src/MCview/AppletPDBViewer.java

   1 package MCview;\r
   2 \r
   3 import java.awt.*;\r
   4 \r
   5 import java.awt.event.*;\r
   6 import jalview.datamodel.*;\r
   7 import jalview.appletgui.*;\r
   8 import java.awt.event.ActionListener;\r
   9 import java.awt.event.ActionEvent;\r
  10 \r
  11 \r
  12 public class AppletPDBViewer extends Frame\r
  13 {\r
  14       PDBEntry pdb;\r
  15       Sequence sequence;\r
  16       AppletPDBCanvas pdbcanvas;\r
  17 \r
  18 \r
  19       public AppletPDBViewer(String pdbtext,\r
  20                        Sequence seq,\r
  21                        SeqCanvas seqcanvas)\r
  22       {\r
  23         sequence = seq;\r
  24 \r
  25         try\r
  26         {\r
  27           jbInit();\r
  28         }\r
  29         catch (Exception ex)\r
  30         {\r
  31           ex.printStackTrace();\r
  32         }\r
  33 \r
  34         pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);\r
  35 \r
  36         add(pdbcanvas, BorderLayout.CENTER);\r
  37 \r
  38         StringBuffer title = new StringBuffer(sequence.getName() + ":");\r
  39 \r
  40         jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400);\r
  41 \r
  42         try{\r
  43         PDBfile pdbfile = new PDBfile(pdbtext, "Paste");\r
  44         pdbcanvas.setPDBFile(pdbfile);\r
  45         }catch(Exception ex){ex.printStackTrace();}\r
  46       }\r
  47 \r
  48 \r
  49       private void jbInit()\r
  50           throws Exception\r
  51       {\r
  52         this.setMenuBar(jMenuBar1);\r
  53         fileMenu.setLabel("File");\r
  54         coloursMenu.setLabel("Colours");\r
  55         mapping.setLabel("View Mapping");\r
  56         mapping.addActionListener(new ActionListener()\r
  57         {\r
  58           public void actionPerformed(ActionEvent e)\r
  59           {\r
  60             mapping_actionPerformed();\r
  61           }\r
  62         });\r
  63         wire.setLabel("Wireframe");\r
  64         wire.addItemListener(new ItemListener()\r
  65         {\r
  66           public void itemStateChanged(ItemEvent e)\r
  67           {\r
  68             wire_actionPerformed();\r
  69           }\r
  70         });\r
  71         depth.setState(true);\r
  72         depth.setLabel("Depthcue");\r
  73         depth.addItemListener(new ItemListener()\r
  74         {\r
  75           public void itemStateChanged(ItemEvent e)\r
  76           {\r
  77             depth_actionPerformed();\r
  78           }\r
  79         });\r
  80         zbuffer.setState(true);\r
  81         zbuffer.setLabel("Z Buffering");\r
  82         zbuffer.addItemListener(new ItemListener()\r
  83         {\r
  84           public void itemStateChanged(ItemEvent e)\r
  85           {\r
  86             zbuffer_actionPerformed();\r
  87           }\r
  88         });\r
  89         charge.setLabel("Charge & Cysteine");\r
  90         charge.addItemListener(new ItemListener()\r
  91         {\r
  92           public void itemStateChanged(ItemEvent e)\r
  93           {\r
  94             charge_actionPerformed();\r
  95           }\r
  96         });\r
  97         hydro.setLabel("Hydrophobicity");\r
  98         hydro.addItemListener(new ItemListener()\r
  99         {\r
 100           public void itemStateChanged(ItemEvent e)\r
 101           {\r
 102             hydro_actionPerformed();\r
 103           }\r
 104         });\r
 105         chain.setLabel("By Chain");\r
 106         chain.addItemListener(new ItemListener()\r
 107         {\r
 108           public void itemStateChanged(ItemEvent e)\r
 109           {\r
 110             chain_actionPerformed();\r
 111           }\r
 112         });\r
 113         seqButton.setState(true);\r
 114         seqButton.setLabel("By Sequence");\r
 115         seqButton.addItemListener(new ItemListener()\r
 116         {\r
 117           public void itemStateChanged(ItemEvent e)\r
 118           {\r
 119             seqButton_actionPerformed();\r
 120           }\r
 121         });\r
 122         molecule.setLabel("By Molecule");\r
 123         molecule.addItemListener(new ItemListener()\r
 124         {\r
 125           public void itemStateChanged(ItemEvent e)\r
 126           {\r
 127             molecule_actionPerformed();\r
 128           }\r
 129         });\r
 130         jMenuBar1.add(fileMenu);\r
 131         jMenuBar1.add(coloursMenu);\r
 132         fileMenu.add(mapping);;\r
 133 \r
 134         coloursMenu.add(seqButton);\r
 135         coloursMenu.add(chain);\r
 136         coloursMenu.add(hydro);\r
 137         coloursMenu.add(charge);\r
 138         coloursMenu.addSeparator();\r
 139         coloursMenu.add(wire);\r
 140         coloursMenu.add(depth);\r
 141         coloursMenu.add(zbuffer);\r
 142         coloursMenu.add(molecule);\r
 143 \r
 144       }\r
 145 \r
 146       MenuBar jMenuBar1 = new MenuBar();\r
 147       Menu fileMenu = new Menu();\r
 148       Menu coloursMenu = new Menu();\r
 149       MenuItem mapping = new MenuItem();\r
 150       CheckboxGroup bg = new CheckboxGroup();\r
 151       CheckboxMenuItem wire = new CheckboxMenuItem();\r
 152       CheckboxMenuItem depth = new CheckboxMenuItem();\r
 153       CheckboxMenuItem zbuffer = new CheckboxMenuItem();\r
 154       CheckboxMenuItem charge = new CheckboxMenuItem();\r
 155 \r
 156 \r
 157       CheckboxMenuItem hydro = new CheckboxMenuItem();\r
 158       CheckboxMenuItem chain = new CheckboxMenuItem();\r
 159       CheckboxMenuItem seqButton = new CheckboxMenuItem();\r
 160       CheckboxMenuItem molecule = new CheckboxMenuItem();\r
 161 \r
 162        public void charge_actionPerformed()\r
 163       {\r
 164         clearButtonGroup();\r
 165         pdbcanvas.pdb.setChargeColours();\r
 166         pdbcanvas.redrawneeded=true;\r
 167         pdbcanvas.repaint();\r
 168       }\r
 169 \r
 170       public void hydro_actionPerformed()\r
 171       {\r
 172         clearButtonGroup();\r
 173         pdbcanvas.pdb.setHydrophobicityColours();\r
 174         pdbcanvas.redrawneeded=true;\r
 175         pdbcanvas.repaint();\r
 176       }\r
 177 \r
 178       public void chain_actionPerformed()\r
 179       {\r
 180         clearButtonGroup();\r
 181         pdbcanvas.pdb.setChainColours();\r
 182         pdbcanvas.redrawneeded=true;\r
 183         pdbcanvas.repaint();\r
 184       }\r
 185 \r
 186       public void zbuffer_actionPerformed()\r
 187       {\r
 188         pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 189         pdbcanvas.redrawneeded=true;\r
 190         pdbcanvas.repaint();\r
 191       }\r
 192 \r
 193       public void molecule_actionPerformed()\r
 194       {\r
 195         pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
 196         pdbcanvas.redrawneeded=true;\r
 197         pdbcanvas.repaint();\r
 198       }\r
 199 \r
 200       public void depth_actionPerformed()\r
 201       {\r
 202       pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 203       pdbcanvas.redrawneeded=true;\r
 204         pdbcanvas.repaint();\r
 205       }\r
 206 \r
 207       public void wire_actionPerformed()\r
 208       {\r
 209         pdbcanvas.wire = ! pdbcanvas.wire;\r
 210         pdbcanvas.redrawneeded=true;\r
 211         pdbcanvas.repaint();\r
 212       }\r
 213 \r
 214       public void seqButton_actionPerformed()\r
 215       {\r
 216         clearButtonGroup();\r
 217         pdbcanvas.bysequence = seqButton.getState();\r
 218         pdbcanvas.updateSeqColours();\r
 219       }\r
 220 \r
 221       void clearButtonGroup()\r
 222       {\r
 223        pdbcanvas.bysequence = false;\r
 224        pdbcanvas.bymolecule = false;\r
 225       }\r
 226 \r
 227       public void mapping_actionPerformed()\r
 228       {\r
 229         jalview.appletgui.CutAndPasteTransfer cap\r
 230             = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
 231         Frame frame = new Frame();\r
 232         frame.add(cap);\r
 233         jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);\r
 234         cap.setText(pdbcanvas.mappingDetails.toString());\r
 235       }\r
 236     }\r