/*
 *                    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 + "]";
        }







}