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,String type,\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, type);\r
  44         pdbcanvas.setPDBFile(pdbfile);\r
  45         }\r
  46         catch(Exception ex){\r
  47           pdbcanvas.errorLoading = true;\r
  48           pdbcanvas.repaint();\r
  49         }\r
  50       }\r
  51 \r
  52 \r
  53       private void jbInit()\r
  54           throws Exception\r
  55       {\r
  56         this.setMenuBar(jMenuBar1);\r
  57         fileMenu.setLabel("File");\r
  58         coloursMenu.setLabel("Colours");\r
  59         mapping.setLabel("View Mapping");\r
  60         mapping.addActionListener(new ActionListener()\r
  61         {\r
  62           public void actionPerformed(ActionEvent e)\r
  63           {\r
  64             mapping_actionPerformed();\r
  65           }\r
  66         });\r
  67         wire.setLabel("Wireframe");\r
  68         wire.addItemListener(new ItemListener()\r
  69         {\r
  70           public void itemStateChanged(ItemEvent e)\r
  71           {\r
  72             wire_actionPerformed();\r
  73           }\r
  74         });\r
  75         depth.setState(true);\r
  76         depth.setLabel("Depthcue");\r
  77         depth.addItemListener(new ItemListener()\r
  78         {\r
  79           public void itemStateChanged(ItemEvent e)\r
  80           {\r
  81             depth_actionPerformed();\r
  82           }\r
  83         });\r
  84         zbuffer.setState(true);\r
  85         zbuffer.setLabel("Z Buffering");\r
  86         zbuffer.addItemListener(new ItemListener()\r
  87         {\r
  88           public void itemStateChanged(ItemEvent e)\r
  89           {\r
  90             zbuffer_actionPerformed();\r
  91           }\r
  92         });\r
  93         charge.setLabel("Charge & Cysteine");\r
  94         charge.addActionListener(new ActionListener()\r
  95         {\r
  96           public void actionPerformed(ActionEvent e)\r
  97           {\r
  98             charge_actionPerformed();\r
  99           }\r
 100         });\r
 101         hydro.setLabel("Hydrophobicity");\r
 102         hydro.addActionListener(new ActionListener()\r
 103         {\r
 104           public void actionPerformed(ActionEvent e)\r
 105           {\r
 106             hydro_actionPerformed();\r
 107           }\r
 108         });\r
 109         chain.setLabel("By Chain");\r
 110         chain.addActionListener(new ActionListener()\r
 111         {\r
 112           public void actionPerformed(ActionEvent e)\r
 113           {\r
 114             chain_actionPerformed();\r
 115           }\r
 116         });\r
 117         seqButton.setLabel("By Sequence");\r
 118         seqButton.addActionListener(new ActionListener()\r
 119         {\r
 120           public void actionPerformed(ActionEvent e){\r
 121             seqButton_actionPerformed();\r
 122           }\r
 123         });\r
 124     allchains.setLabel("All Chains Visible");\r
 125     allchains.addItemListener(new ItemListener()\r
 126     {\r
 127       public void itemStateChanged(ItemEvent itemEvent)\r
 128       {\r
 129         allchains_itemStateChanged(itemEvent);\r
 130       }\r
 131     });\r
 132     jMenuBar1.add(fileMenu);\r
 133         jMenuBar1.add(coloursMenu);\r
 134         fileMenu.add(mapping);;\r
 135 \r
 136         coloursMenu.add(seqButton);\r
 137         coloursMenu.add(chain);\r
 138     coloursMenu.add(hydro);\r
 139     coloursMenu.add(charge);\r
 140     coloursMenu.addSeparator();\r
 141         coloursMenu.add(wire);\r
 142         coloursMenu.add(depth);\r
 143         coloursMenu.add(zbuffer);\r
 144     coloursMenu.add(allchains);\r
 145     allchains.setState(true);\r
 146   }\r
 147 \r
 148       MenuBar jMenuBar1 = new MenuBar();\r
 149       Menu fileMenu = new Menu();\r
 150       Menu coloursMenu = new Menu();\r
 151       MenuItem mapping = new MenuItem();\r
 152       CheckboxGroup bg = new CheckboxGroup();\r
 153       CheckboxMenuItem wire = new CheckboxMenuItem();\r
 154       CheckboxMenuItem depth = new CheckboxMenuItem();\r
 155       CheckboxMenuItem zbuffer = new CheckboxMenuItem();\r
 156 \r
 157       MenuItem charge = new MenuItem();\r
 158       MenuItem hydro = new MenuItem();\r
 159       MenuItem chain = new MenuItem();\r
 160       MenuItem seqButton = new MenuItem();\r
 161 \r
 162      CheckboxMenuItem allchains = new CheckboxMenuItem();\r
 163 \r
 164   public void charge_actionPerformed()\r
 165       {\r
 166         clearButtonGroup();\r
 167         pdbcanvas.pdb.setChargeColours();\r
 168         pdbcanvas.redrawneeded=true;\r
 169         pdbcanvas.repaint();\r
 170       }\r
 171 \r
 172       public void hydro_actionPerformed()\r
 173       {\r
 174         clearButtonGroup();\r
 175         pdbcanvas.pdb.setHydrophobicityColours();\r
 176         pdbcanvas.redrawneeded=true;\r
 177         pdbcanvas.repaint();\r
 178       }\r
 179 \r
 180       public void chain_actionPerformed()\r
 181       {\r
 182         clearButtonGroup();\r
 183         pdbcanvas.pdb.setChainColours();\r
 184         pdbcanvas.redrawneeded=true;\r
 185         pdbcanvas.repaint();\r
 186       }\r
 187 \r
 188       public void zbuffer_actionPerformed()\r
 189       {\r
 190         pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
 191         pdbcanvas.redrawneeded=true;\r
 192         pdbcanvas.repaint();\r
 193       }\r
 194 \r
 195       public void depth_actionPerformed()\r
 196       {\r
 197       pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
 198       pdbcanvas.redrawneeded=true;\r
 199         pdbcanvas.repaint();\r
 200       }\r
 201 \r
 202       public void wire_actionPerformed()\r
 203       {\r
 204         pdbcanvas.wire = ! pdbcanvas.wire;\r
 205         pdbcanvas.redrawneeded=true;\r
 206         pdbcanvas.repaint();\r
 207       }\r
 208 \r
 209       public void seqButton_actionPerformed()\r
 210       {\r
 211         clearButtonGroup();\r
 212         pdbcanvas.bysequence = true;\r
 213         pdbcanvas.updateSeqColours();\r
 214         pdbcanvas.repaint();\r
 215       }\r
 216 \r
 217       void clearButtonGroup()\r
 218       {\r
 219        pdbcanvas.bysequence = false;\r
 220        pdbcanvas.bymolecule = false;\r
 221       }\r
 222 \r
 223       public void mapping_actionPerformed()\r
 224       {\r
 225         jalview.appletgui.CutAndPasteTransfer cap\r
 226             = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
 227         Frame frame = new Frame();\r
 228         frame.add(cap);\r
 229         jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);\r
 230         cap.setText(pdbcanvas.mappingDetails.toString());\r
 231       }\r
 232 \r
 233       public void allchains_itemStateChanged(ItemEvent itemEvent)\r
 234       {\r
 235         pdbcanvas.setAllchainsVisible(allchains.getState());\r
 236       }\r
 237 }\r