override public void Run()
{
try
{
long pos = 0, nextpos;
while (!zap)
{
lock (mutex)
{
nextpos = MoleculeStream.FindNextPosition(istr, pos);
}
if (nextpos < 0)
{
break;
}
filepos.Add(pos);
pos = nextpos;
// inform the main window that is has work to do!
//UPGRADE_ISSUE: Method 'java.awt.EventQueue.invokeLater' was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1000_javaawtEventQueue'"
//EventQueue.invokeLater(new AnonymousClassRunnable(this));
Synch synchDelegate = new Synch(wnd.Synchronize);
synchDelegate(filepos.Count);
}
}
catch (System.IO.IOException e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
SupportClass.OptionPaneSupport.ShowMessageDialog(null, e.ToString(), "Catalog Load Failed", (int)System.Windows.Forms.MessageBoxIcon.Error);
SupportClass.WriteStackTrace(e, Console.Error);
}
}
public virtual Molecule Get(int N)
{
try
{
lock (mutex)
{
return(MoleculeStream.FetchFromPosition(istr, filepos[N]));
}
}
catch (System.IO.IOException e)
{
return(null);
}
}
public virtual void propertyChange(System.Object event_sender, SupportClass.PropertyChangingEventArgs ev)
{
bool update = false;
System.String prop = ev.PropertyName;
if ("directoryChanged".Equals(prop))
// changed directory, do nothing much
{
file = null;
update = true;
}
else if ("SelectedFilesChangedProperty".Equals(prop))
// file just got selected
{
file = (System.IO.FileInfo)ev.NewValue;
update = true;
}
if (update)
{
thumbnail = null;
Molecule mol = null;
if (file != null && System.IO.File.Exists(file.FullName))
{
try
{
//UPGRADE_TODO: Constructor 'java.io.FileInputStream.FileInputStream' was converted to 'System.IO.FileStream.FileStream' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javaioFileInputStreamFileInputStream_javaioFile'"
System.IO.FileStream istr = new System.IO.FileStream(file.FullName, System.IO.FileMode.Open, System.IO.FileAccess.Read);
mol = MoleculeStream.ReadUnknown(istr);
istr.Close();
}
catch (System.IO.IOException)
{
mol = null;
}
}
if (mol == null)
{
mol = new Molecule();
}
Replace(mol);
ScaleToFit();
if (Visible)
{
//UPGRADE_TODO: Method 'java.awt.Component.repaint' was converted to 'System.Windows.Forms.Control.Refresh' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javaawtComponentrepaint'"
Refresh();
}
}
}
public Templates()
{
//UPGRADE_ISSUE: The following fragment of code could not be parsed and was not converted. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1156'"
List <String> list = new List <String>();
// read the list of molecules from the directory file, then create each one of them
Assembly assembly = Assembly.GetExecutingAssembly();
string[] resources = assembly.GetManifestResourceNames();
try
{
// Build the string of resources.
foreach (string resource in resources)
{
if (resource.StartsWith("Genetibase.Chem.NuGenSChem.templ."))
{
list.Add(resource);
}
}
}
catch (IOException e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.Console.Out.WriteLine("Failed to obtain list of templates:\n" + e.ToString());
return;
}
try
{
for (int n = 0; n < list.Count; n++)
{
Stream istr = assembly.GetManifestResourceStream(list[n]);
Molecule mol = MoleculeStream.ReadNative(istr);
templ.Add(mol);
istr.Close();
}
}
catch (System.IO.IOException e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.Console.Out.WriteLine("Failed to obtain particular template:\n" + e.ToString());
return;
}
// sort the molecules by an index of "complexity" (smaller molecules first, carbon-only favoured)
int[] complex = new int[templ.Count];
for (int n = 0; n < templ.Count; n++)
{
Molecule mol = templ[n];
complex[n] = mol.NumAtoms() * 100;
bool nonCH = false;
for (int i = 1; i <= mol.NumAtoms(); i++)
{
if (String.CompareOrdinal(mol.AtomElement(i), "C") != 0 && String.CompareOrdinal(mol.AtomElement(i), "H") != 0)
{
nonCH = true;
}
}
if (!nonCH)
{
complex[n] -= 1000;
}
for (int i = 1; i <= mol.NumBonds(); i++)
{
complex[n] = complex[n] + mol.BondOrder(i);
}
}
int p = 0;
while (p < templ.Count - 1)
{
if (complex[p] > complex[p + 1])
{
int i = complex[p]; complex[p] = complex[p + 1]; complex[p + 1] = i;
Molecule mol = templ[p]; templ[p] = templ[p + 1]; templ[p + 1] = mol;
if (p > 0)
{
p--;
}
}
else
{
p++;
}
}
}
