/*
* 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;
}
/**
* @return true
* @deprecated Always returns true (4.0.0)
*/
@Deprecated
public boolean isPdbDirSplit() {
return true;
}
/**
* @param pdbDirSplit Ignored
* @deprecated Ignored (4.0.0)
*/
@Deprecated
public void setPdbDirSplit(boolean pdbDirSplit) {}
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
+ ", " + newline + " isDomainSplit="
+ isDomainSplit + ", " + newline + " alignPairs=" + alignPairs
+ ", " + newline + " searchFile=" + searchFile + ", " + newline + " saveOutputDir="
+ saveOutputDir + ", " + newline + " nrCPU=" + nrCPU + "]";
}
}