X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e812530c901193acb574caba11c06a5b8fd4142e;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=34ffd4c9f29b404fd1ae937dfe0dfcb5d7133cfb;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java old mode 100755 new mode 100644 index 34ffd4c..e812530 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,1153 +1,1998 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import MCview.*; - -import jalview.analysis.*; - -import jalview.datamodel.*; - - -import jalview.schemes.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import java.util.Vector; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class PopupMenu extends JPopupMenu -{ - JMenu groupMenu = new JMenu(); - JMenuItem groupName = new JMenuItem(); - protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - AlignmentPanel ap; - JMenu sequenceMenu = new JMenu(); - JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; - JMenuItem unGroupMenuItem = new JMenuItem(); - JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); - JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); - JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); - JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); - JMenu editMenu = new JMenu(); - JMenuItem cut = new JMenuItem(); - JMenuItem copy = new JMenuItem(); - JMenuItem upperCase = new JMenuItem(); - JMenuItem lowerCase = new JMenuItem(); - JMenuItem toggle = new JMenuItem(); - - /** - * Creates a new PopupMenu object. - * - * @param ap DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) - { - /////////////////////////////////////////////////////////// - // If this is activated from the sequence panel, the user may want to - // edit or annotate a particular residue. Therefore display the residue menu - // - // If from the IDPanel, we must display the sequence menu - ////////////////////////////////////////////////////////// - this.ap = ap; - sequence = seq; - - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - - try - { - jbInit(); - } - catch (Exception e) - { - e.printStackTrace(); - } - - - if (seq != null) - { - JMenuItem menuItem; - if( seq.getDatasetSequence().getPDBId() != null) - { - java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). - elements(); - while (e.hasMoreElements()) - { - final PDBEntry pdb = (PDBEntry) e.nextElement(); - - menuItem = new JMenuItem(); - menuItem.setText("View PDB entry: " + pdb.getId()); - menuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas); - } - }); - sequenceMenu.add(menuItem); - } - } - - menuItem = new JMenuItem("Hide Sequences"); - menuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hideSequences(false); - } - }); - sequenceMenu.add(menuItem); - - if(ap.av.getSelectionGroup() !=null - && ap.av.getSelectionGroup().getSize(false)>1) - { - menuItem = new JMenuItem("Represent Group with " + seq.getName()); - menuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hideSequences(true); - } - }); - sequenceMenu.add(menuItem); - } - - if (ap.av.hasHiddenRows) - { - final int index = ap.av.alignment.findIndex(seq); - - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) - { - menuItem = new JMenuItem("Reveal"); - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ap.av.showSequence(index); - ap.repaint(); - if (ap.overviewPanel != null) - ap.overviewPanel.updateOverviewImage(); - } - }); - sequenceMenu.add(menuItem); - } - - menuItem = new JMenuItem("Reveal All"); - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ap.av.showAllHiddenSeqs(); - ap.repaint(); - if (ap.overviewPanel != null) - ap.overviewPanel.updateOverviewImage(); - } - }); - - sequenceMenu.add(menuItem); - - - - } - - - } - - - - SequenceGroup sg = ap.av.getSelectionGroup(); - - if (sg != null) - { - groupName.setText(sg.getName()); - - if (sg.cs instanceof ZappoColourScheme) - { - zappoColour.setSelected(true); - } - else if (sg.cs instanceof TaylorColourScheme) - { - taylorColour.setSelected(true); - } - else if (sg.cs instanceof PIDColourScheme) - { - PIDColour.setSelected(true); - } - else if (sg.cs instanceof Blosum62ColourScheme) - { - BLOSUM62Colour.setSelected(true); - } - else if (sg.cs instanceof UserColourScheme) - { - userDefinedColour.setSelected(true); - } - else if (sg.cs instanceof HydrophobicColourScheme) - { - hydrophobicityColour.setSelected(true); - } - else if (sg.cs instanceof HelixColourScheme) - { - helixColour.setSelected(true); - } - else if (sg.cs instanceof StrandColourScheme) - { - strandColour.setSelected(true); - } - else if (sg.cs instanceof TurnColourScheme) - { - turnColour.setSelected(true); - } - else if (sg.cs instanceof BuriedColourScheme) - { - buriedColour.setSelected(true); - } - else if (sg.cs instanceof ClustalxColourScheme) - { - clustalColour.setSelected(true); - } - else - { - noColourmenuItem.setSelected(true); - } - - if (sg.cs!=null && sg.cs.conservationApplied()) - { - conservationMenuItem.setSelected(true); - } - - showText.setSelected(sg.getDisplayText()); - showColourText.setSelected(sg.getColourText()); - showBoxes.setSelected(sg.getDisplayBoxes()); - } - else - { - groupMenu.setVisible(false); - editMenu.setVisible(false); - } - - if (!ap.av.alignment.getGroups().contains(sg)) - { - unGroupMenuItem.setVisible(false); - } - else - { - groupMenu.insertSeparator(3); - } - - if (seq == null) - { - sequenceMenu.setVisible(false); - } - - if(links != null && links.size()>0) - { - JMenu linkMenu = new JMenu("Link"); - JMenuItem item; - for(int i=0; i -1) - { - String id = seq.getName(); - if (id.indexOf("|") > -1) - id = id.substring(id.lastIndexOf("|") + 1); - - url = link.substring(link.indexOf("|") + 1, - link.indexOf("$SEQUENCE_ID$")) - + id + - link.substring(link.indexOf("$SEQUENCE_ID$") + 13); - } - else - url = link.substring(link.lastIndexOf("|")+1); - - - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showLink(url); - } - }); - - linkMenu.add(item); - } - add(linkMenu); - } - } - - - /** - * DOCUMENT ME! - * - * @throws Exception DOCUMENT ME! - */ - private void jbInit() throws Exception - { - groupMenu.setText("Group"); - groupMenu.setText("Group"); - groupName.setText("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupName_actionPerformed(e); - } - }); - sequenceMenu.setText("Sequence"); - sequenceName.setText("Edit Name/Description"); - sequenceName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sequenceName_actionPerformed(e); - } - }); - PIDColour.setFocusPainted(false); - unGroupMenuItem.setText("Remove Group"); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - unGroupMenuItem_actionPerformed(e); - } - }); - - outline.setText("Border colour"); - outline.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - outline_actionPerformed(e); - } - }); - nucleotideMenuItem.setText("Nucleotide"); - nucleotideMenuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - nucleotideMenuItem_actionPerformed(e); - } - }); - colourMenu.setText("Group Colour"); - showBoxes.setText("Boxes"); - showBoxes.setState(true); - showBoxes.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showBoxes_actionPerformed(e); - } - }); - showText.setText("Text"); - showText.setState(true); - showText.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showText_actionPerformed(e); - } - }); - showColourText.setText("Colour Text"); - showColourText.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showColourText_actionPerformed(e); - } - }); - editMenu.setText("Edit"); - cut.setText("Cut"); - cut.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - cut_actionPerformed(e); - } - }); - upperCase.setText("To Upper Case"); - upperCase.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - upperCase_actionPerformed(e); - } - }); - copy.setText("Copy"); - copy.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copy_actionPerformed(e); - } - }); - lowerCase.setText("To Lower Case"); - lowerCase.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - lowerCase_actionPerformed(e); - } - }); - toggle.setText("Toggle Case"); - toggle.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - toggle_actionPerformed(e); - } - }); - add(groupMenu); - add(sequenceMenu); - this.add(editMenu); - groupMenu.add(groupName); - groupMenu.addSeparator(); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.addSeparator(); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); - groupMenu.addSeparator(); - groupMenu.add(outline); - sequenceMenu.add(sequenceName); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideMenuItem); - colourMenu.add(userDefinedColour); - - if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours. - getUserColourSchemes().keys(); - - while (userColours.hasMoreElements()) - { - JMenuItem item = new JMenuItem(userColours. - nextElement().toString()); - item.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.add(item); - } - } - - - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); - editMenu.add(copy); - editMenu.add(cut); - editMenu.add(upperCase); - editMenu.add(lowerCase); - editMenu.add(toggle); - noColourmenuItem.setText("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); - - clustalColour.setText("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setText("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setText("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setText("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setText("Helix propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); - strandColour.setText("Strand propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(e); - } - }); - turnColour.setText("Turn propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); - buriedColour.setText("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(e); - } - }); - abovePIDColour.setText("Above % Identity"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(e); - } - }); - userDefinedColour.setText("User Defined..."); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour.setText("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); - BLOSUM62Colour.setText("BLOSUM62"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); - conservationMenuItem.setText("Conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(e); - } - }); - } - - /** - * DOCUMENT ME! - */ - void refresh() - { - if (ap.overviewPanel != null) - ap.overviewPanel.updateOverviewImage(); - - ap.seqPanel.repaint(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void clustalColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.getSequences(true), - ap.av.alignment.getWidth()); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void zappoColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void taylorColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void helixColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new HelixColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void strandColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new StrandColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void turnColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new TurnColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void buriedColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void nucleotideMenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void abovePIDColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - if(sg.cs==null) - return; - - if (abovePIDColour.isSelected()) - { - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(true), 0, - ap.av.alignment.getWidth())); - - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, - getGroup().getName()); - - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - - SliderPanel.showPIDSlider(); - } - else // remove PIDColouring - { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); - } - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - if (e.getActionCommand().equals("User Defined...")) - new UserDefinedColours(ap, sg); - else - { - UserColourScheme udc = (UserColourScheme) UserDefinedColours. - getUserColourSchemes().get(e.getActionCommand()); - - sg.cs = udc; - } - } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void PIDColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, - ap.av.alignment.getWidth())); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - sg.cs = new Blosum62ColourScheme(); - - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, - ap.av.alignment.getWidth())); - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = null; - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - if(sg.cs==null) - return; - - if (conservationMenuItem.isSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.getSequences(true), 0, - ap.av.alignment.getWidth()); - - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); - - sg.cs.setConservation(c); - - SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); - SliderPanel.showConservationSlider(); - } - else // remove ConservationColouring - { - sg.cs.setConservation(null); - } - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void groupName_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, - "Enter new group name", "Edit group name", - JOptionPane.QUESTION_MESSAGE); - - if (reply == null) - { - return; - } - - sg.setName(reply); - groupName.setText(reply); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); - - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for (int i = 0; i < sg.getSize(false); i++) - { - Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i); - sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); - sb.append("\n"); - } - - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - SequenceGroup getGroup() - { - SequenceGroup sg = ap.av.getSelectionGroup(); - // this method won't add a new group if it already exists - if(sg!=null) - ap.av.alignment.addGroup(sg); - - return sg; - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - void sequenceName_actionPerformed(ActionEvent e) - { - JLabel idlabel = new JLabel( " Sequence Name "); - JLabel desclabel = new JLabel("Sequence Description "); - idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); - desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); - JTextField id = new JTextField(sequence.getName(), 40); - JTextField description = new JTextField(sequence.getDescription(), 40); - JPanel panel = new JPanel(new BorderLayout()); - JPanel panel2 = new JPanel(new BorderLayout()); - panel2.add(idlabel, BorderLayout.WEST); - panel2.add(id, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.NORTH); - panel2 = new JPanel(new BorderLayout()); - panel2.add(desclabel, BorderLayout.WEST); - panel2.add(description, BorderLayout.CENTER); - panel.add(panel2, BorderLayout.SOUTH); - - - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - panel, "Edit Sequence Name/Description", - JOptionPane.OK_CANCEL_OPTION ); - - - if (reply != JOptionPane.OK_OPTION ) - { - return; - } - - String s = id.getText(); - - if (s != null) - { - if (s.indexOf(" ") > -1) - { - JOptionPane.showMessageDialog(ap, - "Spaces have been converted to \"_\"", - "No spaces allowed in Sequence Name", - JOptionPane.WARNING_MESSAGE); - } - - s = s.replace(' ', '_'); - sequence.getDatasetSequence().setName(s); - sequence.setName(s); - ap.repaint(); - } - - sequence.getDatasetSequence().setDescription(description.getText()); - sequence.setDescription(description.getText()); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - void unGroupMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); - ap.av.setSelectionGroup(null); - refresh(); - } - - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void outline_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, "Select Outline Colour", - Color.BLUE); - - if (col != null) - { - sg.setOutlineColour(col); - } - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void showBoxes_actionPerformed(ActionEvent e) - { - getGroup().setDisplayBoxes(showBoxes.isSelected()); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void showText_actionPerformed(ActionEvent e) - { - getGroup().setDisplayText(showText.isSelected()); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void showColourText_actionPerformed(ActionEvent e) - { - getGroup().setColourText(showColourText.isSelected()); - refresh(); - } - - public void showLink(String url) - { - try - { - jalview.util.BrowserLauncher.openURL(url); - } - catch (Exception ex) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Unixers: Couldn't find default web browser." - +"\nAdd the full path to your browser in Preferences.", - "Web browser not found", JOptionPane.WARNING_MESSAGE ); - - - ex.printStackTrace(); - } - } - - void hideSequences(boolean representGroup) - { - SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null || sg.getSize(false)<1) - { - ap.av.hideSequence(sequence); - return; - } - - int index = 0; - while(index < sg.getSize(false)) - { - if(representGroup && sg.getSequenceAt(index)!=sequence) - { - sequence.addHiddenSequence(sg.getSequenceAt(index)); - ap.av.hideSequence(sg.getSequenceAt(index)); - } - else if(!representGroup) - { - ap.av.hideSequence(sg.getSequenceAt(index)); - } - index ++; - } - - ap.av.setSelectionGroup(null); - refresh(); - } - - public void copy_actionPerformed(ActionEvent e) - { - ap.alignFrame.copy_actionPerformed(null); - } - - public void cut_actionPerformed(ActionEvent e) - { - ap.alignFrame.cut_actionPerformed(null); - } - - public void upperCase_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null) - return; - - for(int g=0; g. + */ +package jalview.gui; + +import java.util.*; + +import java.awt.*; +import java.awt.event.*; + +import javax.swing.*; + +import MCview.*; +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; +import jalview.util.GroupUrlLink; +import jalview.util.GroupUrlLink.UrlStringTooLongException; +import jalview.util.UrlLink; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision: 1.118 $ + */ +public class PopupMenu extends JPopupMenu +{ + JMenu groupMenu = new JMenu(); + + JMenuItem groupName = new JMenuItem(); + + protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); + + protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); + + protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + + // protected JRadioButtonMenuItem covariationColour = new + // JRadioButtonMenuItem(); + + JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + + protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + + AlignmentPanel ap; + + JMenu sequenceMenu = new JMenu(); + + JMenuItem sequenceName = new JMenuItem(); + + SequenceI sequence; + + JMenuItem unGroupMenuItem = new JMenuItem(); + + JMenuItem outline = new JMenuItem(); + + JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); + + JMenu colourMenu = new JMenu(); + + JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); + + JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); + + JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); + + JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem(); + + JMenu editMenu = new JMenu(); + + JMenuItem cut = new JMenuItem(); + + JMenuItem copy = new JMenuItem(); + + JMenuItem upperCase = new JMenuItem(); + + JMenuItem lowerCase = new JMenuItem(); + + JMenuItem toggle = new JMenuItem(); + + JMenu pdbMenu = new JMenu(); + + JMenuItem pdbFromFile = new JMenuItem(); + + JMenuItem enterPDB = new JMenuItem(); + + JMenuItem discoverPDB = new JMenuItem(); + + JMenu outputMenu = new JMenu(); + + JMenuItem sequenceFeature = new JMenuItem(); + + JMenuItem textColour = new JMenuItem(); + + JMenu jMenu1 = new JMenu(); + + JMenu structureMenu = new JMenu(); + + JMenu viewStructureMenu = new JMenu(); + + // JMenu colStructureMenu = new JMenu(); + JMenuItem editSequence = new JMenuItem(); + + // JMenuItem annotationMenuItem = new JMenuItem(); + + JMenu groupLinksMenu; + + /** + * Creates a new PopupMenu object. + * + * @param ap + * DOCUMENT ME! + * @param seq + * DOCUMENT ME! + */ + public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) + { + this(ap, seq, links, null); + } + + /** + * + * @param ap + * @param seq + * @param links + * @param groupLinks + */ + public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links, + Vector groupLinks) + { + // ///////////////////////////////////////////////////////// + // If this is activated from the sequence panel, the user may want to + // edit or annotate a particular residue. Therefore display the residue menu + // + // If from the IDPanel, we must display the sequence menu + // //////////////////////////////////////////////////////// + this.ap = ap; + sequence = seq; + + ButtonGroup colours = new ButtonGroup(); + colours.add(noColourmenuItem); + colours.add(clustalColour); + colours.add(zappoColour); + colours.add(taylorColour); + colours.add(hydrophobicityColour); + colours.add(helixColour); + colours.add(strandColour); + colours.add(turnColour); + colours.add(buriedColour); + colours.add(abovePIDColour); + colours.add(userDefinedColour); + colours.add(PIDColour); + colours.add(BLOSUM62Colour); + colours.add(purinePyrimidineColour); + // colours.add(covariationColour); + + for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) + { + JMenuItem item = new JMenuItem( + jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputMenu.add(item); + } + + try + { + jbInit(); + } catch (Exception e) + { + e.printStackTrace(); + } + + JMenuItem menuItem; + if (seq != null) + { + sequenceMenu.setText(sequence.getName()); + + if (seq.getDatasetSequence().getPDBId() != null + && seq.getDatasetSequence().getPDBId().size() > 0) + { + java.util.Enumeration e = seq.getDatasetSequence().getPDBId() + .elements(); + + while (e.hasMoreElements()) + { + final PDBEntry pdb = (PDBEntry) e.nextElement(); + + menuItem = new JMenuItem(); + menuItem.setText(pdb.getId()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence + new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); + // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); + } + + }); + viewStructureMenu.add(menuItem); + + /* + * menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); + * menuItem.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * colourByStructure(pdb.getId()); } }); + * colStructureMenu.add(menuItem); + */ + } + } + else + { + if (ap.av.alignment.isNucleotide() == false) + { + structureMenu.remove(viewStructureMenu); + } + // structureMenu.remove(colStructureMenu); + } + + if (ap.av.alignment.isNucleotide() == true) + { + AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + for (int i = 0; i < aa.length; i++) + { + if (aa[i].getRNAStruc() != null) + { + final String rnastruc = aa[i].getRNAStruc(); + + menuItem = new JMenuItem(); + menuItem.setText("RNA structure - consensus"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq.getSequenceAsString(), rnastruc, seq + .getName(), ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + + // SequenceFeatures[] test = seq.getSequenceFeatures(); + + if (seq.getAnnotation() != null) + { + AlignmentAnnotation seqAnno[] = seq.getAnnotation(); + for (int i = 0; i < seqAnno.length; i++) + { + if (seqAnno[i].getRNAStruc() != null) + { + final String rnastruc = seqAnno[i].getRNAStruc(); + + // TODO: make rnastrucF a bit more nice + menuItem = new JMenuItem(); + menuItem.setText("RNA structure - "+seq.getName()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + // TODO: VARNA does'nt print gaps in the sequence + new AppVarna(seq.getSequenceAsString(), rnastruc, seq + .getName(), ap); + } + }); + viewStructureMenu.add(menuItem); + } + } + } + + + } + + menuItem = new JMenuItem("Hide Sequences"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(false); + } + }); + add(menuItem); + + if (ap.av.getSelectionGroup() != null + && ap.av.getSelectionGroup().getSize() > 1) + { + menuItem = new JMenuItem("Represent Group with " + seq.getName()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(true); + } + }); + sequenceMenu.add(menuItem); + } + + if (ap.av.hasHiddenRows) + { + final int index = ap.av.alignment.findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) + - ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + menuItem = new JMenuItem("Reveal Sequences"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showSequence(index); + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + } + }); + add(menuItem); + } + } + } + // for the case when no sequences are even visible + if (ap.av.hasHiddenRows) { + { + menuItem = new JMenuItem("Reveal All"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showAllHiddenSeqs(); + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + } + }); + + add(menuItem); + } + + } + + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null&& sg.getSize()>0) + { + groupName.setText("Name: "+sg.getName()); + groupName.setText("Edit name and description of current group."); + + if (sg.cs instanceof ZappoColourScheme) + { + zappoColour.setSelected(true); + } + else if (sg.cs instanceof TaylorColourScheme) + { + taylorColour.setSelected(true); + } + else if (sg.cs instanceof PIDColourScheme) + { + PIDColour.setSelected(true); + } + else if (sg.cs instanceof Blosum62ColourScheme) + { + BLOSUM62Colour.setSelected(true); + } + else if (sg.cs instanceof UserColourScheme) + { + userDefinedColour.setSelected(true); + } + else if (sg.cs instanceof HydrophobicColourScheme) + { + hydrophobicityColour.setSelected(true); + } + else if (sg.cs instanceof HelixColourScheme) + { + helixColour.setSelected(true); + } + else if (sg.cs instanceof StrandColourScheme) + { + strandColour.setSelected(true); + } + else if (sg.cs instanceof TurnColourScheme) + { + turnColour.setSelected(true); + } + else if (sg.cs instanceof BuriedColourScheme) + { + buriedColour.setSelected(true); + } + else if (sg.cs instanceof ClustalxColourScheme) + { + clustalColour.setSelected(true); + } + else if (sg.cs instanceof PurinePyrimidineColourScheme) + { + purinePyrimidineColour.setSelected(true); + } + /* + * else if (sg.cs instanceof CovariationColourScheme) { + * covariationColour.setSelected(true); } + */ + else + { + noColourmenuItem.setSelected(true); + } + + if (sg.cs != null && sg.cs.conservationApplied()) + { + conservationMenuItem.setSelected(true); + } + displayNonconserved.setSelected(sg.getShowNonconserved()); + showText.setSelected(sg.getDisplayText()); + showColourText.setSelected(sg.getColourText()); + showBoxes.setSelected(sg.getDisplayBoxes()); + // add any groupURLs to the groupURL submenu and make it visible + if (groupLinks != null && groupLinks.size() > 0) + { + buildGroupURLMenu(sg, groupLinks); + } + // Add a 'show all structures' for the current selection + Hashtable pdbe=new Hashtable(); + SequenceI sqass=null; + for (SequenceI sq: ap.av.getSequenceSelection()) + { + Vector pes = (Vector) sq.getDatasetSequence().getPDBId(); + if (pes!=null) { + for (PDBEntry pe: pes) + { + pdbe.put(pe.getId(), pe); + if (sqass==null) + { + sqass = sq; + } + } + } + } + if (pdbe.size()>0) + { + final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]); + final JMenuItem gpdbview; + if (pdbe.size()==1) + { + structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false))); + } else { + structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures.")); + } + gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment."); + gpdbview.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + } + }); + } + } + else + { + groupMenu.setVisible(false); + editMenu.setVisible(false); + } + + if (!ap.av.alignment.getGroups().contains(sg)) + { + unGroupMenuItem.setVisible(false); + } + + if (seq == null) + { + sequenceMenu.setVisible(false); + structureMenu.setVisible(false); + } + + if (links != null && links.size() > 0) + { + + JMenu linkMenu = new JMenu("Link"); + Vector linkset = new Vector(); + for (int i = 0; i < links.size(); i++) + { + String link = links.elementAt(i).toString(); + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) + { + jalview.bin.Cache.log.error("Exception for URLLink '" + link + + "'", foo); + continue; + } + ; + if (!urlLink.isValid()) + { + jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + continue; + } + final String label = urlLink.getLabel(); + if (seq!=null && urlLink.isDynamic()) + { + + // collect matching db-refs + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( + seq.getDBRef(), new String[] + { urlLink.getTarget() }); + // collect id string too + String id = seq.getName(); + String descr = seq.getDescription(); + if (descr != null && descr.length() < 1) + { + descr = null; + } + + if (dbr != null) + { + for (int r = 0; r < dbr.length; r++) + { + if (id != null && dbr[r].getAccessionId().equals(id)) + { + // suppress duplicate link creation for the bare sequence ID + // string with this link + id = null; + } + // create Bare ID link for this RUL + String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), + true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) + { + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label + "|" + urls[u], + urls[u + 1]); + } + } + } + } + } + if (id != null) + { + // create Bare ID link for this RUL + String[] urls = urlLink.makeUrls(id, true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) + { + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label, urls[u + 1]); + } + } + } + } + // Create urls from description but only for URL links which are regex + // links + if (descr != null && urlLink.getRegexReplace() != null) + { + // create link for this URL from description where regex matches + String[] urls = urlLink.makeUrls(descr, true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + if (!linkset.contains(urls[u] + "|" + urls[u + 1])) + { + linkset.addElement(urls[u] + "|" + urls[u + 1]); + addshowLink(linkMenu, label, urls[u + 1]); + } + } + } + } + } + else + { + if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) + { + linkset.addElement(label + "|" + urlLink.getUrl_prefix()); + // Add a non-dynamic link + addshowLink(linkMenu, label, urlLink.getUrl_prefix()); + } + } + } + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } + } + } + + private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) + { + + // TODO: usability: thread off the generation of group url content so root + // menu appears asap + // sequence only URLs + // ID/regex match URLs + groupLinksMenu = new JMenu("Group Link"); + JMenu[] linkMenus = new JMenu[] + { null, new JMenu("IDS"), new JMenu("Sequences"), + new JMenu("IDS and Sequences") }; // three types of url that might be + // created. + SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); + String[][] idandseqs = GroupUrlLink.formStrings(seqs); + Hashtable commonDbrefs = new Hashtable(); + for (int sq = 0; sq < seqs.length; sq++) + { + + int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq] + .findPosition(sg.getEndRes()); + // just collect ids from dataset sequence + // TODO: check if IDs collected from selecton group intersects with the + // current selection, too + SequenceI sqi = seqs[sq]; + while (sqi.getDatasetSequence() != null) + { + sqi = sqi.getDatasetSequence(); + } + DBRefEntry[] dbr = sqi.getDBRef(); + if (dbr != null && dbr.length > 0) + { + for (int d = 0; d < dbr.length; d++) + { + String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); + Object[] sarray = (Object[]) commonDbrefs.get(src); + if (sarray == null) + { + sarray = new Object[2]; + sarray[0] = new int[] + { 0 }; + sarray[1] = new String[seqs.length]; + + commonDbrefs.put(src, sarray); + } + + if (((String[]) sarray[1])[sq] == null) + { + if (!dbr[d].hasMap() + || (dbr[d].getMap().locateMappedRange(start, end) != null)) + { + ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); + ((int[]) sarray[0])[0]++; + } + } + } + } + } + // now create group links for all distinct ID/sequence sets. + boolean addMenu = false; // indicates if there are any group links to give + // to user + for (int i = 0; i < groupLinks.size(); i++) + { + String link = groupLinks.elementAt(i).toString(); + GroupUrlLink urlLink = null; + try + { + urlLink = new GroupUrlLink(link); + } catch (Exception foo) + { + jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link + + "'", foo); + continue; + } + ; + if (!urlLink.isValid()) + { + jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + continue; + } + final String label = urlLink.getLabel(); + boolean usingNames = false; + // Now see which parts of the group apply for this URL + String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget()); + Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase()); + String[] seqstr, ids; // input to makeUrl + if (idset != null) + { + int numinput = ((int[]) idset[0])[0]; + String[] allids = ((String[]) idset[1]); + seqstr = new String[numinput]; + ids = new String[numinput]; + for (int sq = 0, idcount = 0; sq < seqs.length; sq++) + { + if (allids[sq] != null) + { + ids[idcount] = allids[sq]; + seqstr[idcount++] = idandseqs[1][sq]; + } + } + } + else + { + // just use the id/seq set + seqstr = idandseqs[1]; + ids = idandseqs[0]; + usingNames = true; + } + // and try and make the groupURL! + + Object[] urlset = null; + try + { + urlset = urlLink.makeUrlStubs(ids, seqstr, + "FromJalview" + System.currentTimeMillis(), false); + } catch (UrlStringTooLongException e) + { + } + if (urlset != null) + { + int type = urlLink.getGroupURLType() & 3; + // System.out.println(urlLink.getGroupURLType() + // +" "+((String[])urlset[3])[0]); + // first two bits ofurlLink type bitfield are sequenceids and sequences + // TODO: FUTURE: ensure the groupURL menu structure can be generalised + addshowLink(linkMenus[type], label + + (((type & 1) == 1) ? ("(" + + (usingNames ? "Names" : ltarget) + ")") : ""), + urlLink, urlset); + addMenu = true; + } + } + if (addMenu) + { + groupLinksMenu = new JMenu("Group Links"); + for (int m = 0; m < linkMenus.length; m++) + { + if (linkMenus[m] != null + && linkMenus[m].getMenuComponentCount() > 0) + { + groupLinksMenu.add(linkMenus[m]); + } + } + + groupMenu.add(groupLinksMenu); + } + } + + /** + * add a show URL menu item to the given linkMenu + * + * @param linkMenu + * @param label + * - menu label string + * @param url + * - url to open + */ + private void addshowLink(JMenu linkMenu, String label, final String url) + { + JMenuItem item = new JMenuItem(label); + item.setToolTipText("open URL: " + url); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + showLink(url); + } + + }).start(); + } + }); + + linkMenu.add(item); + } + + /** + * add a late bound groupURL item to the given linkMenu + * + * @param linkMenu + * @param label + * - menu label string + * @param urlgenerator + * GroupURLLink used to generate URL + * @param urlstub + * Object array returned from the makeUrlStubs function. + */ + private void addshowLink(JMenu linkMenu, String label, + final GroupUrlLink urlgenerator, final Object[] urlstub) + { + JMenuItem item = new JMenuItem(label); + item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix() + + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO: + // put + // in + // info + // about + // what + // is + // being + // sent. + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + try + { + showLink(urlgenerator.constructFrom(urlstub)); + } catch (UrlStringTooLongException e) + { + } + } + + }).start(); + } + }); + + linkMenu.add(item); + } + + /** + * DOCUMENT ME! + * + * @throws Exception + * DOCUMENT ME! + */ + private void jbInit() throws Exception + { + groupMenu.setText("Group"); + groupMenu.setText("Selection"); + groupName.setText("Name"); + groupName.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + groupName_actionPerformed(); + } + }); + sequenceMenu.setText("Sequence"); + sequenceName.setText("Edit Name/Description"); + sequenceName.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceName_actionPerformed(); + } + }); + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + unGroupMenuItem_actionPerformed(); + } + }); + + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(); + } + }); + nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideMenuItem_actionPerformed(); + } + }); + colourMenu.setText("Group Colour"); + showBoxes.setText("Boxes"); + showBoxes.setState(true); + showBoxes.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showBoxes_actionPerformed(); + } + }); + showText.setText("Text"); + showText.setState(true); + showText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showText_actionPerformed(); + } + }); + showColourText.setText("Colour Text"); + showColourText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showColourText_actionPerformed(); + } + }); + displayNonconserved.setText("Show Nonconserved"); + displayNonconserved.setState(true); + displayNonconserved.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showNonconserved_actionPerformed(); + } + }); + editMenu.setText("Edit"); + cut.setText("Cut"); + cut.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(); + } + }); + upperCase.setText("To Upper Case"); + upperCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + copy.setText("Copy"); + copy.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(); + } + }); + lowerCase.setText("To Lower Case"); + lowerCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + toggle.setText("Toggle Case"); + toggle.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + pdbMenu.setText("Associate Structure with Sequence"); + pdbFromFile.setText("From File"); + pdbFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(); + } + }); + enterPDB.setText("Enter PDB Id"); + enterPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(); + } + }); + discoverPDB.setText("Discover PDB ids"); + discoverPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(); + } + }); + outputMenu.setText("Output to Textbox..."); + sequenceFeature.setText("Create Sequence Feature"); + sequenceFeature.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(); + } + }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + jMenu1.setText("Group"); + structureMenu.setText("Structure"); + viewStructureMenu.setText("View Structure"); + // colStructureMenu.setText("Colour By Structure"); + editSequence.setText("Edit Sequence..."); + editSequence.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + editSequence_actionPerformed(actionEvent); + } + }); + /* + * annotationMenuItem.setText("By Annotation"); + * annotationMenuItem.addActionListener(new ActionListener() { public void + * actionPerformed(ActionEvent actionEvent) { + * annotationMenuItem_actionPerformed(actionEvent); } }); + */ + + add(groupMenu); + + add(sequenceMenu); + this.add(structureMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.add(sequenceFeature); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); + colourMenu.add(textColour); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideMenuItem); + if (ap.getAlignment().isNucleotide()) { + colourMenu.add(purinePyrimidineColour); + } + // colourMenu.add(covariationColour); + colourMenu.add(userDefinedColour); + + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours + .getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + JMenuItem item = new JMenuItem(userColours.nextElement().toString()); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + // colourMenu.add(annotationMenuItem); + editMenu.add(copy); + editMenu.add(cut); + editMenu.add(editSequence); + editMenu.add(upperCase); + editMenu.add(lowerCase); + editMenu.add(toggle); + pdbMenu.add(pdbFromFile); + pdbMenu.add(enterPDB); + pdbMenu.add(discoverPDB); + jMenu1.add(groupName); + jMenu1.add(unGroupMenuItem); + jMenu1.add(colourMenu); + jMenu1.add(showBoxes); + jMenu1.add(showText); + jMenu1.add(showColourText); + jMenu1.add(outline); + jMenu1.add(displayNonconserved); + structureMenu.add(pdbMenu); + structureMenu.add(viewStructureMenu); + // structureMenu.add(colStructureMenu); + noColourmenuItem.setText("None"); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + noColourmenuItem_actionPerformed(); + } + }); + + clustalColour.setText("Clustalx colours"); + clustalColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + clustalColour_actionPerformed(); + } + }); + zappoColour.setText("Zappo"); + zappoColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + zappoColour_actionPerformed(); + } + }); + taylorColour.setText("Taylor"); + taylorColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + taylorColour_actionPerformed(); + } + }); + hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); + helixColour.setText("Helix propensity"); + helixColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + helixColour_actionPerformed(); + } + }); + strandColour.setText("Strand propensity"); + strandColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + strandColour_actionPerformed(); + } + }); + turnColour.setText("Turn propensity"); + turnColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + turnColour_actionPerformed(); + } + }); + buriedColour.setText("Buried Index"); + buriedColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + buriedColour_actionPerformed(); + } + }); + abovePIDColour.setText("Above % Identity"); + abovePIDColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + abovePIDColour_actionPerformed(); + } + }); + userDefinedColour.setText("User Defined..."); + userDefinedColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + userDefinedColour_actionPerformed(e); + } + }); + PIDColour.setText("Percentage Identity"); + PIDColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + PIDColour_actionPerformed(); + } + }); + BLOSUM62Colour.setText("BLOSUM62"); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + BLOSUM62Colour_actionPerformed(); + } + }); + purinePyrimidineColour.setText("Purine/Pyrimidine"); + purinePyrimidineColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + /* + * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * covariationColour_actionPerformed(); } }); + */ + + conservationMenuItem.setText("Conservation"); + conservationMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); + } + }); + } + + protected void showNonconserved_actionPerformed() + { + getGroup().setShowNonconserved(displayNonconserved.isSelected()); + refresh(); + } + + /** + * call to refresh view after settings change + */ + void refresh() + { + ap.updateAnnotation(); + ap.paintAlignment(true); + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void clustalColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme( + sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void zappoColour_actionPerformed() + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void taylorColour_actionPerformed() + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed() + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void helixColour_actionPerformed() + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void strandColour_actionPerformed() + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void turnColour_actionPerformed() + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void buriedColour_actionPerformed() + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed() + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } + + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); + + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + .getName()); + + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + + SliderPanel.showPIDSlider(); + } + else + // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + + if (e.getActionCommand().equals("User Defined...")) + { + new UserDefinedColours(ap, sg); + } + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; + } + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void PIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (conservationMenuItem.isSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1); + + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); + + sg.cs.setConservation(c); + + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else + // remove ConservationColouring + { + sg.cs.setConservation(null); + } + + refresh(); + } + + public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = getGroup(); + if (sg == null) + { + return; + } + + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, + AnnotationColourGradient.NO_THRESHOLD); + + acg.predefinedColours = true; + sg.cs = acg; + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void groupName_actionPerformed() + { + + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), " Group Name ", + "Group Description ", "Edit Group Name/Description", + ap.alignFrame); + + if (!dialog.accept) + { + return; + } + + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + + /** + * Get selection group - adding it to the alignment if necessary. + * + * @return sequence group to operate on + */ + SequenceGroup getGroup() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + // this method won't add a new group if it already exists + if (sg != null) + { + ap.av.alignment.addGroup(sg); + } + + return sg; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + void sequenceName_actionPerformed() + { + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), " Sequence Name ", + "Sequence Description ", "Edit Sequence Name/Description", + ap.alignFrame); + + if (!dialog.accept) + { + return; + } + + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false); + } + + sequence.setDescription(dialog.getDescription()); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void outline_actionPerformed() + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", + Color.BLUE); + + if (col != null) + { + sg.setOutlineColour(col); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showBoxes_actionPerformed() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } + + public void showLink(String url) + { + try + { + jalview.util.BrowserLauncher.openURL(url); + } catch (Exception ex) + { + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + "Unixers: Couldn't find default web browser." + + "\nAdd the full path to your browser in Preferences.", + "Web browser not found", JOptionPane.WARNING_MESSAGE); + + ex.printStackTrace(); + } + } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) + { + ap.av.hideSequence(new SequenceI[] + { sequence }); + return; + } + + ap.av.setSelectionGroup(null); + + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); + + return; + } + + int gsize = sg.getSize(); + SequenceI[] hseqs; + + hseqs = new SequenceI[gsize]; + + int index = 0; + for (int i = 0; i < gsize; i++) + { + hseqs[index++] = sg.getSequenceAt(i); + } + + ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? + ap.av.sendSelection(); + } + + public void copy_actionPerformed() + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed() + { + ap.alignFrame.cut_actionPerformed(null); + } + + void changeCase(ActionEvent e) + { + Object source = e.getSource(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + sg.getEndRes() + 1); + + String description; + int caseChange; + + if (source == toggle) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if (source == upperCase) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, + caseChange); + + ap.alignFrame.addHistoryItem(caseCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + } + + public void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, 500); + + String[] omitHidden = null; + + System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens + // or we simply trust the user wants + // wysiwig behaviour + SequenceGroup sg = ap.av.getSelectionGroup(); + ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); + omitHidden = ap.av.getViewAsString(true); + Alignment oal = new Alignment(ap.av.getSequenceSelection()); + AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation(); + if (nala != null) + { + for (int i = 0; i < nala.length; i++) + { + AlignmentAnnotation na = nala[i]; + oal.addAnnotation(na); + } + } + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + oal, omitHidden, csel, sg)); + oal = null; + } + + public void pdbFromFile_actionPerformed() + { + jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false)); + chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'"); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true); + } + + } + + public void enterPDB_actionPerformed() + { + String id = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE); + + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id.toUpperCase()); + sequence.getDatasetSequence().addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed() + { + + final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new SequenceI[] + { sequence } + : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + Thread discpdb = new Thread(new Runnable() + { + public void run() + { + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) + .fetchDBRefs(false); + } + + }); + discpdb.start(); + } + + public void sequenceFeature_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) + { + return; + } + + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) + { + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + if (start <= end) + { + seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); + features[rsize] = new SequenceFeature(null, null, null, start, end, + "Jalview"); + rsize++; + } + } + rseqs = new SequenceI[rsize]; + tfeatures = new SequenceFeature[rsize]; + System.arraycopy(seqs, 0, rseqs, 0, rsize); + System.arraycopy(features, 0, tfeatures, 0, rsize); + features = tfeatures; + seqs = rseqs; + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.setShowSeqFeatures(true); + ap.highlightSearchResults(null); + } + } + + public void textColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg != null) + { + new TextColourChooser().chooseColour(ap, sg); + } + } + + public void colourByStructure(String pdbid) + { + Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure( + sequence, pdbid); + + AlignmentAnnotation an = new AlignmentAnnotation("Structure", + "Coloured by " + pdbid, anots); + + ap.av.alignment.addAnnotation(an); + an.createSequenceMapping(sequence, 0, true); + // an.adjustForAlignment(); + ap.av.alignment.setAnnotationIndex(an, 0); + + ap.adjustAnnotationHeight(); + + sequence.addAlignmentAnnotation(an); + + } + + public void editSequence_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + if (sequence == null) + sequence = (Sequence) sg.getSequenceAt(0); + + EditNameDialog dialog = new EditNameDialog( + sequence.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), null, "Edit Sequence ", null, + "Edit Sequence", ap.alignFrame); + + if (dialog.accept) + { + EditCommand editCommand = new EditCommand("Edit Sequences", + EditCommand.REPLACE, dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.hiddenRepSequences), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + + ap.alignFrame.addHistoryItem(editCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + } + } + } + +}