X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f9e0d19d262ed88f4e7bfdfba5c8f19c079c5aa4;hb=refs%2Fheads%2FvamsasDemo;hp=398294b7cd9874d59c3d78a31c2adb7de99d81ca;hpb=116786d279dcb83f05afd625ad6e39627a37e1e8;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 398294b..f9e0d19 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,605 +1,914 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; -import jalview.datamodel.*; +import MCview.*; + import jalview.analysis.*; + +import jalview.datamodel.*; + + import jalview.schemes.*; + import java.awt.*; -import javax.swing.*; import java.awt.event.*; -import jalview.io.*; -import MCview.*; +import javax.swing.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class PopupMenu extends JPopupMenu { - JMenu groupMenu = new JMenu(); - JMenuItem analyze = new JMenuItem(); - JMenu defineMenu = new JMenu(); - JMenuItem groupName = new JMenuItem(); - JMenuItem groupAnnotation = 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(); - JMenu residueMenu = new JMenu(); - JMenuItem annotateResidue = new JMenuItem(); - - Sequence sequence; - JMenuItem unGroupMenuItem = new JMenuItem(); - JMenuItem pdbMenuItem = new JMenuItem(); - JMenuItem outline = new JMenuItem(); - - 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(); } - - SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg!=null) + 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) { - 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 ConservationColourScheme) - conservationMenuItem.setSelected(true); + /////////////////////////////////////////////////////////// + // 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); + } } - - if(seq!=null) - residueMenu.setVisible(false); - else - sequenceMenu.setVisible(false); - - } - private void jbInit() throws Exception - { - groupMenu.setText("Group"); - analyze.setText("Analyze"); - analyze.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - analyze_actionPerformed(e); - } - }); - defineMenu.setText("Define"); - groupName.setText("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupName_actionPerformed(e); - } - }); - groupAnnotation.setEnabled(false); - groupAnnotation.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupAnnotation_actionPerformed(e); - } - }); - sequenceMenu.setText("Sequence"); - sequenceName.setText("Edit name"); - sequenceName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sequenceName_actionPerformed(e); - } - }); - residueMenu.setText("Residue"); - annotateResidue.setEnabled(false); - annotateResidue.setActionCommand("annotate residue"); - annotateResidue.setText("annotate residue???"); - 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() + /** + * DOCUMENT ME! + * + * @throws Exception DOCUMENT ME! + */ + private void jbInit() throws Exception { - public void actionPerformed(ActionEvent e) - { - outline_actionPerformed(e); - } - }); - add(groupMenu); - this.add(sequenceMenu); - this.add(residueMenu); - groupMenu.add(defineMenu); - groupMenu.add(unGroupMenuItem); - groupMenu.addSeparator(); - groupMenu.add(analyze); - defineMenu.add(groupName); - defineMenu.add(groupAnnotation); - defineMenu.addSeparator(); - defineMenu.add(outline); - defineMenu.addSeparator(); - defineMenu.add(noColourmenuItem); - defineMenu.add(clustalColour); - defineMenu.add(zappoColour); - defineMenu.add(taylorColour); - defineMenu.add(hydrophobicityColour); - defineMenu.add(helixColour); - defineMenu.add(strandColour); - defineMenu.add(turnColour); - defineMenu.add(buriedColour); - defineMenu.add(userDefinedColour); - defineMenu.add(PIDColour); - defineMenu.add(BLOSUM62Colour); - defineMenu.addSeparator(); - defineMenu.add(abovePIDColour); - defineMenu.add(conservationMenuItem); - - sequenceMenu.add(sequenceName); - sequenceMenu.add(pdbMenuItem); - residueMenu.add(annotateResidue); - - noColourmenuItem.setText("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); + 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); + } + }); + + 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); + } + }); + } - clustalColour.setText("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setText("Zappo colour scheme"); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setText("Taylor colour scheme"); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setText("By 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! + */ + void refresh() { - 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 PID threshold only"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(e); - } - }); - userDefinedColour.setText("User defined colours"); - 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 score"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); - conservationMenuItem.setText("By 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 ); - if( superG !=null) - superG.setSuperGroupProperties( sg ); - - 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(); - } - - - protected void abovePIDColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - if (abovePIDColour.isSelected()) - { - 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(); + SequenceGroup sg = getGroup(); + if(sg!=null) + { + SuperGroup superG = ap.av.alignment.getSuperGroup(sg); + + if (superG != null) + { + superG.setSuperGroupProperties(sg); + } + } + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); + + ap.seqPanel.repaint(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void clustalColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg.sequences, + ap.av.alignment.getWidth()); + refresh(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void zappoColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new ZappoColourScheme(); + refresh(); } - else // remove PIDColouring + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void taylorColour_actionPerformed(ActionEvent e) { - ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; - rcs.setThreshold(0); - sg.cs = rcs; + getGroup().cs = new TaylorColourScheme(); + refresh(); } - refresh(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void helixColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void strandColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - JInternalFrame frame = new JInternalFrame(); - UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup()); - frame.setContentPane(chooser); - Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 ); - frame.setResizable(false); - frame.setIconifiable(false); - frame.setMaximizable(false); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void turnColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void buriedColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } - protected void PIDColour_actionPerformed(ActionEvent e) - { + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; - 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()); + } + refresh(); + } - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = null; - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); - protected void conservationMenuItem_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()); - if(conservationMenuItem.isSelected()) + 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(); + } - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.sequences, 0, - ap.av.alignment.getWidth()); - - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + sg.cs = new Blosum62ColourScheme(); - sg.cs = ccs; + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); - 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 groupAnnotation_actionPerformed(ActionEvent e) - { - - } - - 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); - } - - - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - JInternalFrame frame = new JInternalFrame(); - cap.formatForOutput(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for(int i=0; i -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + s = s.replace(' ', '_'); + sequence.setName(s); + ap.repaint(); + } + } - if(s!=null) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed(ActionEvent e) { - sequence.setName(s); - ap.repaint(); + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); } - } - - void unGroupMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getSelectionGroup(); - ap.av.alignment.deleteGroup(sg); - ap.av.setSelectionGroup(null); - ap.repaint(); - } - void pdbMenuItem_actionPerformed(ActionEvent e) - { - if(sequence.getPDBId()==null) - return; - - try + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void outline_actionPerformed(ActionEvent e) { - EBIFetchClient ebi = new EBIFetchClient(); - String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null); + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", + Color.BLUE); + + if (col != null) + { + sg.setOutlineColour(col); + } - PDBfile pdb = new PDBfile(result); - sequence.setPDBfile(pdb); + refresh(); + } - ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true; - ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence; - // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed(ActionEvent e) + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } - rotCanvas rc = new rotCanvas(pdb); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(rc); - Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showText_actionPerformed(ActionEvent e) + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); } - catch (Exception ex) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showColourText_actionPerformed(ActionEvent e) { - ex.printStackTrace(); + getGroup().setColourText(showColourText.isSelected()); + refresh(); } - } - 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); - } + 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(); + } + } }