Examples with BigString org.vcell.util.BigString used on opensource projects

Example 41 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class BNGOutput method insertEntitiesInNetFile.

public void insertEntitiesInNetFile(String entities, String kind) {
    if (entities == null) {
        return;
    }
    HashSet<Integer> netFileIndices = new HashSet<Integer>();
    for (int i = 0; i < bng_filenames.length; i++) {
        if (bng_filenames[i].toLowerCase().endsWith(BNG_NET_FILE_SUFFIX)) {
            netFileIndices.add(i);
        }
    }
    if (netFileIndices.size() != 1) {
        throw new RuntimeException("BioNetGen was unable to generate reaction network.");
    }
    int location = netFileIndices.iterator().next();
    String s = bng_fileContents[location].toString();
    String prologue = s.substring(0, s.indexOf("begin " + kind));
    String epilogue = s.substring(s.indexOf("end " + kind));
    String d = prologue;
    d += "begin " + kind + "\n";
    d += entities;
    d += epilogue;
    bng_fileContents[location] = new BigString(d);
}

Example 42 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class BNGOutput method extractCompartmentsFromNetFile.

public void extractCompartmentsFromNetFile() {
    HashSet<Integer> netFileIndices = new HashSet<Integer>();
    for (int i = 0; i < bng_filenames.length; i++) {
        if (bng_filenames[i].toLowerCase().endsWith(BNG_NET_FILE_SUFFIX)) {
            netFileIndices.add(i);
        }
    }
    if (netFileIndices.size() != 1) {
        throw new RuntimeException("BioNetGen was unable to generate reaction network.");
    }
    int location = netFileIndices.iterator().next();
    String s = bng_fileContents[location].toString();
    String p = BNGOutputFileParser.extractCompartments(s);
    bng_fileContents[location] = new BigString(p);
}

Example 43 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method saveMathModel.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString saveMathModel(BigString mathModelXML, String[] independentSims) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.saveMathModel()");
        BigString savedMathModelXML = dbServerProxy.saveMathModel(mathModelXML, independentSims);
        return savedMathModelXML;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 44 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method saveMathModelAs.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString saveMathModelAs(BigString mathModelXML, String newName, String[] independentSims) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.saveMathModel(newName=" + newName + ")");
        BigString savedMathModelXML = dbServerProxy.saveMathModelAs(mathModelXML, newName, independentSims);
        return savedMathModelXML;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 45 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method getGeometryXML.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString getGeometryXML(KeyValue geometryKey) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getGeometryXML(key=" + geometryKey + ")");
        BigString geometryXML = dbServerProxy.getGeometryXML(geometryKey);
        return geometryXML;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}