! - */ - public void moveSelectedSequences(boolean up) + else { - SequenceGroup sg = viewport.getSelectionGroup(); + for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) + { + SequenceI seq = viewport.alignment.getSequenceAt(i); - if (sg == null) + if (!sg.sequences.contains(seq)) { - return; + continue; } - if (up) + SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + + if (sg.sequences.contains(temp)) { - for (int i = 1; i < viewport.alignment.getHeight(); i++) - { - SequenceI seq = viewport.alignment.getSequenceAt(i); + continue; + } - if (!sg.sequences.contains(seq)) - { - continue; - } + viewport.alignment.getSequences().setElementAt(temp, i); + viewport.alignment.getSequences().setElementAt(seq, i + 1); + } + } - SequenceI temp = viewport.alignment.getSequenceAt(i - 1); + alignPanel.repaint(); + } - if (sg.sequences.contains(temp)) - { - continue; - } + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + Desktop.jalviewClipboard = null; + } - 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.sequences.contains(seq)) - { - continue; - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void copy_actionPerformed(ActionEvent e) + { + if (viewport.getSelectionGroup() == null) + { + return; + } - SequenceI temp = viewport.alignment.getSequenceAt(i + 1); + SequenceGroup sg = viewport.getSelectionGroup(); - if (sg.sequences.contains(temp)) - { - continue; - } + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - viewport.alignment.getSequences().setElementAt(temp, i); - viewport.alignment.getSequences().setElementAt(seq, i + 1); - } - } + Hashtable orderedSeqs = new Hashtable(); + SequenceI[] seqs = new SequenceI[sg.getSize()]; - alignPanel.repaint(); + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.alignment.findIndex(seq); + orderedSeqs.put(index + "", seq); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void copy_actionPerformed(ActionEvent e) + int index = 0, startRes, endRes; + char ch; + + for (int i = 0; i < sg.getSize(); i++) { - if (viewport.getSelectionGroup() == null) + SequenceI seq = null; + + while (seq == null) + { + if (orderedSeqs.containsKey(index + "")) { - return; - } + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; - SequenceGroup sg = viewport.getSelectionGroup(); + break; + } + else + { + index++; + } + } - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - StringBuffer buffer = new StringBuffer(); + //FIND START RES + //Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); - Hashtable orderedSeqs = new Hashtable(); + //FIND END RES + //Need to find the residue preceeding index if gap + endRes = 0; - for (int i = 0; i < sg.getSize(); i++) + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.alignment.findIndex(seq); - orderedSeqs.put(index + "", seq); + endRes++; } + } - int index = 0, startRes, endRes; - char ch; + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI seq = null; + seqs[i] = new Sequence(seq.getName(), + seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1), + startRes, + endRes); + seqs[i].setDescription(seq.getDescription()); + seqs[i].setDBRef(seq.getDBRef()); + seqs[i].setSequenceFeatures(seq.getSequenceFeatures()); + seqs[i].setDatasetSequence(seq.getDatasetSequence()); + + } + + FastaFile ff = new FastaFile(); + ff.addJVSuffix( viewport.showJVSuffix ); + c.setContents(new StringSelection( ff.print(seqs)), this); + Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()}; + } + + /** + * 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) + { + addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, + HistoryItem.PASTE)); + paste(false); + } + + /** + * DOCUMENT ME! + * + * @param newAlignment DOCUMENT ME! + */ + void paste(boolean newAlignment) + { + try + { + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); + + if (contents == null) + { + return; + } - while (seq == null) - { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; + String str = (String) contents.getTransferData(DataFlavor.stringFlavor); + if(str.length()<1) + return; + + String format = new IdentifyFile().Identify(str, "Paste"); + SequenceI[] sequences; + + 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); + } + + if (newAlignment) + { + + Alignment alignment = new Alignment(sequences); + + if(Desktop.jalviewClipboard!=null) + alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] ); + else + alignment.setDataset( null ); - break; - } - else - { - index++; - } - } - //FIND START RES - //Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); + AlignFrame af = new AlignFrame(alignment); + String newtitle = new String("Copied sequences"); - //FIND END RES - //Need to find the residue preceeding index if gap - endRes = 0; + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } - for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++) + Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + } + else + { + //!newAlignment + for (int i = 0; i < sequences.length; i++) + { + Sequence newseq = new Sequence(sequences[i].getName(), + sequences[i].getSequence(), sequences[i].getStart(), + sequences[i].getEnd()); + viewport.alignment.addSequence(newseq); + if(sequences[i].getDatasetSequence()==null) + { + //////////////////////////// + //Datset needs extension; + ///////////////////////////// + Sequence ds = new Sequence(sequences[i].getName(), + AlignSeq.extractGaps("-. ", sequences[i].getSequence()), + sequences[i].getStart(), + sequences[i].getEnd()); + newseq.setDatasetSequence(ds); + viewport.alignment.getDataset().addSequence(ds); + } + else + { + newseq.setDatasetSequence(sequences[i].getDatasetSequence()); + if(sequences[i].getDatasetSequence().getAnnotation()!=null) { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) + for(int aa=0; aa0) - { - endRes += seq.getStart() -1; - } - - buffer.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + } } - - c.setContents(new StringSelection(buffer.toString()), null); + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void pasteNew_actionPerformed(ActionEvent e) + catch (Exception ex) { - paste(true); + ex.printStackTrace(); + System.out.println("Exception whilst pasting: "+ex); + // could be anything being pasted in here } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void pasteThis_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); - paste(false); - } - /** - * DOCUMENT ME! - * - * @param newAlignment DOCUMENT ME! - */ - void paste(boolean newAlignment) - { - try - { - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - Transferable contents = c.getContents(this); + } - if (contents == null) - { - return; - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void cut_actionPerformed(ActionEvent e) + { + copy_actionPerformed(null); + delete_actionPerformed(null); + } - String str = (String) contents.getTransferData(DataFlavor.stringFlavor); - StringTokenizer st = new StringTokenizer(str); - ArrayList seqs = new ArrayList(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void delete_actionPerformed(ActionEvent e) + { - 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); + if (viewport.getSelectionGroup() == null) + { + return; + } - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.add(sequence); - } - } - if (newAlignment) - { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - seqs.toArray(newSeqs); + SequenceGroup sg = viewport.getSelectionGroup(); - AlignFrame af = new AlignFrame(new Alignment(newSeqs)); - String newtitle = new String("Copied sequences"); - if (title.startsWith("Copied sequences")) - { - newtitle = title; - } - else - { - newtitle = newtitle.concat("- from " + title); - } - 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) + //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); - // could be anything being pasted in here + return; + } + j++; + }while(j<=sg.getEndRes()); + } } - /** - * 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) + addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, + HistoryItem.HIDE)); + + + for (int i = 0; i < sg.sequences.size(); i++) { - boolean seqsdeleted = false; + SequenceI seq = sg.getSequenceAt(i); + int index = viewport.getAlignment().findIndex(seq); - if (viewport.getSelectionGroup() == null) - { - return; - } + seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); + // If the cut affects all sequences, remove highlighted columns + if (sg.sequences.size() == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) - allSequences = true; + if (seq.getSequence().length() < 1) + { + viewport.getAlignment().deleteSequence(seq); + } + else + { + viewport.getAlignment().getSequences().setElementAt(seq, index); + } + } - for (int i = 0; i < sg.sequences.size(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); + viewport.setSelectionGroup(null); + viewport.alignment.deleteGroup(sg); - // If the cut affects all sequences, remove highlighted columns - if(allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1); - } + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); - if (seq.getSequence().length() < 1) - { - seqsdeleted = true; - viewport.getAlignment().deleteSequence(seq); - } - else - { - viewport.getAlignment().getSequences().setElementAt(seq, index); - } - } - viewport.setSelectionGroup(null); - viewport.alignment.deleteGroup(sg); + 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) + { + viewport.setSelectionGroup(null); + viewport.getColumnSelection().clear(); + viewport.setSelectionGroup(null); + alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); + alignPanel.idPanel.idCanvas.searchResults = null; + 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); + } - if (seqsdeleted) - { - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - } + Vector groups = viewport.alignment.getGroups(); - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.get(i); - if (viewport.getAlignment().getHeight() < 1) + if (!sg.adjustForRemoveLeft(min)) { - try - { - this.setClosed(true); - } - catch (Exception ex) - { - } + viewport.alignment.deleteGroup(sg); } + } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } + } - /** - * 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 remove2RightMenuItem_actionPerformed(ActionEvent e) + { + ColumnSelection colSel = viewport.getColumnSelection(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + if (colSel.size() > 0) { - SequenceGroup sg = new SequenceGroup(); + 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); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + if (!sg.adjustForRemoveRight(max)) { - sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); + viewport.alignment.deleteGroup(sg); } + } - sg.setEndRes(viewport.alignment.getWidth()-1); - viewport.setSelectionGroup(sg); - PaintRefresher.Refresh(null, viewport.alignment); + 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)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + //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().sequences != null + && viewport.getSelectionGroup().sequences.size() > 0) + { + seqs = viewport.getSelectionGroup().sequences; + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes()+1; + } + else { - viewport.setSelectionGroup(null); - viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); - alignPanel.annotationPanel.activeRes = null; - PaintRefresher.Refresh(null, viewport.alignment); + seqs = viewport.alignment.getSequences(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) + for (int i = 0; i < seqs.size(); i++) { - SequenceGroup sg = viewport.getSelectionGroup(); + current = (SequenceI) seqs.elementAt(i); + jSize = current.getLength(); - if (sg == null) - { - selectAllSequenceMenuItem_actionPerformed(null); + // Removing a range is much quicker than removing gaps + // one by one for long sequences + int j = start; + int rangeStart=-1, rangeEnd=-1; - return; + do + { + if (jalview.util.Comparison.isGap(current.getCharAt(j))) + { + if(rangeStart==-1) + { + rangeStart = j; + rangeEnd = j+1; + } + else + { + rangeEnd++; + } + j++; } - - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + else { - sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false); + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + j-=rangeEnd-rangeStart; + jSize-=rangeEnd-rangeStart; + rangeStart = -1; + rangeEnd = -1; + } + else + j++; } - - PaintRefresher.Refresh(null, viewport.alignment); + } + while (j < end && j < jSize); + if(rangeStart>-1) + { + current.deleteChars(rangeStart, rangeEnd); + } } - /** - * 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)); + viewport.setStartRes(seq.findIndex(startRes)-1); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } + public void alignmentChanged() + { + if(viewport.vconsensus!=null) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); - Vector groups = viewport.alignment.getGroups(); + viewport.alignment.adjustSequenceAnnotations(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.get(i); + alignPanel.repaint(); + } - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } + void resetAllColourSchemes() + { + ColourSchemeI cs = viewport.globalColourScheme; + if(cs!=null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). + resetClustalX(viewport.alignment.getSequences(), + viewport.alignment.getWidth()); + } - alignPanel.repaint(); - } + 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); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void remove2RightMenuItem_actionPerformed(ActionEvent e) + int s, sSize = viewport.alignment.getGroups().size(); + for(s=0; s 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); + SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s); + if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme) + { + ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth()); + } + sg.recalcConservation(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void padGapsMenuitem_actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment, + HistoryItem.HIDE)); + if (viewport.getAlignment().padGaps()) + alignmentChanged(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void findMenuItem_actionPerformed(ActionEvent e) + { + JInternalFrame frame = new JInternalFrame(); + Finder finder = new Finder(viewport, alignPanel, frame); + frame.setContentPane(finder); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + Desktop.addInternalFrame(frame, "Find", 340, 110); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void font_actionPerformed(ActionEvent e) + { + new FontChooser(alignPanel); + } + + public void smoothFont_actionPerformed(ActionEvent e) + { + viewport.antiAlias = smoothFont.isSelected(); + alignPanel.annotationPanel.image = null; + alignPanel.repaint(); + } + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void seqLimit_actionPerformed(ActionEvent e) + { + viewport.setShowJVSuffix(seqLimits.isSelected()); + + 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) + { + viewport.setWrapAlignment(wrapMenuItem.isSelected()); + alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); + scaleAbove.setVisible(wrapMenuItem.isSelected()); + scaleLeft.setVisible(wrapMenuItem.isSelected()); + scaleRight.setVisible(wrapMenuItem.isSelected()); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void scaleAbove_actionPerformed(ActionEvent e) + { + viewport.setScaleAboveWrapped(scaleAbove.isSelected()); + alignPanel.repaint(); + } + + /** + * 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(); + } + + /** + * 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) + { + viewport.setShowText(viewTextMenuItem.isSelected()); + alignPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { + viewport.setRenderGaps(renderGapsMenuItem.isSelected()); + alignPanel.repaint(); + } + + public void fetchSeqFeatures_actionPerformed(ActionEvent e) + { + if (!viewport.alignment.isNucleotide()) + { + new SequenceFeatureFetcher(viewport. + alignment, + alignPanel); + viewport.setShowSequenceFeatures(true); + showSeqFeatures.setSelected(true); + } + } + + + public void featureSettings_actionPerformed(ActionEvent e) + { + new FeatureSettings(viewport, alignPanel); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void showSeqFeatures_actionPerformed(ActionEvent evt) + { + viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); + alignPanel.repaint(); + 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()); + } + + /** + * 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); + } + + /** + * 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 annotationColour_actionPerformed(ActionEvent e) + { + new AnnotationColourChooser(viewport, alignPanel); + } + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void applyToAllGroups_actionPerformed(ActionEvent e) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); + } + + /** + * DOCUMENT ME! + * + * @param cs DOCUMENT ME! + */ + void changeColour(ColourSchemeI cs) + { + int threshold = 0; + + if(cs!=null) + { + if (viewport.getAbovePIDThreshold()) + { + threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, + "Background"); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); + cs.setThreshold(threshold, + viewport.getIgnoreGapsConsensus()); - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } + viewport.setGlobalColourScheme(cs); + } + else + { + cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } - Vector groups = viewport.alignment.getGroups(); + if (viewport.getConservationSelected()) + { - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.get(i); + Alignment al = (Alignment) viewport.alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); - alignPanel.repaint(); - } - } + cs.setConservation(c); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, HistoryItem.HIDE)); + cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, + "Background")); + } + else + { + cs.setConservation(null); + } - viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + cs.setConsensus(viewport.vconsensus); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); - - SequenceI current; - int jSize; + viewport.setGlobalColourScheme(cs); - Vector seqs = null; + if (viewport.getColourAppliesToAllGroups()) + { + Vector groups = viewport.alignment.getGroups(); - int start = 0; - int end = viewport.alignment.getWidth(); + for (int i = 0; i < groups.size(); i++) + { + SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + if (cs == null) + { + sg.cs = null; + continue; + } - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + if (cs instanceof ClustalxColourScheme) + { + sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + } + else if (cs instanceof UserColourScheme) { - seqs = viewport.getSelectionGroup().sequences; - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); + sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours()); } else { - seqs = viewport.alignment.getSequences(); + try + { + sg.cs = (ColourSchemeI) cs.getClass().newInstance(); + } + catch (Exception ex) + { + } } - for (int i = 0; i < seqs.size(); i++) + if (viewport.getAbovePIDThreshold() + || cs instanceof PIDColourScheme + || cs instanceof Blosum62ColourScheme) { - current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); + sg.cs.setThreshold(threshold, + viewport.getIgnoreGapsConsensus()); - int j = start; - - do - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - current.deleteCharAt(j); - j--; - jSize--; - } - - j++; - } - while (j < end && j < jSize); + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.getWidth())); } + else + sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void padGapsMenuitem_actionPerformed(ActionEvent e) - { - addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment, - HistoryItem.HIDE)); - - SequenceI current; - int Width = viewport.getAlignment().getWidth(); - for (int i = 0; i < viewport.getAlignment().getSequences().size(); - i++) + if (viewport.getConservationSelected()) { - current = viewport.getAlignment().getSequenceAt(i); - - if (current.getLength() < Width) - { - current.insertCharAt(Width - 1, viewport.getGapCharacter()); - } + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.sequences, 0, + viewport.alignment.getWidth() - 1); + c.calculate(); + c.verdict(false, viewport.ConsPercGaps); + sg.cs.setConservation(c); } - - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + else + sg.cs.setConservation(null); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void findMenuItem_actionPerformed(ActionEvent e) + if (alignPanel.getOverviewPanel() != 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); + alignPanel.getOverviewPanel().updateOverviewImage(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void font_actionPerformed(ActionEvent e) - { - FontChooser fc = new FontChooser(alignPanel); - } + alignPanel.repaint(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void fullSeqId_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void modifyPID_actionPerformed(ActionEvent e) + { + if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) { - viewport.setShowFullId(fullSeqId.isSelected()); - - alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.repaint(); + SliderPanel.setPIDSliderSource(alignPanel, + viewport.getGlobalColourScheme(), + "Background"); + SliderPanel.showPIDSlider(); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void colourTextMenuItem_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void modifyConservation_actionPerformed(ActionEvent e) + { + if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) { - viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.repaint(); + SliderPanel.setConservationSlider(alignPanel, + viewport.globalColourScheme, + "Background"); + SliderPanel.showConservationSlider(); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void wrapMenuItem_actionPerformed(ActionEvent e) - { - viewport.setWrapAlignment(wrapMenuItem.isSelected()); - alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); - scaleAbove.setVisible(wrapMenuItem.isSelected()); - scaleLeft.setVisible(wrapMenuItem.isSelected()); - scaleRight.setVisible(wrapMenuItem.isSelected()); - alignPanel.repaint(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { + viewport.setConservationSelected(conservationMenuItem.isSelected()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void scaleAbove_actionPerformed(ActionEvent e) - { - viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.repaint(); - } + viewport.setAbovePIDThreshold(false); + abovePIDThreshold.setSelected(false); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void scaleLeft_actionPerformed(ActionEvent e) - { - viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.repaint(); - } + changeColour(viewport.getGlobalColourScheme()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void scaleRight_actionPerformed(ActionEvent e) - { - viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.repaint(); - } + modifyConservation_actionPerformed(null); + } - /** - * 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 abovePIDThreshold_actionPerformed(ActionEvent e) + { + viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void viewTextMenuItem_actionPerformed(ActionEvent e) - { - viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.repaint(); - } + conservationMenuItem.setSelected(false); + viewport.setConservationSelected(false); + + changeColour(viewport.getGlobalColourScheme()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + modifyPID_actionPerformed(null); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void userDefinedColour_actionPerformed(ActionEvent e) + { + if (e.getActionCommand().equals("User Defined...")) { - viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.repaint(); + new UserDefinedColours(alignPanel, null); } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void sequenceFeatures_actionPerformed(ActionEvent evt) + else { - viewport.showSequenceFeatures(sequenceFeatures.isSelected()); - - if (viewport.showSequenceFeatures && - !((Alignment) viewport.alignment).featuresAdded) - { - SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, - alignPanel); - ((Alignment) viewport.alignment).featuresAdded = true; - } + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); - alignPanel.repaint(); + changeColour(udc); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void annotationPanelMenuItem_actionPerformed(ActionEvent e) - { - if (annotationPanelMenuItem.isSelected() && - viewport.getWrapAlignment()) - { - annotationPanelMenuItem.setSelected(false); - - return; - } + public void updateUserColourMenu() + { - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); + 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--; + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void overviewMenuItem_actionPerformed(ActionEvent e) + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) { - if (alignPanel.overviewPanel != null) - { - return; - } + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); - 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() + while (userColours.hasMoreElements()) + { + final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours. + nextElement().toString()); + radioItem.setName("USER_DEFINED"); + radioItem.addMouseListener(new MouseAdapter() { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + public void mousePressed(MouseEvent evt) + { + if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt)) { - alignPanel.setOverviewPanel(null); + 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); + } + }); - alignPanel.setOverviewPanel(overview); + 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) + { + RedundancyPanel sp = new RedundancyPanel(alignPanel, this); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(sp); + Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, + 100, false); + } + + /** + * 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(viewport); + } + + /** + * 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) + { + final TreePanel tp; + + if ( (viewport.getSelectionGroup() != null) && + (viewport.getSelectionGroup().getSize() > 3)) + { + int s = 0; + SequenceGroup sg = viewport.getSelectionGroup(); + + /* 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); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - changeColour(null); - } + return; + } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void clustalColour_actionPerformed(ActionEvent e) - { - changeColour(new ClustalxColourScheme( - viewport.alignment.getSequences(), viewport.alignment.getWidth())); + title = title + " on region"; + tp = new TreePanel(viewport, + viewport.getSelectionGroup().sequences, type, pwType, + sg.getStartRes(), sg.getEndRes()); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void zappoColour_actionPerformed(ActionEvent e) + else { - changeColour(new ZappoColourScheme()); - } + //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; + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void taylorColour_actionPerformed(ActionEvent e) - { - changeColour(new TaylorColourScheme()); + tp = new TreePanel(viewport, + viewport.getAlignment().getSequences(), type, pwType, + 0, + viewport.alignment.getWidth()); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void hydrophobicityColour_actionPerformed(ActionEvent e) - { - changeColour(new HydrophobicColourScheme()); - } + addTreeMenuItem(tp, title); + viewport.setCurrentTree(tp.getTree()); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void helixColour_actionPerformed(ActionEvent e) - { - changeColour(new HelixColourScheme()); - } + Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void strandColour_actionPerformed(ActionEvent e) + /** + * 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() { - changeColour(new StrandColourScheme()); - } + public void actionPerformed(ActionEvent e) + { + addHistoryItem(new HistoryItem("Sort", viewport.alignment, + HistoryItem.SORT)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void turnColour_actionPerformed(ActionEvent e) - { - changeColour(new TurnColourScheme()); - } + // TODO: JBPNote - have to map order entries to curent SequenceI pointers + AlignmentSorter.sortBy(viewport.getAlignment(), order); + alignPanel.repaint(); + } + }); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void buriedColour_actionPerformed(ActionEvent e) - { - changeColour(new BuriedColourScheme()); - } + /** + * 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++; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void nucleotideColour_actionPerformed(ActionEvent e) + if (treeCount == 1) { - changeColour(new NucleotideColourScheme()); + sort.add(sortByTreeMenu); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void applyToAllGroups_actionPerformed(ActionEvent e) + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() { - viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); - } + 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 cs DOCUMENT ME! - */ - void changeColour(ColourSchemeI cs) + treePanel.addInternalFrameListener(new javax.swing.event. + InternalFrameAdapter() { - int threshold = 0; + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + treeCount--; + sortByTreeMenu.remove(item); - if (viewport.getAbovePIDThreshold()) + if (treeCount == 0) { - threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, - "Background"); + 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() > 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()]; + + for (int i = 0; i < sz; i++) + { + msa[i] = (SequenceI) seqs.getSequenceAt(i); + } + } + else + { + Vector seqs = viewport.getAlignment().getSequences(); - if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(threshold); - } - else if (cs instanceof ScoreColourScheme) - { - ((ScoreColourScheme) cs).setThreshold(threshold); - } + if (seqs.size() > 1) + { + msa = new SequenceI[seqs.size()]; - viewport.setGlobalColourScheme(cs); - } - else if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(0); - } - else if (cs instanceof ScoreColourScheme) + for (int i = 0; i < seqs.size(); i++) { - ((ScoreColourScheme) cs).setThreshold(0); + msa[i] = (SequenceI) seqs.elementAt(i); } + } + } + return msa; + } - if (viewport.getConservationSelected()) - { - ConservationColourScheme ccs = null; - - 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); + /** + * 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; - ccs = new ConservationColourScheme(c, cs); + 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(); - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - ccs.setConsensus(viewport.vconsensus); - viewport.setGlobalColourScheme(ccs); + if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned()) + { + seq = (SequenceI) seqs.getSequenceAt(0); + } + else + { + int sz; + msa = new SequenceI[sz = seqs.getSize()]; - ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, - "Background"); + for (int i = 0; i < sz; i++) + { + msa[i] = (SequenceI) seqs.getSequenceAt(i); } - else - { - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - if (cs != null) - { - cs.setConsensus(viewport.vconsensus); - } - - 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; - } - else if (cs instanceof ClustalxColourScheme) - { - sg.cs = new ClustalxColourScheme(sg.sequences, 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()) - { - if (sg.cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) sg.cs).setThreshold(threshold); - } - else if (sg.cs instanceof ScoreColourScheme) - { - ((ScoreColourScheme) sg.cs).setThreshold(threshold); - } - - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - sg.getWidth())); - } + } + } + else + { + Vector seqs = viewport.getAlignment().getSequences(); - if (viewport.getConservationSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, 0, - viewport.alignment.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - - ConservationColourScheme ccs = new ConservationColourScheme(c, - sg.cs); - - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - sg.getWidth())); - sg.cs = ccs; - } - else if (cs != null) - { - // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS! - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - sg.getWidth())); - } - } - } + if ( (seqs.size() == 1) || !viewport.alignment.isAligned()) + { + seq = (SequenceI) seqs.elementAt(0); + } + else + { + msa = new SequenceI[seqs.size()]; - if (alignPanel.getOverviewPanel() != null) + for (int i = 0; i < seqs.size(); i++) { - alignPanel.getOverviewPanel().updateOverviewImage(); + msa[i] = (SequenceI) seqs.elementAt(i); } - - alignPanel.repaint(); + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void modifyPID_actionPerformed(ActionEvent e) + if (msa != null) { - if (viewport.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getGlobalColourScheme(), "Background"); - SliderPanel.showPIDSlider(); - } + return msa; } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void modifyConservation_actionPerformed(ActionEvent e) + else { - if (viewport.getConservationSelected()) - { - SliderPanel.setConservationSlider(alignPanel, - viewport.globalColourScheme, "Background"); - SliderPanel.showConservationSlider(); - } + if (seq != null) + { + return new SequenceI[] + { + seq}; + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); - - ColourSchemeI cs = viewport.getGlobalColourScheme(); - - if (cs instanceof ConservationColourScheme) - { - changeColour(((ConservationColourScheme) cs).cs); - } - else - { - changeColour(cs); - } - - modifyConservation_actionPerformed(null); + 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(); + } } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void abovePIDThreshold_actionPerformed(ActionEvent e) - { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); + 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; - ColourSchemeI cs = viewport.getGlobalColourScheme(); - - if (cs instanceof ConservationColourScheme) - { - changeColour(((ConservationColourScheme) cs).cs); - } - else - { - changeColour(cs); - } + try + { + nf.parse(); - modifyPID_actionPerformed(null); - } + if (nf.getTree() != null) + { + tp = new TreePanel(viewport, + viewport.getAlignment().getSequences(), nf, + "FromFile", + title); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void userDefinedColour_actionPerformed(ActionEvent e) - { - new UserDefinedColours(alignPanel, null); - } + tp.setSize(w,h); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void PIDColour_actionPerformed(ActionEvent e) - { - changeColour(new PIDColourScheme()); - } + if(x>0 && y>0) + tp.setLocation(x,y); - /** - * 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(); + Desktop.addInternalFrame(tp, title, w, h); + addTreeMenuItem(tp, title); + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void sortIDMenuItem_actionPerformed(ActionEvent e) + catch (Exception ex) { - addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - HistoryItem.SORT)); - AlignmentSorter.sortByID(viewport.getAlignment()); - alignPanel.repaint(); + ex.printStackTrace(); } - /** - * 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(); - } + return tp; + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + class PrintThread + extends Thread + { + public void run() { - RedundancyPanel sp = new RedundancyPanel(alignPanel, this); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(sp); - Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, - 100, false); - } + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + printJob.setPrintable(alignPanel, pf); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) - { - if ((viewport.getSelectionGroup() == null) || - (viewport.getSelectionGroup().getSize() < 2)) + if (printJob.printDialog()) + { + try { - JOptionPane.showInternalMessageDialog(this, - "You must select at least 2 sequences.", "Invalid Selection", - JOptionPane.WARNING_MESSAGE); + printJob.print(); } - else + catch (Exception PrintException) { - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500); + 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"); + 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()); - /** - * 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; - } + }); + 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()); - try - { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(pcaPanel); - Desktop.addInternalFrame(frame, "Principal component analysis", - 400, 400); + } + + }); + msawsmenu.add(methodR); + + } } - catch (java.lang.OutOfMemoryError ex) - { - JOptionPane.showInternalMessageDialog(this, - "Too many sequences selected\nfor Principal Component Analysis!!", - "Out of memory", JOptionPane.WARNING_MESSAGE); + 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)); + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + else { - NewTreePanel("AV", "PID", "Average distance tree using PID"); + 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. + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); - } + /* public void vamsasStore_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) - { - NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); - } + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Export to Vamsas file"); + chooser.setToolTipText("Export"); + + int value = chooser.showSaveDialog(this); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + if (value == JalviewFileChooser.APPROVE_OPTION) { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); + jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); + //vs.store(chooser.getSelectedFile().getAbsolutePath() ); + vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this); } + }*/ - /** - * DOCUMENT ME! - * - * @param type DOCUMENT ME! - * @param pwType DOCUMENT ME! - * @param title DOCUMENT ME! - */ - void NewTreePanel(String type, String pwType, String title) - { - final TreePanel tp; - if ((viewport.getSelectionGroup() != null) && - (viewport.getSelectionGroup().getSize() > 3)) - { - int s = 0; - SequenceGroup sg = viewport.getSelectionGroup(); - /* 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; - } - } - title = title + " on region"; - tp = new TreePanel(viewport, - viewport.getSelectionGroup().sequences, type, pwType, - sg.getStartRes(), sg.getEndRes()); - } - 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; - } +public void showTranslation_actionPerformed(ActionEvent e) +{ + int s, sSize = viewport.alignment.getHeight(); + 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()]; - 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()]; +/*public void tabSelected() + { + int index = tabbedPane.getSelectedIndex(); + viewport = (AlignViewport)viewports.elementAt(index); + alignPanel = (AlignmentPanel)alignPanels.elementAt(index); + }*/ - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } +/** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ +public boolean parseGroupsFile(String file) +{ + try + { + BufferedReader in = new BufferedReader(new FileReader(file)); + SequenceI seq = null; + String line, type, desc, token; + + int index, start, end; + StringTokenizer st; + SequenceFeature sf; + int lineNo = 0; + String featureGroup = null; + while ( (line = in.readLine()) != null) + { + lineNo++; + st = new StringTokenizer(line, "\t"); + if (st.countTokens() == 2) + { + type = st.nextToken(); + if (type.equalsIgnoreCase("startgroup")) + { + featureGroup = st.nextToken(); + } + else if (type.equalsIgnoreCase("endgroup")) + { + //We should check whether this is the current group, + //but at present theres no way of showing more than 1 group + st.nextToken(); + featureGroup = null; + } + else + { + UserColourScheme ucs = new UserColourScheme(st.nextToken()); + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, + ucs.findColour("A")); + } + continue; } - if (msa != null) + while (st.hasMoreElements()) { - jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", - title, msa, false, true); - } - } + desc = 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! - * - * @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; + start = Integer.parseInt(st.nextToken()); + end = Integer.parseInt(st.nextToken()); - 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()]; + seq = viewport.alignment.getSequenceAt(index); - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); + type = st.nextToken(); - if (seqs.size() > 1) - { - msa = new SequenceI[seqs.size()]; + if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null) + { + // Probably the old style groups file + UserColourScheme ucs = new UserColourScheme(type); + alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A")); + } - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } + sf = new SequenceFeature(type, desc, "", start, end); + sf.setFeatureGroup(featureGroup); - if (msa != null) - { - jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", - title, msa, true, true); + seq.getDatasetSequence().addSequenceFeature(sf); } + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void jpred_actionPerformed(ActionEvent e) + catch (Exception ex) { - SequenceI seq = null; - SequenceI[] msa = null; + ex.printStackTrace(); + System.out.println("Error parsing groups file: " + ex); + return false; + } - 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(); + viewport.showSequenceFeatures = true; + showSeqFeatures.setSelected(true); + alignPanel.repaint(); + return true; +} - if ((seqs.getSize() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.getSequenceAt(0); - } - else - { - int sz; - msa = new SequenceI[sz = seqs.getSize()]; +public void dragEnter(DropTargetDragEvent evt) +{} - for (int i = 0; i < sz; i++) - { - msa[i] = (SequenceI) seqs.getSequenceAt(i); - } - } - } - else - { - Vector seqs = viewport.getAlignment().getSequences(); +public void dragExit(DropTargetEvent evt) +{} - if ((seqs.size() == 1) || !viewport.alignment.isAligned()) - { - seq = (SequenceI) seqs.elementAt(0); - } - else - { - msa = new SequenceI[seqs.size()]; +public void dragOver(DropTargetDragEvent evt) +{} - for (int i = 0; i < seqs.size(); i++) - { - msa[i] = (SequenceI) seqs.elementAt(i); - } - } - } +public void dropActionChanged(DropTargetDragEvent evt) +{} - 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 drop(DropTargetDropEvent evt) +{ + Transferable t = evt.getTransferable(); + java.util.List files = null; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) + try { - // 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()]; - - 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); - } - } - } + 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; + } - if (msa != null) - { - MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa, - false, true); + java.net.URI uri = new java.net.URI(s); + java.io.File file = new java.io.File(uri); + files.add(file); } + } } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) + catch (Exception 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"); + e.printStackTrace(); + } - int value = chooser.showOpenDialog(null); + if (files != null) + { + try + { + boolean isAnnotation = false; - if (value == JalviewFileChooser.APPROVE_OPTION) + for (int i = 0; i < files.size(); i++) { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + String file = files.get(i).toString(); - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, - "File"); - viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); - } - catch (Exception ex) + isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file); + + if( !isAnnotation ) + { + boolean isGroupsFile = parseGroupsFile(file); + if (!isGroupsFile) { - JOptionPane.showMessageDialog(Desktop.desktop, - "Problem reading tree file", ex.getMessage(), - JOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - } - } + String protocol = "File"; + String format = new IdentifyFile().Identify(file, protocol); + SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format); - /** - * DOCUMENT ME! - * - * @param nf DOCUMENT ME! - * @param title DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public TreePanel ShowNewickTree(NewickFile nf, String title) - { - TreePanel tp = null; + FastaFile ff = new FastaFile(); + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + c.setContents(new StringSelection(ff.print(sequences)), this); - try - { - nf.parse(); + this.paste(false); - if (nf.getTree() != null) - { - tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), nf, "FromFile", - title); - Desktop.addInternalFrame(tp, title, 600, 500); - addTreeMenuItem(tp, title); } + } } - catch (Exception ex) - { - ex.printStackTrace(); - } - - return tp; - } - class PrintThread extends Thread - { - public void run() + if(isAnnotation) { - PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); - printJob.setPrintable(alignPanel, pf); + int height = alignPanel.annotationPanel.adjustPanelHeight(); + alignPanel.annotationScroller.setPreferredSize( + new Dimension(alignPanel.annotationScroller.getWidth(), + height)); - if (printJob.printDialog()) - { - try - { - printJob.print(); - } - catch (Exception PrintException) - { - PrintException.printStackTrace(); - } - } + alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension( + alignPanel.annotationSpaceFillerHolder.getWidth(), + height)); + + alignPanel.addNotify(); } + } + catch (Exception ex) + { + ex.printStackTrace(); + } } } + +}