+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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 3
- * of the License, or (at your option) any later version.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package MCview;
-
-import jalview.appletgui.AlignmentPanel;
-import jalview.appletgui.EmbmenuFrame;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.CheckboxGroup;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-
-public class AppletPDBViewer extends EmbmenuFrame
- implements ActionListener, ItemListener
-{
- AppletPDBCanvas pdbcanvas;
-
- public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, DataSourceType protocol)
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
-
- embedMenuIfNeeded(pdbcanvas);
- add(pdbcanvas, BorderLayout.CENTER);
-
- StringBuffer title = new StringBuffer(
- seq[0].getName() + ":" + pdbcanvas.pdbentry.getFile());
-
- jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
-
- }
-
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- if (evt.getSource() == mapping)
- {
- jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
- false, null);
- Frame frame = new Frame();
- frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.getString("label.pdb_sequence_mapping"), 500,
- 600);
- cap.setText(pdbcanvas.mappingDetails.toString());
-
- }
- else if (evt.getSource() == charge)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChargeColours();
- }
-
- else if (evt.getSource() == chain)
- {
- pdbcanvas.bysequence = false;
- pdbcanvas.pdb.setChainColours();
- }
- else if (evt.getSource() == seqButton)
- {
- pdbcanvas.bysequence = true;
- pdbcanvas.colourBySequence();
-
- }
- else if (evt.getSource() == zappo)
- {
- pdbcanvas.setColours(new ZappoColourScheme());
- }
- else if (evt.getSource() == taylor)
- {
- pdbcanvas.setColours(new TaylorColourScheme());
- }
- else if (evt.getSource() == hydro)
- {
- pdbcanvas.setColours(new HydrophobicColourScheme());
- }
- else if (evt.getSource() == helix)
- {
- pdbcanvas.setColours(new HelixColourScheme());
- }
- else if (evt.getSource() == strand)
- {
- pdbcanvas.setColours(new StrandColourScheme());
- }
- else if (evt.getSource() == turn)
- {
- pdbcanvas.setColours(new TurnColourScheme());
- }
- else if (evt.getSource() == buried)
- {
- pdbcanvas.setColours(new BuriedColourScheme());
- }
- else if (evt.getSource() == user)
- {
- pdbcanvas.bysequence = false;
- new jalview.appletgui.UserDefinedColours(pdbcanvas);
- }
-
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
-
- }
-
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt.getSource() == allchains)
- {
- pdbcanvas.setAllchainsVisible(allchains.getState());
- }
- else if (evt.getSource() == wire)
- {
- pdbcanvas.wire = !pdbcanvas.wire;
- }
- else if (evt.getSource() == depth)
- {
- pdbcanvas.depthcue = !pdbcanvas.depthcue;
- }
- else if (evt.getSource() == zbuffer)
- {
- pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
- }
- pdbcanvas.redrawneeded = true;
- pdbcanvas.repaint();
- }
-
- private void jbInit() throws Exception
- {
- setMenuBar(jMenuBar1);
- fileMenu.setLabel(MessageManager.getString("action.file"));
- coloursMenu.setLabel(MessageManager.getString("label.colours"));
- mapping.setLabel(MessageManager.getString("label.view_mapping"));
- mapping.addActionListener(this);
- wire.setLabel(MessageManager.getString("label.wireframe"));
- wire.addItemListener(this);
- depth.setState(true);
- depth.setLabel(MessageManager.getString("label.depthcue"));
- depth.addItemListener(this);
- zbuffer.setState(true);
- zbuffer.setLabel(MessageManager.getString("label.z_buffering"));
- zbuffer.addItemListener(this);
- charge.setLabel(MessageManager.getString("label.charge_cysteine"));
- charge.addActionListener(this);
- hydro.setLabel(
- MessageManager.getString("label.colourScheme_hydrophobic"));
- hydro.addActionListener(this);
- chain.setLabel(MessageManager.getString("action.by_chain"));
- chain.addActionListener(this);
- seqButton.setLabel(MessageManager.getString("action.by_sequence"));
- seqButton.addActionListener(this);
- allchains
- .setLabel(MessageManager.getString("label.all_chains_visible"));
- allchains.addItemListener(this);
- viewMenu.setLabel(MessageManager.getString("action.view"));
- zappo.setLabel(MessageManager.getString("label.colourScheme_zappo"));
- zappo.addActionListener(this);
- taylor.setLabel(MessageManager.getString("label.colourScheme_taylor"));
- taylor.addActionListener(this);
- helix.setLabel(MessageManager
- .getString("label.colourScheme_helix_propensity"));
- helix.addActionListener(this);
- strand.setLabel(MessageManager
- .getString("label.colourScheme_strand_propensity"));
- strand.addActionListener(this);
- turn.setLabel(
- MessageManager.getString("label.colourScheme_turn_propensity"));
- turn.addActionListener(this);
- buried.setLabel(
- MessageManager.getString("label.colourScheme_buried_index"));
- buried.addActionListener(this);
- user.setLabel(MessageManager.getString("action.user_defined"));
- user.addActionListener(this);
- jMenuBar1.add(fileMenu);
- jMenuBar1.add(coloursMenu);
- jMenuBar1.add(viewMenu);
- fileMenu.add(mapping);
- ;
-
- coloursMenu.add(seqButton);
- coloursMenu.add(chain);
- coloursMenu.add(charge);
- coloursMenu.add(zappo);
- coloursMenu.add(taylor);
- coloursMenu.add(hydro);
- coloursMenu.add(helix);
- coloursMenu.add(strand);
- coloursMenu.add(turn);
- coloursMenu.add(buried);
- coloursMenu.add(user);
- viewMenu.add(wire);
- viewMenu.add(depth);
- viewMenu.add(zbuffer);
- viewMenu.add(allchains);
- allchains.setState(true);
- }
-
- MenuBar jMenuBar1 = new MenuBar();
-
- Menu fileMenu = new Menu();
-
- Menu coloursMenu = new Menu();
-
- MenuItem mapping = new MenuItem();
-
- CheckboxGroup bg = new CheckboxGroup();
-
- CheckboxMenuItem wire = new CheckboxMenuItem();
-
- CheckboxMenuItem depth = new CheckboxMenuItem();
-
- CheckboxMenuItem zbuffer = new CheckboxMenuItem();
-
- MenuItem charge = new MenuItem();
-
- MenuItem hydro = new MenuItem();
-
- MenuItem chain = new MenuItem();
-
- MenuItem seqButton = new MenuItem();
-
- CheckboxMenuItem allchains = new CheckboxMenuItem();
-
- Menu viewMenu = new Menu();
-
- MenuItem turn = new MenuItem();
-
- MenuItem strand = new MenuItem();
-
- MenuItem helix = new MenuItem();
-
- MenuItem taylor = new MenuItem();
-
- MenuItem zappo = new MenuItem();
-
- MenuItem buried = new MenuItem();
-
- MenuItem user = new MenuItem();
-
- // End StructureListener
- // //////////////////////////
-
-}
git://source.jalview.org / jalview.git / blobdiff