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

Example 16 with Species

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

the class ReactStepDbDriver method getSpecies.

/**
 * getModel method comment.
 */
public Species[] getSpecies(QueryHashtable dbc, Connection con, User user) throws SQLException, DataAccessException {
    // log.print("ReactStepDbDriver.getSpecies()");
    String sql;
    sql = " SELECT " + speciesTable.getTableName() + ".* " + " FROM " + speciesTable.getTableName() + "," + ModelTable.table.getTableName() + "," + SpeciesContextModelTable.table.getTableName() + " WHERE " + ModelTable.table.ownerRef.getQualifiedColName() + " = " + user.getID() + " AND " + SpeciesContextModelTable.table.modelRef.getQualifiedColName() + " = " + ModelTable.table.id.getQualifiedColName() + " AND " + SpeciesContextModelTable.table.speciesRef.getQualifiedColName() + " = " + speciesTable.id.getQualifiedColName() + " ORDER BY " + speciesTable.commonName.getQualifiedColName();
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    java.util.Vector speciesList = new java.util.Vector();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            Species s = getSpecies(dbc, rset, con);
            speciesList.addElement(s);
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // 
    if (speciesList.size() == 0) {
        return null;
    } else {
        Species[] speciesArray = new Species[speciesList.size()];
        speciesList.copyInto(speciesArray);
        return speciesArray;
    }
}

Example 17 with Species

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

the class ReactStepDbDriver method getSpecies.

/**
 * getModel method comment.
 */
public Species getSpecies(QueryHashtable dbc, Connection con, KeyValue speciesID) throws SQLException, DataAccessException, ObjectNotFoundException {
    // 
    // try to get Species from the object cache
    // 
    Species species = (Species) dbc.get(speciesID);
    if (species != null) {
        return species;
    }
    if (speciesID == null) {
        throw new IllegalArgumentException("Improper parameters for getSpecies");
    }
    // log.print("ReactStepDbDriver.getSpecies(speciesID=" + speciesID + ")");
    String sql;
    sql = " SELECT * " + " FROM " + speciesTable.getTableName() + " WHERE " + speciesTable.id + " = " + speciesID;
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            species = getSpecies(dbc, rset, con);
        } else {
            throw new org.vcell.util.ObjectNotFoundException("Species id=" + speciesID + " not found");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // MIRIAMTable.table.setMIRIAMAnnotation(con, species, speciesID);
    return species;
}

Example 18 with Species

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

the class ReactionCartoonTool method pasteReactionsAndSpecies.

private void pasteReactionsAndSpecies(Structure structure) {
    final String RXSPECIES_PASTERX = "Reactions";
    final String RXSPECIES_SPECIES = "Species";
    ReactionSpeciesCopy reactionSpeciesCopy = (ReactionSpeciesCopy) SimpleTransferable.getFromClipboard(VCellTransferable.REACTION_SPECIES_ARRAY_FLAVOR);
    if (reactionSpeciesCopy != null) {
        // TODO: here we may want to warn the user about compartment number / type / name mismatch
        // between the source and the destination
        String response = null;
        if ((reactionSpeciesCopy.getReactStepArr() != null || reactionSpeciesCopy.getReactionRuleArr() != null) && reactionSpeciesCopy.getSpeciesContextArr() != null) {
            String msg = "There are ";
            msg += reactionSpeciesCopy.getSpeciesContextArr().length + " Species and ";
            int rlen = 0;
            if (reactionSpeciesCopy.getReactStepArr() != null)
                rlen += reactionSpeciesCopy.getReactStepArr().length;
            if (reactionSpeciesCopy.getReactionRuleArr() != null)
                rlen += reactionSpeciesCopy.getReactionRuleArr().length;
            msg += rlen + " Reactions / Rules on the clipboard, choose which set to paste.";
            response = DialogUtils.showWarningDialog(getGraphPane(), "Choose Species or Reactions to paste", msg, new String[] { RXSPECIES_SPECIES, RXSPECIES_PASTERX, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
            if (response == null || response.equals(RXSPECIES_CANCEL)) {
                return;
            }
        }
        if (reactionSpeciesCopy.getSpeciesContextArr() != null && (response == null || response.equals(RXSPECIES_SPECIES))) {
            IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
            Vector<BioModelEntityObject> pastedSpeciesContextV = new Vector<BioModelEntityObject>();
            for (int i = 0; i < reactionSpeciesCopy.getSpeciesContextArr().length; i++) {
                String rootSC = speciesContextRootFinder(reactionSpeciesCopy.getSpeciesContextArr()[i]);
                pastedSpeciesContextV.add(pasteSpecies(getGraphPane(), reactionSpeciesCopy.getSpeciesContextArr()[i].getSpecies(), rootSC, getModel(), structure, true, speciesHash, null));
                copyRelativePosition(getGraphModel(), reactionSpeciesCopy.getSpeciesContextArr()[i], pastedSpeciesContextV.lastElement());
            }
            ReactionCartoonTool.selectAndSaveDiagram(ReactionCartoonTool.this, pastedSpeciesContextV);
        }
        if (reactionSpeciesCopy.getReactStepArr() != null && reactionSpeciesCopy.getReactionRuleArr() == null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            pasteReactionSteps(getGraphPane(), reactionSpeciesCopy.getReactStepArr(), getModel(), structure, true, null, ReactionCartoonTool.this);
        } else if (reactionSpeciesCopy.getReactionRuleArr() != null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            pasteReactionsAndRules(getGraphPane(), reactionSpeciesCopy, getModel(), structure, ReactionCartoonTool.this);
        }
    // try {
    // for(MolecularType mtOurs : mtNewList) {
    // rbmmcOurs.addMolecularType(mtOurs, false);
    // }
    // } catch (ModelException | PropertyVetoException e) {
    // e.printStackTrace();
    // }
    // 
    // // ReactionRules
    // if(reactionSpeciesCopy.getReactionRuleArr() != null) {
    // for(ReactionRule rrTheirs : reactionSpeciesCopy.getReactionRuleArr()) {
    // 
    // }
    // }
    }
}

Example 19 with Species

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

the class GeneratedSpeciesTableRow method deriveSpecies.

private void deriveSpecies(String inputString, Model tempModel) {
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                tempModel.addFeature(strStructure);
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        // System.out.println(sp.toString());
        species = new SpeciesContext(new Species("a", ""), structure, sp);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
    }
}

Example 20 with Species

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

the class ViewGeneratedSpeciesPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedSpeciesTableRow speciesTableRow = tableModel.getValueAt(selectedRow);
    String inputString = speciesTableRow.getExpression();
    // System.out.println(selectedRows[0] + ": " + inputString);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            // we'll just assume there's only one, may want to throw exception if more
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
        spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanel, sc, issueManager);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
        // error (red circle)
        spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
        shapePanel.repaint();
    }
    int xOffset = spls.getRightEnd() + 45;
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}