Subversion Repositories wimsdev

/*

    Sketch Elements: Chemistry molecular diagram drawing tool.

    (c) 2005 Dr. Alex M. Clark

    Released as GNUware, under the Gnu Public License (GPL)

    See www.gnu.org for details.

*/

package WIMSchem;

import java.io.*;

import java.net.*;

import java.util.*;

// For obtaining the template list.

public class Templates

{

    ArrayList<Molecule> templ=new ArrayList<Molecule>();

    // jm.evers: copies... of functions in applet. Should be reorganised !!

    public static byte [] loadURL(URL url) throws IOException {

        int bufSize = 1024 * 2;

        byte [] buf = new byte[bufSize];

        ByteArrayOutputStream bout = new ByteArrayOutputStream();

        BufferedInputStream   in   = new BufferedInputStream(url.openStream());

        int n;

        while ((n = in.read(buf)) > 0){

            bout.write(buf, 0, n);

        }

        try

        { in.close(); } catch (Exception ignored) { }

        return bout.toByteArray();

    }

    public static String loadFile(String fname) throws IOException {

        byte[] bytes = loadURL(new URL("file:" + fname));

        return new String(bytes);

    }

    public static String load(String fileOrURL) throws IOException {

        try {

            URL url = new URL(fileOrURL);

            return new String(loadURL(url));

        } catch (Exception e) { return loadFile(fileOrURL);}

    }

    public Templates(Class cls)

    {

        ArrayList<String> list=new ArrayList<String>();

        // jm.evers : if an param template is defined, load them in the ArrayList.

        if( MainApplet.templateURL != null ){

            for(int p=0; p<MainApplet.templateURL.length ;p++ ){

                try {

                    //Molecule mol = MoleculeStream.readMDLMOL(new BufferedReader(new StringReader((load(MainApplet.templateURL[p])).toString())));    

                    Molecule mol = MoleculeStream.readUnknown(new BufferedReader(new StringReader((load(MainApplet.templateURL[p])).toString())));    

                    templ.add(mol);

                    System.out.println("loading template no"+p);

                } catch (IOException e) {System.out.println("FAILED loading template"+p+"\n Are you using correct MDLMol or Native files??");}

            }

        }

        else   

        {    // read the list of molecules from the directory file, then create each one of them

            try

            {

                InputStream istr=cls.getResourceAsStream("/templ/list");

                BufferedReader in=new BufferedReader(new InputStreamReader(istr));

                String line;

                while ((line=in.readLine())!=null) {list.add(line);}

                istr.close();

            }

            catch (IOException e)

            {

                System.out.println("Failed to obtain list of jar included default templates:\n"+e.toString());

                return;

            }

            try

            {

                for (int n=0;n<list.size();n++)

                {

                    InputStream istr=cls.getResourceAsStream("/templ/"+list.get(n));

                    Molecule mol=MoleculeStream.readNative(istr);

                    templ.add(mol);

                    istr.close();

                }

            }

            catch (IOException e)

            {

                System.out.println("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.size()];

        for (int n=0;n<templ.size();n++)

        {

            Molecule mol=templ.get(n);

            complex[n]=mol.numAtoms()*100;

            boolean nonCH=false;

            for (int i=1;i<=mol.numAtoms();i++)

                if (mol.atomElement(i).compareTo("C")!=0 && mol.atomElement(i).compareTo("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.size()-1)

        {

            if (complex[p]>complex[p+1])

            {

                int i=complex[p]; complex[p]=complex[p+1]; complex[p+1]=i;

                Molecule mol=templ.get(p); templ.set(p,templ.get(p+1)); templ.set(p+1,mol);

                if (p>0) p--;

            }

            else p++;

        }

    }

    public int numTemplates() {return templ.size();}

    public Molecule getTemplate(int N) {return templ.get(N);}

    public void addTemplate(Molecule Mol) {templ.add(Mol);}

}