X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f1a38f5475b4193e0f2077803b049d566f193a89;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=55aea5ec725bbf6648ddfee32942202796b4d485;hpb=f744d455e1b6bae50524152edf2fe8c78a8dffab;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 55aea5e..f1a38f5 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -18,20 +18,18 @@ */ package jalview.gui; -import MCview.*; - -import jalview.analysis.*; - -import jalview.datamodel.*; - - -import jalview.schemes.*; +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.*; /** * DOCUMENT ME! @@ -39,1037 +37,1342 @@ import javax.swing.*; * @author $author$ * @version $Revision$ */ -public class PopupMenu extends JPopupMenu +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 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(); + 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(); /** - * Creates a new PopupMenu object. - * - * @param ap DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - public PopupMenu(final AlignmentPanel ap, Sequence seq) - { - /////////////////////////////////////////////////////////// - // 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) + * 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); + + 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) { - e.printStackTrace(); + outputText_actionPerformed(e); } + }); + + outputMenu.add(item); + } + + try + { + jbInit(); + } + catch (Exception e) + { + e.printStackTrace(); + } + + if (seq != null) + { + sequenceMenu.setText(sequence.getName()); + JMenuItem menuItem; + if (seq.getDatasetSequence().getPDBId() != null) + { + java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). + elements(); - if (seq != null) + while (e.hasMoreElements()) { - JMenuItem menuItem; - if( seq.getDatasetSequence().getPDBId() != null) + final PDBEntry pdb = (PDBEntry) e.nextElement(); + + menuItem = new JMenuItem(); + menuItem.setText("View PDB entry: " + pdb.getId()); + menuItem.addActionListener(new java.awt.event.ActionListener() { - java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). - elements(); - while (e.hasMoreElements()) + public void actionPerformed(ActionEvent e) { - 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); + 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); + } + }); + 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); + } - /* 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.hasHiddenRows) + { + final int index = ap.av.alignment.findIndex(seq); - if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1) + if (ap.av.adjustForHiddenSeqs(index) - + ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + menuItem = new JMenuItem("Reveal Sequences"); + menuItem.addActionListener(new ActionListener() { - menuItem = new JMenuItem("Represent Group with " + seq.getName()); - menuItem.addActionListener(new java.awt.event.ActionListener() + public void actionPerformed(ActionEvent e) { - public void actionPerformed(ActionEvent e) + ap.av.showSequence(index); + if (ap.overviewPanel != null) { - hideSequences(true); + ap.overviewPanel.updateOverviewImage(); } - }); - sequenceMenu.add(menuItem); - }*/ + } + }); + add(menuItem); + } + 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(); - SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) + { + groupName.setText(sg.getName()); - 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 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); + } - 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); + } - 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); + } + + if (seq == null) + { + sequenceMenu.setVisible(false); + pdbMenu.setVisible(false); + } + + if (links != null && links.size() > 0) + { + JMenu linkMenu = new JMenu("Link"); + JMenuItem item; + for (int i = 0; i < links.size(); i++) + { + String link = links.elementAt(i).toString(); + final String label = link.substring(0, link.indexOf("|")); + item = new JMenuItem(label); + final String url; - if (!ap.av.alignment.getGroups().contains(sg)) + if (link.indexOf("$SEQUENCE_ID$") > -1) { - unGroupMenuItem.setVisible(false); + 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 { - groupMenu.insertSeparator(3); + url = link.substring(link.lastIndexOf("|") + 1); } - if (seq == null) - { - sequenceMenu.setVisible(false); - } - else + item.addActionListener(new java.awt.event.ActionListener() { - java.util.Vector links = Preferences.sequenceURLLinks; + public void actionPerformed(ActionEvent e) + { + showLink(url); + } + }); - JMenu linkMenu = new JMenu("Link"); - JMenuItem item; - for(int i=0; i-1) - id = id.substring(id.lastIndexOf("|")+1); + /** + * 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(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } - final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$")) - + id + - link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + 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()); - item.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - showLink(url); - } - }); + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - linkMenu.add(item); - } - add(linkMenu); - } + SliderPanel.showPIDSlider(); + } + else // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } + refresh(); + } - /** - * 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() + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + + if (e.getActionCommand().equals("User Defined...")) { - public void actionPerformed(ActionEvent e) - { - copy_actionPerformed(e); - } - }); - lowerCase.setText("To Lower Case"); - lowerCase.addActionListener(new ActionListener() + new UserDefinedColours(ap, sg); + } + else { - public void actionPerformed(ActionEvent e) - { - lowerCase_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(); + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); - 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); - } - } + 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(); + } - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); - editMenu.add(copy); - editMenu.add(cut); - editMenu.add(upperCase); - editMenu.add(lowerCase); - 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! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); - /** - * DOCUMENT ME! - */ - void refresh() - { - if (ap.overviewPanel != null) - ap.overviewPanel.updateOverviewImage(); + sg.cs = new Blosum62ColourScheme(); - ap.seqPanel.repaint(); - } + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void clustalColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, - ap.av.alignment.getWidth()); - refresh(); - } + 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 noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void taylorColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) { - getGroup().cs = new TaylorColourScheme(); - refresh(); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + if (conservationMenuItem.isSelected()) { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } + 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); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void helixColour_actionPerformed(ActionEvent e) + sg.cs.setConservation(c); + + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring { - getGroup().cs = new HelixColourScheme(); - refresh(); + sg.cs.setConservation(null); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void strandColour_actionPerformed(ActionEvent e) + 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"); + + if (!dialog.accept) { - getGroup().cs = new StrandColourScheme(); - refresh(); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void turnColour_actionPerformed(ActionEvent e) + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + } + + /** + * 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) { - getGroup().cs = new TurnColourScheme(); - refresh(); + ap.av.alignment.addGroup(sg); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void buriedColour_actionPerformed(ActionEvent e) + 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"); + + if (!dialog.accept) { - getGroup().cs = new BuriedColourScheme(); - refresh(); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void nucleotideMenuItem_actionPerformed(ActionEvent e) + if (dialog.getName() != null) { - getGroup().cs = new NucleotideColourScheme(); - refresh(); + 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.repaint(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void abovePIDColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - if(sg.cs==null) - return; + sequence.setDescription(dialog.getDescription()); - if (abovePIDColour.isSelected()) - { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, - getGroup().getName()); + } - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); + } - SliderPanel.showPIDSlider(); - } - else // remove PIDColouring - { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void outline_actionPerformed() + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", + Color.BLUE); - refresh(); + if (col != null) + { + sg.setOutlineColour(col); } - /** - * 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.sequences, 0, - ap.av.alignment.getWidth())); - refresh(); - } + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } - sg.cs = new Blosum62ColourScheme(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } - refresh(); + public void showLink(String url) + { + try + { + jalview.util.BrowserLauncher.openURL(url); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed(ActionEvent e) + catch (Exception ex) { - getGroup().cs = null; - refresh(); + 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(); } + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void conservationMenuItem_actionPerformed(ActionEvent e) + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) { - SequenceGroup sg = getGroup(); - if(sg.cs==null) - return; - - if (conservationMenuItem.isSelected()) - { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, 0, - ap.av.alignment.getWidth()); - - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + ap.av.hideSequence(new SequenceI[] + {sequence}); + return; + } - sg.cs.setConservation(c); + ap.av.setSelectionGroup(null); - SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); - SliderPanel.showConservationSlider(); - } - else // remove ConservationColouring - { - sg.cs.setConservation(null); - } + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); - refresh(); + return; } - /** - * 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; - } + int gsize = sg.getSize(); + SequenceI[] hseqs; - sg.setName(reply); - groupName.setText(reply); - } + hseqs = new SequenceI[gsize]; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void analyze_actionPerformed(ActionEvent e) + int index = 0; + for (int i = 0; i < gsize; i++) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); + hseqs[index++] = sg.getSequenceAt(i); + } - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); + ap.av.hideSequence(hseqs); + } - for (int i = 0; i < sg.sequences.size(); i++) - { - Sequence tmp = (Sequence) sg.sequences.get(i); - sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); - sb.append("\n"); - } + public void copy_actionPerformed() + { + ap.alignFrame.copy_actionPerformed(null); + } - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); - } + public void cut_actionPerformed() + { + ap.alignFrame.cut_actionPerformed(null); + } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - SequenceGroup getGroup() + void changeCase(ActionEvent e) + { + Object source = e.getSource(); + SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); + if (sg != null) { - 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; - } + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; - /** - * 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 ) + do + { + if (ap.av.hasHiddenColumns) { - return; + if (start == 0) + { + start = ap.av.colSel.adjustForHiddenColumns(start); + } + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = sg.getEndRes() + 1; + } + if (end > sg.getEndRes()) + { + end = sg.getEndRes() + 1; + } } - String s = id.getText(); + regions.addElement(new int[] + {start, end}); - if (s != null) + if (ap.av.hasHiddenColumns) { - 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(); + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; } + } + while (end < sg.getEndRes()); - sequence.getDatasetSequence().setDescription(description.getText()); - sequence.setDescription(description.getText()); - } + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } - /** - * 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(); - } + 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; + } - /** - * 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); + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), + startEnd, caseChange + ); - if (col != null) - { - sg.setOutlineColour(col); - } + ap.alignFrame.addHistoryItem(caseCommand); - refresh(); - } + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); - /** - * 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(); - } + 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; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void showColourText_actionPerformed(ActionEvent e) + if (ap.av.hasHiddenColumns) { - getGroup().setColourText(showColourText.isSelected()); - refresh(); + System.out.println("PROMPT USER HERE"); + omitHidden = ap.av.getViewAsString(true); } - 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 ); + cap.setText(new FormatAdapter().formatSequences( + e.getActionCommand(), + ap.av.getSelectionAsNewSequence(), + omitHidden)); + } + 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"); + chooser.setToolTipText("Load a PDB file"); - ex.printStackTrace(); - } - } + int value = chooser.showOpenDialog(null); - void hideSequences(boolean representGroup) + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) { - SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null || sg.getSize()<1) + PDBEntry entry = new PDBEntry(); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + try { - ap.av.hideSequence(sequence); - return; - } + MCview.PDBfile pdbfile = new MCview.PDBfile(choice, + jalview.io.AppletFormatAdapter.FILE); - int index = 0; - while(index < sg.sequences.size()) + if (pdbfile.id == null) { - if(representGroup && sg.getSequenceAt(index)!=sequence) + String reply = JOptionPane.showInternalInputDialog( + Desktop.desktop, + "Couldn't find a PDB id in the file supplied." + + "Please enter an Id to identify this structure.", + "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); + if (reply == null) { - sequence.addHiddenSequence(sg.getSequenceAt(index)); - ap.av.hideSequence(sg.getSequenceAt(index)); - } - else if(!representGroup) - { - ap.av.hideSequence(sg.getSequenceAt(index)); + return; } - index ++; + + entry.setId(reply); } + else + { + entry.setId(pdbfile.id); + } + } + catch (java.io.IOException ex) + { + ex.printStackTrace(); + } - ap.av.setSelectionGroup(null); - refresh(); + entry.setFile(choice); + sequence.getDatasetSequence().addPDBId(entry); } - public void copy_actionPerformed(ActionEvent e) + } + + public void enterPDB_actionPerformed() { - ap.alignFrame.copy_actionPerformed(null); + 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); + sequence.getDatasetSequence() + .addPDBId(entry); + } } - public void cut_actionPerformed(ActionEvent e) + public void discoverPDB_actionPerformed() { - ap.alignFrame.cut_actionPerformed(null); + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); } - public void upperCase_actionPerformed(ActionEvent e) + public void sequenceFeature_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null) + if (sg == null) + { return; + } - for(int g=0; g