X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f1a38f5475b4193e0f2077803b049d566f193a89;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=4928189ba6148bae5315638a397e23ce4f975aff;hpb=00506d5a86e6f2c09529134ef8ddbf114656b681;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4928189..f1a38f5 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,47 +1,104 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * 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 jalview.analysis.*; -import jalview.schemes.*; -import javax.swing.*; +import java.util.*; + +import java.awt.*; import java.awt.event.*; +import javax.swing.*; +import MCview.*; +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; -public class PopupMenu extends JPopupMenu +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class PopupMenu + extends JPopupMenu { - JMenuItem residueMenu = new JMenuItem(); 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 hydrophobicityColour = new + JRadioButtonMenuItem(); protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem abovePIDColour = 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 JMenuItem conservationColourIncMenuItem = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - - - AlignViewport av; - SeqPanel seqPanel; - - public PopupMenu(AlignViewport av, SeqPanel sp) + AlignmentPanel ap; + JMenu sequenceMenu = new JMenu(); + JMenuItem sequenceName = new JMenuItem(); + Sequence sequence; + JMenuItem unGroupMenuItem = new JMenuItem(); + JMenuItem outline = new JMenuItem(); + JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); + JMenu colourMenu = new JMenu(); + JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); + JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); + JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); + JMenu editMenu = new JMenu(); + JMenuItem cut = new JMenuItem(); + JMenuItem copy = new JMenuItem(); + JMenuItem upperCase = new JMenuItem(); + JMenuItem lowerCase = new JMenuItem(); + JMenuItem toggle = new JMenuItem(); + JMenu pdbMenu = new JMenu(); + JMenuItem pdbFromFile = new JMenuItem(); + JMenuItem enterPDB = new JMenuItem(); + JMenuItem discoverPDB = new JMenuItem(); + JMenu outputMenu = new JMenu(); + JMenuItem sequenceFeature = new JMenuItem(); + JMenuItem textColour = new JMenuItem(); + JMenu jMenu1 = new JMenu(); + + /** + * Creates a new PopupMenu object. + * + * @param ap DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) { - this.av = av; - seqPanel = sp; + /////////////////////////////////////////////////////////// + // 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); @@ -58,143 +115,518 @@ public class PopupMenu extends JPopupMenu colours.add(PIDColour); colours.add(BLOSUM62Colour); + for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) + { + JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[ + i]); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + outputMenu.add(item); + } + try { jbInit(); } - catch(Exception e) + catch (Exception e) { e.printStackTrace(); } - SequenceGroup sg = av.getRubberbandGroup(); - groupName.setText( sg.getName() ); + if (seq != null) + { + sequenceMenu.setText(sequence.getName()); + + JMenuItem menuItem; + if (seq.getDatasetSequence().getPDBId() != null) + { + java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). + elements(); + + while (e.hasMoreElements()) + { + final PDBEntry pdb = (PDBEntry) e.nextElement(); + + menuItem = new JMenuItem(); + menuItem.setText("View PDB entry: " + pdb.getId()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas); + } + }); + sequenceMenu.add(menuItem); + } + } + + menuItem = new JMenuItem("Hide Sequences"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(false); + } + }); + add(menuItem); + + if (ap.av.getSelectionGroup() != null + && ap.av.getSelectionGroup().getSize() > 1) + { + menuItem = new JMenuItem("Represent Group with " + seq.getName()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(true); + } + }); + sequenceMenu.add(menuItem); + } + + if (ap.av.hasHiddenRows) + { + final int index = ap.av.alignment.findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) - + ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + menuItem = new JMenuItem("Reveal Sequences"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showSequence(index); + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + } + }); + add(menuItem); + } + + menuItem = new JMenuItem("Reveal All"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showAllHiddenSeqs(); + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + } + }); + + add(menuItem); + } + + } + + SequenceGroup sg = ap.av.getSelectionGroup(); + + 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()); + } + else + { + groupMenu.setVisible(false); + editMenu.setVisible(false); + } + + if (!ap.av.alignment.getGroups().contains(sg)) + { + unGroupMenuItem.setVisible(false); + } + + if (seq == null) + { + sequenceMenu.setVisible(false); + pdbMenu.setVisible(false); + } + + if (links != null && links.size() > 0) + { + JMenu linkMenu = new JMenu("Link"); + JMenuItem item; + for (int i = 0; i < links.size(); i++) + { + String link = links.elementAt(i).toString(); + final String label = link.substring(0, link.indexOf("|")); + item = new JMenuItem(label); + final String url; + + if (link.indexOf("$SEQUENCE_ID$") > -1) + { + String id = seq.getName(); + if (id.indexOf("|") > -1) + { + id = id.substring(id.lastIndexOf("|") + 1); + } + + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + } + else + { + url = link.substring(link.lastIndexOf("|") + 1); + } + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showLink(url); + } + }); + + linkMenu.add(item); + } + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } + } } - private void jbInit() throws Exception + + /** + * DOCUMENT ME! + * + * @throws Exception DOCUMENT ME! + */ + private void jbInit() + throws Exception { - residueMenu.setText("Residue"); groupMenu.setText("Group"); - copyGroup.setText("Copy region to new Alignment"); - copyGroup.addActionListener(new java.awt.event.ActionListener() + groupMenu.setText("Selection"); + groupName.setText("Name"); + groupName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - copyGroup_actionPerformed(e); + groupName_actionPerformed(); } }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() + sequenceMenu.setText("Sequence"); + sequenceName.setText("Edit Name/Description"); + sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - moveGroup_actionPerformed(e); + sequenceName_actionPerformed(); } }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - deleteSequences_actionPerformed(e); + unGroupMenuItem_actionPerformed(); } }); - analyze.setText("Analyze"); - analyze.addActionListener(new java.awt.event.ActionListener() + + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - analyze_actionPerformed(e); + outline_actionPerformed(); } }); - defineMenu.setText("Define"); - groupName.setText("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() + nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideMenuItem_actionPerformed(); + } + }); + colourMenu.setText("Group Colour"); + showBoxes.setText("Boxes"); + showBoxes.setState(true); + showBoxes.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showBoxes_actionPerformed(); + } + }); + showText.setText("Text"); + showText.setState(true); + showText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showText_actionPerformed(); + } + }); + showColourText.setText("Colour Text"); + showColourText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showColourText_actionPerformed(); + } + }); + editMenu.setText("Edit"); + cut.setText("Cut"); + cut.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - groupName_actionPerformed(e); + cut_actionPerformed(); } }); - groupAnnotation.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() + upperCase.setText("To Upper Case"); + upperCase.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - groupAnnotation_actionPerformed(e); + changeCase(e); } }); + copy.setText("Copy"); + copy.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(); + } + }); + lowerCase.setText("To Lower Case"); + lowerCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + toggle.setText("Toggle Case"); + toggle.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + pdbMenu.setText("Associate Structure with Sequence"); + pdbFromFile.setText("From File"); + pdbFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(); + } + }); + enterPDB.setText("Enter PDB Id"); + enterPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(); + } + }); + discoverPDB.setText("Discover PDB ids"); + discoverPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(); + } + }); + outputMenu.setText("Output to Textbox..."); + sequenceFeature.setText("Create Sequence Feature"); + sequenceFeature.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(); + } + }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + jMenu1.setText("Group"); add(groupMenu); - 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.addSeparator(); - defineMenu.add(conservationMenuItem); - defineMenu.add(conservationColourIncMenuItem); - defineMenu.addSeparator(); - defineMenu.add(abovePIDColour); - defineMenu.add(PIDColour); - defineMenu.add(BLOSUM62Colour); + add(sequenceMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.add(sequenceFeature); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenu); + colourMenu.add(textColour); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideMenuItem); + colourMenu.add(userDefinedColour); + + if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + JMenuItem item = new JMenuItem(userColours. + nextElement().toString()); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + editMenu.add(copy); + editMenu.add(cut); + editMenu.add(upperCase); + editMenu.add(lowerCase); + editMenu.add(toggle); + pdbMenu.add(pdbFromFile); + pdbMenu.add(enterPDB); + pdbMenu.add(discoverPDB); + jMenu1.add(groupName); + jMenu1.add(unGroupMenuItem); + jMenu1.add(colourMenu); + jMenu1.add(showBoxes); + jMenu1.add(showText); + jMenu1.add(showColourText); + jMenu1.add(outline); noColourmenuItem.setText("None"); - noColourmenuItem.setSelected(true); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); + noColourmenuItem_actionPerformed(); } }); - clustalColour.setEnabled(false); - clustalColour.setSelected(false); clustalColour.setText("Clustalx colours"); clustalColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(e); + clustalColour_actionPerformed(); } }); - zappoColour.setText("Zappo colour scheme"); + zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(e); + zappoColour_actionPerformed(); } }); - taylorColour.setText("Taylor colour scheme"); + taylorColour.setText("Taylor"); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(e); + taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText("By hydrophobicity"); + hydrophobicityColour.setText("Hydrophobicity"); hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - hydrophobicityColour_actionPerformed(e); + hydrophobicityColour_actionPerformed(); } }); helixColour.setText("Helix propensity"); @@ -202,7 +634,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(e); + helixColour_actionPerformed(); } }); strandColour.setText("Strand propensity"); @@ -210,7 +642,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(e); + strandColour_actionPerformed(); } }); turnColour.setText("Turn propensity"); @@ -218,27 +650,26 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(e); + turnColour_actionPerformed(); } }); - buriedColour.setText("Buried index"); + buriedColour.setText("Buried Index"); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(e); + buriedColour_actionPerformed(); } }); - abovePIDColour.setEnabled(false); - abovePIDColour.setText("Above PID threshold only"); + abovePIDColour.setText("Above % Identity"); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(e); + abovePIDColour_actionPerformed(); } }); - userDefinedColour.setText("User defined colours"); + userDefinedColour.setText("User Defined..."); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -246,275 +677,702 @@ public class PopupMenu extends JPopupMenu userDefinedColour_actionPerformed(e); } }); - PIDColour.setEnabled(false); - PIDColour.setText("By PID"); + PIDColour.setText("Percentage Identity"); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(e); + PIDColour_actionPerformed(); } }); - BLOSUM62Colour.setText("By BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(e); + BLOSUM62Colour_actionPerformed(); } }); - conservationMenuItem.setText("By conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(e); - } - }); - - conservationColourIncMenuItem.setEnabled(false); - conservationColourIncMenuItem.setText("Conservation Colour Increment"); - conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener() + conservationMenuItem.setText("Conservation"); + conservationMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - conservationColourIncMenuItem_actionPerformed(e); + conservationMenuItem_actionPerformed(); } }); - - } + /** + * DOCUMENT ME! + */ void refresh() { - seqPanel.seqCanvas.paintFlag=true; - seqPanel.repaint(); + if (ap.overviewPanel != null) + { + ap.overviewPanel.updateOverviewImage(); + } + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } - protected void clustalColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void clustalColour_actionPerformed() { - + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); + refresh(); } - protected void zappoColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); } - protected void taylorColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); } - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); } - protected void helixColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); } - protected void strandColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); } - protected void turnColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); } - protected void buriedColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed() + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } - protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } -} -/* -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); + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), + sg.getEndRes() + 1)); - }*/ + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - protected void abovePIDColour_actionPerformed(ActionEvent e) - { + SliderPanel.showPIDSlider(); + } + else // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } + refresh(); } - + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void userDefinedColour_actionPerformed(ActionEvent e) { + SequenceGroup sg = getGroup(); + if (e.getActionCommand().equals("User Defined...")) + { + new UserDefinedColours(ap, sg); + } + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; + } + refresh(); } - protected void PIDColour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void PIDColour_actionPerformed() { - + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1)); + refresh(); } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() { - getGroup().cs = new Blosum62ColourScheme(av); + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av. + hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1)); + refresh(); } - - protected void noColourmenuItem_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed() { SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (conservationMenuItem.isSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(ap.av. + hiddenRepSequences), + sg.getStartRes(), + sg.getEndRes() + 1); - Alignment al = (Alignment)av.getAlignment(); - Conservation c = new Conservation("Group", al.cons, - ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(), - sg.getEndRes() ); + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); - c.calculate(); - c.verdict(false, 100); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + sg.cs.setConservation(c); - sg.cs = ccs; + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring + { + sg.cs.setConservation(null); + } - refresh(); + refresh(); } - protected void groupAnnotation_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void groupName_actionPerformed() { + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), + " Group Name ", + "Group Description ", + "Edit Group Name/Description"); + + if (!dialog.accept) + { + return; + } + + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); } - protected void groupName_actionPerformed(ActionEvent e) + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + SequenceGroup getGroup() { - SequenceGroup sg = getGroup(); - String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE); - if(reply==null) + SequenceGroup sg = ap.av.getSelectionGroup(); + // this method won't add a new group if it already exists + if (sg != null) + { + ap.av.alignment.addGroup(sg); + } + + return sg; + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void sequenceName_actionPerformed() + { + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), + " Sequence Name ", + "Sequence Description ", + "Edit Sequence Name/Description"); + + if (!dialog.accept) + { return; + } + + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + sequence.setName(dialog.getName().replace(' ', '_')); + ap.repaint(); + } + + sequence.setDescription(dialog.getDescription()); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void outline_actionPerformed() + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", + Color.BLUE); + + if (col != null) + { + sg.setOutlineColour(col); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } - sg.setName(reply); - groupName.setText(reply); + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); } - /* public void deleteSelectedMenuItem_actionPerformed(ActionEvent e) + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } + + public void showLink(String url) + { + try { - addHistoryItem("delete selection"); + 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(); + } + } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) + { + ap.av.hideSequence(new SequenceI[] + {sequence}); + return; + } + + ap.av.setSelectionGroup(null); - for (int i=0;i < viewport.getSelection().size(); i++) - viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i)); + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); - viewport.getSelection().clear(); - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); - alignPanel.RefreshPanels(); + return; } - public void moveSelectedMenuItem_actionPerformed(ActionEvent e) + int gsize = sg.getSize(); + SequenceI[] hseqs; + + hseqs = new SequenceI[gsize]; + + int index = 0; + for (int i = 0; i < gsize; i++) { - copySelectedMenuItem_actionPerformed(null); - deleteSelectedMenuItem_actionPerformed(null); - alignPanel.repaint(); + hseqs[index++] = sg.getSequenceAt(i); } - public void copySelectedMenuItem_actionPerformed(ActionEvent e) + ap.av.hideSequence(hseqs); + } + + public void copy_actionPerformed() + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed() + { + ap.alignFrame.cut_actionPerformed(null); + } + + void changeCase(ActionEvent e) + { + Object source = e.getSource(); + SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); + if (sg != null) { - if(viewport.getSelection().size()==0) - return; + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do + { + if (ap.av.hasHiddenColumns) + { + if (start == 0) + { + start = ap.av.colSel.adjustForHiddenColumns(start); + } + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + { + end = sg.getEndRes() + 1; + } + if (end > sg.getEndRes()) + { + end = sg.getEndRes() + 1; + } + } + + regions.addElement(new int[] + {start, end}); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + } + while (end < sg.getEndRes()); - SequenceI[] s = new Sequence[viewport.getSelection().size()]; - for (int i=0; i < viewport.getSelection().size(); i++) { - s[i] = new Sequence(viewport.getSelection().sequenceAt(i)); + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } + + String description; + int caseChange; + + if (source == toggle) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; } - 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); + else if (source == upperCase) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(ap.av.hiddenRepSequences), + startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } -*/ - protected void copyGroup_actionPerformed(ActionEvent e) + } + + public void outputText_actionPerformed(ActionEvent e) { - SequenceGroup sg = av.getRubberbandGroup(); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, + 500); + + String[] omitHidden = null; - 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); + if (ap.av.hasHiddenColumns) + { + System.out.println("PROMPT USER HERE"); + omitHidden = ap.av.getViewAsString(true); + } + + cap.setText(new FormatAdapter().formatSequences( + e.getActionCommand(), + ap.av.getSelectionAsNewSequence(), + omitHidden)); } - protected void moveGroup_actionPerformed(ActionEvent e) + public void pdbFromFile_actionPerformed() { + jalview.io.JalviewFileChooser chooser + = new jalview.io.JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY")); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Select a PDB file"); + chooser.setToolTipText("Load a PDB file"); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + PDBEntry entry = new PDBEntry(); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + try + { + MCview.PDBfile pdbfile = new MCview.PDBfile(choice, + jalview.io.AppletFormatAdapter.FILE); + + if (pdbfile.id == null) + { + String reply = JOptionPane.showInternalInputDialog( + Desktop.desktop, + "Couldn't find a PDB id in the file supplied." + + "Please enter an Id to identify this structure.", + "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); + if (reply == null) + { + return; + } + + entry.setId(reply); + } + else + { + entry.setId(pdbfile.id); + } + } + catch (java.io.IOException ex) + { + ex.printStackTrace(); + } + + entry.setFile(choice); + sequence.getDatasetSequence().addPDBId(entry); + } } - protected void deleteSequences_actionPerformed(ActionEvent e) + public void enterPDB_actionPerformed() { - SequenceGroup sg = av.getRubberbandGroup(); - for (int i=0;i < sg.sequences.size(); i++) - av.getAlignment().deleteSequence(sg.getSequenceAt(i)); + String id = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE); - av.alignment.deleteGroup(sg); - av.resetSeqLimits(seqPanel.seqCanvas.getHeight()); - seqPanel.parent.RefreshPanels(); + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id); + sequence.getDatasetSequence() + .addPDBId(entry); + } + } + public void discoverPDB_actionPerformed() + { + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); } - protected void analyze_actionPerformed(ActionEvent e) + public void sequenceFeature_actionPerformed() { - 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(); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) + { + return; + } - for(int i=0; i