X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=311421140d1a0dfce80dd3c4b09162f813b7fa7d;hb=7c12f8eb9879172c5c437143ca5eb811a8daf5c7;hp=19698b7f13495587fd2b9c5f44b9c2f5f2b81fdc;hpb=ff3c6d412fe13784cde1e15a12567d6537f4151c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 19698b7..3114211 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,793 +1,931 @@ +/* + * 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 javax.swing.*; + +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 copyGroup = new JMenuItem(); - JMenuItem moveGroup = new JMenuItem(); - JMenuItem deleteSequences = new JMenuItem(); - 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(); - - SequenceI sequence; - - public PopupMenu(AlignmentPanel ap, SequenceI 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.getRubberbandGroup(); - 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) + /** + * DOCUMENT ME! + * + * @throws Exception DOCUMENT ME! + */ + private void jbInit() throws Exception { - residueMenu.setVisible(false); - sequenceName.setText( sequence.getName() ); + 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); + } + }); } - else - sequenceMenu.setVisible(false); - - } - private void jbInit() throws Exception - { - groupMenu.setText("Group"); - copyGroup.setText("Copy region to new Alignment"); - copyGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copyGroup_actionPerformed(e); - } - }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveGroup_actionPerformed(e); - } - }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSequences_actionPerformed(e); - } - }); - 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.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupAnnotation_actionPerformed(e); - } - }); - sequenceMenu.setText("Sequence"); - sequenceName.setText("sequenceName"); - sequenceName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - sequenceName_actionPerformed(e); - } - }); - residueMenu.setText("Residue"); - annotateResidue.setText("annotate residue???"); - PIDColour.setFocusPainted(false); - add(groupMenu); - this.add(sequenceMenu); - this.add(residueMenu); - groupMenu.add(defineMenu); - groupMenu.addSeparator(); - groupMenu.add(copyGroup); - groupMenu.add(moveGroup); - groupMenu.add(deleteSequences); - groupMenu.addSeparator(); - groupMenu.add(analyze); - defineMenu.add(groupName); - defineMenu.add(groupAnnotation); - 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); - residueMenu.add(annotateResidue); - - 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 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() + /** + * DOCUMENT ME! + */ + void refresh() { - 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() - { - 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() - { - ap.seqPanel.seqCanvas.paintFlag=true; - ap.seqPanel.repaint(); - } - - protected void clustalColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new ClustalxColourScheme(); - 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(); - } + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); - protected void buriedColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - -/* -public void conservationColourIncMenuItem_actionPerformed(ActionEvent e) -{ -ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel); -JInternalFrame frame = new JInternalFrame(); -frame.setContentPane(cip); -Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90); -frame.setMaximizable(false); - - }*/ - - - protected void abovePIDColour_actionPerformed(ActionEvent e) - { - SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs ); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(sp); - Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90); - frame.setMaximizable(false); - - } - - - 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); + 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(); + } - protected void PIDColour_actionPerformed(ActionEvent e) - { + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void zappoColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void taylorColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - getGroup().cs = new Blosum62ColourScheme(ap.av); - 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(); + } - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = null; - refresh(); - } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void strandColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void turnColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(), - sg.getEndRes() ); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void buriedColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } - c.calculate(); - c.verdict(false, 100); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } - sg.cs = ccs; + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; - refresh(); - } + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); -/* - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme( null ); - changeColour(); - } - - - public void clustalColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme(new ClustalxColourScheme( )); - conservationMenuItem.setSelected(false); - abovePIDThreshold.setSelected(false); - changeColour(); - } - - public void zappoColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme(new ZappoColourScheme() ); - changeColour(); - } - - public void taylorColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme(new TaylorColourScheme() ); - changeColour(); - } - - - public void hydrophobicityColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme( new HydrophobicColourScheme() ); - changeColour(); - } - - public void helixColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme( new HelixColourScheme() ); - changeColour(); - } - - - public void strandColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme(new StrandColourScheme() ); - changeColour(); - } - - - public void turnColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme(new TurnColourScheme() ); - changeColour(); - } - - - public void buriedColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme( new BuriedColourScheme() ); - changeColour(); - } - - void changeColour() - { - if(abovePIDThreshold.isSelected()) - abovePIDThreshold_actionPerformed(null); - else if(conservationMenuItem.isSelected()) - conservationMenuItem_actionPerformed(null); - - alignPanel.seqPanel.seqCanvas.paintFlag = true; - alignPanel.repaint(); - } - - void addConservationOrPIDColour() - { - int x=0, y=0, threshold = 70; - - if(sliderFrame!=null) - try - { - x = sliderFrame.getX(); - y = sliderFrame.getY(); - SliderPanel sp = (SliderPanel) sliderFrame.getContentPane(); - threshold = sp.getValue(); - sliderFrame.setClosed(true); - } - catch (Exception ex) - { ex.printStackTrace(); } + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); - ColourSchemeI oldCs = viewport.getGlobalColourScheme(); + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - ConservationColourScheme ccs = null; - if (oldCs instanceof ConservationColourScheme) - ccs = (ConservationColourScheme) oldCs; + SliderPanel.showPIDSlider(); + } + else // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } - if(conservationMenuItem.isSelected()) - { - Alignment al = (Alignment)viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, al.getSequences(), 0, - al.getWidth() ); + refresh(); + } - c.calculate(); - c.verdict(false, 100); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); - if(ccs!=null) - ccs = new ConservationColourScheme(c, ccs.cs); + if (e.getActionCommand().equals("User Defined...")) + new UserDefinedColours(ap, sg); else - ccs = new ConservationColourScheme(c, oldCs); - - viewport.setGlobalColourScheme( ccs ); - - } - else if(oldCs instanceof ConservationColourScheme) - { - oldCs = ccs.cs; - viewport.setGlobalColourScheme( oldCs ); - } - - - if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() ) - { - sliderFrame = new JInternalFrame(); - sliderFrame.setMaximizable(false); - sliderFrame.setResizable(false); - - SliderPanel sp = null; - if (conservationMenuItem.isSelected()) { - if(threshold > 50) - threshold = 30; - sp = new SliderPanel(alignPanel, threshold, true,ccs); - Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90); - threshold = 0; - } - else if (abovePIDThreshold.isSelected()) - { - sp = new SliderPanel(alignPanel, threshold, false, oldCs); - sp.cs = oldCs; - Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90); - } - - sliderFrame.setContentPane(sp); - if(x!=0 && y!=0) - sliderFrame.setLocation(x,y); + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); + sg.cs = udc; + } } - else - threshold = 0; + /** + * 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(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); - if (oldCs instanceof ResidueColourScheme) - { - ResidueColourScheme rcs = (ResidueColourScheme) oldCs; - rcs.setThreshold(threshold); - } - else if (oldCs instanceof ScoreColourScheme) - { - ScoreColourScheme scs = (ScoreColourScheme) oldCs; - scs.setThreshold(threshold); - } + sg.cs = new Blosum62ColourScheme(); - alignPanel.seqPanel.seqCanvas.paintFlag = true; - alignPanel.repaint(); - - } - - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - if(abovePIDThreshold.isSelected()) - abovePIDThreshold.setSelected(false); - - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - addConservationOrPIDColour(); - } - - JInternalFrame sliderFrame; - public void abovePIDThreshold_actionPerformed(ActionEvent e) - { - if(conservationMenuItem.isSelected()) - conservationMenuItem.setSelected(false); - - addConservationOrPIDColour(); - } - - - - public void userDefinedColour_actionPerformed(ActionEvent e) - { - JInternalFrame frame = new JInternalFrame(); - UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null); - frame.setContentPane(chooser); - Desktop.addInternalFrame(frame,"User defined colours", 450,540 ); - frame.setResizable(false); - frame.setIconifiable(false); - frame.setMaximizable(false); - } - - public void PIDColour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme( new PIDColourScheme() ); - alignPanel.setColourScheme( ); - } - - - public void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) ); - alignPanel.setColourScheme(); - } -*/ -////////////////////////////////////// - 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 copyGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - - SequenceI[] s = new Sequence[sg.sequences.size()]; - for (int i=0; i < sg.sequences.size(); i++) - { - s[i] = new Sequence( sg.getSequenceAt(i)); - s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) ); - } - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if (newHeight > 500) - newHeight = 500; - Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight); - } + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); - protected void moveGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); + refresh(); + } - SequenceI[] s = new Sequence[sg.sequences.size()]; + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = null; + refresh(); + } - for (int i=0; i < sg.sequences.size(); i++) - s[i] = new Sequence( sg.getSequenceAt(i)); + /** + * 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(); + } - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if(newHeight>500) - newHeight=500; - Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void groupName_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter new group name", "Edit group name", + JOptionPane.QUESTION_MESSAGE); + + if (reply == null) + { + return; + } + + sg.setName(reply); + groupName.setText(reply); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void analyze_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(cap); + Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); + + SequenceGroup sg = getGroup(); + StringBuffer sb = new StringBuffer(); + + for (int i = 0; i < sg.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()); + } - for (int i=0; i < sg.sequences.size(); i++) - ap.av.alignment.deleteSequence(sg.getSequenceAt(i)); + /** + * 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; + } - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.RefreshPanels(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void sequenceName_actionPerformed(ActionEvent e) + { + JLabel idlabel = new JLabel( " Sequence Name "); + JLabel desclabel = new JLabel("Sequence Description "); + idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); + desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); + JTextField id = new JTextField(sequence.getName(), 40); + JTextField description = new JTextField(sequence.getDescription(), 40); + JPanel panel = new JPanel(new BorderLayout()); + JPanel panel2 = new JPanel(new BorderLayout()); + panel2.add(idlabel, BorderLayout.WEST); + panel2.add(id, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.NORTH); + panel2 = new JPanel(new BorderLayout()); + panel2.add(desclabel, BorderLayout.WEST); + panel2.add(description, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.SOUTH); + + + int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + panel, "Edit Sequence Name/Description", + JOptionPane.OK_CANCEL_OPTION ); + + + if (reply != JOptionPane.OK_OPTION ) + { + return; + } + + String s = id.getText(); + + if (s != null) + { + if (s.indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + s = s.replace(' ', '_'); + sequence.getDatasetSequence().setName(s); + sequence.setName(s); + ap.repaint(); + } + + sequence.getDatasetSequence().setDescription(description.getText()); + sequence.setDescription(description.getText()); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); + } - } - protected void deleteSequences_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - for (int i=0;i < sg.sequences.size(); i++) - ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i)); + /** + * 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); - ap.av.alignment.deleteGroup(sg); - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.seqPanel.parent.RefreshPanels(); + if (col != null) + { + sg.setOutlineColour(col); + } - } + refresh(); + } - 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(); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed(ActionEvent e) + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } - for(int i=0; i