[ViewVC] Diff of: OpenMD/trunk/src/selection/SelectionEvaluator.cpp

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC

+namespace oopse {
-+
+bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
-+
+    this->filename = filename;
-+
+    this->script = script;
-+
+    if (! compiler.compile(filename, script)) {
-+
+        error = true;
-+
+        errorMessage = compiler.getErrorMessage();
-+
+        return false;
-+
+    }
-+
-+
+    pc = 0;
-+
+    aatoken = compiler.getAatokenCompiled();
-+
+    linenumbers = compiler.getLineNumbers();
-+
+    lineIndices = compiler.getLineIndices();
-+
+    return true;
-+
-+
+void SelectionEvaluator::clearState() {
-+
+    for (int i = scriptLevelMax; --i >= 0; )
-+
+        stack[i] = null;
-+
+    scriptLevel = 0;
-+
+    error = false;
-+
+    errorMessage = null;
-+
+}
-+
-+
+bool SelectionEvaluator::loadScriptString(const std::string& script) {
-+
+    clearState();
-+
+    return loadScript(null, script);
-+
+}
-+
-+
+bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
-+
+    clearState();
-+
+    return loadScriptFileInternal(filename);
-+
+}
-+
-+
-+
+void SelectionEvaluator::instructionDispatchLoop(){
-+
-+
+    while ( pc < aatoken.length) {
-+
+        statement = aatoken[pc++];
-+
+        statementLength = statement.length;
-+
+        Token token = statement[0];
-+
+        switch (token.tok) {
-+
+            case Token.define:
-+
+                define();
-+
+            break;
-+
+            case Token.select:
-+
+                select();
-+
+            break;
-+
+            default:
-+
+                unrecognizedCommand(token);
-+
+            return;
-+
+        }
-+
+    }
-+
+}
-+
-+
+  void SelectionEvaluator::predefine(String script) {
-+
+    if (compiler.compile("#predefine", script)) {
-+
+      Token [][] aatoken = compiler.getAatokenCompiled();
-+
+      if (aatoken.length != 1) {
-+
+        viewer.scriptStatus("predefinition does not have exactly 1 command:"
-+
+                            + script);
-+
+        return;
-+
+      }
-+
+      Token[] statement = aatoken[0];
-+
+      if (statement.length > 2) {
-+
+        int tok = statement[1].tok;
-+
+        if (tok == Token.identifier ||
-+
+            (tok & Token.predefinedset) == Token.predefinedset) {
-+
+          String variable = (String)statement[1].value;
-+
+          variables.put(variable, statement);
-+
+        } else {
-+
+          viewer.scriptStatus("invalid variable name:" + script);
-+
+        }
-+
+      } else {
-+
+        viewer.scriptStatus("bad predefinition length:" + script);
-+
+      }
-+
+    } else {
-+
+      viewer.scriptStatus("predefined set compile error:" + script +
-+
+                          "\ncompile error:" + compiler.getErrorMessage());
-+
+    }
-+
+  }
-+
-+
-+
-+
+  BitSet SelectionEvaluator::expression(Token[] code, int pcStart) throws ScriptException {
-+
+    int numberOfAtoms = viewer.getAtomCount();
-+
+    BitSet bs;
-+
+    BitSet[] stack = new BitSet[10];
-+
+    int sp = 0;
-+
-+
+    for (int pc = pcStart; ; ++pc) {
-+
+      Token instruction = code[pc];
-+
+      if (logMessages)
-+
+        viewer.scriptStatus("instruction=" + instruction);
-+
+      switch (instruction.tok) {
-+
+      case Token.expressionBegin:
-+
+        break;
-+
+      case Token.expressionEnd:
-+
+        break expression_loop;
-+
+      case Token.all:
-+
+        bs = stack[sp++] = new BitSet(numberOfAtoms);
-+
+        for (int i = numberOfAtoms; --i >= 0; )
-+
+          bs.set(i);
-+
+        break;
-+
+      case Token.none:
-+
+        stack[sp++] = new BitSet();
-+
+        break;
-+
+      case Token.opOr:
-+
+        bs = stack[--sp];
-+
+        stack[sp-1].or(bs);
-+
+        break;
-+
+      case Token.opAnd:
-+
+        bs = stack[--sp];
-+
+        stack[sp-1].and(bs);
-+
+        break;
-+
+      case Token.opNot:
-+
+        bs = stack[sp - 1];
-+
+        notSet(bs);
-+
+        break;
-+
+      case Token.within:
-+
+        bs = stack[sp - 1];
-+
+        stack[sp - 1] = new BitSet();
-+
+        withinInstruction(instruction, bs, stack[sp - 1]);
-+
+        break;
-+
+      case Token.selected:
-+
+        stack[sp++] = copyBitSet(viewer.getSelectionSet());
-+
+        break;
-+
+      case Token.y:
-+
+      case Token.amino:
-+
+      case Token.backbone:
-+
+      case Token.solvent:
-+
+      case Token.identifier:
-+
+      case Token.sidechain:
-+
+      case Token.surface:
-+
+        stack[sp++] = lookupIdentifierValue((String)instruction.value);
-+
+        break;
-+
+      case Token.opLT:
-+
+      case Token.opLE:
-+
+      case Token.opGE:
-+
+      case Token.opGT:
-+
+      case Token.opEQ:
-+
+      case Token.opNE:
-+
+        bs = stack[sp++] = new BitSet();
-+
+        comparatorInstruction(instruction, bs);
-+
+        break;
-+
+      default:
-+
+        unrecognizedExpression();
-+
+      }
-+
+    }
-+
+    if (sp != 1)
-+
+      evalError("atom expression compiler error - stack over/underflow");
-+
+    return stack[0];
-+
+  }
-+
-+
-+
-+
+  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
-+
+    int comparator = instruction.tok;
-+
+    int property = instruction.intValue;
-+
+    float propertyValue = 0; // just for temperature
-+
+    int comparisonValue = ((Integer)instruction.value).intValue();
-+
+    int numberOfAtoms = viewer.getAtomCount();
-+
+    Frame frame = viewer.getFrame();
-+
+    for (int i = 0; i < numberOfAtoms; ++i) {
-+
+      Atom atom = frame.getAtomAt(i);
-+
+      switch (property) {
-+
+      case Token.atomno:
-+
+        propertyValue = atom.getAtomNumber();
-+
+        break;
-+
+      case Token.elemno:
-+
+        propertyValue = atom.getElementNumber();
-+
+        break;
-+
+      case Token.temperature:
-+
+        propertyValue = atom.getBfactor100();
-+
+        if (propertyValue < 0)
-+
+          continue;
-+
+        propertyValue /= 100;
-+
+        break;
-+
+      case Token._atomID:
-+
+        propertyValue = atom.getSpecialAtomID();
-+
+        if (propertyValue < 0)
-+
+          continue;
-+
+        break;
-+
+      case Token._structure:
-+
+        propertyValue = getProteinStructureType(atom);
-+
+        if (propertyValue == -1)
-+
+          continue;
-+
+        break;
-+
+      case Token.radius:
-+
+        propertyValue = atom.getRasMolRadius();
-+
+        break;
-+
+      case Token._bondedcount:
-+
+        propertyValue = atom.getCovalentBondCount();
-+
+        break;
-+
+      case Token.model:
-+
+        propertyValue = atom.getModelTagNumber();
-+
+        break;
-+
+      default:
-+
+        unrecognizedAtomProperty(property);
-+
+      }
-+
+      boolean match = false;
-+
+      switch (comparator) {
-+
+      case Token.opLT:
-+
+        match = propertyValue < comparisonValue;
-+
+        break;
-+
+      case Token.opLE:
-+
+        match = propertyValue <= comparisonValue;
-+
+        break;
-+
+      case Token.opGE:
-+
+        match = propertyValue >= comparisonValue;
-+
+        break;
-+
+      case Token.opGT:
-+
+        match = propertyValue > comparisonValue;
-+
+        break;
-+
+      case Token.opEQ:
-+
+        match = propertyValue == comparisonValue;
-+
+        break;
-+
+      case Token.opNE:
-+
+        match = propertyValue != comparisonValue;
-+
+        break;
-+
+      }
-+
+      if (match)
-+
+        bs.set(i);
-+
+    }
-+
+  }
-+
-+
+void SelectionEvaluator::withinInstruction(Token instruction, BitSet bs, BitSet bsResult)
-+
-+
+    Object withinSpec = instruction.value;
-+
+    if (withinSpec instanceof Float) {
-+
+        withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
-+
+        return;
-+
+    }
-+
+    evalError("Unrecognized within parameter:" + withinSpec);
-+
+}
-+
-+
+  void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
-+
+    Frame frame = viewer.getFrame();
-+
+    for (int i = frame.getAtomCount(); --i >= 0; ) {
-+
+      if (bs.get(i)) {
-+
+        Atom atom = frame.getAtomAt(i);
-+
+        AtomIterator iterWithin =
-+
+          frame.getWithinIterator(atom, distance);
-+
+        while (iterWithin.hasNext())
-+
+          bsResult.set(iterWithin.next().getAtomIndex());
-+
+      }
-+
+    }
-+
+  }
-+
-+
+  void SelectionEvaluator::define() throws ScriptException {
-+
+    String variable = (String)statement[1].value;
-+
+    variables.put(variable, (expression(statement, 2)));
-+
+  }
-+
+}
-+
-+
+  void SelectionEvaluator::predefine(Token[] statement) {
-+
+    String variable = (String)statement[1].value;
-+
+    variables.put(variable, statement);
-+
+  }
-+
-+
+  void SelectionEvaluator::select(){
-+
+    // NOTE this is called by restrict()
-+
+    if (statementLength == 1) {
-+
+      viewer.selectAll();
-+
+      if (!viewer.getRasmolHydrogenSetting())
-+
+        viewer.excludeSelectionSet(getHydrogenSet());
-+
+      if (!viewer.getRasmolHeteroSetting())
-+
+        viewer.excludeSelectionSet(getHeteroSet());
-+
+    } else {
-+
+      viewer.setSelectionSet(expression(statement, 1));
-+
+    }
-+
+    viewer.scriptStatus("" + viewer.getSelectionCount() + " atoms selected");
-+
+  }
-+
-+
+  }

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents): Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs. Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC

Diff Legend

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC