public void actionPerformed(final ActionEvent ae) {
final boolean saveInteractionsFlag = LigandExplorer.saveInteractionsFlag;
LigandExplorer.saveInteractionsFlag = false;
final StructureModel model = LigandExplorer.sgetModel();
// final LXGlGeometryViewer glViewer = LigandExplorer.sgetGlGeometryViewer();
// **J check to make sure all text fields have three
// characters in them; if not, make the correction
String philicText2 = philicFLF2.getText();
switch (philicText2.length()) {
case 0:
philicText2 = "0.0";
philicFLF2.setText(philicText2);
break;
case 1:
philicText2 = philicText2 + ".0";
philicFLF2.setText(philicText2);
break;
case 2:
philicText2 = philicText2 + "0";
philicFLF2.setText(philicText2);
}
String phobicText2 = phobicFLF2.getText();
switch (phobicText2.length()) {
case 0:
phobicText2 = "0.0";
phobicFLF2.setText(phobicText2);
break;
case 1:
phobicText2 = phobicText2 + ".0";
phobicFLF2.setText(phobicText2);
break;
case 2:
phobicText2 = phobicText2 + "0";
phobicFLF2.setText(phobicText2);
}
String l_h2o_pText2 = l_h2o_pflf2.getText();
switch (l_h2o_pText2.length()) {
case 0:
l_h2o_pText2 = "0.0";
l_h2o_pflf2.setText(l_h2o_pText2);
break;
case 1:
l_h2o_pText2 = l_h2o_pText2 + ".0";
l_h2o_pflf2.setText(l_h2o_pText2);
break;
case 2:
l_h2o_pText2 = l_h2o_pText2 + "0";
l_h2o_pflf2.setText(l_h2o_pText2);
}
String otherText2 = otherFLF2.getText();
switch (otherText2.length()) {
case 0:
otherText2 = "0.0";
otherFLF2.setText(otherText2);
break;
case 1:
otherText2 = otherText2 + ".0";
otherFLF2.setText(otherText2);
break;
case 2:
otherText2 = otherText2 + "0";
otherFLF2.setText(otherText2);
}
String neighborText1 = neighborFLF1.getText();
switch (neighborText1.length()) {
case 0:
neighborText1 = "0.0";
neighborFLF1.setText(neighborText1);
break;
case 1:
neighborText1 = neighborText1 + ".0";
neighborFLF1.setText(neighborText1);
break;
case 2:
neighborText1 = neighborText1 + "0";
neighborFLF1.setText(neighborText1);
}
if (model.hasStructures()) {
final Structure structure = model.getStructures().get(0);
final TreePath treeSelection[] = ligandJList.getSelectionPaths();
if (treeSelection != null) {
Residue residues[] = null;
DefaultMutableTreeNode node =
(DefaultMutableTreeNode) treeSelection[0].getLastPathComponent();
StructureComponent nodeValue = (StructureComponent) node.getUserObject();
if (nodeValue instanceof Chain) {
assert (treeSelection.length == 1);
Chain chain = (Chain) nodeValue;
if (chain.getBird() != null) {
residues = getBirdResidues(structure, chain);
} else {
residues = new Residue[chain.getResidueCount()];
for (int ix = 0; ix < chain.getResidueCount(); ix++) {
residues[ix] = chain.getResidue(ix);
}
}
} else if (nodeValue instanceof Residue) {
int ix = 0;
residues = new Residue[treeSelection.length];
for (TreePath path : treeSelection) {
node = (DefaultMutableTreeNode) path.getLastPathComponent();
nodeValue = (StructureComponent) node.getUserObject();
assert (nodeValue instanceof Residue);
residues[ix] = (Residue) nodeValue;
ix++;
}
}
if (residues != null) {
LigandExplorer.sgetSceneController().setLigandResidues(residues);
}
}
final float philicf2 = Float.parseFloat(philicText2);
final float phobicf2 = Float.parseFloat(phobicText2);
final float l_h2o_pf2 = Float.parseFloat(l_h2o_pText2);
final float otherf2 = Float.parseFloat(otherText2);
final float neighborf1 = Float.parseFloat(neighborText1);
// Thread runner = new Thread() {
//
// public void run() {
try {
LigandExplorer.sgetSceneController()
.processLeftPanelEvent(
structure,
l_h2o_pf2,
box.isSelected(),
hydrogenBondBox.isSelected(),
philicf2,
hydrophobicBox.isSelected(),
phobicf2,
metalInteractionBox.isSelected(),
otherf2,
distanceBox.isSelected(),
neighborf1,
neighborBox.isSelected(),
saveInteractionsFlag);
} catch (final Exception e) {
e.printStackTrace();
Status.progress(
100, "Error while processing your options...Please select different options");
}
// }
// };
// runner.start();
// remove current surfaces from display list and add them again to ensure
// transparent surfaces are drawn on top of the interactions
LigandExplorer.sgetGlGeometryViewer().surfaceRemoved(structure);
LigandExplorer.sgetGlGeometryViewer().surfaceAdded(structure);
} else {
// add a display message here, ask user to load a
// structure, do this later
}
}
