-package MCview;\r
-\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-import jalview.io.EBIFetchClient;\r
-import java.awt.event.ActionListener;\r
-import java.awt.event.ActionEvent;\r
-\r
-public class PDBViewer extends JInternalFrame implements Runnable\r
-{\r
- PDBEntry pdb;\r
- Sequence sequence;\r
- PDBCanvas pdbcanvas;\r
-\r
-\r
- public PDBViewer(PDBEntry entry,\r
- Sequence seq,\r
- SeqCanvas seqcanvas)\r
- {\r
-\r
- pdb = entry;\r
- sequence = seq;\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
-\r
- setContentPane(pdbcanvas);\r
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
- if(pdb.getProperty()!=null)\r
- {\r
- title.append( " Method: " );\r
- title.append(pdb.getProperty().get("method"));\r
- title.append( " Chain:" );\r
- title.append( pdb.getProperty().get("chains"));\r
- }\r
-\r
- Desktop.addInternalFrame(this,title.toString(),400, 400);\r
- }\r
-\r
- public void run()\r
- {\r
- try\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");\r
-\r
- PDBfile pdbfile = new PDBfile(result);\r
-\r
- pdbcanvas.setPDBFile(pdbfile);\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- pdbcanvas.keyPressed(evt);\r
- }\r
- });\r
-\r
- this.setJMenuBar(jMenuBar1);\r
- fileMenu.setText("File");\r
- coloursMenu.setText("Colours");\r
- saveMenu.setActionCommand("Save Image");\r
- saveMenu.setText("Save As");\r
- png.setText("PNG");\r
- png.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- png_actionPerformed(e);\r
- }\r
- });\r
- eps.setText("EPS");\r
- eps.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- eps_actionPerformed(e);\r
- }\r
- });\r
- mapping.setText("View Mapping");\r
- mapping.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- mapping_actionPerformed(e);\r
- }\r
- });\r
- wire.setText("Wireframe");\r
- wire.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- wire_actionPerformed(e);\r
- }\r
- });\r
- depth.setSelected(true);\r
- depth.setText("Depthcue");\r
- depth.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- depth_actionPerformed(e);\r
- }\r
- });\r
- zbuffer.setSelected(true);\r
- zbuffer.setText("Z Buffering");\r
- zbuffer.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zbuffer_actionPerformed(e);\r
- }\r
- });\r
- charge.setText("Charge & Cysteine");\r
- charge.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- charge_actionPerformed(e);\r
- }\r
- });\r
- hydro.setText("Hydrophobicity");\r
- hydro.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydro_actionPerformed(e);\r
- }\r
- });\r
- chain.setText("By Chain");\r
- chain.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- chain_actionPerformed(e);\r
- }\r
- });\r
- seqButton.setSelected(true);\r
- seqButton.setText("By Sequence");\r
- seqButton.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- seqButton_actionPerformed(e);\r
- }\r
- });\r
- molecule.setText("By Molecule");\r
- molecule.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- molecule_actionPerformed(e);\r
- }\r
- });\r
- allchains.setSelected(true);\r
- allchains.setText("Show All Chains");\r
- allchains.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- allchains_itemStateChanged(e);\r
- }\r
- });\r
- jMenuBar1.add(fileMenu);\r
- jMenuBar1.add(coloursMenu);\r
- fileMenu.add(saveMenu);\r
- fileMenu.add(mapping);\r
- saveMenu.add(png);\r
- saveMenu.add(eps);\r
- coloursMenu.add(seqButton);\r
- coloursMenu.add(chain);\r
- coloursMenu.add(hydro);\r
- coloursMenu.add(charge);\r
- coloursMenu.addSeparator();\r
- coloursMenu.add(wire);\r
- coloursMenu.add(depth);\r
- coloursMenu.add(zbuffer);\r
- coloursMenu.add(molecule);\r
- coloursMenu.add(allchains);\r
- ButtonGroup bg = new ButtonGroup();\r
- bg.add(seqButton);\r
- bg.add(chain);\r
- bg.add(hydro);\r
- bg.add(charge);\r
- }\r
-\r
- JMenuBar jMenuBar1 = new JMenuBar();\r
- JMenu fileMenu = new JMenu();\r
- JMenu coloursMenu = new JMenu();\r
- JMenu saveMenu = new JMenu();\r
- JMenuItem png = new JMenuItem();\r
- JMenuItem eps = new JMenuItem();\r
- JMenuItem mapping = new JMenuItem();\r
- JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
- JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
- JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void eps_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.EPS);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void png_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.PNG);\r
- }\r
-\r
- void makePDBImage(int type)\r
- {\r
- int width = pdbcanvas.getWidth();\r
- int height = pdbcanvas.getHeight();\r
-\r
- jalview.util.ImageMaker im;\r
-\r
- if (type == jalview.util.ImageMaker.PNG)\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.PNG,\r
- "Make PNG image from view",\r
- width, height,\r
- null, null);\r
- else\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.EPS,\r
- "Make EPS file from view",\r
- width, height,\r
- null, this.getTitle());\r
-\r
- if (im.getGraphics() != null)\r
- {\r
- pdbcanvas.drawAll(im.getGraphics(), width, height);\r
- im.writeImage();\r
- }\r
- }\r
- public void charge_actionPerformed(ActionEvent e)\r
- {\r
- clearButtonGroup();\r
- pdbcanvas.pdb.setChargeColours();\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void hydro_actionPerformed(ActionEvent e)\r
- {\r
- clearButtonGroup();\r
- pdbcanvas.pdb.setHydrophobicityColours();\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void chain_actionPerformed(ActionEvent e)\r
- {\r
- clearButtonGroup();\r
- pdbcanvas.pdb.setChainColours();\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void zbuffer_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void molecule_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void depth_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void wire_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.wire = ! pdbcanvas.wire;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void seqButton_actionPerformed(ActionEvent e)\r
- {\r
- clearButtonGroup();\r
- pdbcanvas.bysequence = seqButton.isSelected();\r
- pdbcanvas.updateSeqColours();\r
- }\r
-\r
- void clearButtonGroup()\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.bymolecule = false;\r
- }\r
-\r
- public void mapping_actionPerformed(ActionEvent e)\r
- {\r
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
- cap.setText(pdbcanvas.mappingDetails.toString());\r
- }\r
-\r
- public void allchains_itemStateChanged(ItemEvent e)\r
- {\r
- pdbcanvas.setAllchainsVisible(allchains.getState());\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.OOMWarning;
+import jalview.gui.UserDefinedColours;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+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.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.PrintWriter;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.SwingUtilities;
+
+public class PDBViewer extends JInternalFrame implements Runnable
+{
+
+ /**
+ * The associated sequence in an alignment
+ */
+ PDBCanvas pdbcanvas;
+
+ PDBEntry pdbentry;
+
+ SequenceI[] seq;
+
+ String[] chains;
+
+ AlignmentPanel ap;
+
+ String protocol;
+
+ String tmpPDBFile;
+
+ public PDBViewer(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ AlignmentPanel ap, String protocol)
+ {
+ this.pdbentry = pdbentry;
+ this.seq = seq;
+ this.chains = chains;
+ this.ap = ap;
+ this.protocol = protocol;
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ StringBuffer title = new StringBuffer(seq[0].getName() + ":"
+ + pdbentry.getFile());
+
+ pdbcanvas = new PDBCanvas();
+
+ setContentPane(pdbcanvas);
+
+ if (pdbentry.getFile() != null)
+ {
+ try
+ {
+ tmpPDBFile = pdbentry.getFile();
+ PDBfile pdbfile = new PDBfile(false, false, false, tmpPDBFile,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ else
+ {
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ if (pdbentry.getProperty() != null)
+ {
+ if (pdbentry.getProperty().get("method") != null)
+ {
+ title.append(" Method: ");
+ title.append(pdbentry.getProperty().get("method"));
+ }
+ if (pdbentry.getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdbentry.getProperty().get("chains"));
+ }
+ }
+ Desktop.addInternalFrame(this, title.toString(), 400, 400);
+ }
+
+ public void run()
+ {
+ try
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ String query = "pdb:" + pdbentry.getId();
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ .getAbsolutePath());
+
+ if (pdbentry.getFile() != null)
+ {
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
+ }
+ } catch (Exception ex)
+ {
+ pdbcanvas.errorMessage = "Error retrieving file: " + pdbentry.getId();
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ this.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ pdbcanvas.keyPressed(evt);
+ }
+ });
+
+ this.setJMenuBar(jMenuBar1);
+ fileMenu.setText(MessageManager.getString("action.file"));
+ coloursMenu.setText(MessageManager.getString("label.colours"));
+ saveMenu.setActionCommand(MessageManager.getString("action.save_image"));
+ saveMenu.setText(MessageManager.getString("action.save_as"));
+ png.setText("PNG");
+ png.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ png_actionPerformed(e);
+ }
+ });
+ eps.setText("EPS");
+ eps.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ eps_actionPerformed(e);
+ }
+ });
+ mapping.setText(MessageManager.getString("label.view_mapping"));
+ mapping.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ mapping_actionPerformed(e);
+ }
+ });
+ wire.setText(MessageManager.getString("label.wireframe"));
+ wire.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ wire_actionPerformed(e);
+ }
+ });
+ depth.setSelected(true);
+ depth.setText(MessageManager.getString("label.depthcue"));
+ depth.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ depth_actionPerformed(e);
+ }
+ });
+ zbuffer.setSelected(true);
+ zbuffer.setText(MessageManager.getString("label.z_buffering"));
+ zbuffer.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zbuffer_actionPerformed(e);
+ }
+ });
+ charge.setText(MessageManager.getString("label.charge_cysteine"));
+ charge.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ charge_actionPerformed(e);
+ }
+ });
+ chain.setText(MessageManager.getString("action.by_chain"));
+ chain.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ chain_actionPerformed(e);
+ }
+ });
+ seqButton.setSelected(true);
+ seqButton.setText(MessageManager.getString("action.by_sequence"));
+ seqButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ seqButton_actionPerformed(e);
+ }
+ });
+ allchains.setSelected(true);
+ allchains.setText(MessageManager.getString("label.show_all_chains"));
+ allchains.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ allchains_itemStateChanged(e);
+ }
+ });
+ zappo.setText(MessageManager.getString("label.zappo"));
+ zappo.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappo_actionPerformed(e);
+ }
+ });
+ taylor.setText(MessageManager.getString("label.taylor"));
+ taylor.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylor_actionPerformed(e);
+ }
+ });
+ hydro.setText(MessageManager.getString("label.hydrophobicity"));
+ hydro.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydro_actionPerformed(e);
+ }
+ });
+ helix.setText(MessageManager.getString("label.helix_propensity"));
+ helix.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helix_actionPerformed(e);
+ }
+ });
+ strand.setText(MessageManager.getString("label.strand_propensity"));
+ strand.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strand_actionPerformed(e);
+ }
+ });
+ turn.setText(MessageManager.getString("label.turn_propensity"));
+ turn.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turn_actionPerformed(e);
+ }
+ });
+ buried.setText(MessageManager.getString("label.buried_index"));
+ buried.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buried_actionPerformed(e);
+ }
+ });
+ user.setText(MessageManager.getString("action.user_defined"));
+ user.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ user_actionPerformed(e);
+ }
+ });
+ viewMenu.setText(MessageManager.getString("action.view"));
+ background
+ .setText(MessageManager.getString("action.background_colour"));
+ background.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ background_actionPerformed(e);
+ }
+ });
+ savePDB.setText(MessageManager.getString("label.pdb_file"));
+ savePDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ savePDB_actionPerformed(e);
+ }
+ });
+ jMenuBar1.add(fileMenu);
+ jMenuBar1.add(coloursMenu);
+ jMenuBar1.add(viewMenu);
+ fileMenu.add(saveMenu);
+ fileMenu.add(mapping);
+ saveMenu.add(savePDB);
+ saveMenu.add(png);
+ saveMenu.add(eps);
+ 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);
+ coloursMenu.add(background);
+ ButtonGroup bg = new ButtonGroup();
+ bg.add(seqButton);
+ bg.add(chain);
+ bg.add(charge);
+ bg.add(zappo);
+ bg.add(taylor);
+ bg.add(hydro);
+ bg.add(helix);
+ bg.add(strand);
+ bg.add(turn);
+ bg.add(buried);
+ bg.add(user);
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+ .getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColours.nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isControlDown()
+ || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop,
+ MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ coloursMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ user_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ user_actionPerformed(evt);
+ }
+ });
+ coloursMenu.add(radioItem);
+ bg.add(radioItem);
+ }
+ }
+
+ viewMenu.add(wire);
+ viewMenu.add(depth);
+ viewMenu.add(zbuffer);
+ viewMenu.add(allchains);
+ }
+
+ JMenuBar jMenuBar1 = new JMenuBar();
+
+ JMenu fileMenu = new JMenu();
+
+ JMenu coloursMenu = new JMenu();
+
+ JMenu saveMenu = new JMenu();
+
+ JMenuItem png = new JMenuItem();
+
+ JMenuItem eps = new JMenuItem();
+
+ JMenuItem mapping = new JMenuItem();
+
+ JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
+
+ JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+
+ JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+
+ JMenu viewMenu = new JMenu();
+
+ JMenuItem background = new JMenuItem();
+
+ JMenuItem savePDB = new JMenuItem();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+ }
+
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
+ {
+ int width = pdbcanvas.getWidth();
+ int height = pdbcanvas.getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle());
+ }
+ else
+ {
+
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle());
+ }
+
+ if (im.getGraphics() != null)
+ {
+ pdbcanvas.drawAll(im.getGraphics(), width, height);
+ im.writeImage();
+ }
+ }
+
+ public void charge_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChargeColours();
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void hydro_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void chain_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChainColours();
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void zbuffer_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void molecule_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bymolecule = !pdbcanvas.bymolecule;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void depth_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.depthcue = !pdbcanvas.depthcue;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void wire_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.wire = !pdbcanvas.wire;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void seqButton_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = true;
+ pdbcanvas.updateSeqColours();
+ }
+
+ public void mapping_actionPerformed(ActionEvent e)
+ {
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ try
+ {
+ cap.setText(pdbcanvas.mappingDetails.toString());
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Opening sequence to structure mapping report", oom);
+ cap.dispose();
+ }
+ }
+
+ public void allchains_itemStateChanged(ItemEvent e)
+ {
+ pdbcanvas.setAllchainsVisible(allchains.getState());
+ }
+
+ public void zappo_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new ZappoColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void taylor_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new TaylorColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void helix_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new HelixColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void strand_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new StrandColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void turn_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new TurnColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void buried_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new BuriedColourScheme());
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+
+ public void user_actionPerformed(ActionEvent e)
+ {
+ if (e.getActionCommand().equals(
+ MessageManager.getString("action.user_defined")))
+ {
+ // new UserDefinedColours(pdbcanvas, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ .getUserColourSchemes().get(e.getActionCommand());
+
+ pdbcanvas.pdb.setColours(udc);
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+ }
+
+ public void background_actionPerformed(ActionEvent e)
+ {
+ java.awt.Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_backgroud_colour"),
+ pdbcanvas.backgroundColour);
+
+ if (col != null)
+ {
+ pdbcanvas.backgroundColour = col;
+ pdbcanvas.redrawneeded = true;
+ pdbcanvas.repaint();
+ }
+ }
+
+ public void savePDB_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ BufferedReader in = new BufferedReader(new FileReader(tmpPDBFile));
+ File outFile = chooser.getSelectedFile();
+
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+ while ((data = in.readLine()) != null)
+ {
+ if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
+ {
+ out.println(data);
+ }
+ }
+ out.close();
+ in.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff