gt: 				+ ", " + newline + " isDomainSplit="
context: /*
   *                    BioJava development code
   *
   * This code may be freely distributed and modified under the
   * terms of the GNU Lesser General Public Licence.  This should
   * be distributed with the code.  If you do not have a copy,
   * see:
   *
   *      http://www.gnu.org/copyleft/lesser.html
   *
   * Copyright for this code is held jointly by the individual
   * authors.  These should be listed in @author doc comments.
   *
   * For more information on the BioJava project and its aims,
   * or to join the biojava-l mailing list, visit the home page
   * at:
   *
   *      http://www.biojava.org/
   *
   */
  package org.biojava.nbio.structure.align.ce;
  
  
  /** a simple bean that contains the parameters that can get set at startup
   *
   * @author Andreas Prlic
   *
   */
  public class StartupParameters {
  
  
  
  	String pdbFilePath;
  	String cacheFilePath;
  	String outFile;
  	String pdb1;
  	String pdb2;
  	String file1;
  	String file2;
  	String showDBresult;
  	boolean printXML;
  	boolean printFatCat;
  	boolean show3d;
  	boolean autoFetch;
  	boolean printCE;
  	boolean showMenu;
  	boolean printPDB;
  	boolean isDomainSplit;
  
  
  	// for DB searches
  	String alignPairs;
  	String searchFile;
  	String saveOutputDir;
  	int nrCPU;
  
  
  	private static final String newline = System.getProperty("line.separator");
  
  	public StartupParameters(){
  		show3d = false;
  		printXML = false;
  		printPDB = false;
  		printFatCat = false;
  		autoFetch = false;
  		showMenu = false;
  		isDomainSplit = true;
  		nrCPU = Runtime.getRuntime().availableProcessors() -1;
  		if ( nrCPU < 1)
  			nrCPU = 1;
  	}
  
  	/** An input file to be used for the DB search
  	 *
  	 * @return
  	 */
  	public String getSearchFile() {
  		return searchFile;
  	}
  	public void setSearchFile(String searchFile) {
  		this.searchFile = searchFile;
  	}
  
  
  	/** The file that contains a list of PDB pairs to be aligned
  	 *
  	 * @return
  	 */
  	public String getAlignPairs() {
  		return alignPairs;
  	}
  
  	public void setAlignPairs(String alignPairs) {
  		this.alignPairs = alignPairs;
  	}
  
  	public String getSaveOutputDir() {
  		return saveOutputDir;
  	}
  
  	public void setSaveOutputDir(String saveOutputDir) {
  		this.saveOutputDir = saveOutputDir;
  	}
  
  	public boolean isShowMenu() {
  		return showMenu;
  	}
  
  	public void setShowMenu(boolean showMenu) {
  		this.showMenu = showMenu;
  	}
  
  	/** Display the output string in CE style
  	 *
  	 * @return flag
  	 */
  	public boolean isPrintCE() {
  		return printCE;
  	}
  
  	/** Display the output string in CE style
  	 *
  	 * @param printCE a flag
  	 */
  	public void setPrintCE(boolean printCE) {
  		this.printCE = printCE;
  	}
  
  
  	public String getPdb1() {
  		return pdb1;
  	}
  	/** mandatory argument to set the first PDB (and optionally chain ID) to be aligned.
  	 *
  	 * @param pdb1
  	 */
  	public void setPdb1(String pdb1) {
  		this.pdb1 = pdb1;
  	}
  	public String getPdb2() {
  		return pdb2;
  	}
  
  	/** mandatory argument to set the second PDB (and optionally chain ID) to be aligned.
  	 *  @param pdb2
  	 */
  	public void setPdb2(String pdb2) {
  		this.pdb2 = pdb2;
  	}
  
  	public boolean isPrintXML() {
  		return printXML;
  	}
  	public void setPrintXML(boolean printXML) {
  		this.printXML = printXML;
  	}
  	public boolean isPrintFatCat() {
  		return printFatCat;
  	}
  	public void setPrintFatCat(boolean printFatCat) {
  		this.printFatCat = printFatCat;
  	}
  
  	public String getPdbFilePath() {
  		return pdbFilePath;
  	}
  
  	/** mandatory argument to set the location of PDB files.
  	 *
  	 * @param pdbFilePath
  	 */
  	public void setPdbFilePath(String pdbFilePath) {
  		this.pdbFilePath = pdbFilePath;
  	}
  
  	public String getCacheFilePath() {
  		return cacheFilePath;
  	}
  
  	public void setCacheFilePath(String cacheFilePath) {
  		this.cacheFilePath = cacheFilePath;
  	}
  
  	public boolean isShow3d() {
  		return show3d;
  	}
  	public void setShow3d(boolean show3d) {
  		this.show3d = show3d;
  	}
  	public String getOutFile() {
  		return outFile;
  	}
  	public void setOutFile(String outFile) {
  		this.outFile = outFile;
  	}
  	public boolean isAutoFetch() {
  		return autoFetch;
  	}
  	public void setAutoFetch(boolean autoFetch) {
  		this.autoFetch = autoFetch;
  	}
  	public String getShowDBresult() {
  		return showDBresult;
  	}
  	public void setShowDBresult(String showDBresult) {
  		this.showDBresult = showDBresult;
  	}
  
  	public int getNrCPU() {
  		return nrCPU;
  	}
  	public void setNrCPU(int nrCPU) {
  		this.nrCPU = nrCPU;
  	}
  
  	public String getFile1()
  	{
  		return file1;
  	}
  
  	public void setFile1(String file1)
  	{
  		this.file1 = file1;
  	}
  
  	public String getFile2()
  	{
  		return file2;
  	}
  
  	public void setFile2(String file2)
  	{
  		this.file2 = file2;
  	}
  
  
  
  	/** When writing the results to a file, don;t write as XML but write aligned PDB file
  	 *
  	 * @return flag
  	 */
  	public boolean isOutputPDB() {
  		return printPDB;
  	}
  	/** When writing the results to a file, don;t write as XML but write aligned PDB file
  	 *
  	 * @param printPDB flag to print aligned PDB
  	 */
  	public void setOutputPDB(boolean printPDB) {
  		this.printPDB = printPDB;
  	}
  
  
  
  
  
  	public boolean isDomainSplit() {
  		return isDomainSplit;
  	}
  
  	public void setDomainSplit(boolean isDomainSplit) {
  		this.isDomainSplit = isDomainSplit;
  	}
  
  	@Override
  	public String toString() {
  		return "StartupParameters [pdbFilePath=" + pdbFilePath
  				+ ", " + newline + " cacheFilePath=" + cacheFilePath + ", " + newline + " outFile=" + outFile
  				+ ", " + newline + " pdb1=" + pdb1 + ", " + newline + " pdb2=" + pdb2 + ", " + newline + " file1=" + file1
  				+ ", " + newline + " file2=" + file2 + ", " + newline + " showDBresult=" + showDBresult
  				+ ", " + newline + " printXML=" + printXML + ", " + newline + " printFatCat=" + printFatCat
  				+ ", " + newline + " show3d=" + show3d + ", " + newline + " autoFetch=" + autoFetch
  				+ ", " + newline + " printCE=" + printCE + ", " + newline + " showMenu=" + showMenu
  				+ ", " + newline + " printPDB=" + printPDB
  