package com.github.celldynamics.quimp.filesystem;
   
   import com.github.celldynamics.quimp.BOAState;
   import com.github.celldynamics.quimp.BOA_;
   import com.github.celldynamics.quimp.QParams;
   import com.github.celldynamics.quimp.QParamsQconf;
   import com.github.celldynamics.quimp.SnakePluginList;
   import com.github.celldynamics.quimp.ViewUpdater;
   import com.github.celldynamics.quimp.filesystem.converter.FormatConverter;
  import com.github.celldynamics.quimp.plugin.engine.PluginFactory;
  import com.github.celldynamics.quimp.plugin.qanalysis.STmap;
  
  /**
   * Integrate outputs from every module of QuimP.
   * 
   * <p>All modules can add here their configuration sets. This structure is used for exchanging data
   * between modules. It can be dynamically modified.
   * 
   * @author p.baniukiewicz
   * @see FormatConverter
   * @see QParams
   * @see QParamsQconf
   */
  public class DataContainer implements IQuimpSerialize {
  
    /**
     * Indicate that BOAState module is not null.
     */
    public static final int BOA_RUN = 1024;
    /**
     * Indicate that ECMM module is not null (it has been run already on those data).
     */
    public static final int ECMM_RUN = 2048;
    /**
     * Indicate that ANA module is not null (it has been run already on those data).
     */
    public static final int ANA_RUN = 4096;
    /**
     * Indicate that Q module is not null (it has been run already on those data).
     */
    public static final int Q_RUN = 8192;
    /**
     * Indicate that QCONF contains statistics.
     */
    public static final int STATS_AVAIL = 16384;
  
    /**
     * Object to store all BOA state. Can be <tt>null</tt> when module has not been run yet.
     */
    public BOAState BOAState;
    /**
     * Object to store ECCM output. Can be <tt>null</tt> when module has not been run yet.
     */
    public OutlinesCollection ECMMState;
    /**
     * Hold ANA state.
     */
    public ANAParamCollection ANAState;
    /**
     * Store maps generated by Q Analysis plugin for every OutlineHandler from ECMMState. Can be
     * <tt>null</tt> when module has not been run yet.
     * 
     * <p>The order of STmap object in this array is correlated with the order of OutlineHandlers in
     * <tt>ECMMState</tt>, thus <i>n-th</i> STmap has been calculated from <i>n-th</i> Outline by Q
     * Analysis module.
     */
    public STmap[] QState;
    /**
     * Store statistics for cells computed for outlines and fluorescence data.
     */
    public StatsCollection Stats;
  
    private transient PluginFactory pf;
    private transient ViewUpdater vu;
  
    /**
     * Default constructor. Create empty data containers.
     */
    public DataContainer() {
      BOAState = null;
      ECMMState = null;
      ANAState = null;
      QState = null;
    }
  
    /**
     * Create DataContainer with attached {@link PluginFactory PluginFactory} and {@link ViewUpdater
     * ViewUpdater}.
     * 
     * @param pf {@link PluginFactory PluginFactory} object reference
     * @param vu {@link ViewUpdater ViewUpdater} object reference
     */
    public DataContainer(final PluginFactory pf, final ViewUpdater vu) {
      this();
      this.pf = pf;
      this.vu = vu;
    }
  
    /**
    * getBOAState.
    * 
    * @return the bOAState
    */
   public BOAState getBOAState() {
     return BOAState;
   }
 
   /**
    * getECMMState.
    * 
    * @return the eCMMState
    */
   public OutlinesCollection getEcmmState() {
     return ECMMState;
   }
 
   /**
    * getQState.
    * 
    * @return the qState
    */
   public STmap[] getQState() {
     return QState;
   }
 
   /**
    * getANAState.
    * 
    * @return the aNAState
    */
   public ANAParamCollection getANAState() {
     return ANAState;
   }
 
   /**
    * getStats.
    * 
    * @return the stats
    */
   public StatsCollection getStats() {
     return Stats;
   }
 
   /**
    * Get information about available modules in object.
    * 
    * @return Flags according to loaded modules.
    * @see com.github.celldynamics.quimp.filesystem.QconfLoader
    */
   public int validateDataContainer() {
     int ret = QconfLoader.QCONF_INVALID;
     // check for all modules
     if (getBOAState() != null) {
       ret += DataContainer.BOA_RUN;
     }
     if (getEcmmState() != null) {
       ret += DataContainer.ECMM_RUN;
     }
     if (getANAState() != null) {
       ret += DataContainer.ANA_RUN;
     }
     if (getQState() != null) {
       if (getQState().length > 0) {
         int count = 0;
         for (STmap tmp : getQState()) {
           if (tmp != null && tmp.getT() != 0) {
             count++;
           }
         }
         if (count == getQState().length) { // qstate can be !null but contain invalid
           // data, e.g fluoro[3] array with initial default vales but empty. This is e,g, after
           // paQP-QCONF conversion. So check resolution T (array size)
           ret += DataContainer.Q_RUN;
         }
       }
     }
     if (getStats() != null) {
       ret += DataContainer.STATS_AVAIL;
     }
     return ret;
   }
 
   /**
    * Called before serialization.
    * 
    * <p>Call similar method for all stored object allowing them for self-preparation for normal
    * operations after loading
    */
   @Override
   public void beforeSerialize() {
     if (BOAState != null) {
       BOAState.beforeSerialize(); // serialize first stored data
     }
     if (ECMMState != null) {
       ECMMState.beforeSerialize(); // serialize second stored data
     }
     if (ANAState != null) {
       ANAState.beforeSerialize();
     }
     if (QState != null) {
       for (STmap stM : QState) {
         if (stM != null) {
           stM.beforeSerialize();
         }
       }
     }
     if (Stats != null) {
       Stats.beforeSerialize();
     }
 
   }
 
   /**
    * Called after serialization.
    * 
    * <p>Call similar method for all stored object allowing them for self-preparation for saving
    */
   @Override
   public void afterSerialize() throws Exception {
     if (BOAState != null) {
       BOAState.snakePluginList = new SnakePluginList(BOA_.NUM_SNAKE_PLUGINS, pf, vu);
       BOAState.afterSerialize();
       for (SnakePluginList sl : BOAState.snakePluginListSnapshots) {
         sl.updateRefs(pf, vu);
       }
     }
     if (ECMMState != null) {
       ECMMState.afterSerialize();
     }
     if (ANAState != null) {
       ANAState.afterSerialize();
     }
     if (QState != null) {
       for (STmap stM : QState) {
         if (stM != null) {
           stM.afterSerialize();
         }
       }
     }
     if (Stats != null) {
       Stats.afterSerialize();
     }
   }
 }