--- /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 mc_view;
+
+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