Examples with RbmObservable cbit.vcell.model.RbmObservable used on opensource projects

Example 26 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class SpeciesPatternLargeShape method paintSelf.

public void paintSelf(Graphics g, boolean bPaintContour) {
    Graphics2D g2 = (Graphics2D) g;
    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    if (shapePanel.getDisplayMode() == DisplayMode.participantSignatures) {
        if (bMatchesSignature == true) {
            paintMatchesSignatureContour(g);
        }
    } else if (bPaintContour && (owner instanceof RbmObservable || owner instanceof ReactionRule)) {
        paintContour(g);
    }
    // TODO: bring this back once we add compartments to species patterns
    paintCompartment(g);
    if (speciesShapes.isEmpty()) {
        // paint empty dummy
        MolecularTypeLargeShape.paintDummy(g, xPos, yPos, shapePanel);
    }
    for (MolecularTypeLargeShape stls : speciesShapes) {
        stls.paintSelf(g);
    }
    if (owner instanceof RbmObservable) {
        // endText = "Right click here to add a molecule.";
        endText = "";
    }
    // // matches between molecular types - only within reaction rules
    // if(owner instanceof ReactionRule) {
    // Color colorOld = g2.getColor();
    // Font fontOld = g.getFont();
    // 
    // Font font = MolecularComponentLargeShape.deriveComponentFontBold(graphicsContext);
    // Color fontColor = Color.gray;
    // Color lineColor = Color.lightGray;
    // g2.setFont(font);
    // g2.setColor(fontColor);
    // for(MolecularTypeLargeShape mtls : speciesShapes) {
    // MolecularTypePattern mtp = mtls.getMolecularTypePattern();
    // if(!mtp.hasExplicitParticipantMatch()) {
    // continue;				// nothing to do if no explicit match
    // }
    // int x = mtls.getX()+10;
    // int y = mtls.getY()-7;
    // if(((ReactionRule)owner).isReactant(sp)) {
    // g2.drawLine(x, y, x, y+6);									// vertical line
    // g2.drawLine(x+1, y, x+1, y+6);
    // 
    // g2.drawLine(x, y, x+10, y);									// line to right
    // g2.drawLine(x, y+1, x+10, y+1);
    // 
    // g2.drawString(mtp.getParticipantMatchLabel(), x+12, y+4);
    // } else {
    // g2.drawLine(x, y, x, y+6);
    // g2.drawLine(x+1, y, x+1, y+6);
    // 
    // g2.drawLine(x, y, x-10, y);									// line to left
    // g2.drawLine(x, y+1, x-10, y+1);
    // 
    // g2.drawString(mtp.getParticipantMatchLabel(), x+3, y+4);	// the match label
    // }
    // }
    // g2.setFont(fontOld);
    // g2.setColor(colorOld);
    // }
    // --- ------- Bonds between components ------------------------------------------------------------------------
    // initial height of vertical bar of matched bond
    int yDouble = 18;
    if (shapePanel != null) {
        // arbitrary factor, to be determined
        int Ratio = 1;
        // negative if going smaller
        int zoomFactor = shapePanel.getZoomFactor() * Ratio;
        yDouble += zoomFactor;
    }
    // distance between 2 vertical line segments of "exists" bond
    int yExists = 5;
    // separation between 2 vertical line segments of "exists" bond
    int ysExists = 3;
    if (shapePanel != null) {
        // negative if going smaller
        double zoomFactor = (double) (shapePanel.getZoomFactor()) / 3.0;
        yExists += (int) zoomFactor;
        ysExists += (int) zoomFactor;
    }
    // bond related attributes
    // offset of the bond id - we assume there will never be more than 99
    final int xOneLetterOffset = 7;
    final int xTwoLetterOffset = 13;
    // default y distance between 2 adjacent bars
    int separ = 5;
    for (int i = 0; i < bondSingles.size(); i++) {
        BondSingle bs = bondSingles.get(i);
        Color colorOld = g2.getColor();
        Font fontOld = g.getFont();
        Color fontColor = Color.red;
        Color lineColor = Color.red;
        if (AbstractComponentShape.isHidden(owner, bs.mcp)) {
            fontColor = getDefaultColor(Color.gray);
            lineColor = getDefaultColor(Color.lightGray);
        } else {
            fontColor = getDefaultColor(Color.black);
            lineColor = getDefaultColor(Color.gray);
        }
        if (bs.mcp.getBondType().equals(BondType.Possible)) {
            // ?  (Possible)
            Graphics gc = shapePanel.getGraphics();
            if (shapePanel.getZoomFactor() >= LargeShapeCanvas.SmallestZoomFactorWithText) {
                Font font = MolecularComponentLargeShape.deriveComponentFontBold(gc, shapePanel);
                g2.setFont(font);
                g2.setColor(fontColor);
                g2.drawString(bs.mcp.getBondType().symbol, bs.from.x - xOneLetterOffset, bs.from.y + yLetterOffset);
            }
            g2.setColor(lineColor);
            g2.drawLine(bs.from.x, bs.from.y, bs.from.x, bs.from.y + ysExists);
            g2.setColor(getDefaultColor(Color.gray));
            g2.drawLine(bs.from.x + 1, bs.from.y, bs.from.x + 1, bs.from.y + ysExists);
            g2.setColor(lineColor);
            g2.drawLine(bs.from.x, bs.from.y + yExists, bs.from.x, bs.from.y + yExists + ysExists);
            g2.setColor(getDefaultColor(Color.gray));
            g2.drawLine(bs.from.x + 1, bs.from.y + yExists, bs.from.x + 1, bs.from.y + yExists + ysExists);
            g2.setColor(lineColor);
            g2.drawLine(bs.from.x, bs.from.y + yExists * 2, bs.from.x, bs.from.y + yExists * 2 + ysExists);
            g2.setColor(getDefaultColor(Color.gray));
            g2.drawLine(bs.from.x + 1, bs.from.y + yExists * 2, bs.from.x + 1, bs.from.y + yExists * 2 + ysExists);
        } else if (bs.mcp.getBondType().equals(BondType.Exists)) {
            // g2.setColor(plusSignGreen);								// draw a green '+' sign
            // g2.drawLine(bs.from.x-8, bs.from.y+6, bs.from.x-3, bs.from.y+6);	// horizontal
            // g2.drawLine(bs.from.x-8, bs.from.y+7, bs.from.x-3, bs.from.y+7);
            // g2.drawLine(bs.from.x-6, bs.from.y+4, bs.from.x-6, bs.from.y+9);	// vertical
            // g2.drawLine(bs.from.x-5, bs.from.y+4, bs.from.x-5, bs.from.y+9);
            g2.setColor(lineColor);
            g2.drawLine(bs.from.x, bs.from.y, bs.from.x, bs.from.y + yExists * 2 + ysExists);
            g2.setColor(getDefaultColor(Color.gray));
            g2.drawLine(bs.from.x + 1, bs.from.y, bs.from.x + 1, bs.from.y + yExists * 2 + ysExists);
        } else {
        // g2.setColor(Color.red.darker());									// draw a dark red '-' sign
        // g2.drawLine(bs.from.x-10, bs.from.y+5, bs.from.x-4, bs.from.y+5);	// horizontal
        // g2.drawLine(bs.from.x-10, bs.from.y+6, bs.from.x-4, bs.from.y+6);
        // g2.drawLine(bs.from.x-6, bs.from.y+4, bs.from.x-6, bs.from.y+9);	// vertical
        // g2.drawLine(bs.from.x-5, bs.from.y+4, bs.from.x-5, bs.from.y+9);
        // for BondType.None we show nothing at all
        // below small black vertical line ended in a red "x" (comment out if not wanted)
        // g2.setColor(lineColor);
        // g2.drawLine(bs.from.x, bs.from.y, bs.from.x, bs.from.y+7);
        // g2.setColor(Color.gray);
        // g2.drawLine(bs.from.x+1, bs.from.y, bs.from.x+1, bs.from.y+7);
        // 
        // int vo = 8;
        // g2.setColor(Color.red);
        // g2.drawLine(bs.from.x-3, bs.from.y+2+vo, bs.from.x+4, bs.from.y-2+vo);
        // g2.setColor(Color.gray);
        // g2.drawLine(bs.from.x-3, bs.from.y+3+vo, bs.from.x+4, bs.from.y-1+vo);
        // 
        // g2.setColor(Color.red);
        // g2.drawLine(bs.from.x-3, bs.from.y-2+vo, bs.from.x+4, bs.from.y+2+vo);
        // g2.setColor(Color.gray);
        // g2.drawLine(bs.from.x-3, bs.from.y-1+vo, bs.from.x+4, bs.from.y+3+vo);
        // below small black vertical line (comment out if not wanted)
        // int vo = 10;
        // g2.setColor(lineColor);
        // g2.drawLine(bs.from.x, bs.from.y, bs.from.x, bs.from.y+vo);
        // g2.setColor(Color.gray);
        // g2.drawLine(bs.from.x+1, bs.from.y, bs.from.x+1, bs.from.y+vo);
        // 
        // small horizontal red line at the end of the vertical one
        // g2.setColor(Color.gray);
        // g2.drawLine(bs.from.x-1, bs.from.y+vo-1, bs.from.x+2, bs.from.y+vo-1);
        // g2.setColor(Color.gray);
        // g2.drawLine(bs.from.x-1, bs.from.y+vo, bs.from.x+2, bs.from.y+vo);
        }
        g.setFont(fontOld);
        g2.setColor(colorOld);
    }
    switch(// variable distance on y between bonds, we draw them closer when there are many of them
    bondPairs.size()) {
        case 1:
        case 2:
            separ = 5;
            break;
        case 3:
        case 4:
            separ = 4;
            break;
        case 5:
        case 6:
            separ = 3;
            break;
        case 7:
        case 8:
        case 9:
            separ = 2;
            break;
        default:
            separ = 1;
    }
    for (int i = 0; i < bondPairs.size(); i++) {
        BondPair bp = bondPairs.get(i);
        Color colorOld = g2.getColor();
        Font fontOld = g.getFont();
        if (shapePanel.isShowDifferencesOnly()) {
            g2.setColor(getDefaultColor(Color.gray));
        } else {
            g2.setColor(getDefaultColor(GraphConstants.bondHtmlColors[bp.id % GraphConstants.bondHtmlColors.length]));
        }
        g2.drawLine(bp.from.x, bp.from.y, bp.from.x, bp.from.y + yDouble + i * separ);
        g2.drawLine(bp.to.x, bp.to.y, bp.to.x, bp.to.y + yDouble + i * separ);
        g2.drawLine(bp.from.x, bp.from.y + yDouble + i * separ, bp.to.x, bp.to.y + yDouble + i * separ);
        Graphics gc = shapePanel.getGraphics();
        if (shapePanel.getZoomFactor() >= LargeShapeCanvas.SmallestZoomFactorWithText) {
            Font font = MolecularComponentLargeShape.deriveComponentFontBold(gc, shapePanel);
            g.setFont(font);
            String nr = bp.id + "";
            if (nr.length() < 2) {
                g2.drawString(nr, bp.from.x - xOneLetterOffset, bp.from.y + yLetterOffset);
                g2.drawString(nr, bp.to.x - xOneLetterOffset, bp.to.y + yLetterOffset);
            } else {
                g2.drawString(nr, bp.from.x - xTwoLetterOffset, bp.from.y + yLetterOffset);
                g2.drawString(nr, bp.to.x - xTwoLetterOffset, bp.to.y + yLetterOffset);
            }
        }
        g2.setColor(getDefaultColor(Color.lightGray));
        g2.drawLine(bp.from.x + 1, bp.from.y + 1, bp.from.x + 1, bp.from.y + yDouble + i * separ);
        g2.drawLine(bp.to.x + 1, bp.to.y + 1, bp.to.x + 1, bp.to.y + yDouble + i * separ);
        g2.drawLine(bp.from.x, bp.from.y + yDouble + i * separ + 1, bp.to.x + 1, bp.to.y + yDouble + i * separ + 1);
        g.setFont(fontOld);
        g2.setColor(colorOld);
    }
    if (!endText.isEmpty()) {
        Color colorOld = g2.getColor();
        g2.setColor(getDefaultColor(Color.black));
        g.drawString(endText, getRightEnd() + 20, yPos + 20);
        g2.setColor(colorOld);
    }
}

Example 27 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class SpeciesPatternLargeShape method getStructure.

public Structure getStructure() {
    Structure structure = null;
    if (owner instanceof ReactionRule) {
        ReactionRule rr = (ReactionRule) owner;
        ReactantPattern rp = rr.getReactantPattern(sp);
        ProductPattern pp = rr.getProductPattern(sp);
        if (rp != null) {
            structure = rp.getStructure();
        } else if (pp != null) {
            structure = pp.getStructure();
        } else {
            structure = ((ReactionRule) owner).getStructure();
        }
    } else if (owner instanceof SpeciesContext && ((SpeciesContext) owner).hasSpeciesPattern()) {
        structure = ((SpeciesContext) owner).getStructure();
    } else if (owner instanceof RbmObservable) {
        structure = ((RbmObservable) owner).getStructure();
    }
    return structure;
}

Example 28 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class SpeciesPatternRoundShape method paintSelf.

public void paintSelf(Graphics g, boolean bPaintContour) {
    Graphics2D g2 = (Graphics2D) g;
    Font fontOld = g2.getFont();
    Color colorOld = g2.getColor();
    g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
    // if(bPaintContour && (owner instanceof RbmObservable || owner instanceof ReactionRule)) {
    // paintContour(g);
    // }
    // paintCompartment(g);	// TODO: bring this back once we add compartments to species patterns
    // 
    // if(speciesShapes.isEmpty()) {		// paint empty dummy
    // MolecularTypeLargeShape.paintDummy(g, xPos, yPos, shapePanel);
    // }
    // g2.setPaint(Color.green.darker().darker());
    // Ellipse2D circle = new Ellipse2D.Double(xPos, yPos, 2*radius, 2*radius);
    // g2.fill(circle);
    // paint the bonds first as circles
    // as we keep painting other shapes over the bonds, all the unwanted parts of the bonds will get hidden
    // 
    // for(Pair<Integer, Integer> p : bondsSet) {
    // 
    // MolecularTypeRoundShape mtrsFrom = speciesShapes.get(p.one);
    // MolecularTypeRoundShape mtrsTo = speciesShapes.get(p.two);
    // 
    // //			Point p1 = new Point(mtrsFrom.xPos + MolecularTypeRoundShape.radius, mtrsFrom.yPos + MolecularTypeRoundShape.radius);
    // //			Point p2 = new Point(mtrsTo.xPos + MolecularTypeRoundShape.radius, mtrsTo.yPos + MolecularTypeRoundShape.radius);
    // Point p1 = new Point(mtrsFrom.xPos, mtrsFrom.yPos);
    // Point p2 = new Point(mtrsTo.xPos, mtrsTo.yPos);
    // 
    // int dx = Math.abs(p1.x - p2.x);
    // int dy = Math.abs(p1.y - p2.y);
    // double len = Math.sqrt(Math.pow((double)dx, 2) + Math.pow((double)dy, 2));
    // 
    // Point m = new Point((p1.x+p2.x)/2, (p1.y+p2.y)/2);
    // //			Point c = new Point(m.x+dy-MolecularTypeRoundShape.radius, m.y+dx-MolecularTypeRoundShape.radius);
    // Point c = new Point(m.x+dy, m.y+dx);
    // 
    // 
    // //			Ellipse2D circle2 = new Ellipse2D.Double(c.x, c.y, len, len);
    // Ellipse2D circle2 = new Ellipse2D.Double(c.x-8, c.y-8, len+9, len+9);
    // g2.setPaint(Color.gray);
    // g2.draw(circle2);
    // 
    // 
    // }
    Ellipse2D circle2 = new Ellipse2D.Double(xPos, yPos, 2 * radius, 2 * radius);
    g2.setPaint(Color.lightGray);
    g2.draw(circle2);
    g.setFont(fontOld);
    g.setColor(colorOld);
    for (MolecularTypeRoundShape mtls : speciesShapes) {
        mtls.paintSelf(g);
    }
    if (owner instanceof RbmObservable) {
        // endText = "Right click here to add a molecule.";
        endText = "";
    }
    if (!endText.isEmpty()) {
        g.drawString(endText, getRightEnd() + 20, yPos + 20);
    }
}

Example 29 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class AbstractMathMapping method getMathSymbol0.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
protected final String getMathSymbol0(SymbolTableEntry ste, GeometryClass geometryClass) throws MappingException {
    String steName = ste.getName();
    if (ste instanceof Kinetics.KineticsParameter) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("KineticsParameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ReactionRule.ReactionRuleNameScope) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("Reaction Rule Parameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof ProbabilityParameter) {
        // be careful here, to see if we need mangle the reaction name
        ProbabilityParameter probParm = (ProbabilityParameter) ste;
        return probParm.getName() + PARAMETER_PROBABLIITY_RATE_SUFFIX;
    }
    if (ste instanceof SpeciesConcentrationParameter) {
        SpeciesConcentrationParameter concParm = (SpeciesConcentrationParameter) ste;
        return concParm.getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof SpeciesCountParameter) {
        SpeciesCountParameter countParm = (SpeciesCountParameter) ste;
        return countParm.getSpeciesContext().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof ObservableConcentrationParameter) {
        ObservableConcentrationParameter concParm = (ObservableConcentrationParameter) ste;
        return concParm.getObservable().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof ObservableCountParameter) {
        ObservableCountParameter countParm = (ObservableCountParameter) ste;
        return countParm.getObservable().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof RbmObservable) {
        RbmObservable observable = (RbmObservable) ste;
        return observable.getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof EventAssignmentOrRateRuleInitParameter) {
        EventAssignmentOrRateRuleInitParameter eventInitParm = (EventAssignmentOrRateRuleInitParameter) ste;
        // + MATH_FUNC_SUFFIX_EVENTASSIGN_OR_RATE_INIT;
        return eventInitParm.getName();
    }
    if (ste instanceof RateRuleRateParameter) {
        RateRuleRateParameter rateRuleRateParm = (RateRuleRateParameter) ste;
        // + MATH_FUNC_SUFFIX_RATERULE_RATE;
        return rateRuleRateParm.getName();
    }
    if (ste instanceof Model.ReservedSymbol) {
        return steName;
    }
    if (ste instanceof Membrane.MembraneVoltage) {
        return steName;
    }
    if (ste instanceof Structure.StructureSize) {
        Structure structure = ((Structure.StructureSize) ste).getStructure();
        StructureMapping.StructureMappingParameter sizeParameter = simContext.getGeometryContext().getStructureMapping(structure).getSizeParameter();
        return getMathSymbol(sizeParameter, geometryClass);
    }
    if (ste instanceof ProxyParameter) {
        ProxyParameter pp = (ProxyParameter) ste;
        return getMathSymbol0(pp.getTarget(), geometryClass);
    }
    // 
    if (ste instanceof ModelParameter) {
        ModelParameter mp = (ModelParameter) ste;
        return mp.getName();
    }
    if (ste instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
        SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) ste;
        SpeciesContext speciesContext = ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext();
        SpeciesContextMapping scm = getSpeciesContextMapping(speciesContext);
        String speciesContextVarName = null;
        if (scm.getVariable() != null) {
            speciesContextVarName = scm.getVariable().getName();
        } else {
            speciesContextVarName = speciesContext.getName();
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
            return speciesContextVarName + MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scsParm.getUnitDefinition().getSymbol());
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
            return speciesContextVarName + MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate) {
            return speciesContextVarName + PARAMETER_DIFFUSION_RATE_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXm) {
            return speciesContextVarName + PARAMETER_BOUNDARY_XM_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXp) {
            return speciesContextVarName + PARAMETER_BOUNDARY_XP_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYm) {
            return speciesContextVarName + PARAMETER_BOUNDARY_YM_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYp) {
            return speciesContextVarName + PARAMETER_BOUNDARY_YP_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZm) {
            return speciesContextVarName + PARAMETER_BOUNDARY_ZM_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZp) {
            return speciesContextVarName + PARAMETER_BOUNDARY_ZP_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityX) {
            return speciesContextVarName + PARAMETER_VELOCITY_X_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityY) {
            return speciesContextVarName + PARAMETER_VELOCITY_Y_SUFFIX;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityZ) {
            return speciesContextVarName + PARAMETER_VELOCITY_Z_SUFFIX;
        }
    }
    if (ste instanceof ElectricalDevice.ElectricalDeviceParameter) {
        ElectricalDevice.ElectricalDeviceParameter edParm = (ElectricalDevice.ElectricalDeviceParameter) ste;
        ElectricalDevice electricalDevice = (ElectricalDevice) edParm.getNameScope().getScopedSymbolTable();
        if (electricalDevice instanceof MembraneElectricalDevice) {
            String nameWithScope = ((MembraneElectricalDevice) electricalDevice).getMembraneMapping().getMembrane().getNameScope().getName();
            if (edParm.getRole() == ElectricalDevice.ROLE_TotalCurrent) {
                return PARAMETER_TOTAL_CURRENT_PREFIX + nameWithScope;
            }
            if (edParm.getRole() == ElectricalDevice.ROLE_TransmembraneCurrent) {
                return PARAMETER_TRANSMEMBRANE_CURRENT_PREFIX + nameWithScope;
            }
        // }else if (electricalDevice instanceof CurrentClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // }else if (electricalDevice instanceof VoltageClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ElectricalStimulus.ElectricalStimulusNameScope) {
        LocalParameter esParm = (LocalParameter) ste;
        String nameWithScope = esParm.getNameScope().getName();
        if (esParm.getRole() == ElectricalStimulus.ElectricalStimulusParameterType.TotalCurrent) {
            return PARAMETER_TOTAL_CURRENT_PREFIX + nameWithScope;
        } else if (esParm.getRole() == ElectricalStimulus.ElectricalStimulusParameterType.Voltage) {
            return PARAMETER_VOLTAGE_PREFIX + nameWithScope;
        }
    }
    if (ste instanceof StructureMapping.StructureMappingParameter) {
        StructureMapping.StructureMappingParameter smParm = (StructureMapping.StructureMappingParameter) ste;
        Structure structure = ((StructureMapping) (smParm.getNameScope().getScopedSymbolTable())).getStructure();
        String nameWithScope = structure.getNameScope().getName();
        int role = smParm.getRole();
        if (role == StructureMapping.ROLE_InitialVoltage) {
            return smParm.getName();
        } else if (role == StructureMapping.ROLE_SpecificCapacitance) {
            return PARAMETER_SPECIFIC_CAPACITANCE_PREFIX + nameWithScope;
        } else if (role == StructureMapping.ROLE_Size) {
            if (simContext.getGeometry().getDimension() == 0) {
                // if geometry is compartmental, make sure compartment sizes are set if referenced in model.
                if (smParm.getExpression() == null || smParm.getExpression().isZero()) {
                    throw new MappingException("\nIn non-spatial application '" + getSimulationContext().getName() + "', " + "size of structure '" + structure.getName() + "' must be assigned a " + "positive value if referenced in the model.\n\nPlease go to 'Structure Mapping' tab to check the size.");
                }
            }
            return PARAMETER_SIZE_FUNCTION_PREFIX + nameWithScope;
        } else if (role == StructureMapping.ROLE_AreaPerUnitArea) {
            return "AreaPerUnitArea_" + nameWithScope;
        } else if (role == StructureMapping.ROLE_AreaPerUnitVolume) {
            return "AreaPerUnitVolume_" + nameWithScope;
        } else if (role == StructureMapping.ROLE_VolumePerUnitArea) {
            return "VolumePerUnitArea_" + nameWithScope;
        } else if (role == StructureMapping.ROLE_VolumePerUnitVolume) {
            return "VolumePerUnitVolume_" + nameWithScope;
        }
    }
    // 
    if (ste instanceof SpeciesContext) {
        SpeciesContext sc = (SpeciesContext) ste;
        SpeciesContextMapping scm = getSpeciesContextMapping(sc);
        if (scm == null) {
            throw new RuntimeException("Species '" + sc.getName() + "' is referenced in model but may have been deleted. " + "Find its references in '" + GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_BIOMODEL_PARAMETERS + "'.");
        }
        // 
        if (geometryClass instanceof SubVolume) {
            // 
            if (scm.getVariable() != null && !scm.getVariable().getName().equals(steName)) {
                return scm.getVariable().getName();
            }
        // 
        // for reactions within a surface, may need "_INSIDE" or "_OUTSIDE" for jump condition
        // 
        } else if (geometryClass instanceof SurfaceClass) {
            // 
            // if the speciesContext is also within the surface, replace SpeciesContext name with Variable name
            // 
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(sc.getStructure());
            if (sm.getGeometryClass() == geometryClass) {
                if (scm.getVariable() != null && !(scm.getVariable().getName().equals(ste.getName()))) {
                    return scm.getVariable().getName();
                }
            // 
            // if the speciesContext is "inside" or "outside" the membrane
            // 
            } else if (sm.getGeometryClass() instanceof SubVolume && ((SurfaceClass) geometryClass).isAdjacentTo((SubVolume) sm.getGeometryClass())) {
                SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
                if (!scs.isConstant()) {
                    if (!scs.isDiffusing() && !scs.isWellMixed()) {
                        throw new MappingException("Enable diffusion in Application '" + simContext.getName() + "'. This must be done for any species (e.g '" + sc.getName() + "') in flux reactions.\n\n" + "To save or run simulations, set the diffusion rate to a non-zero " + "value in Initial Conditions or disable those reactions in Specifications->Reactions.");
                    }
                }
                if (scm.getVariable() != null) {
                    return scm.getVariable().getName();
                }
            } else {
                throw new MappingException("species '" + sc.getName() + "' interacts with surface '" + geometryClass.getName() + "', but is not mapped spatially adjacent");
            }
        }
    }
    return getNameScope().getSymbolName(ste);
}

Example 30 with RbmObservable

use of cbit.vcell.model.RbmObservable in project vcell by virtualcell.

the class MolecularComponentLargeShape method setComponentColor.

private Color setComponentColor() {
    boolean highlight = isHighlighted();
    if (owner == null) {
        return highlight == true ? componentBad.brighter() : componentBad;
    }
    Color componentColor = highlight == true ? componentBad.brighter() : componentBad;
    if (owner instanceof MolecularType) {
        componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
    } else if (owner instanceof SpeciesContext) {
        if (shapePanel != null && !shapePanel.isShowNonTrivialOnly()) {
            componentColor = componentHidden;
        } else {
            componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
        }
    } else if (mcp != null && owner instanceof RbmObservable) {
        if (shapePanel != null && !shapePanel.isEditable()) {
            componentColor = componentHidden;
        } else {
            componentColor = highlight == true ? componentHidden.brighter() : componentHidden;
        }
        if (mcp.getBondType() != BondType.Possible) {
            componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
        }
    } else if (owner instanceof ReactionRule) {
        ReactionRule reactionRule = (ReactionRule) owner;
        if (shapePanel.getDisplayMode() == DisplayMode.participantSignatures) {
            componentColor = componentHidden;
            if (shapePanel.isShowNonTrivialOnly() == true) {
                if (mcp.getBondType() != BondType.Possible) {
                    componentColor = componentPaleYellow;
                } else {
                    componentColor = componentHidden;
                }
            }
            if (shapePanel.isShowDifferencesOnly()) {
                switch(shapePanel.hasBondChanged(reactionRule.getName(), mcp)) {
                    case CHANGED:
                        componentColor = Color.orange;
                        break;
                    case ANALYSISFAILED:
                        ArrayList<Issue> issueList = new ArrayList<Issue>();
                        reactionRule.gatherIssues(new IssueContext(), issueList);
                        boolean bRuleHasErrorIssues = false;
                        for (Issue issue : issueList) {
                            if (issue.getSeverity() == Severity.ERROR) {
                                bRuleHasErrorIssues = true;
                                break;
                            }
                        }
                        if (bRuleHasErrorIssues) {
                            componentColor = componentHidden;
                        } else {
                            System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                            componentColor = Color.red.darker();
                        }
                        break;
                    default:
                        break;
                }
            }
        } else if (shapePanel.getDisplayMode() == DisplayMode.rules) {
            componentColor = componentHidden;
            if (shapePanel.isShowNonTrivialOnly() == true) {
                if (mcp.getBondType() != BondType.Possible) {
                    componentColor = componentPaleYellow;
                } else {
                    componentColor = componentHidden;
                }
            }
            if (shapePanel.isShowDifferencesOnly()) {
                switch(shapePanel.hasBondChanged(mcp)) {
                    case CHANGED:
                        componentColor = Color.orange;
                        break;
                    case ANALYSISFAILED:
                        ArrayList<Issue> issueList = new ArrayList<Issue>();
                        reactionRule.gatherIssues(new IssueContext(), issueList);
                        boolean bRuleHasErrorIssues = false;
                        for (Issue issue : issueList) {
                            if (issue.getSeverity() == Severity.ERROR) {
                                bRuleHasErrorIssues = true;
                                break;
                            }
                        }
                        if (bRuleHasErrorIssues) {
                            componentColor = componentHidden;
                        } else {
                            System.err.println("ReactionRule Analysis failed, but there are not Error Issues with ReactionRule " + reactionRule.getName());
                            componentColor = Color.red.darker();
                        }
                        break;
                    default:
                        break;
                }
            }
        } else {
            componentColor = highlight == true ? componentHidden.brighter() : componentHidden;
            if (mcp.getBondType() != BondType.Possible) {
                componentColor = highlight == true ? componentPaleYellow.brighter() : componentPaleYellow;
            }
        }
    }
    if (hasErrorIssues(owner, mcp, mc)) {
        componentColor = highlight == true ? componentBad.brighter() : componentBad;
    }
    return componentColor;
}