-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.jbgui;\r
-\r
-import javax.swing.*;\r
-import java.awt.event.ActionListener;\r
-import java.awt.event.ActionEvent;\r
-\r
-public class GStructureViewer extends JInternalFrame\r
-{\r
- public GStructureViewer()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setJMenuBar(menuBar);\r
- fileMenu.setText("File");\r
- savemenu.setActionCommand("Save Image");\r
- savemenu.setText("Save As");\r
- pdbFile.setText("PDB File");\r
- pdbFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- pdbFile_actionPerformed(actionEvent);\r
- }\r
- });\r
- png.setText("PNG");\r
- png.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- png_actionPerformed(actionEvent);\r
- }\r
- });\r
- eps.setText("EPS");\r
- eps.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- eps_actionPerformed(actionEvent);\r
- }\r
- });\r
- viewMapping.setText("View Mapping");\r
- viewMapping.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- viewMapping_actionPerformed(actionEvent);\r
- }\r
- });\r
- viewMenu.setText("View");\r
- chainMenu.setText("Show Chain");\r
- jMenu2.setText("Colours");\r
- backGround.setText("Background Colour...");\r
- backGround.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- backGround_actionPerformed(actionEvent);\r
- }\r
- });\r
- seqColour.setSelected(true);\r
- seqColour.setText("By Sequence");\r
- seqColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- seqColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- chainColour.setText("By Chain");\r
- chainColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- chainColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- chargeColour.setText("Charge & Cysteine");\r
- chargeColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- chargeColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- zappoColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- taylorColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- hydroColour.setText("Hydro");\r
- hydroColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- hydroColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- strandColour.setText("Strand");\r
- strandColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- strandColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- helixColour.setText("Helix");\r
- helixColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- helixColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- turnColour.setText("Turn");\r
- turnColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- turnColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- buriedColour.setText("Buried");\r
- buriedColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- buriedColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- userColour.setText("User Defined ...");\r
- userColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- userColour_actionPerformed(actionEvent);\r
- }\r
- });\r
- menuBar.add(fileMenu);\r
- menuBar.add(viewMenu);\r
- menuBar.add(jMenu2);\r
- fileMenu.add(savemenu);\r
- fileMenu.add(viewMapping);\r
- savemenu.add(pdbFile);\r
- savemenu.add(png);\r
- savemenu.add(eps);\r
- viewMenu.add(chainMenu);\r
- jMenu2.add(seqColour);\r
- jMenu2.add(chainColour);\r
- jMenu2.add(chargeColour);\r
- jMenu2.add(zappoColour);\r
- jMenu2.add(taylorColour);\r
- jMenu2.add(hydroColour);\r
- jMenu2.add(helixColour);\r
- jMenu2.add(strandColour);\r
- jMenu2.add(turnColour);\r
- jMenu2.add(buriedColour);\r
- jMenu2.add(userColour);\r
- jMenu2.add(backGround);\r
- }\r
-\r
- JMenuBar menuBar = new JMenuBar();\r
- JMenu fileMenu = new JMenu();\r
- JMenu savemenu = new JMenu();\r
- JMenuItem pdbFile = new JMenuItem();\r
- JMenuItem png = new JMenuItem();\r
- JMenuItem eps = new JMenuItem();\r
- JMenuItem viewMapping = new JMenuItem();\r
- JMenu viewMenu = new JMenu();\r
- protected JMenu chainMenu = new JMenu();\r
- JMenu jMenu1 = new JMenu();\r
- JMenu jMenu2 = new JMenu();\r
- JMenuItem backGround = new JMenuItem();\r
- protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();\r
- JMenuItem chainColour = new JMenuItem();\r
- JMenuItem chargeColour = new JMenuItem();\r
- JMenuItem zappoColour = new JMenuItem();\r
- JMenuItem taylorColour = new JMenuItem();\r
- JMenuItem hydroColour = new JMenuItem();\r
- JMenuItem strandColour = new JMenuItem();\r
- JMenuItem helixColour = new JMenuItem();\r
- JMenuItem turnColour = new JMenuItem();\r
- JMenuItem buriedColour = new JMenuItem();\r
- JMenuItem userColour = new JMenuItem();\r
- public void pdbFile_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void png_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void eps_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void viewMapping_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void seqColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void chainColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void chargeColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void hydroColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void strandColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void turnColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void buriedColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void userColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void backGround_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\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 jalview.jbgui;
+
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.util.MessageManager;
+
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+
+public abstract class GStructureViewer extends JInternalFrame implements
+ JalviewStructureDisplayI
+{
+ // private AAStructureBindingModel bindingModel;
+
+ protected JMenu savemenu = new JMenu();
+
+ protected JMenu viewMenu = new JMenu();
+
+ protected JMenu chainMenu = new JMenu();
+
+ protected JMenu viewerActionMenu = new JMenu();
+
+ protected JMenuItem alignStructs = new JMenuItem();
+
+ protected JMenuItem fitToWindow = new JMenuItem();
+
+ protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
+
+ protected JMenuItem helpItem = new JMenuItem();
+
+ protected JLabel statusBar = new JLabel();
+
+ protected JPanel statusPanel = new JPanel();
+
+ /**
+ * Constructor
+ */
+ public GStructureViewer()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ JMenuBar menuBar = new JMenuBar();
+ this.setJMenuBar(menuBar);
+
+ JMenu fileMenu = new JMenu();
+ fileMenu.setText(MessageManager.getString("action.file"));
+
+ savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+ savemenu.setText(MessageManager.getString("action.save_as"));
+
+ JMenuItem pdbFile = new JMenuItem();
+ pdbFile.setText(MessageManager.getString("label.pdb_file"));
+ pdbFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ pdbFile_actionPerformed(actionEvent);
+ }
+ });
+
+ JMenuItem png = new JMenuItem();
+ png.setText("PNG");
+ png.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ png_actionPerformed(actionEvent);
+ }
+ });
+
+ JMenuItem eps = new JMenuItem();
+ eps.setText("EPS");
+ eps.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ eps_actionPerformed(actionEvent);
+ }
+ });
+
+ JMenuItem viewMapping = new JMenuItem();
+ viewMapping.setText(MessageManager.getString("label.view_mapping"));
+ viewMapping.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ viewMapping_actionPerformed(actionEvent);
+ }
+ });
+ viewMenu.setText(MessageManager.getString("action.view"));
+
+ chainMenu.setText(MessageManager.getString("action.show_chain"));
+
+ fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
+ fitToWindow.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ fitToWindow_actionPerformed();
+ }
+ });
+
+ JMenu colourMenu = new JMenu();
+ colourMenu.setText(MessageManager.getString("label.colours"));
+
+ JMenuItem backGround = new JMenuItem();
+ backGround
+ .setText(MessageManager.getString("action.background_colour"));
+ backGround.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ backGround_actionPerformed(actionEvent);
+ }
+ });
+ seqColour.setSelected(false);
+ seqColour.setText(MessageManager.getString("action.by_sequence"));
+ seqColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ seqColour_actionPerformed(actionEvent);
+ }
+ });
+ chainColour.setText(MessageManager.getString("action.by_chain"));
+ chainColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chainColour_actionPerformed(actionEvent);
+ }
+ });
+ chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
+ chargeColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ chargeColour_actionPerformed(actionEvent);
+ }
+ });
+ zappoColour.setText(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ zappoColour_actionPerformed(actionEvent);
+ }
+ });
+ taylorColour.setText(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ taylorColour_actionPerformed(actionEvent);
+ }
+ });
+ hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydroColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ hydroColour_actionPerformed(actionEvent);
+ }
+ });
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ strandColour_actionPerformed(actionEvent);
+ }
+ });
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ helixColour_actionPerformed(actionEvent);
+ }
+ });
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ turnColour_actionPerformed(actionEvent);
+ }
+ });
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ buriedColour_actionPerformed(actionEvent);
+ }
+ });
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ purinePyrimidineColour_actionPerformed(actionEvent);
+ }
+ });
+
+ userColour.setText(MessageManager.getString("action.user_defined"));
+ userColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ userColour_actionPerformed(actionEvent);
+ }
+ });
+ viewerColour.setSelected(false);
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
+ viewerColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ viewerColour_actionPerformed(actionEvent);
+ }
+ });
+
+ JMenu helpMenu = new JMenu();
+ helpMenu.setText(MessageManager.getString("action.help"));
+ helpItem.setText(MessageManager.getString("label.jmol_help"));
+ helpItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ showHelp_actionPerformed(actionEvent);
+ }
+ });
+ alignStructs
+ .setText(MessageManager.getString("label.align_structures"));
+ alignStructs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alignStructs_actionPerformed(actionEvent);
+ }
+ });
+ viewerActionMenu.setText(MessageManager.getString("label.jmol"));
+ menuBar.add(fileMenu);
+ menuBar.add(viewMenu);
+ menuBar.add(colourMenu);
+ menuBar.add(viewerActionMenu);
+ viewerActionMenu.setVisible(false);
+ menuBar.add(helpMenu);
+ fileMenu.add(savemenu);
+ fileMenu.add(viewMapping);
+ savemenu.add(pdbFile);
+ savemenu.add(png);
+ savemenu.add(eps);
+ viewMenu.add(chainMenu);
+
+ colourMenu.add(seqColour);
+ colourMenu.add(chainColour);
+ colourMenu.add(chargeColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydroColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(userColour);
+ colourMenu.add(viewerColour);
+ colourMenu.add(backGround);
+
+ ButtonGroup colourButtons = new ButtonGroup();
+
+ colourButtons.add(seqColour);
+ colourButtons.add(chainColour);
+ colourButtons.add(chargeColour);
+ colourButtons.add(zappoColour);
+ colourButtons.add(taylorColour);
+ colourButtons.add(hydroColour);
+ colourButtons.add(helixColour);
+ colourButtons.add(strandColour);
+ colourButtons.add(turnColour);
+ colourButtons.add(buriedColour);
+ colourButtons.add(purinePyrimidineColour);
+ colourButtons.add(userColour);
+ colourButtons.add(viewerColour);
+
+ helpMenu.add(helpItem);
+ viewerActionMenu.add(alignStructs);
+
+ statusPanel.setLayout(new GridLayout());
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ }
+
+ protected void fitToWindow_actionPerformed()
+ {
+ }
+
+ protected void viewerColour_actionPerformed(ActionEvent actionEvent)
+ {
+ }
+
+ protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ {
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void png_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void eps_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void viewMapping_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void seqColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void chainColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void chargeColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void zappoColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void taylorColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void hydroColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void helixColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void strandColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void turnColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void buriedColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void userColour_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void backGround_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
+ {
+
+ }
+
+ // {
+ // return bindingModel;
+ // }
+
+ // public void setBindingModel(AAStructureBindingModel bindingModel)
+ // {
+ // this.bindingModel = bindingModel;
+ // }
+
+}
git://source.jalview.org / jalview.git / blobdiff