+++ /dev/null
-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;
- }
-
-
-}
git://source.jalview.org / jalview.git / blobdiff