import jalview.datamodel.*;\r
import jalview.schemes.*;\r
\r
+\r
public class AppletPDBViewer\r
extends Frame implements ActionListener, ItemListener\r
{\r
AppletPDBCanvas pdbcanvas;\r
- public AppletPDBViewer(String pdbtext, String type,\r
- Sequence seq,\r
- SeqCanvas seqcanvas)\r
- {\r
\r
+ public AppletPDBViewer(PDBEntry pdbentry,\r
+ SequenceI[] seq,\r
+ AlignmentPanel ap,\r
+ String protocol)\r
+ {\r
try\r
{\r
jbInit();\r
ex.printStackTrace();\r
}\r
\r
- pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);\r
+ pdbcanvas = new AppletPDBCanvas(pdbentry, seq, ap, protocol);\r
+\r
\r
add(pdbcanvas, BorderLayout.CENTER);\r
\r
- StringBuffer title = new StringBuffer(seq.getName() + ":");\r
+ System.out.println(seq[0].getName()+" ASFA");\r
+\r
+ StringBuffer title = new StringBuffer(seq[0].getName()\r
+ + ":"\r
+ + pdbcanvas.pdbentry.getFile());\r
\r
jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);\r
\r
- try\r
- {\r
- PDBfile pdbfile = new PDBfile(pdbtext, type);\r
- pdbcanvas.setPDBFile(pdbfile);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- pdbcanvas.errorLoading = true;\r
- pdbcanvas.repaint();\r
- }\r
}\r
\r
+\r
+\r
public void actionPerformed(ActionEvent evt)\r
{\r
if (evt.getSource() == mapping)\r
{\r
- mapping_actionPerformed();\r
- }\r
- else if (evt.getSource() == wire)\r
- {\r
- wire_actionPerformed();\r
- }\r
- else if (evt.getSource() == depth)\r
- {\r
- depth_actionPerformed();\r
- }\r
- else if (evt.getSource() == zbuffer)\r
- {\r
- zbuffer_actionPerformed();\r
+ jalview.appletgui.CutAndPasteTransfer cap\r
+ = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,\r
+ 600);\r
+ cap.setText(pdbcanvas.mappingDetails.toString());\r
+\r
}\r
else if (evt.getSource() == charge)\r
{\r
- charge_actionPerformed();\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setChargeColours();\r
}\r
\r
else if (evt.getSource() == chain)\r
{\r
- chain_actionPerformed();\r
+ pdbcanvas.bysequence = false;\r
+ pdbcanvas.pdb.setChainColours();\r
}\r
else if (evt.getSource() == seqButton)\r
{\r
- seqButton_actionPerformed();\r
+ pdbcanvas.bysequence = true;\r
+ pdbcanvas.colourBySequence(pdbcanvas.ap.getSequenceRenderer(),\r
+ pdbcanvas.ap.av.getShowSequenceFeatures() ?\r
+ pdbcanvas.ap.getFeatureRenderer() : null);\r
+\r
}\r
else if (evt.getSource() == zappo)\r
{\r
pdbcanvas.bysequence = false;\r
new jalview.appletgui.UserDefinedColours(pdbcanvas);\r
}\r
+\r
+ pdbcanvas.redrawneeded = true;\r
+ pdbcanvas.repaint();\r
+\r
}\r
\r
public void itemStateChanged(ItemEvent evt)\r
{\r
if (evt.getSource() == allchains)\r
{\r
- allchains_itemStateChanged();\r
+ pdbcanvas.setAllchainsVisible(allchains.getState());\r
}\r
else if (evt.getSource() == wire)\r
{\r
- wire_actionPerformed();\r
+ pdbcanvas.wire = !pdbcanvas.wire;\r
}\r
else if (evt.getSource() == depth)\r
{\r
- depth_actionPerformed();\r
+ pdbcanvas.depthcue = !pdbcanvas.depthcue;\r
}\r
else if (evt.getSource() == zbuffer)\r
{\r
- zbuffer_actionPerformed();\r
+ pdbcanvas.zbuffer = !pdbcanvas.zbuffer;\r
}\r
+ pdbcanvas.redrawneeded = true;\r
+ pdbcanvas.repaint();\r
}\r
\r
private void jbInit()\r
MenuItem buried = new MenuItem();\r
MenuItem user = new MenuItem();\r
\r
- public void charge_actionPerformed()\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setChargeColours();\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void chain_actionPerformed()\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setChainColours();\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void zbuffer_actionPerformed()\r
- {\r
- pdbcanvas.zbuffer = !pdbcanvas.zbuffer;\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void depth_actionPerformed()\r
- {\r
- pdbcanvas.depthcue = !pdbcanvas.depthcue;\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void wire_actionPerformed()\r
- {\r
- pdbcanvas.wire = !pdbcanvas.wire;\r
- pdbcanvas.redrawneeded = true;\r
- pdbcanvas.repaint();\r
- }\r
\r
- public void seqButton_actionPerformed()\r
- {\r
- pdbcanvas.bysequence = true;\r
- pdbcanvas.updateSeqColours();\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void mapping_actionPerformed()\r
- {\r
- jalview.appletgui.CutAndPasteTransfer cap\r
- = new jalview.appletgui.CutAndPasteTransfer(false, null);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);\r
- cap.setText(pdbcanvas.mappingDetails.toString());\r
- }\r
+//End StructureListener\r
+////////////////////////////\r
\r
- public void allchains_itemStateChanged()\r
- {\r
- pdbcanvas.setAllchainsVisible(allchains.getState());\r
- }\r
\r
}\r