src/MCview/AppletPDBViewer.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package MCview;\r
  20 \r
  21 import java.awt.*;\r
  22 \r
  23 import java.awt.event.*;\r
  24 import jalview.datamodel.*;\r
  25 import jalview.appletgui.*;\r
  26 import java.awt.event.ActionListener;\r
  27 import java.awt.event.ActionEvent;\r
  28 \r
  29 \r
  30 public class AppletPDBViewer extends Frame\r
  31 {\r
  32       PDBEntry pdb;\r
  33       Sequence sequence;\r
  34       AppletPDBCanvas pdbcanvas;\r
  35 \r
  36 \r
  37       public AppletPDBViewer(String pdbtext,String type,\r
  38                        Sequence seq,\r
  39                        SeqCanvas seqcanvas)\r
  40       {\r
  41         sequence = seq;\r
  42 \r
  43         try\r
  44         {\r
  45           jbInit();\r
  46         }\r
  47         catch (Exception ex)\r
  48         {\r
  49           ex.printStackTrace();\r
  50         }\r
  51 \r
  52         pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);\r
  53 \r
  54         add(pdbcanvas, BorderLayout.CENTER);\r
  55 \r
  56         StringBuffer title = new StringBuffer(sequence.getName() + ":");\r
  57 \r
  58         jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400);\r
  59 \r
  60         try{\r
  61         PDBfile pdbfile = new PDBfile(pdbtext, type);\r
  62         pdbcanvas.setPDBFile(pdbfile);\r
  63         }\r
  64         catch(Exception ex){\r
  65           pdbcanvas.errorLoading = true;\r
  66           pdbcanvas.repaint();\r
  67         }\r
  68       }\r
  69 \r
  70 \r
  71       private void jbInit()\r
  72           throws Exception\r
  73       {\r
  74         this.setMenuBar(jMenuBar1);\r
  75         fileMenu.setLabel("File");\r
  76         coloursMenu.setLabel("Colours");\r
  77         mapping.setLabel("View Mapping");\r
  78         mapping.addActionListener(new ActionListener()\r
  79         {\r
  80           public void actionPerformed(ActionEvent e)\r
  81           {\r
  82             mapping_actionPerformed();\r
  83           }\r
  84         });\r
  85         wire.setLabel("Wireframe");\r
  86         wire.addItemListener(new ItemListener()\r
  87         {\r
  88           public void itemStateChanged(ItemEvent e)\r
  89           {\r
  90             wire_actionPerformed();\r
  91           }\r
  92         });\r
  93         depth.setState(true);\r
  94         depth.setLabel("Depthcue");\r
  95         depth.addItemListener(new ItemListener()\r
  96         {\r
  97           public void itemStateChanged(ItemEvent e)\r
  98           {\r
  99             depth_actionPerformed();\r
 100           }\r
 101         });\r
 102         zbuffer.setState(true);\r
 103         zbuffer.setLabel("Z Buffering");\r
 104         zbuffer.addItemListener(new ItemListener()\r
 105         {\r
 106           public void itemStateChanged(ItemEvent e)\r
 107           {\r
 108             zbuffer_actionPerformed();\r
 109           }\r
 110         });\r
 111         charge.setLabel("Charge & Cysteine");\r
 112         charge.addActionListener(new ActionListener()\r
 113         {\r
 114           public void actionPerformed(ActionEvent e)\r
 115           {\r
 116             charge_actionPerformed();\r
 117           }\r
 118         });\r
 119         hydro.setLabel("Hydrophobicity");\r
 120         hydro.addActionListener(new ActionListener()\r
 121         {\r
 122           public void actionPerformed(ActionEvent e)\r
 123           {\r
 124             hydro_actionPerformed();\r
 125           }\r
 126         });\r
 127         chain.setLabel("By Chain");\r
 128         chain.addActionListener(new ActionListener()\r
 129         {\r
 130           public void actionPerformed(ActionEvent e)\r
 131           {\r
 132             chain_actionPerformed();\r
 133           }\r
 134         });\r
 135         seqButton.setLabel("By Sequence");\r
 136         seqButton.addActionListener(new ActionListener()\r
 137         {\r
 138           public void actionPerformed(ActionEvent e){\r
 139             seqButton_actionPerformed();\r
 140           }\r
 141         });\r
 142     allchains.setLabel("All Chains Visible");\r
 143     allchains.addItemListener(new ItemListener()\r
 144     {\r
 145       public void itemStateChanged(ItemEvent itemEvent)\r
 146       {\r
 147         allchains_itemStateChanged(itemEvent);\r
 148       }\r
 149     });\r
 150     jMenuBar1.add(fileMenu);\r
 151         jMenuBar1.add(coloursMenu);\r
 152         fileMenu.add(mapping);;\r
 153 \r
 154         coloursMenu.add(seqButton);\r
 155         coloursMenu.add(chain);\r
 156     coloursMenu.add(hydro);\r
 157     coloursMenu.add(charge);\r
 158     coloursMenu.addSeparator();\r
 159         coloursMenu.add(wire);\r
 160         coloursMenu.add(depth);\r
 161         coloursMenu.add(zbuffer);\r
 162     coloursMenu.add(allchains);\r
 163     allchains.setState(true);\r
 164   }\r
 165 \r
 166       MenuBar jMenuBar1 = new MenuBar();\r
 167       Menu fileMenu = new Menu();\r
 168       Menu coloursMenu = new Menu();\r
 169       MenuItem mapping = new MenuItem();\r
 170       CheckboxGroup bg = new CheckboxGroup();\r
 171       CheckboxMenuItem wire = new CheckboxMenuItem();\r
 172       CheckboxMenuItem depth = new CheckboxMenuItem();\r
 173       CheckboxMenuItem zbuffer = new CheckboxMenuItem();\r
 174 \r
 175       MenuItem charge = new MenuItem();\r
 176       MenuItem hydro = new MenuItem();\r
 177       MenuItem chain = new MenuItem();\r
 178       MenuItem seqButton = new MenuItem();\r
 179 \r
 180      CheckboxMenuItem allchains = new CheckboxMenuItem();\r
 181 \r
 182   public void charge_actionPerformed()\r
 183       {\r
 184         clearButtonGroup();\r
 185         pdbcanvas.pdb.setChargeColours();\r
 186         pdbcanvas.redrawneeded=true;\r
 187         pdbcanvas.repaint();\r
 188       }\r
 189 \r
 190       public void hydro_actionPerformed()\r
 191       {\r
 192         clearButtonGroup();\r
 193        // pdbcanvas.pdb.setHydrophobicityColours();\r
 194         pdbcanvas.redrawneeded=true;\r
 195         pdbcanvas.repaint();\r
 196       }\r
 197 \r
 198       public void chain_actionPerformed()\r
 199       {\r
 200         clearButtonGroup();\r
 201         pdbcanvas.pdb.setChainColours();\r
 202         pdbcanvas.redrawneeded=true;\r
 203         pdbcanvas.repaint();\r
 204       }\r
 205 \r
 206       public void zbuffer_actionPerformed()\r
 207       {\r
 208         pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 209         pdbcanvas.redrawneeded=true;\r
 210         pdbcanvas.repaint();\r
 211       }\r
 212 \r
 213       public void depth_actionPerformed()\r
 214       {\r
 215       pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 216       pdbcanvas.redrawneeded=true;\r
 217         pdbcanvas.repaint();\r
 218       }\r
 219 \r
 220       public void wire_actionPerformed()\r
 221       {\r
 222         pdbcanvas.wire = ! pdbcanvas.wire;\r
 223         pdbcanvas.redrawneeded=true;\r
 224         pdbcanvas.repaint();\r
 225       }\r
 226 \r
 227       public void seqButton_actionPerformed()\r
 228       {\r
 229         clearButtonGroup();\r
 230         pdbcanvas.bysequence = true;\r
 231         pdbcanvas.updateSeqColours();\r
 232         pdbcanvas.repaint();\r
 233       }\r
 234 \r
 235       void clearButtonGroup()\r
 236       {\r
 237        pdbcanvas.bysequence = false;\r
 238        pdbcanvas.bymolecule = false;\r
 239       }\r
 240 \r
 241       public void mapping_actionPerformed()\r
 242       {\r
 243         jalview.appletgui.CutAndPasteTransfer cap\r
 244             = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
 245         Frame frame = new Frame();\r
 246         frame.add(cap);\r
 247         jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);\r
 248         cap.setText(pdbcanvas.mappingDetails.toString());\r
 249       }\r
 250 \r
 251       public void allchains_itemStateChanged(ItemEvent itemEvent)\r
 252       {\r
 253         pdbcanvas.setAllchainsVisible(allchains.getState());\r
 254       }\r
 255 }\r