X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=311421140d1a0dfce80dd3c4b09162f813b7fa7d;hb=391968dd70ca76090306df9b5852bbef10ab4ede;hp=d563e095b7533e9fad60bc38113f59e556b35d1f;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d563e09..3114211 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -18,682 +18,914 @@ */ package jalview.gui; -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; - import MCview.*; + import jalview.analysis.*; + import jalview.datamodel.*; -import jalview.io.*; + + import jalview.schemes.*; -public class PopupMenu - extends JPopupMenu +import java.awt.*; +import java.awt.event.*; + +import javax.swing.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class PopupMenu extends JPopupMenu { - JMenu groupMenu = new JMenu(); - JMenuItem groupName = new JMenuItem(); - protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem hydrophobicityColour = new - JRadioButtonMenuItem(); - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - AlignmentPanel ap; - JMenu sequenceMenu = new JMenu(); - JMenuItem sequenceName = new JMenuItem(); - Sequence sequence; - JMenuItem unGroupMenuItem = new JMenuItem(); - JMenuItem pdbMenuItem = 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(); - - public PopupMenu(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) - { - e.printStackTrace(); + 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(); + + /** + * 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) + { + e.printStackTrace(); + } + + + if ((seq != null) + && seq.getDatasetSequence().getPDBId() != null) + { + java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements(); + while(e.hasMoreElements()) + { + final PDBEntry pdb = (PDBEntry)e.nextElement(); + + JMenuItem pdbMenuItem = new JMenuItem(); + pdbMenuItem.setText("View PDB entry: "+pdb.getId()); + pdbMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas); + } + }); + sequenceMenu.add(pdbMenuItem); + } + + } + + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + groupName.setText(sg.getName()); + + if (sg.cs instanceof ZappoColourScheme) + { + zappoColour.setSelected(true); + } + else if (sg.cs instanceof TaylorColourScheme) + { + taylorColour.setSelected(true); + } + else if (sg.cs instanceof PIDColourScheme) + { + PIDColour.setSelected(true); + } + else if (sg.cs instanceof Blosum62ColourScheme) + { + BLOSUM62Colour.setSelected(true); + } + else if (sg.cs instanceof UserColourScheme) + { + userDefinedColour.setSelected(true); + } + else if (sg.cs instanceof HydrophobicColourScheme) + { + hydrophobicityColour.setSelected(true); + } + else if (sg.cs instanceof HelixColourScheme) + { + helixColour.setSelected(true); + } + else if (sg.cs instanceof StrandColourScheme) + { + strandColour.setSelected(true); + } + else if (sg.cs instanceof TurnColourScheme) + { + turnColour.setSelected(true); + } + else if (sg.cs instanceof BuriedColourScheme) + { + buriedColour.setSelected(true); + } + else if (sg.cs instanceof ClustalxColourScheme) + { + clustalColour.setSelected(true); + } + else + { + noColourmenuItem.setSelected(true); + } + + if (sg.cs!=null && sg.cs.conservationApplied()) + { + conservationMenuItem.setSelected(true); + } + + showText.setSelected(sg.getDisplayText()); + showColourText.setSelected(sg.getColourText()); + showBoxes.setSelected(sg.getDisplayBoxes()); + } + + if (!ap.av.alignment.getGroups().contains(sg)) + { + unGroupMenuItem.setVisible(false); + } + else + { + groupMenu.insertSeparator(3); + } + + if (seq == null) + { + sequenceMenu.setVisible(false); + } + else + { + java.util.Vector links = Preferences.sequenceURLLinks; + + JMenu linkMenu = new JMenu("Link"); + JMenuItem item; + for(int i=0; i-1) + id = id.substring(id.lastIndexOf("|")+1); + + final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showLink(url); + } + }); + + linkMenu.add(item); + } + add(linkMenu); + } } - SequenceGroup sg = ap.av.getSelectionGroup(); + /** + * DOCUMENT ME! + * + * @throws Exception DOCUMENT ME! + */ + private void jbInit() throws Exception + { + groupMenu.setText("Group"); + groupMenu.setText("Define"); + 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/Desciption"); + 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); + } + }); + add(groupMenu); + add(sequenceMenu); + groupMenu.add(groupName); + groupMenu.addSeparator(); + groupMenu.add(unGroupMenuItem); + groupMenu.add(colourMenu); + groupMenu.addSeparator(); + groupMenu.add(showBoxes); + groupMenu.add(showText); + groupMenu.add(showColourText); + groupMenu.addSeparator(); + groupMenu.add(outline); + sequenceMenu.add(sequenceName); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideMenuItem); + colourMenu.add(userDefinedColour); + + if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + JMenuItem item = new JMenuItem(userColours. + nextElement().toString()); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + + + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + 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); + } + }); + } - if (sg != null) + /** + * DOCUMENT ME! + */ + void refresh() { - groupName.setText(sg.getName()); + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); - 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 ConservationColourScheme) - { - conservationMenuItem.setSelected(true); - } + ap.seqPanel.repaint(); + } - showText.setSelected(sg.getDisplayText()); - showColourText.setSelected(sg.getColourText()); - showBoxes.setSelected(sg.getDisplayBoxes()); + /** + * 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(); } - if (!ap.av.alignment.getGroups().contains(sg)) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void zappoColour_actionPerformed(ActionEvent e) { - unGroupMenuItem.setVisible(false); + getGroup().cs = new ZappoColourScheme(); + refresh(); } - else + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void taylorColour_actionPerformed(ActionEvent e) { - groupMenu.insertSeparator(3); + getGroup().cs = new TaylorColourScheme(); + refresh(); } - if (seq == null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed(ActionEvent e) { - sequenceMenu.setVisible(false); + getGroup().cs = new HydrophobicColourScheme(); + refresh(); } - } - - private void jbInit() - throws Exception - { - groupMenu.setText("Group"); - groupMenu.setText("Define"); - 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"); - 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); - } - }); - pdbMenuItem.setText("View PDB structure"); - pdbMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pdbMenuItem_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); - } - }); - add(groupMenu); - add(sequenceMenu); - 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); - sequenceMenu.add(pdbMenuItem); - 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); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); - 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() + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void helixColour_actionPerformed(ActionEvent e) { - 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); - } - }); - } - - void refresh() - { - SequenceGroup sg = getGroup(); - SuperGroup superG = ap.av.alignment.getSuperGroup(sg); + getGroup().cs = new HelixColourScheme(); + refresh(); + } - if (superG != null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void strandColour_actionPerformed(ActionEvent e) { - superG.setSuperGroupProperties(sg); + getGroup().cs = new StrandColourScheme(); + refresh(); } - ap.seqPanel.repaint(); - } - - protected void clustalColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, - ap.av.alignment.getWidth()); - refresh(); - } - - protected void zappoColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } - - protected void taylorColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } - - protected void helixColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new HelixColourScheme(); - refresh(); - } - - protected void strandColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new StrandColourScheme(); - refresh(); - } - - protected void turnColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new TurnColourScheme(); - refresh(); - } - - protected void buriedColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - public void nucleotideMenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } - - protected void abovePIDColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - if (abovePIDColour.isSelected()) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void turnColour_actionPerformed(ActionEvent e) { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); - - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, - getGroup().getName()); - - if (sg.cs instanceof ResidueColourScheme) - { - ( (ResidueColourScheme) sg.cs).setThreshold(threshold); - } - else if (sg.cs instanceof ScoreColourScheme) - { - ( (ScoreColourScheme) sg.cs).setThreshold(threshold); - } - - SliderPanel.showPIDSlider(); + getGroup().cs = new TurnColourScheme(); + refresh(); } - else // remove PIDColouring + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void buriedColour_actionPerformed(ActionEvent e) { - ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; - rcs.setThreshold(0); - sg.cs = rcs; + getGroup().cs = new BuriedColourScheme(); + refresh(); } - refresh(); - } - - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - new UserDefinedColours(ap, getGroup()); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } - 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(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); - sg.cs = new Blosum62ColourScheme(); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - refresh(); - } + SliderPanel.showPIDSlider(); + } + else // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = null; - refresh(); - } + refresh(); + } - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); + /** + * 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(); + } - if (conservationMenuItem.isSelected()) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.sequences, 0, - ap.av.alignment.getWidth()); + SequenceGroup sg = getGroup(); - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); + sg.cs = new Blosum62ColourScheme(); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); - sg.cs = ccs; - - SliderPanel.setConservationSlider(ap, ccs, sg.getName()); - SliderPanel.showConservationSlider(); + refresh(); } - else // remove ConservationColouring + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) { - ConservationColourScheme ccs = (ConservationColourScheme) sg.cs; - sg.cs = ccs.cs; + getGroup().cs = null; + refresh(); } - refresh(); - } - - 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); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; + + if (conservationMenuItem.isSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, sg.sequences, 0, + ap.av.alignment.getWidth()); + + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); + + sg.cs.setConservation(c); + + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring + { + sg.cs.setConservation(null); + } + + refresh(); + } - if (reply == null) - { - 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; + } + + sg.setName(reply); + groupName.setText(reply); } - sg.setName(reply); - groupName.setText(reply); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void analyze_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(cap); + Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); + + SequenceGroup sg = getGroup(); + StringBuffer sb = new StringBuffer(); + + for (int i = 0; i < sg.sequences.size(); i++) + { + Sequence tmp = (Sequence) sg.sequences.get(i); + sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); + sb.append("\n"); + } + + sb.append("Something amazing will happen soon"); + cap.setText(sb.toString()); + } - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); + /** + * 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); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); + return sg; + } - 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"); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void sequenceName_actionPerformed(ActionEvent e) + { + JLabel idlabel = new JLabel( " Sequence Name "); + JLabel desclabel = new JLabel("Sequence Description "); + idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); + desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); + JTextField id = new JTextField(sequence.getName(), 40); + JTextField description = new JTextField(sequence.getDescription(), 40); + JPanel panel = new JPanel(new BorderLayout()); + JPanel panel2 = new JPanel(new BorderLayout()); + panel2.add(idlabel, BorderLayout.WEST); + panel2.add(id, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.NORTH); + panel2 = new JPanel(new BorderLayout()); + panel2.add(desclabel, BorderLayout.WEST); + panel2.add(description, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.SOUTH); + + + int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + panel, "Edit Sequence Name/Description", + JOptionPane.OK_CANCEL_OPTION ); + + + if (reply != JOptionPane.OK_OPTION ) + { + return; + } + + String s = id.getText(); + + if (s != null) + { + if (s.indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + s = s.replace(' ', '_'); + sequence.getDatasetSequence().setName(s); + sequence.setName(s); + ap.repaint(); + } + + sequence.getDatasetSequence().setDescription(description.getText()); + sequence.setDescription(description.getText()); } - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); - } + /** + * 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(); + } - SequenceGroup getGroup() - { - SequenceGroup sg = ap.av.getSelectionGroup(); - // this method won't add a new group if it already exists - ap.av.alignment.addGroup(sg); + /** + * 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); - return sg; - } + if (col != null) + { + sg.setOutlineColour(col); + } - void sequenceName_actionPerformed(ActionEvent e) - { - String id = sequence.getName(); - String s = (String) JOptionPane.showInternalInputDialog(ap, - "Edit sequence name", - "Edit sequence name (" + sequence.getName() + ")", - JOptionPane.PLAIN_MESSAGE, null, null, id); + refresh(); + } - if (s != null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed(ActionEvent e) { - sequence.setName(s); - ap.repaint(); + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); } - } - - void unGroupMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); - ap.av.setSelectionGroup(null); - refresh(); - } - - void pdbMenuItem_actionPerformed(ActionEvent e) - { - if (sequence.getPDBId() == null) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showText_actionPerformed(ActionEvent e) { - return; + getGroup().setDisplayText(showText.isSelected()); + refresh(); } - try + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showColourText_actionPerformed(ActionEvent e) { - EBIFetchClient ebi = new EBIFetchClient(); - String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, - null); - - PDBfile pdb = new PDBfile(result); - - rotCanvas rc = new rotCanvas(pdb, sequence, ap.av); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(rc); - Desktop.addInternalFrame(frame, - sequence.getName() + " " + sequence.getPDBId(), - 400, 400); + getGroup().setColourText(showColourText.isSelected()); + refresh(); } - catch (Exception ex) + + public void showLink(String url) { - ex.printStackTrace(); - } - } + 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 ); - protected void outline_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, "Select Outline Colour", - Color.BLUE); - if (col != null) - { - sg.setOutlineColour(col); + ex.printStackTrace(); + } } - - refresh(); - } - - public void showBoxes_actionPerformed(ActionEvent e) - { - getGroup().setDisplayBoxes(showBoxes.isSelected()); - refresh(); - } - - public void showText_actionPerformed(ActionEvent e) - { - getGroup().setDisplayText(showText.isSelected()); - refresh(); - } - - public void showColourText_actionPerformed(ActionEvent e) - { - getGroup().setColourText(showColourText.isSelected()); - refresh(); - } }