X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fcontrolers%2FControleurScriptParser.java;fp=src2%2Ffr%2Forsay%2Flri%2Fvarna%2Fcontrolers%2FControleurScriptParser.java;h=0000000000000000000000000000000000000000;hb=a1225b9392dc7657d5cef12907385b07527d6122;hp=4688f91acd1eb70724a482c54598cbf7722c8e48;hpb=b513684c725997c77341f30ce4e584cf9f7cdfed;p=jalview.git

diff --git a/src2/fr/orsay/lri/varna/controlers/ControleurScriptParser.java b/src2/fr/orsay/lri/varna/controlers/ControleurScriptParser.java
deleted file mode 100644
index 4688f91..0000000
--- a/src2/fr/orsay/lri/varna/controlers/ControleurScriptParser.java
+++ /dev/null
@@ -1,551 +0,0 @@
-package fr.orsay.lri.varna.controlers;
-
-import java.awt.Color;
-import java.io.StreamTokenizer;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-
-import fr.orsay.lri.varna.VARNAPanel;
-import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
-import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType;
-import fr.orsay.lri.varna.models.rna.ModeleColorMap;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-public class ControleurScriptParser {
-    private static String SCRIPT_ERROR_PREFIX = "Error";	
-
-
-	private static class Command{
-		Function _f;
-		Vector<Argument> _argv; 
-		public Command(Function f, Vector<Argument> argv)
-		{
-			_f = f;
-			_argv = argv;
-		}
-	}; 
-
-	private static abstract class Argument{
-		ArgumentType _t;
-		
-		public Argument(ArgumentType t)
-		{
-			_t = t;
-		}
-		
-		public ArgumentType getType()
-		{
-			return _t;
-		}
-		
-		public abstract String toString();
-		
-	}; 
-	
-
-	private static class NumberArgument extends Argument{
-		Number _val; 
-		public NumberArgument(Number val)
-		{
-			super(ArgumentType.NUMBER_TYPE);
-			_val = val;
-		}
-		public Number getNumber()
-		{
-			return _val;
-		}
-		public String toString()
-		{
-			return _val.toString();
-		}
-	}; 
-	
-	private static class ColorArgument extends Argument{
-		Color _val; 
-		public ColorArgument(Color val)
-		{
-			super(ArgumentType.COLOR_TYPE);
-			_val = val;
-		}
-		public Color getColor()
-		{
-			return _val;
-		}
-		public String toString()
-		{
-			return _val.toString();
-		}
-	}; 
-
-	private static class BooleanArgument extends Argument{
-		boolean _val; 
-		public BooleanArgument(boolean val)
-		{
-			super(ArgumentType.BOOLEAN_TYPE);
-			_val = val;
-		}
-		public boolean getBoolean()
-		{
-			return _val;
-		}
-		public String toString()
-		{
-			return ""+_val;
-		}
-	}; 
-
-	private static class StringArgument extends Argument{
-		String _val; 
-		public StringArgument(String val)
-		{
-			super(ArgumentType.STRING_TYPE);
-			_val = val;
-		}
-		public String toString()
-		{
-			return _val.toString();
-		}
-	}; 
-
-	private static class ArrayArgument extends Argument{
-		Vector<Argument> _val; 
-		public ArrayArgument(Vector<Argument> val)
-		{
-			super(ArgumentType.ARRAY_TYPE);
-			_val = val;
-		}
-		public int getSize()
-		{
-			return _val.size();
-		}
-		public Argument getArgument(int i)
-		{
-			return _val.get(i);
-		}
-		public String toString()
-		{
-			return _val.toString();
-		}
-	}; 
-	
-	
-	private enum ArgumentType{
-		STRING_TYPE,
-		NUMBER_TYPE,
-		BOOLEAN_TYPE,
-		ARRAY_TYPE,
-		COLOR_TYPE
-	};
-    
-    
-    private enum Function{
-		ADD_CHEM_PROB("addchemprob",new ArgumentType[] {ArgumentType.NUMBER_TYPE,ArgumentType.NUMBER_TYPE,ArgumentType.STRING_TYPE,ArgumentType.NUMBER_TYPE,ArgumentType.COLOR_TYPE,ArgumentType.BOOLEAN_TYPE}),
-    	ERASE_SEQ("eraseseq",new ArgumentType[] {}),
-		RESET_CHEM_PROB("resetchemprob",new ArgumentType[] {}),
-		SET_COLOR_MAP_MIN("setcolormapminvalue",new ArgumentType[]{ArgumentType.NUMBER_TYPE}),
-		SET_COLOR_MAP_MAX("setcolormapmaxvalue",new ArgumentType[]{ArgumentType.NUMBER_TYPE}),
-		SET_COLOR_MAP("setcolormap",new ArgumentType[]{ArgumentType.STRING_TYPE}),
-		SET_CUSTOM_COLOR_MAP("setcustomcolormap",new ArgumentType[]{ArgumentType.ARRAY_TYPE}),
-		SET_SEQ("setseq",new ArgumentType[]{ArgumentType.STRING_TYPE}),
-		SET_STRUCT("setstruct",new ArgumentType[]{ArgumentType.STRING_TYPE}),
-		SET_STRUCT_SMOOTH("setstructsmooth",new ArgumentType[] {ArgumentType.STRING_TYPE}),
-		SET_TITLE("settitle",new ArgumentType[] {ArgumentType.STRING_TYPE}),
-		SET_RNA("setrna",new ArgumentType[]{ArgumentType.STRING_TYPE,ArgumentType.STRING_TYPE}),
-		SET_RNA_SMOOTH("setrnasmooth",new ArgumentType[]{ArgumentType.STRING_TYPE,ArgumentType.STRING_TYPE}),
-		SET_SELECTION("setselection",new ArgumentType[]{ArgumentType.ARRAY_TYPE}),
-		SET_VALUES("setvalues",new ArgumentType[]{ArgumentType.ARRAY_TYPE}),
-		TOGGLE_SHOW_COLOR_MAP("toggleshowcolormap",new ArgumentType[]{}),
-		REDRAW("redraw",new ArgumentType[] {ArgumentType.STRING_TYPE}),
-		UNKNOWN("N/A",new ArgumentType[] {});
-		
-		String _funName;
-		ArgumentType[] _args;
-		Function(String funName, ArgumentType[] args)
-		{
-			_funName = funName;
-			_args = args;
-		}
-		ArgumentType[] getPrototype()
-		{
-			return this._args;
-		}
-		String getFunName()
-		{
-			return this._funName;
-		}
-		
-	};
-	
-	private static Hashtable<String,Function> _name2Fun = new Hashtable<String,Function>();  
-	private static Hashtable<Function,ArgumentType[]> _fun2Prot = new Hashtable<Function,ArgumentType[]>();
-	
-	
-	private static void initFunctions()
-	{
-		if (_name2Fun.size()>0)
-		{ return; }
-		Function[] funs = Function.values();
-		for(int i=0;i<funs.length;i++)
-		{
-			Function fun = funs[i];
-			_name2Fun.put(fun.getFunName(),fun);
-			_fun2Prot.put(fun,fun.getPrototype());
-		}			
-	}
-	
-	private static Function getFunction(String f)
-	{
-		String s = f.trim().toLowerCase();
-		if (_name2Fun.containsKey(s))
-			return _name2Fun.get(s);
-		return Function.UNKNOWN;
-	}
-
-	private static ArgumentType[] getPrototype(Function f)
-	{
-		if (_fun2Prot.containsKey(f))
-			return _fun2Prot.get(f);
-		return new ArgumentType[0];
-	}	
-	
-    public static void executeScript(VARNAPanel vp, String cmdtxt) throws Exception
-    {
-    	Vector<Command> cmds = parseScript(cmdtxt);
-    	for(int i=0;i<cmds.size();i++)
-    	{
-    		Command cmd = cmds.get(i);
-    		switch(cmd._f)
-    		{
-    			case ADD_CHEM_PROB:
-    			{
-    				int from = (int)((NumberArgument) cmd._argv.get(0)).getNumber().intValue();
-    				int to = (int)((NumberArgument) cmd._argv.get(1)).getNumber().intValue();
-    				ChemProbAnnotationType t = ChemProbAnnotation.annotTypeFromString(((StringArgument) cmd._argv.get(2)).toString());
-    				double intensity = ((NumberArgument) cmd._argv.get(3)).getNumber().doubleValue();
-    				Color c = ((ColorArgument) cmd._argv.get(4)).getColor();
-    				boolean out = ((BooleanArgument) cmd._argv.get(5)).getBoolean();
-    				vp.getRNA().addChemProbAnnotation(new ChemProbAnnotation(
-    						vp.getRNA().getBaseAt(from),
-    						vp.getRNA().getBaseAt(to),
-    						t,
-    						intensity,
-    						c,
-    						out));
-    			}
-    			break;
-    			case ERASE_SEQ:
-    			{
-    				vp.eraseSequence();
-    			}
-    			break;
-    			case RESET_CHEM_PROB:
-    			{
-    				vp.getRNA().clearChemProbAnnotations();
-    				vp.repaint();
-    			}
-    			break;
-    			case SET_COLOR_MAP_MIN:
-    			{
-    				vp.setColorMapMinValue(((NumberArgument) cmd._argv.get(0)).getNumber().doubleValue());
-    			}
-    			break;
-    			case SET_COLOR_MAP_MAX:
-    			{
-    				vp.setColorMapMaxValue(((NumberArgument) cmd._argv.get(0)).getNumber().doubleValue());
-    			}
-    			break;
-    			case SET_COLOR_MAP:
-    			{
-    				vp.setColorMap(ModeleColorMap.parseColorMap(cmd._argv.get(0).toString()));
-    			}
-    			break;
-    			case SET_CUSTOM_COLOR_MAP:
-    			{
-    				ModeleColorMap cm = new ModeleColorMap();
-    				//System.out.println("a"+cmd._argv.get(0));
-    				ArrayArgument arg = (ArrayArgument) cmd._argv.get(0);
-    				for (int j=0;j<arg.getSize();j++)
-    				{
-    					Argument a = arg.getArgument(j);
-    					if (a._t==ArgumentType.ARRAY_TYPE)
-    					{ 
-    	    				//System.out.println("%");
-    						ArrayArgument aarg = (ArrayArgument) a; 
-    						if (aarg.getSize()==2)
-    						{
-    							Argument a1 = aarg.getArgument(0);
-    							Argument a2 = aarg.getArgument(1);
-        	    				//System.out.println("& |"+a1+"| ["+a1.getType()+"] |"+a2+"| ["+a2.getType()+"]");
-    							if ((a1.getType()==ArgumentType.NUMBER_TYPE)&&(a2.getType()==ArgumentType.COLOR_TYPE))
-    							{
-            	    				//System.out.println("+");
-    								cm.addColor(((NumberArgument)a1).getNumber().doubleValue(),((ColorArgument)a2).getColor());
-    							}
-    						}
-    					}
-    				}    				
-    				vp.setColorMap(cm);
-    			}
-    			break;
-    			case SET_RNA:
-    			{
-    				String seq = cmd._argv.get(0).toString();
-    				String str = cmd._argv.get(1).toString();
-    				vp.drawRNA(seq, str);
-    			}
-    			break;
-    			case SET_RNA_SMOOTH:
-    			{
-    				String seq = cmd._argv.get(0).toString();
-    				String str = cmd._argv.get(1).toString();
-    				vp.drawRNAInterpolated(seq, str);
-    				vp.repaint();
-    			}
-    			break;
-    			case SET_SELECTION:
-    			{
-    				ArrayArgument arg = (ArrayArgument) cmd._argv.get(0);
-    				ArrayList<Integer> vals = new ArrayList<Integer>();
-    				for (int j=0;j<arg.getSize();j++)
-    				{
-    					Argument a = arg.getArgument(j);
-    					if (a._t==ArgumentType.NUMBER_TYPE)
-    					{ 
-    						NumberArgument narg = (NumberArgument) a; 
-    						vals.add(narg.getNumber().intValue()); 
-    					}
-    				}    				
-    				vp.setSelection(vals);
-    				vp.repaint();
-    			}
-    			break;	
-    			case SET_SEQ:
-    			{
-    				String seq = cmd._argv.get(0).toString();
-    				vp.setSequence(seq);
-    			}
-    			break;
-    			case SET_STRUCT:
-    			{
-    				String seq = vp.getRNA().getSeq();
-    				String str = cmd._argv.get(0).toString();
-    				vp.drawRNA(seq, str);
-    			}
-    			break;
-    			case SET_STRUCT_SMOOTH:
-    			{
-    				String seq = vp.getRNA().getSeq();
-    				String str = cmd._argv.get(0).toString();
-    				vp.drawRNAInterpolated(seq, str);
-    				vp.repaint();
-    			}
-    			break;
-    			case SET_TITLE:
-    			{
-    				vp.setTitle(cmd._argv.get(0).toString());
-    			}
-    			break;
-    			case SET_VALUES:
-    			{
-    				ArrayArgument arg = (ArrayArgument) cmd._argv.get(0);
-    				Double[] vals = new Double[arg.getSize()];
-    				for (int j=0;j<arg.getSize();j++)
-    				{
-    					Argument a = arg.getArgument(j);
-    					if (a._t==ArgumentType.NUMBER_TYPE)
-    					{ 
-    						NumberArgument narg = (NumberArgument) a; 
-    						vals[j] = narg.getNumber().doubleValue(); 
-    					}
-    				}    				
-    				vp.setColorMapValues(vals);
-    				vp.repaint();
-    			}
-    			break;
-    			case REDRAW:
-    			{
-    				int mode = -1;
-    				String modeStr = cmd._argv.get(0).toString().toLowerCase(); 
-    				if (modeStr.equals("radiate"))
-    					mode = RNA.DRAW_MODE_RADIATE;
-    				else if (modeStr.equals("circular"))
-    					mode = RNA.DRAW_MODE_CIRCULAR;
-    				else if (modeStr.equals("naview"))
-    					mode = RNA.DRAW_MODE_NAVIEW;
-    				else if (modeStr.equals("linear"))
-    					mode = RNA.DRAW_MODE_LINEAR;
-    				if (mode != -1)
-    				  vp.drawRNA(vp.getRNA(), mode);
-    			}
-    			break;
-    			case TOGGLE_SHOW_COLOR_MAP:
-    			{
-    				vp.setColorMapVisible(!vp.getColorMapVisible());
-    			}
-    			break;
-    			default:
-    				throw new Exception(SCRIPT_ERROR_PREFIX+": Method '"+cmd._f+"' unimplemented.");
-    		}
-    		vp.repaint();
-    	}
-    }
-
-	
-	
-	private static Color parseColor(String s)
-	{
-		Color result = null;
-		try {result = Color.decode(s); }
-		catch (Exception e) {}
-		return result;
-	}
-
-	private static Boolean parseBoolean(String s)
-	{
-		Boolean result = null;
-		if (s.toLowerCase().equals("true"))
-			result = new Boolean(true);
-		if (s.toLowerCase().equals("false"))
-			result = new Boolean(false);
-		return result;
-	}
-
-	
-	private static Vector<Argument> parseArguments(StreamTokenizer st, boolean parType) throws Exception
-	{
-		Vector<Argument> result = new Vector<Argument>();
-		while((st.ttype!=')' && parType) || (st.ttype!=']' && !parType))
-		{
-			st.nextToken();
-			  //System.out.println(""+ (parType?"Par.":"Bra.")+" "+(char)st.ttype);
-			switch(st.ttype)
-			{
-			  case(StreamTokenizer.TT_NUMBER):
-			  {
-				  result.add(new NumberArgument(st.nval));
-			  }
-			  break;
-			  case(StreamTokenizer.TT_WORD):
-			  {
-				  Color c = parseColor(st.sval);
-				  if (c!=null)
-				  {
-					 result.add(new ColorArgument(c));
-				  }
-				  else
-				  {
-					  Boolean b = parseBoolean(st.sval);
-					  if (b!=null)
-					  {
-						 result.add(new BooleanArgument(b));
-					  }
-					  else
-					  {
-						 result.add(new StringArgument(st.sval));					  
-					  }
-				  }
-			  }
-			  break;
-			  case('"'):
-			  {
-				  result.add(new StringArgument(st.sval));
-			  }
-			  break;
-			  case('['):
-			  {
-				  result.add(new ArrayArgument(parseArguments(st, false)));
-			  }
-			  break;
-			  case('('):
-			  {
-				  result.add(new ArrayArgument(parseArguments(st, true)));
-			  }
-			  break;
-			  case(')'):
-			  {
-				  if (parType)
-				    return result;
-				  else
-					throw new Exception(SCRIPT_ERROR_PREFIX+": Opening "+(parType?"parenthesis":"bracket")+" matched with a closing "+(!parType?"parenthesis":"bracket"));					  
-			  }
-			  case(']'):
-			  {
-				  if (!parType)
-				    return result;
-				  else
-					throw new Exception(SCRIPT_ERROR_PREFIX+": Opening "+(parType?"parenthesis":"bracket")+" matched with a closing "+(!parType?"parenthesis":"bracket"));					  
-			  }
-			  case(','):
-				  break;
-			  case(StreamTokenizer.TT_EOF):
-			  {
-				  throw new Exception(SCRIPT_ERROR_PREFIX+": Unmatched opening "+(parType?"parenthesis":"bracket"));
-			  }
-			  
-			}
-		}
-		return result;
-	}
-	
-	
-	private static Command parseCommand(String cmd) throws Exception
-	{
-		int cut = cmd.indexOf("(");
-		if (cut==-1)
-		{
-			throw new Exception(SCRIPT_ERROR_PREFIX+": Syntax error");
-		}
-		String fun = cmd.substring(0,cut);
-		Function f  = getFunction(fun);
-		if (f==Function.UNKNOWN)
-		{ throw new Exception(SCRIPT_ERROR_PREFIX+": Unknown function \""+fun+"\""); }
-		StreamTokenizer st = new StreamTokenizer(new StringReader(cmd.substring(cut+1)));
-		st.eolIsSignificant(false);
-		st.parseNumbers();
-		st.quoteChar('\"');
-		st.ordinaryChar('=');
-		st.ordinaryChar(',');
-		st.ordinaryChar('[');
-		st.ordinaryChar(']');
-		st.ordinaryChar('(');
-		st.ordinaryChar(')');
-		st.wordChars('#', '#');
-		Vector<Argument> argv = parseArguments(st,true);
-		checkArgs(f,argv);
-		Command result = new Command(f,argv); 
-		return result;
-	}
-	
-	private static boolean checkArgs(Function f, Vector<Argument> argv) throws Exception
-	{
-		ArgumentType[] argtypes = getPrototype(f);
-		if (argtypes.length!=argv.size())
-			throw new Exception(SCRIPT_ERROR_PREFIX+": Wrong number of argument for function \""+f+"\".");
-		for (int i=0;i<argtypes.length;i++)
-		{
-			if (argtypes[i] != argv.get(i)._t)
-			{
-				throw new Exception(SCRIPT_ERROR_PREFIX+": Bad type ("+argtypes[i]+"!="+argv.get(i)._t+") for argument #"+(i+1)+" in function \""+f+"\".");
-			}
-		}
-		return true;
-	}
-	
-	private static Vector<Command> parseScript(String cmd) throws Exception
-	{
-		initFunctions();
-		Vector<Command> cmds = new Vector<Command>();
-		String[] data = cmd.split(";");
-		for (int i=0;i<data.length;i++)
-		{
-			cmds.add(parseCommand(data[i].trim()));
-		}
-		return cmds;
-	}
-	
-	
-}