CMView-jung/cmview/Start.java

package cmview;
import java.io.*;
import java.sql.SQLException;
import java.util.Properties;
import java.util.TreeMap;
import java.util.concurrent.Executors;
import java.util.concurrent.ThreadPoolExecutor;

import javax.swing.JColorChooser;
import javax.swing.JFileChooser;
import javax.swing.JPanel;
import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;

import proteinstructure.PdbCodeNotFoundError;

import tools.MySQLConnection;

import cmview.datasources.Model;
import cmview.datasources.ModelConstructionError;
import cmview.datasources.PdbaseModel;

/**
 * Main class to start contact map viewer application.
 * Contains static main function, constants and some helper functions.
 */
public class Start {

        static final long serialVersionUID = 1l;
        
        // internal constants (not user changeable)
        public static final String              APP_NAME =                              "CMView";                       // name of this application
        public static final String              VERSION =                               "0.8.5";                        // current version of this application (should match manifest)
        public static final String              NULL_CHAIN_CODE =               "NULL";                         // used by Pdb/Graph objects for the empty pdbChainCode
        public static final int                 NO_SEQ_SEP_VAL =                -1;                                     // default seq sep value indicating that no seq sep has been specified
        public static final String              NO_SEQ_SEP_STR =                "none";                         // text output if some seqsep variable equals NO_SEQ_SEP_VAL
        public static final String              RESOURCE_DIR =                  "/resources/";          // path within the jar archive where resources are located
        public static final String              PYMOL_HOST =                    "localhost";            // currently, the XMLRPC server in Pymol only supports localhost
        public static final String              PYMOL_PORT =                    "9123";                         // default port, if port is blocked, pymol will increase automatically
        public static final String              PYMOL_SERVER_URL =              "http://"+PYMOL_HOST+":"+PYMOL_PORT; // TODO: set this later so that the two above may change
                
        // The following config file name may be overwritten by a command line switch
        public static String                    CONFIG_FILE_NAME =              "cmview.cfg";           // default name of config file (can be overridden by cmd line param)
        
        // The following 'constants' can be overwritten by the user's config file. In the code, they are being used as if they were (final) constants
        // and the only time when they may change is during startup. Note that for each variable that ought to be user changeable, i.e. read from cfg file
        // there has to be a line in the applyUserProperties method. The preassigned values are the default and being used unless overwritten by the user.
        // Additioanlly, values that should appear in the example config file should be added to the getSelectedProperties method.

        // environment
        public static String                    TEMP_DIR = System.getProperty("java.io.tmpdir");
        
        // user customizations
        public static int                       INITIAL_SCREEN_SIZE = 800;                      // initial size of the contactMapPane in pixels
        public static boolean                   USE_DATABASE = true;                            // if false, all functions involving a database will be hidden 
        public static boolean                   USE_PYMOL = true;                                       // if false, all pymol specific functionality will be hidden
        public static boolean                   INCLUDE_GROUP_INTERNALS = true; // this flag shall indicate strongly experimental stuff, use it to disable features in release versions
        public static boolean                   PRELOAD_PYMOL = true;                           // if true, pymol is preloaded on startup
        public static boolean                   SHUTDOWN_PYMOL_ON_EXIT = true;          // if true, pymol is shutdown on exit
        
        public static boolean                   SHOW_RULERS_ON_STARTUP = true;          // if true, rulers will be shown by default
        public static boolean                   FORCE_DSSP = false;                                     // if true, secondary structure will be always taken from DSSP (if available)
        public static String                    DSSP_EXECUTABLE = "/project/StruPPi/Software/dssp/dsspcmbi";
        public static String                    DSSP_PARAMETERS = "--";
        public static String                    PDB_FTP_URL = "ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/mmCIF/";
        
        // constants not in config file yet
        public static String                    DIST_MAP_CONTACT_TYPE = "Ca";   // contact type to be used for distance map calculation (only single atom allowed)
        public static boolean                   SHOW_ICON_BAR = true;                           // if true, icon bar is used
        public static boolean                   ICON_BAR_FLOATABLE = false;                     // if true, icon bar can be dragged out of the window (buggy, don't use)
        
        // pymol connection
        public static String                    PYMOL_EXECUTABLE =              "/project/StruPPi/bin/pymol-1.0"; // to start pymol automatically
        public static String                    PYMOL_PARAMETERS =      "-R -q";                                // run xmlrpc server and skip splash screen
        public static long                              PYMOL_CONN_TIMEOUT =    15000;                                  // pymol connection time out in milliseconds
        
        // database connection
        public static String                    DB_HOST = "white";                                                              // TODO: change to dummy name
        public static String                    DB_USER = getUserName();                                                // guess user name
        public static String                    DB_PWD = "nieve";                                                               // TODO: change to tiger
        
        // default values for loading contact maps
        public static String                    DEFAULT_GRAPH_DB =                      "pdb_reps_graph";       // shown in load from graph db dialog
        public static String                    DEFAULT_PDB_DB =                        "pdbase";                       // for loading from command line
        public static String                    DEFAULT_MSDSD_DB =                      "msdsd_00_07_a";        // used when loading structures for cm file graphs
        public static String                    DEFAULT_CONTACT_TYPE =          "Ca";                           // loading from command line and shown in LoadDialog
        public static double                    DEFAULT_DISTANCE_CUTOFF =       8.0;                            // dito
        private static final int        DEFAULT_MIN_SEQSEP =            NO_SEQ_SEP_VAL;         // dito, but not user changeable at the moment
        private static final int        DEFAULT_MAX_SEQSEP =            NO_SEQ_SEP_VAL;         // dito, but not user changeable at the moment
        
        // internal status variables
        protected static boolean                database_found = true;
        protected static boolean                pymol_found = true;
        protected static boolean                dssp_found = true;                      // check later whether dssp can be used
        protected static Properties             userProperties;                         // properties read from the user's config file
        protected static Properties             selectedProperties;                     // selected default properties for the example config file
        
        // global session variables (use getter methods)
        private static MySQLConnection conn;
        private static JFileChooser fileChooser;
        private static JColorChooser colorChooser;
        private static PyMolAdaptor pymolAdaptor;
        
        // the thread pool
        public static ThreadPoolExecutor threadPool =  (ThreadPoolExecutor) Executors.newCachedThreadPool();
        
        // mapping pdb-code to mmCIF files in the tmp-directory
        private static TreeMap<String, String> pdbCode2file = new TreeMap<String, String>();
        
        /**
         * Gets the filename of the local copy of the structure file corresponding 
         * to the given pdb code. 
         * @param pdbCode  pdb code
         * @return  path to the file of the given pdb code. Returns null if there 
         *  is no such file. 
         */
        public static String getFilename2PdbCode(String pdbCode) {
                return pdbCode2file.get(pdbCode.toLowerCase());
        }
        
        /**
         * Sets the name of the local copy of the structure file corresponding to 
         * the given pdb code.
         * @param pdbCode  pdb code
         * @param filename  name of the file corresponding to <code>pdbCode</code>
         */
        public static void setFilename2PdbCode(String pdbCode, String filename) {
                pdbCode2file.put(pdbCode, filename);
        }       
        
        /** 
         * Get user name from operating system (for use as database username). 
         * */
        private static String getUserName() {
                String user = null;
                user = System.getProperty("user.name");
                if(user == null) {
                        System.err.println("Could not get user name from operating system.");
                }
                return user;
        }
                
        /**
         * Returns a property object with the default values for selected customizable variables.
         * These are the variables that we expect users to commonly change. They are written
         * when the users selects the 'write example config file' from the Help menu.
         * Other possible customizable variables should be mentioned somewhere in the manual.
         */
        private static Properties getSelectedProperties() {

                Properties d = new Properties();
                
                // properties which the user will have to change
                d.setProperty("PYMOL_EXECUTABLE",PYMOL_EXECUTABLE);             
                d.setProperty("DB_HOST",DB_HOST);
                d.setProperty("DB_USER",DB_USER);
                d.setProperty("DB_PWD",DB_PWD);
                                
                // properties which the user may want to change
                d.setProperty("INITIAL_SCREEN_SIZE",new Integer(INITIAL_SCREEN_SIZE).toString());
                d.setProperty("USE_DATABASE",new Boolean(USE_DATABASE).toString());
                d.setProperty("USE_PYMOL",new Boolean(USE_PYMOL).toString());
                d.setProperty("PRELOAD_PYMOL",new Boolean(PRELOAD_PYMOL).toString());
                d.setProperty("SHUTDOWN_PYMOL_ON_EXIT",new Boolean(SHUTDOWN_PYMOL_ON_EXIT).toString());
                d.setProperty("DEFAULT_CONTACT_TYPE",DEFAULT_CONTACT_TYPE);
                d.setProperty("DEFAULT_DISTANCE_CUTOFF",new Double(DEFAULT_DISTANCE_CUTOFF).toString());
                d.setProperty("DSSP_EXECUTABLE", DSSP_EXECUTABLE);
                d.setProperty("FORCE_DSSP", new Boolean(FORCE_DSSP).toString());
                d.setProperty("SHOW_RULERS_ON_STARTUP", new Boolean(SHOW_RULERS_ON_STARTUP).toString());
                
                // properties which will become obsolete when loading from online pdb is implemented
                d.setProperty("DEFAULT_PDB_DB",DEFAULT_PDB_DB);
                d.setProperty("DEFAULT_GRAPH_DB", DEFAULT_GRAPH_DB);
                d.setProperty("DEFAULT_MSDSD_DB",DEFAULT_MSDSD_DB);
                
                // properties that should be changed only if problems arise
                // these will be mentioned in the documentation somewhere but not in the example config file
                //d.setProperty("TEMP_DIR",TEMP_DIR);
                //d.setProperty("PYMOL_PARAMETERS",PYMOL_PARAMETERS);
                //d.setProperty("PYMOL_CONN_TIMEOUT",new Long(PYMOL_CONN_TIMEOUT).toString());
                //d.setProperty("DSSP_PARAMETERS", DSSP_PARAMETERS);
                
                return d;
        }

        /**
         * Loads user properties from the given configuration file.
         * Returns null on failure;
         * @throws IOException 
         * @throws FileNotFoundException 
         */
        private static Properties loadUserProperties(String fileName) throws FileNotFoundException, IOException {
                Properties p = new Properties();
                p.load(new FileInputStream(fileName));
                return p;
        }

        /**
         * Overwrite the local constants with the values from the given properties object
         */
        private static void applyUserProperties(Properties p) {

                // The logic here is: First, take the value from the user config file,
                // if that is not found, keep the variable value unchanged.
                // Note that any value in the user config file that is not being processed here is ignored.
                
                TEMP_DIR = p.getProperty("TEMP_DIR",TEMP_DIR);
                INITIAL_SCREEN_SIZE = Integer.valueOf(p.getProperty("INITIAL_SCREEN_SIZE", new Integer(INITIAL_SCREEN_SIZE).toString()));
                USE_DATABASE = Boolean.valueOf(p.getProperty("USE_DATABASE", new Boolean(USE_DATABASE).toString()));
                USE_PYMOL = Boolean.valueOf(p.getProperty("USE_PYMOL", new Boolean(USE_PYMOL).toString()));
                PRELOAD_PYMOL = Boolean.valueOf(p.getProperty("PRELOAD_PYMOL", new Boolean(PRELOAD_PYMOL).toString()));
                SHUTDOWN_PYMOL_ON_EXIT = Boolean.valueOf(p.getProperty("SHUTDOWN_PYMOL_ON_EXIT", new Boolean(SHUTDOWN_PYMOL_ON_EXIT).toString()));
                SHOW_RULERS_ON_STARTUP = Boolean.valueOf(p.getProperty("SHOW_RULERS_ON_STARTUP", new Boolean(SHOW_RULERS_ON_STARTUP).toString()));
                
                PYMOL_PARAMETERS = p.getProperty("PYMOL_PARAMETERS", PYMOL_PARAMETERS);
                PYMOL_EXECUTABLE = p.getProperty("PYMOL_EXECUTABLE", PYMOL_EXECUTABLE);         
                PYMOL_CONN_TIMEOUT = Long.valueOf(p.getProperty("PYMOL_CONN_TIMEOUT",new Long(PYMOL_CONN_TIMEOUT).toString()));
                
                DSSP_EXECUTABLE = p.getProperty("DSSP_EXECUTABLE",DSSP_EXECUTABLE);
                DSSP_PARAMETERS = p.getProperty("DSSP_PARAMETERS",DSSP_PARAMETERS);
                FORCE_DSSP = Boolean.valueOf(p.getProperty("FORCE_DSSP", new Boolean(FORCE_DSSP).toString()));
                
                DB_HOST = p.getProperty("DB_HOST", DB_HOST);
                DB_USER = p.getProperty("DB_USER", DB_USER);
                DB_PWD = p.getProperty("DB_PWD", DB_PWD);

                DEFAULT_PDB_DB = p.getProperty("DEFAULT_PDB_DB", DEFAULT_PDB_DB);
                DEFAULT_CONTACT_TYPE = p.getProperty("DEFAULT_CONTACT_TYPE", DEFAULT_CONTACT_TYPE);
                DEFAULT_DISTANCE_CUTOFF = Double.valueOf(p.getProperty("DEFAULT_DISTANCE_CUTOFF", new Double(DEFAULT_DISTANCE_CUTOFF).toString()));
                
                DEFAULT_GRAPH_DB = p.getProperty("DEFAULT_GRAPH_DB", DEFAULT_GRAPH_DB);
                DEFAULT_MSDSD_DB = p.getProperty("DEFAULT_MSDSD_DB", DEFAULT_MSDSD_DB);

        }
        
        /** 
         * Copy external resources (data files and executables) from the jar archive to a temp directory.
         * The files are marked to be deleted on exit. Use getResourcePath() to access resources later.
         * */
        private static void unpackResources() {         
                unpackResource(PyMolAdaptor.PYMOLFUNCTIONS_SCRIPT);
        }       
        
        /** 
         * Copy the resource file 'resource' from the resource dir in the jar file to the temp directory.
         * The resource will be marked as to be deleted. Use getResourcePath() to access resource later. 
         */
        private static void unpackResource(String resource) {
                
                String source = RESOURCE_DIR + resource;
                File target = new File(TEMP_DIR, resource);

                try{
                        try {
                                target.createNewFile();
                        } catch (IOException e) {
                                System.err.println("Failed to create file " + target);
                                throw e;
                        }

                        InputStream inp = Runtime.getRuntime().getClass().getResourceAsStream(source);
                        BufferedInputStream in = new BufferedInputStream(inp);
                        FileOutputStream out = new FileOutputStream(target);

                        try {
                                int ch;            
                                while((ch = in.read()) != -1)
                                        out.write(ch);
                                in.close();
                                out.close();
                        } catch (IOException e) {
                                System.err.println("Failed to read from " + source);
                                throw e;
                        }
                }
                catch(IOException e) {
                        System.err.println("Severe error: Failed to create resource " + target);
                }
                finally {
                        target.deleteOnExit();
                }
        
        }
        
        /** 
         * Return the absolute path to the unpacked resource with the given name.
         * Will always return a file object but the resource may not exists unless
         * it has been created with unpackResource() previously. 
         */
        protected static String getResourcePath(String resource) {
                return new File(TEMP_DIR, resource).getAbsolutePath();
        }
        
        /** 
         * Set native OSlook and feel (is possible). 
         */
        private static void setLookAndFeel() {
                try {
                    // Set System L&F
                UIManager.setLookAndFeel(
                    //looks[2].getClassName());
                        UIManager.getSystemLookAndFeelClassName());
            } 
            catch (UnsupportedLookAndFeelException e) {
               System.out.println(e);
            }
            catch (ClassNotFoundException e) {
                       System.out.println(e);          // handle exception
            }
            catch (InstantiationException e) {
                       System.out.println(e);          // handle exception
            }
            catch (IllegalAccessException e) {
                       System.out.println(e);          // handle exception
            }
        }
        
        /**
         * Runs external pymol executable if possible. Return true on success, false otherwise.
         */
        private static boolean runPymol() {
                try {
                        System.out.println("Starting PyMol...");
                        File f = new File(PYMOL_EXECUTABLE);
                        if(!f.exists()) {
                                System.err.println(PYMOL_EXECUTABLE + " does not exist.");
                                // try to start pymol anyways because on Mac f.exists() returns false even though the file is there
                        }
                        Runtime.getRuntime().exec(f.getCanonicalPath() + " " + PYMOL_PARAMETERS);
                } catch(IOException e) {
                        return false;
                }
                return true;                            
        }
        
        /**
         * Try connecting to the database server. Returns true on success, false otherwise.
         */
        private static boolean tryConnectingToDb() {
                try {
                        conn = new MySQLConnection(DB_HOST, DB_USER, DB_PWD);
                }
                catch(Exception e) {
                        return false;
                }
                return true;
        }       
        
        /**
         * Preload a model based on the command line parameters.
         * Returns the model or null on failure.
         * TODO: Do proper command line parsing with switches to preload files or structures from online pdb
         */
        private static Model preloadModel(String[] args) {
                Model mod = null;
                // parameters should be pdb code and chain code
                if(USE_DATABASE && database_found) {
                        String pdbCode = args[0];
                        String chainCode;
                        if(args.length > 1) {
                                chainCode = args[1];
                        } else {
                                chainCode = NULL_CHAIN_CODE;
                        }
                        try {
                                mod = new PdbaseModel(pdbCode, DEFAULT_CONTACT_TYPE, DEFAULT_DISTANCE_CUTOFF, DEFAULT_MIN_SEQSEP, DEFAULT_MAX_SEQSEP, DEFAULT_PDB_DB);
                                mod.load(chainCode, 1);
                        } catch(ModelConstructionError e) {
                                System.err.println("Could not load structure for given command line parameters:");
                                System.err.println(e.getMessage());
                        } catch (PdbCodeNotFoundError e) {
                                System.err.println("Could not load structure for given command line parameters:");
                                System.err.println(e.getMessage());
                        } catch (SQLException e) {
                                System.err.println("Could not load structure for given command line parameters:");
                                System.err.println(e.getMessage());
                        }                       
                } else {
                        System.err.println("No database. Ignoring command line parameters.");
                }
                return mod;
        }
        
        /**
         * Returns true iff the given path is a directory which is writable.
         */
        private static boolean isWritableDir(String path) {
                File f = new File(path);
                if(!f.isDirectory()) return false;
                if(!f.canWrite()) return false;
                return true;
        }

        /*---------------------------- public methods ---------------------------*/

        /**
         * Writes an example configuration file with the default values for selected user
         * customizable variables. The file will be written in the current directory.
         * The values are taken from the variable selectedProperties which has to be
         * initialized previously using getSelectedProperties().
         * @throws IOException 
         * @throws FileNotFoundException 
         */
        public static void writeExampleConfigFile(String fileName) throws FileNotFoundException, IOException {
                Properties d = selectedProperties;
                String comment = "Properties file for " + APP_NAME + " " + VERSION;
                d.store(new FileOutputStream(fileName), comment);
        }
        
        /**
         * Returns true if a database connection is expected to be available. This is to avoid
         * trying to connect when it is clear that the trial will fail.
         */
        public static boolean isDatabaseConnectionAvailable() {
                return Start.USE_DATABASE && Start.database_found;
        }
        
        /**
         * Returns true if a connection to pymol is expected to be available. This is to avoid
         * trying to connect when it is clear that the trial will fail.
         */
        public static boolean isPyMolConnectionAvailable() {
                return Start.USE_PYMOL && Start.pymol_found;
        }
        
        /**
         * Returns true if external dssp application is available.
         */
        public static boolean isDsspAvailable() {
                return dssp_found;
        }

        /**
         * Return the global db connection for this session.
         * @return The MySQLConnection object
         */
        public static MySQLConnection getDbConnection() {
                return conn;
        }
        
        /**
         * Return the global fileChooser for this session.
         * @return A JFileChooser to be used whenever possible.
         */     
        public static JFileChooser getFileChooser() {
                return fileChooser;
        }
         
         /**
          * Return the global colorChooser for this session.
          * @return A JColorChooser to be used whenever possible.
          */    
         public static JColorChooser getColorChooser() {
                  return colorChooser;
          }
        
         /** 
          * Return the global pymolAdaptor of this session.
          * @return The PyMolAdaptor object
          */
         public static PyMolAdaptor getPyMolAdaptor() {
                 return pymolAdaptor;
         }
         
        
        /**
         * Main method to start CMView application
         * @param args command line arguments
         */
        public static void main(String args[]){
                
                System.out.println("Starting " + APP_NAME + " " + VERSION + " - Interactive contact map viewer");
                
                // TODO: check whether config file is passed as command line parameter, otherwise use default one
                
                // load configuration
                selectedProperties = getSelectedProperties();
                try {
                        Properties p = loadUserProperties(CONFIG_FILE_NAME);
                        System.out.println("Loading configuration file " + CONFIG_FILE_NAME);
                        userProperties = p;
                        applyUserProperties(userProperties);
                } catch (FileNotFoundException e) {
                        System.out.println("No configuration file found. Using default settings.");
                } catch (IOException e) {
                        System.err.println("Error while reading from file " + CONFIG_FILE_NAME + ". Using default settings.");
                }
                                
                // TODO: apply command line arguments here
                                
                // add shutdown hook
        Runtime.getRuntime().addShutdownHook(new Thread() {
            public void run() {
                System.out.println("Shutting down");
                if(isPyMolConnectionAvailable() && SHUTDOWN_PYMOL_ON_EXIT) {
                        pymolAdaptor.shutdown(PYMOL_SERVER_URL);
                }
            }
        });
                
                // check temp directory
                System.out.println("Using temporary directory " + TEMP_DIR);
                if(isWritableDir(TEMP_DIR)) {
                        unpackResources();
                } else {
                        System.err.println("Error: Can not write to temporary directory. Some features may not function correctly.");
                }
                
                // connect to pymol
                if(USE_PYMOL) {
                        pymolAdaptor = new PyMolAdaptor(PYMOL_SERVER_URL);
                        if(pymolAdaptor.tryConnectingToPymol(100) == true) { // running pymol server found
                                System.out.println("PyMol server found. Connected.");
                                pymol_found = true;
                        } else {
                                if(PRELOAD_PYMOL) {
                                        if(runPymol() == false) {
                                                //System.err.println("Warning: Failed to start PyMol automatically. Please manually start Pymol with the -R parameter.");       
                                                System.err.println("Failed. (You can try to restart this application after manually starting pymol with the -R parameter)");
                                                pymol_found = false;
                                        } else {
                                                System.out.println("Connecting to PyMol server...");
                                                if(pymolAdaptor.tryConnectingToPymol(PYMOL_CONN_TIMEOUT) == false) {
                                                        System.err.println("Failed. (You can try to restart this application after manually starting pymol with the -R parameter)");
                                                        pymol_found = false;
                                                } else {
                                                        System.out.println("Connected.");
                                                        pymol_found = true;
                                                }                                               
                                        }
                                }
                        }
                        if(!pymol_found) {
                                System.err.println("Could not connect to PyMol server. Some functionality will not be available.");
                        }
                }
                
                // connect to database
                if(USE_DATABASE) {
                        System.out.println("Connecting to database...");
                        if(tryConnectingToDb() == false) {
                                System.err.println("No database found. Some functionality will not be available.");
                                database_found = false;
                        } else {
                                System.out.println("Connected.");
                                database_found = true;
                        }
                }

                setLookAndFeel();
                
                // initialize session variables
                fileChooser = new JFileChooser();
                colorChooser = new JColorChooser();
                colorChooser.setPreviewPanel(new JPanel()); // removing the preview panel
                
                // start gui without a model or preload contact map based on command line parameters
                String wintitle = "Contact Map Viewer";
                Model mod = null;
                View view = new View(mod, wintitle);
                if (args.length>=1){
                        mod = preloadModel(args);
                        if(mod != null) {
                                view.spawnNewViewWindow(mod);
                        }
                }
        }
}
Revision:	249
Committed:	Tue Dec 4 15:27:58 2007 UTC (11 years, 2 months ago) by lpetzo
File size:	22875 byte(s)
Log Message:	class Start: - some changes in function preloadModel(...) due to the new loading scheme for models - changed default settings for the contact type and the contact distance according to Michael's suggestions class View: - adapted new loading scheme for the models - implemented chain code and model serial Getters for the retrieval of all present chain codes and model serials in the source