X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f1a38f5475b4193e0f2077803b049d566f193a89;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=d5ddd1bbceb5f055ccc48157be84603ea09a4720;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d5ddd1b..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) 2006 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 @@ -18,21 +18,18 @@ */ package jalview.gui; -import MCview.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.commands.ChangeCaseCommand; +import java.util.*; import java.awt.*; import java.awt.event.*; - import javax.swing.*; -import java.util.Vector; -import jalview.io.FormatAdapter; - +import MCview.*; +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; /** * DOCUMENT ME! @@ -40,35 +37,37 @@ import jalview.io.FormatAdapter; * @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(); @@ -85,358 +84,364 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); /** - * 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++) + * 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) + { + 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(); + + while (e.hasMoreElements()) { - JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] ); + final PDBEntry pdb = (PDBEntry) e.nextElement(); - item.addActionListener(new java.awt.event.ActionListener() + menuItem = new JMenuItem(); + menuItem.setText("View PDB entry: " + pdb.getId()); + menuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - outputText_actionPerformed(e); + new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas); } }); - - outputMenu.add(item); + sequenceMenu.add(menuItem); } + } - - try - { - jbInit(); - } - catch (Exception e) + menuItem = new JMenuItem("Hide Sequences"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) { - e.printStackTrace(); + hideSequences(false); } + }); + add(menuItem); - - if (seq != null) + 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() { - sequenceMenu.setText(sequence.getName()); - - JMenuItem menuItem; - if( seq.getDatasetSequence().getPDBId() != null) + public void actionPerformed(ActionEvent e) { - 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); - } + hideSequences(true); } + }); + 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.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); + } - if (ap.av.hasHiddenRows) + menuItem = new JMenuItem("Reveal All"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) { - final int index = ap.av.alignment.findIndex(seq); - - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) + ap.av.showAllHiddenSeqs(); + if (ap.overviewPanel != null) { - 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); + ap.overviewPanel.updateOverviewImage(); } - - 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); } + }); + 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); + } - SequenceGroup sg = ap.av.getSelectionGroup(); + showText.setSelected(sg.getDisplayText()); + showColourText.setSelected(sg.getColourText()); + showBoxes.setSelected(sg.getDisplayBoxes()); + } + else + { + groupMenu.setVisible(false); + editMenu.setVisible(false); + } - if (sg != null) - { - groupName.setText(sg.getName()); + if (!ap.av.alignment.getGroups().contains(sg)) + { + unGroupMenuItem.setVisible(false); + } - 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 (seq == null) + { + sequenceMenu.setVisible(false); + pdbMenu.setVisible(false); + } - if (sg.cs!=null && sg.cs.conservationApplied()) - { - conservationMenuItem.setSelected(true); - } + 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; - showText.setSelected(sg.getDisplayText()); - showColourText.setSelected(sg.getColourText()); - showBoxes.setSelected(sg.getDisplayBoxes()); - } - else + if (link.indexOf("$SEQUENCE_ID$") > -1) { - groupMenu.setVisible(false); - editMenu.setVisible(false); - } + String id = seq.getName(); + if (id.indexOf("|") > -1) + { + id = id.substring(id.lastIndexOf("|") + 1); + } - if (!ap.av.alignment.getGroups().contains(sg)) - { - unGroupMenuItem.setVisible(false); + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); } - - - if (seq == null) + else { - sequenceMenu.setVisible(false); - pdbMenu.setVisible(false); + url = link.substring(link.lastIndexOf("|") + 1); } - if(links != null && links.size()>0) + item.addActionListener(new java.awt.event.ActionListener() { - 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); + showLink(url); } - if(sequence!=null) - sequenceMenu.add(linkMenu); - else - add(linkMenu); - } + }); + + linkMenu.add(item); + } + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } } + } + /** + * 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(); + } + }); - /** - * DOCUMENT ME! - * - * @throws Exception DOCUMENT ME! - */ - private void jbInit() throws Exception + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() { - 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(); - } - }); + 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(); + } + }); editMenu.setText("Edit"); cut.setText("Cut"); cut.addActionListener(new ActionListener() @@ -523,620 +528,633 @@ public class PopupMenu extends JPopupMenu jMenu1.setText("Group"); add(groupMenu); - add(sequenceMenu); - groupMenu.add(editMenu); - groupMenu.add(outputMenu); - groupMenu.add(sequenceFeature); - groupMenu.add(jMenu1); - sequenceMenu.add(sequenceName); - sequenceMenu.add(pdbMenu); - 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); - colourMenu.add(userDefinedColour); - - if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours. - getUserColourSchemes().keys(); + add(sequenceMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.add(sequenceFeature); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenu); + 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); + 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); + 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); + 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(); + } + }); + conservationMenuItem.setText("Conservation"); + conservationMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); + } + }); + } + + /** + * DOCUMENT ME! + */ + void refresh() + { + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + } - 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); - } - } + /** + * 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(); + } - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); - editMenu.add(copy); - editMenu.add(cut); - 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); - 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(); - } - }); - conservationMenuItem.setText("Conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void taylorColour_actionPerformed() + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } - /** - * DOCUMENT ME! - */ - void refresh() - { - if (ap.overviewPanel != null) - ap.overviewPanel.updateOverviewImage(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed() + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } - PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void helixColour_actionPerformed() + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } - /** - * 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 strandColour_actionPerformed() + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void zappoColour_actionPerformed() - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void turnColour_actionPerformed() + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void taylorColour_actionPerformed() - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void buriedColour_actionPerformed() + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed() - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed() + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void helixColour_actionPerformed() + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) { - getGroup().cs = new HelixColourScheme(); - refresh(); + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void strandColour_actionPerformed() + if (abovePIDColour.isSelected()) { - getGroup().cs = new StrandColourScheme(); - refresh(); - } + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void turnColour_actionPerformed() + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); + + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + + SliderPanel.showPIDSlider(); + } + else // remove PIDColouring { - getGroup().cs = new TurnColourScheme(); - refresh(); + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void buriedColour_actionPerformed() + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + + if (e.getActionCommand().equals("User Defined...")) { - getGroup().cs = new BuriedColourScheme(); - refresh(); + new UserDefinedColours(ap, sg); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void nucleotideMenuItem_actionPerformed() + else { - getGroup().cs = new NucleotideColourScheme(); - refresh(); + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; } + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void abovePIDColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - if(sg.cs==null) - return; + /** + * 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(); + } - if (abovePIDColour.isSelected()) - { - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), - sg.getEndRes() + 1)); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, - getGroup().getName()); + sg.cs = new Blosum62ColourScheme(); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1)); - SliderPanel.showPIDSlider(); - } - else // remove PIDColouring - { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); - } + refresh(); + } - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + 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 conservationMenuItem_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void BLOSUM62Colour_actionPerformed() + if (conservationMenuItem.isSelected()) { - SequenceGroup sg = getGroup(); + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(ap.av. + hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1); - sg.cs = new Blosum62ColourScheme(); + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences), - sg.getStartRes(), - sg.getEndRes() + 1)); + sg.cs.setConservation(c); - refresh(); + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed() + else // remove ConservationColouring { - getGroup().cs = null; - refresh(); + sg.cs.setConservation(null); } - /** - * 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); + refresh(); + } - SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); - SliderPanel.showConservationSlider(); - } - else // remove ConservationColouring - { - sg.cs.setConservation(null); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void groupName_actionPerformed() + { - refresh(); - } + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), + " Group Name ", + "Group Description ", + "Edit Group Name/Description"); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void groupName_actionPerformed() + if (!dialog.accept) { + return; + } - SequenceGroup sg = getGroup(); - EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), - " Group Name ", - "Group Description ", - "Edit Group Name/Description"); - - if (!dialog.accept) - { - return; - } + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + } - 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) + { + 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"); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - SequenceGroup getGroup() + if (!dialog.accept) { - 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; + return; } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - void sequenceName_actionPerformed() + if (dialog.getName() != null) { - EditNameDialog dialog = new EditNameDialog(sequence.getName(), - sequence.getDescription(), - " Sequence Name ", - "Sequence Description ", - "Edit Sequence Name/Description"); + if (dialog.getName().indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } - if (!dialog.accept) - { - return; - } + sequence.setName(dialog.getName().replace(' ', '_')); + ap.repaint(); + } - 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.setDescription(dialog.getDescription()); - sequence.setName(dialog.getName().replace(' ', '_')); - ap.repaint(); - } + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); - 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); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - void unGroupMenuItem_actionPerformed() - { - SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); - ap.av.setSelectionGroup(null); - refresh(); + if (col != null) + { + sg.setOutlineColour(col); } + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void outline_actionPerformed() - { - SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, "Select Outline Colour", - Color.BLUE); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } - if (col != null) - { - sg.setOutlineColour(col); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void showBoxes_actionPerformed() + public void showLink(String url) + { + try { - getGroup().setDisplayBoxes(showBoxes.isSelected()); - refresh(); + jalview.util.BrowserLauncher.openURL(url); } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void showText_actionPerformed() + catch (Exception ex) { - getGroup().setDisplayText(showText.isSelected()); - 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! - */ - public void showColourText_actionPerformed() + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) { - getGroup().setColourText(showColourText.isSelected()); - refresh(); + ap.av.hideSequence(new SequenceI[] + {sequence}); + return; } - 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(); - } - } + ap.av.setSelectionGroup(null); - void hideSequences(boolean representGroup) + if (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); + ap.av.hideRepSequences(sequence, sg); - return; - } - - int gsize = sg.getSize(); - SequenceI[] hseqs; + return; + } - hseqs = new SequenceI[gsize]; + int gsize = sg.getSize(); + SequenceI[] hseqs; - int index = 0; - for (int i = 0; i < gsize; i++) - { - hseqs[index++] = sg.getSequenceAt(i); - } + hseqs = new SequenceI[gsize]; - ap.av.hideSequence(hseqs); + int index = 0; + for (int i = 0; i < gsize; i++) + { + hseqs[index++] = sg.getSequenceAt(i); } + ap.av.hideSequence(hseqs); + } + public void copy_actionPerformed() { ap.alignFrame.copy_actionPerformed(null); @@ -1161,14 +1179,20 @@ public class PopupMenu extends JPopupMenu { if (ap.av.hasHiddenColumns) { - if(start==0) + 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; + } } regions.addElement(new int[] @@ -1188,16 +1212,15 @@ public class PopupMenu extends JPopupMenu startEnd[i] = (int[]) regions.elementAt(i); } - String description; int caseChange; - if(source==toggle) + if (source == toggle) { description = "Toggle Case"; caseChange = ChangeCaseCommand.TOGGLE_CASE; } - else if(source==upperCase) + else if (source == upperCase) { description = "To Upper Case"; caseChange = ChangeCaseCommand.TO_UPPER; @@ -1215,9 +1238,8 @@ public class PopupMenu extends JPopupMenu ap.alignFrame.addHistoryItem(caseCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.getAlignment().getSequences()); } } @@ -1230,9 +1252,9 @@ public class PopupMenu extends JPopupMenu "Alignment output - " + e.getActionCommand(), 600, 500); - String [] omitHidden = null; + String[] omitHidden = null; - if(ap.av.hasHiddenColumns) + if (ap.av.hasHiddenColumns) { System.out.println("PROMPT USER HERE"); omitHidden = ap.av.getViewAsString(true); @@ -1244,52 +1266,55 @@ public class PopupMenu extends JPopupMenu 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"); - - int value = chooser.showOpenDialog(null); - - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - PDBEntry entry = new PDBEntry(); - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - try - { - MCview.PDBfile pdbfile = new MCview.PDBfile(choice, - jalview.io.AppletFormatAdapter.FILE); - - if (pdbfile.id == null) - { - 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) - return; - - entry.setId(reply); - } - else - entry.setId(pdbfile.id); - } - catch (java.io.IOException ex) - { - ex.printStackTrace(); - } - - entry.setFile(choice); - sequence.getDatasetSequence().addPDBId(entry); - } + 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"); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + PDBEntry entry = new PDBEntry(); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + try + { + MCview.PDBfile pdbfile = new MCview.PDBfile(choice, + jalview.io.AppletFormatAdapter.FILE); + + if (pdbfile.id == null) + { + 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) + { + return; + } + + entry.setId(reply); + } + else + { + entry.setId(pdbfile.id); + } + } + catch (java.io.IOException ex) + { + ex.printStackTrace(); + } + + entry.setFile(choice); + sequence.getDatasetSequence().addPDBId(entry); + } } @@ -1310,25 +1335,27 @@ public class PopupMenu extends JPopupMenu public void discoverPDB_actionPerformed() { new jalview.io.DBRefFetcher( - ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); } public void sequenceFeature_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg==null) + if (sg == null) + { return; + } - int gSize= sg.getSize(); - SequenceI [] seqs = new SequenceI[gSize]; - SequenceFeature [] features = new SequenceFeature[gSize]; + int gSize = sg.getSize(); + SequenceI[] seqs = new SequenceI[gSize]; + SequenceFeature[] features = new SequenceFeature[gSize]; for (int i = 0; i < gSize; i++) { seqs[i] = sg.getSequenceAt(i).getDatasetSequence(); int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - features[i] = new SequenceFeature(null,null, null,start,end,"Jalview"); + features[i] = new SequenceFeature(null, null, null, start, end, "Jalview"); } if (ap.seqPanel.seqCanvas.getFeatureRenderer() @@ -1344,6 +1371,8 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); if (sg != null) + { new TextColourChooser().chooseColour(ap, sg); + } } }