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.

    11/2013 rewrite based on SketchEl 1.21: (08/Nov/2008) to include export of SVG.

    More recent verions than 1.21 do not improve the Applet or SVG export.

    jm.evers

*/  

package WIMSchem;

import java.io.*;

import java.awt.*;

import java.awt.event.*;

import java.util.*;

import javax.swing.*;

import java.net.*;

import java.applet.AppletContext;

import java.text.*;

public class MainApplet extends JApplet implements ComponentListener

{

    MainPanel mainPanel=null;

    long id;

    String zoom_js;

    public static String g_id = "g_SVG_1000000";/* used for SVG zoom in/out */

    public static String svg_id = "SVG_1000000";/* used for SVG zoom in/out */

    /* jm.evers addition to configure applet */

    static String[] TOOLS={"TOOL_CURSOR","TOOL_ROTATOR","TOOL_ERASOR","TOOL_DIALOG","TOOL_EDIT",

    "TOOL_SETATOM","TOOL_SINGLE","TOOL_DOUBLE","TOOL_TRIPLE","TOOL_ZERO",

    "TOOL_INCLINED","TOOL_DECLINED","TOOL_UNKNOWN","TOOL_CHARGE","TOOL_UNDO",

    "TOOL_REDO","TOOL_TEMPLATE","TOOL_CUT","TOOL_COPY","TOOL_PASTE",

    "TOOL_UNSELECT","TOOL_SELECT"};

    static String[] MENUS={"MENU_BLOCK","MENU_SELECT","MENU_TRANSFORM","MENU_ZOOM","MENU_SHOW","MENU_HYDROGEN","MENU_STEREO","MENU_HELP"};

    static int TOOL_COUNT = TOOLS.length;

    static int MENU_COUNT = MENUS.length;

    public static String[] templateURL;

    public static AppletContext applet_context;

    public static String[] myAtoms;

    public static int rotation;

    public static boolean viewC;

    public static boolean viewH;

    public static boolean[] TOOL_SELECTION;

    public static boolean[] MENU_SELECTION;

    public static boolean USER_SELECTION = false;

    public static int GLOBAL_ALPHA = 140;

    public static int ATOM_SELECT_HTML_COLOR; /* the default Atom click colour for user interaction when selecting atoms */

    public static int BOND_SELECT_HTML_COLOR; /* the default bond click colour for user interaction when selecting atoms */

    public static Color ATOM_SELECT_COLOR;/* the colour for not-by-param-selected-atoms */

    public static Color BOND_SELECT_COLOR;/* the colour for not-by-param-selected-bonds */

    public static int[] ExternalAtomSelection; /* atom line numbers in MDLmol file */

    public static Color SelectedAtomColorArray[];/* atom corresponding colours for line numbers in MDLmol file */

    public static int[] ExternalBondSelection;/* bonding line numbers in MDLmol file */

    public static Color SelectedBondColorArray[];;/* corresponding bonding colours for line numbers in MDLmol file */

    public static int SelectedAtomColorInt[]; /* int color numbers set by params used in svg export */

    public static int SelectedBondColorInt[]; /* colors set by params used in svg export */

    public static boolean ATOM_BUTTONS = true; /* button row with atoms SOUTH */

    public static boolean SUPERUSER_SELECTION = false; /* if true the exported SVG will be coloured according params */

    public static String language;

    public void init(){

        ATOM_BUTTONS = getBool("atom_button_row",false); /* if set an extra row of buttons will be shown  */

        USER_SELECTION = getBool("user_selection",false);

        if( USER_SELECTION ){

            GLOBAL_ALPHA = getInt("color_alpha",140);

            /* some people forget the importance of alpha...this should be removed */

            if( GLOBAL_ALPHA > 250 ){GLOBAL_ALPHA = 140;}

            ATOM_SELECT_COLOR = getColor("default_atom_select_color",GLOBAL_ALPHA,255,0,0);/* RGB */

            BOND_SELECT_COLOR = getColor("default_bond_select_color",GLOBAL_ALPHA,0,0,255);/* RGB */

            ATOM_SELECT_HTML_COLOR = RGB2int("default_atom_select_color",0x0000ff);/* int for svg */

            BOND_SELECT_HTML_COLOR = RGB2int("default_bond_select_color",0x00ff00);/* int for svg */

        }

        zoom_js = "";

        language = getLanguage();

        TOOL_SELECTION = getTools();

        MENU_SELECTION = getMenus();

        ExternalAtomSelection = SetAtomSelection();

        ExternalBondSelection = SetBondSelection();

        rotation = getInt("rotation",0);

        myAtoms = GetMyAtoms(); /* read parm atoms to tailomade atomselection*/

        templateURL = getTemplateURL();/* read params template1...template_n and use these insteadof default ones */

        viewC =  getBool("show_carbon",true);

        viewH = getBool("show_hydrogen",true);

        System.out.println("viewC = "+viewC+"\nviewH = "+viewH);

        getContentPane().setLayout(new BorderLayout());

        mainPanel=new MainPanel(null,MainPanel.MODE_APPLET,null);

        getContentPane().add(mainPanel,BorderLayout.CENTER);

        addComponentListener(this);

        getFile();/* read param file and load it if param showfile is set */

        repaint(1000);

    }

    public String getAppletInfo()

    {

        return "WIMSchem: Applet version of chemistry\nmolecular diagram drawing tool.";

    }

    /*

        replace the current molecule with the content of the string, which can be any of the formats which WIMSchem

        is able to read out from a file; returns true if successful

    */

    public boolean SetMoleculeNative(String Source) {

        try{

            Molecule mol=MoleculeStream.readNative(new BufferedReader(new StringReader(Source.toString())));

            mainPanel.setMolecule(mol);

            mainPanel.repaint();

            return true;

        } catch (IOException e) { System.out.println("problems parsing:\n"+Source.toString()+"\n"+e);}

        return false;

    }

    public boolean SetMoleculeMDLMol(String Source){

        try{

            Molecule mol = MoleculeStream.readMDLMOL(new BufferedReader(new StringReader(Source.toString())));

            mainPanel.setMolecule(mol);

            mainPanel.repaint();

            return true;

        } catch (IOException e) { System.out.println("problems parsing:\n"+Source.toString()+"\n"+e);}

        return false;

    }

    public boolean SetMolecule(String Source, boolean is_molfile)

    {

        try

        {

            Molecule mol;

            if(is_molfile){

             mol = MoleculeStream.readMDLMOL(new BufferedReader(new StringReader(Source.toString())));

            }

            else

            {

             mol = MoleculeStream.readUnknown(new BufferedReader(new StringReader(Source.toString())));

            }

            mainPanel.setMolecule(mol);

            mainPanel.repaint();

            return true;

        }

        catch (IOException e){ System.out.println("error in applet : setMolecule( String Source ) :\ncan not parse : "+Source.toString());}

        return false;

    }

    /*

        appends the indicated molecular source to the current molecule,

        in the same way as the paste feature; otherwise works

        the same as SetMolecule

    */

    public boolean AppendMolecule(String Source, boolean is_molfile)

    {

        try

        {

            Molecule mol;

            if(is_molfile){

             mol = MoleculeStream.readMDLMOL(new BufferedReader(new StringReader(Source.toString())));

            }

            else

            {

             mol = MoleculeStream.readUnknown(new BufferedReader(new StringReader(Source.toString())));

            }

            mainPanel.addMolecule(mol);

            mainPanel.repaint();

            return true;

        }

        catch (IOException e) { System.out.println("error in applet : appendMolelcule( String Source ) : "+e.toString());}

        return false;

    }

    /*

        return the string representation of the molecule, in WIMSchem native format

    */

    public String GetMoleculeNative()

    {

        try

        {

            StringWriter sw=new StringWriter();

            BufferedWriter bw=new BufferedWriter(sw);

            MoleculeStream.writeNative(bw,mainPanel.molData());

            return sw.toString();

        }

        catch (IOException e) {}

        return null;

    }

    /*

        return the string representation of the molecule, in MDL MOL-file format

    */

    public String GetMoleculeMDLMol()

    {

        try

        {

            StringWriter sw = new StringWriter();

            BufferedWriter bw = new BufferedWriter(sw);

            MoleculeStream.writeMDLMOL(bw,mainPanel.molData());

            return sw.toString();

        }

        catch (IOException e) {}

        return "error getting MDLMol file from applet";

    }

    public int RGB2int(String p, int d){ /* convert 255,0,255 -> ff00ff*/

        String param = getParameter(p);

        if( param != null && param.length()>0 ){

            int k = 0;String hex = "";String tmp="";

            StringTokenizer q = new StringTokenizer(param, ",");

            int c = q.countTokens();

            if( c != 3){System.out.println("use R,G,B for colours ; use param color_alpha for transparency"); return d;}

            for( int a = 0; a < 3 ; a++){

                k = Integer.parseInt(q.nextToken(), 10);

                tmp = Integer.toHexString(k);

                while (tmp.length()<2) tmp="0"+tmp;

                hex = hex+""+tmp;

            }

            return Integer.parseInt(hex,16);

        }

        else

        {

            return d;

        }

    }

    public void componentHidden(ComponentEvent e){}

    public void componentMoved(ComponentEvent e){}

    public void componentResized(ComponentEvent e){}

    public void componentShown(ComponentEvent e){

        mainPanel.scaleToFit();

        mainPanel.repaint();

    }

    /*

        jm.evers additions to configuring applet

    */

    public String getSelected(){

        int num=0;

        String reply="";

        Molecule mol = (mainPanel.editor).molData();

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

            if( (mainPanel.editor).selected[n-1] ){ reply = reply+mol.atomElement(n-1)+"\n";}

        }

        return reply;

    }

    public String getSVG(String type){

        SVGMolecule svgmol;

        if( type.equals("1") ){ /* get the student reply*/

            try{

                System.out.println("ok : exporting user drawing to SVG");

                svgmol = new SVGMolecule((mainPanel.editor).molData());

            }catch(Exception e){return e.toString();}

        }

        else

        {

         /*

             check if we have a param 'name=file2' : reserved for the correctmolecule in mdlmol --> svg

             using javascript:getSVG(2)

         */

            type = getString("file2");

            USER_SELECTION = false; /* disable colours of studentreply in correct answer svg ! */    

            SUPERUSER_SELECTION = true; /* if appropriate set html colours to applet colours */

            if( type != null ){ /* ok found param file2 */

                try{

                    String correct_answer = loadAny(type);

                    Molecule answer_mol = MoleculeStream.readMDLMOL(new BufferedReader(new StringReader(correct_answer.toString())));

                    svgmol = new SVGMolecule(answer_mol);

                    System.out.println("ok : exporting file2 to SVG");

                }catch(Exception e){return e.toString();}

            }

            else

            {

                /* use the drawing in the applet for export to svg*/

                try{

                    svgmol = new SVGMolecule((mainPanel.editor).molData());

                    System.out.println("ok : exporting molecule in applet window to SVG\npossibly colouring atoms and bonds\naccording to color params");

                }catch(Exception e){return e.toString();}

            }

        }

        double zoom_factor = getDouble("zoomfactor",1.00);

        if( zoom_factor != 1.00 ){ /* simple static in/out zoom, no pan */

            id = System.currentTimeMillis();

            g_id = ("g_SVG_"+id).toString();

            svg_id = ("SVG_"+id).toString();

            zoom_js="<script type=\"text/javascript\">"+

            "var flip = 0;"+

            "function SVG_zoom(svg,g,w0,h0){"+

             "var svg = document.getElementById(svg);"+

             "var g = document.getElementById(g);"+

             "var f = "+zoom_factor+";"+

             "if( flip == 1 ){"+

              "flip = 0;"+

              "var w1 = parseInt(w0*f);"+

              "var h1 = parseInt(h0*f);"+

              "svg.setAttributeNS(null, 'viewBox', '0 0 '+w1+' '+h1);"+

              "svg.setAttributeNS(null, 'width',w1);"+

              "svg.setAttributeNS(null, 'height',h1);"+

              "g.setAttributeNS(null,'transform','matrix('+f+' 0 0 '+f+' 0 0)');"+

             "}else{"+

              "flip = 1;"+

              "svg.setAttributeNS(null, 'viewBox', '0 0 '+w0+' '+h0);"+

              "svg.setAttributeNS(null, 'width',w0);"+

              "svg.setAttributeNS(null, 'height',h0);"+

              "g.setAttributeNS(null,'transform','matrix(1 0 0 1 0 0)');"+

              "};};</script>";

        }

        svgmol.draw();

        String reply = "";

        reply = (svgmol + zoom_js).toString();

        return reply.replaceAll("(\\n|\\r|\\  )", " ");

    }

    public boolean[] getTools(){ /* jm.evers: configuring toolbar through appletparams  */

     String param;

     boolean[] TOOL_SELECTION = new boolean[TOOL_COUNT];

     for(int p = 0;p < TOOL_COUNT ; p++){ /* adjust if more buttons are added MainPanel */

      param = getParameter(TOOLS[p]);

      TOOL_SELECTION[p] = false;

      if( param != null ){if(param.equalsIgnoreCase("yes") || param.equals("1")){ TOOL_SELECTION[p] = true;} }

     }

      return TOOL_SELECTION;

    }

    public boolean[] getMenus(){ /* jm.evers: configuring menubar through appletparams  */

     String param;

     boolean[] MENU_SELECTION = new boolean[MENU_COUNT];

     for(int p = 0;p < MENU_COUNT ; p++){ /* adjust if more buttons are added MainPanel */

      param = getParameter(MENUS[p]);

      MENU_SELECTION[p] = false;

      if( param != null && param.length() > 0){if(param.equalsIgnoreCase("yes") || param.equals("1")){ MENU_SELECTION[p] = true;} }

     }

      return MENU_SELECTION;

    }

    public String[] getTemplateURL(){

        // jm.evers : retreive an unknown amount of templates via params called template1,template2...

        // these templates will be called by Template.java

        String param = getParameter("template1");

        if( param != null && param.length()>0 ){

            int p=0;

            while( param!=null && param.length()!=0 ){

                p++; /* unknown amount...let's count */

                param = getParameter("template"+p);

            }

            String[] templateURL = new String[p-1];

            for(int s = 1;s < p; s++){ /* fill the array with url's */

                param = getParameter("template"+s);

                System.out.println("loading template url : "+param);

                templateURL[s - 1] = param;

            }

            return templateURL;

        }

        else

        {

            return null;

        }

    }

    public boolean getFile(){

    /*

        jm.evers : try to load a file as string from the URL given in the params

    */

        String showfile = getParameter("showfile");

        if(showfile != null && showfile.length()>0){

            if(showfile.equalsIgnoreCase("yes") ||  showfile.equals("1") ){

                String filename = getParameter("file");

                if (filename != null && filename.length() > 0){

                /*

                    jm.evers: is param showfile is set, draw to canvas...

                */

                    String demomol = loadAny(filename);

                    if( demomol.indexOf("V2000") < 1 ){

                        SetMolecule(demomol,false);

                    }

                    else

                    {

                        SetMolecule(demomol,true);

                    }

                    return true;

                }

            }

        }

        else

        {

            System.out.println("not using external file loading");

        }

        return false;

    }

    public String getString( String p ){

        String param = getParameter(p);

        if( param != null  && param.length()>0){

            return  param.toString();

        }

        return null;

    }

    public Boolean getBool(String p , boolean d ){

    /* jm.evers 27/12/2008 */

        String param = getParameter(p);

        if( param != null && param.length()>0 ){

            param = param.toLowerCase();

            if(param.equals("1") || param.equalsIgnoreCase("yes") || param.equalsIgnoreCase("true") ){

                return true;

            }

            if(param.equals("0") || param.equalsIgnoreCase("no") ||  param.equalsIgnoreCase("false")){

                return false;

            }

        }

        return d;

    }

    /*

        routine to read an 'int' from some applet param 'p'

    */

    public int getInt(String p, int d){/* jm.evers 27/12/2008 */

        String param = getParameter(p);

        if( param != null  && param.length()>0){

            return Integer.parseInt( param );

        }

        return d;

        /*

            we don't want to trip over a wrong param...use default

        */

    }

    /*

        routine to read a 'double' from some applet param 'p'

    */

    public double getDouble(String p, double d){/* jm.evers 27/12/2008 */

        String param = getParameter(p);

        if( param != null  && param.length()>0){

            return Double.parseDouble( param );

        }

        return d;

        /*

            we don't want to trip over a wrong param...

        */

    }

    /*

        routine to read a color from some applet param 'p'

    */

    public Color getColor(String p, int alpha, int r0,int g0,int b0 ){

        String param = getParameter(p);

        if( param != null && param.length()>0){

            String k;int R1=0,G1=0,B1=0,rgb=0;

            StringTokenizer q = new StringTokenizer(param, ",");

            int c = q.countTokens();

            if( c != 3){System.out.println("use R,G,B for colours ; use param color_alpha for transparency"); return new Color(0,0,255,255);}

            for( int a = 0; a < 3 ; a++){

                k = q.nextToken();

                rgb = Integer.parseInt(k, 10);

                if( rgb < 0 ){ rgb = 0; }

                if( rgb > 255 ){ rgb = 255; }

                if(a == 0){ R1 = rgb;}

                else

                if(a == 1){G1 = rgb;}

                else B1 = rgb;

            }

            return new Color(R1,G1,B1,alpha);

        }

        else

        {

            return new Color(r0,g0,b0,alpha);

        }

    }

    /*

        jm.evers: reading atoms from params

    */

    public String[] GetMyAtoms(){

        String param = getParameter("atoms");

        if( param != null && param.length()>0){

            return String2Array( param );

        }

        else

        {

            return null;

        }

    }

    public String getLanguage(){

    /*

        jm.evers: reading language. default english

    */

     String param = getParameter("language");

     if(param != null && param.length() == 2){return  param.toLowerCase();}

     return "en";

    }

/* called via javascript */

    public String ReadAtomSelection(){

     boolean[] S = EditorPane.atomselection;

     String selection="";

     for (int p = 1;p < S.length; p++){ /* starts with 1 */

      if(S[p]){ /* is selected */

       if(selection != ""){ selection = selection +","+p; } else { selection=""+p; }

      }

     }

     return selection;

    }

    public String ReadBondSelection(){

     boolean[] S = EditorPane.bondselection;

      String selection="";

      for (int p=0;p<S.length;p++){

       if(S[p]){ /* is selected */

        if(selection == ""){ selection = ""+p; } else { selection = selection+","+p; }

       }

      }

      return selection;

    }

/* jm.evers : routines to load a file direct or via network */

    public String loadAny(String filename){

     String demomol = "";

     try{

        return (load(filename)).toString();

     }catch(Exception e){System.out.println("HMMMM");}

     return demomol;

    }

    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 {

     try{

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

        return new String(bytes);

     }catch(Exception e ){System.out.println("loadFile error :"+e.toString());}

     return null;

    }

    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 String[] String2Array(String t){

        /*

            jm.evers: parsing params into array...fieldseparators are "," ":" ";" " "

        */

        StringTokenizer q;

        if(t.indexOf(",")!=-1){

            q = new StringTokenizer(t, ",");

        }

        else

        {

            if(t.indexOf(":")!=-1){

                q = new StringTokenizer(t, ":");

            }

            else

            {

                if(t.indexOf(";")!=-1){

                    q = new StringTokenizer(t, ";");

                }

                else

                {

                    if(t.indexOf(" ")>2){

                        q = new StringTokenizer(t, " ");

                    }

                    else

                    {

                        return null;

                    }

                }

            }

        }

        int max = q.countTokens();if( max > 50 ){ max = 50;}

        String[] tmp = new String[max];String s="";

        for( int p = 0 ; p<max ; p++){

            s=q.nextToken();

            if(s.length()==1 || s.length()==2){

                System.out.println("atom = "+s);

                tmp[p]=s;

            }

        }

        return tmp;

    }

    public void send_to_wims(int type){

    /*

        DO NOT USE THIS FOR SENDING SVG/XML !!!

        THIS WILL GIVE TROUBLE WIH TOO LARGE STRINGS:

        [quote] The requested URL's length exceeds the capacity limit for this server.

        BETTER USE:

        <form  action="$wims_ref_name?form-data$session" method="post" enctype="multipart/form-data" >

    */

        applet_context = this.getAppletContext();

        String wims_ref_name = getString("wims_ref_name");

        String session = getString("session");

        String module = getString("module");

        String replyargs = getString("replyarguments"); /* reply2=*/

        if( wims_ref_name == null ){

            System.out.println("param wims_ref_name is not set POST will not work !!");

        }

        else

        {

            String student_MDL_molecule = GetMoleculeMDLMol();

            String student_svg_molecule = getSVG("1");

            String correct_svg_molecule = getSVG("2");

            String reply = "";

            switch(type){

                case 0: reply = student_MDL_molecule;break;

                case 1: reply = student_svg_molecule+"\n"+student_MDL_molecule;break;

                case 2: reply = correct_svg_molecule+"\n"+student_svg_molecule+"\n"+student_MDL_molecule;break;

                default: reply = "send_to_wims(type) \ntype=1: MDLmol student drawing\ntype=2: student SVG \\n MDLmol student drawing\ntype=3: answer SVG \\n student SVG \\n MDLmol student drawing ";

            }

            try{reply = URLEncoder.encode(reply,"UTF-8"); }catch(Exception e){reply = e.toString();}

            String back_url_string = wims_ref_name+"?session="+session+"&module="+module+"&cmd=reply&"+replyargs;

            back_url_string = back_url_string.replaceAll(" ",""); /* no space in url */

            URL backurl;

            try {backurl=new URL(back_url_string+reply);

                applet_context.showDocument(backurl,"_self");

            } catch (MalformedURLException e){backurl=null;System.out.println("could not send  to wims "+back_url_string);}

        }

    }

    /*  

        set bonds and atoms via applet param

    */

    public int[] SetAtomSelection(){

        String param = getParameter("select_atoms");

        if(param != null && param.length()>0){

            String k;int rgb=0;int R1=255;int G1=0;int B1=0;//red

            param=param.replaceAll(";",",");param=param.replaceAll(":",",");

            StringTokenizer i = new StringTokenizer(param, ",");

            int max=i.countTokens();

            ExternalAtomSelection = new int[max];

            SelectedAtomColorArray = new Color[max];

            SelectedAtomColorInt = new int[max];

            String ColorParam;

            for(int p=0;p<max;p++){

                ExternalAtomSelection[p] = Integer.parseInt(i.nextToken());

                // now try to find the color belonging to this selected atom

                SelectedAtomColorInt[p] = RGB2int("select_atom_color"+ExternalAtomSelection[p]+"",0x00ff00);

                ColorParam=getParameter("select_atom_color"+ExternalAtomSelection[p]);

                if(ColorParam != null && ColorParam.length()>0){

                    ColorParam=ColorParam.replaceAll(":",",");ColorParam=ColorParam.replace(";",",");

                    StringTokenizer q = new StringTokenizer(ColorParam, ",");

                    for( int a=0; a<3 ; a++){

                        k=q.nextToken();

                        rgb=Integer.parseInt(k, 10);

                        if(rgb<0){rgb=0;}if(rgb>255){rgb=255;}

                        if(a == 0){R1 = rgb;}

                        else

                        {

                            if(a == 1){G1 = rgb;}

                            else{B1 = rgb;}

                        }

                    }

                    SelectedAtomColorArray[p] = new  Color(R1,G1,B1,GLOBAL_ALPHA);

                }

                else

                {

                    SelectedAtomColorArray[p] = ATOM_SELECT_COLOR;

                }

            }

            SUPERUSER_SELECTION = true;

        }else{ ExternalAtomSelection = null;}

        return ExternalAtomSelection;

    }

    /*  

        set bonds and atoms via applet param

    */