package baseCode.bio.geneset;
   
   import java.io.BufferedInputStream;
   import java.io.BufferedReader;
   import java.io.FileInputStream;
   import java.io.IOException;
   import java.io.InputStream;
   import java.io.InputStreamReader;
   import java.io.Writer;
  import java.util.ArrayList;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.Comparator;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.Iterator;
  import java.util.LinkedHashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  import java.util.StringTokenizer;
  import java.util.Vector;
  
  import javax.swing.table.AbstractTableModel;
  import javax.swing.table.TableModel;
  
  import baseCode.util.FileTools;
  import baseCode.util.StatusViewer;
  
  /***
   * Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.
   * <p>
   * Maintains the following important data structures, all derived from the input file:
   * 
   * <pre>
   * 
   *  
   *   
   *    
   *     
   *      
   *       
   *        
   *         
   *          
   *           
   *                                                    probe-&gt;Classes -- each value is a Set of the Classes that a probe belongs to.
   *                                                    Classes-&gt;probe -- each value is a Set of the probes that belong to a class
   *                                                    probe-&gt;gene -- each value is the gene name corresponding to the probe.
   *                                                    gene-&gt;list of probes -- each value is a list of probes corresponding to a gene
   *                                                    probe-&gt;description -- each value is a text description of the probe (actually...of the gene)
   *                
   *            
   *           
   *          
   *         
   *        
   *       
   *      
   *     
   *    
   *   
   *  
   * </pre>
   * 
   * <p>
   * Copyright (c) 2004 Columbia University
   * </p>
   * 
   * @author Paul Pavlidis
   * @author Shamhil Merchant
   * @author Homin Lee
   * @version $Id: GeneAnnotations.java,v 1.7 2004/12/27 22:25:56 pavlidis Exp $
   */
  
  public class GeneAnnotations {
  
     /***
      * The maximum size of gene sets ever considered.
      */
     private static final int PRACTICAL_MAXIMUM_GENESET_SIZE = 1000;
  
     /***
      * The minimum size of a 'set' of genes.
      */
     private static final int ABSOLUTE_MINIMUM_GENESET_SIZE = 2;
  
     private Map probeToGeneSetMap; //stores probe->Classes map todo why are contents an arraylist, should be a set?
     private Map geneSetToProbeMap; //stores Classes->probes map
     private Map probeToGeneName;
     private Map probeToDescription;
     private Map geneToProbeList;
     private Map geneToGeneSetMap;
     private Map geneSetToGeneMap; //stores Classes->genes map. use to get a list
     // of classes.
  
     private Vector sortedGeneSets;
     private Map geneSetToRedundantMap;
     Vector selectedProbes;
    private Vector selectedSets;
 
    private StatusViewer messenger;
 
    /***
     * This is for creating GeneAnnotations by reading from a file
     * 
     * @param filename String
     * @param messenger StatusViewer to print status updates to.
     * @throws IOException
     */
    public GeneAnnotations( String filename, StatusViewer messenger )
          throws IOException {
 
       setUpDataStructures();
       this.messenger = messenger;
 
       this.read( filename );
 
       setUp();
    }
 
    /***
     * This is for creating GeneAnnotations by pruning a copy.
     * 
     * @param geneData GeneAnnotations copy to prune from
     * @param activeProbes Set only include these probes
     */
    public GeneAnnotations( GeneAnnotations geneData, Set activeProbes ) {
 
       // FIXME - shallow copies here could cause problems.
 
       // CAREFUL this is a shallow copy! This is okay?
       probeToGeneSetMap = new LinkedHashMap( geneData.probeToGeneSetMap );
 
       // make a deep copy of the classToProbeMap, which is a map of sets. Shallow copy is BAD.
       this.geneSetToProbeMap = new LinkedHashMap();
       for ( Iterator iter = geneData.geneSetToProbeMap.keySet().iterator(); iter
             .hasNext(); ) {
          String key = ( String ) iter.next();
          this.geneSetToProbeMap.put( key, new ArrayList(
                ( ArrayList ) geneData.geneSetToProbeMap.get( key ) ) );
       }
 
       probeToGeneName = new HashMap( geneData.probeToGeneName ); // shallow copy, okay
       probeToDescription = new HashMap( geneData.probeToDescription ); // shallow copy, okay
       geneToProbeList = new HashMap( geneData.geneToProbeList ); // shallow copy, okay?
       geneToGeneSetMap = new HashMap( geneData.geneToGeneSetMap ); // shallow copy, okay?
       geneSetToRedundantMap = new HashMap( geneData.geneSetToRedundantMap );
 
       Vector allProbes = new Vector( probeToGeneName.keySet() );
       for ( Iterator iter = allProbes.iterator(); iter.hasNext(); ) {
          String probe = ( String ) iter.next();
          if ( !activeProbes.contains( probe ) ) { // remove probes not in data set.
             removeProbeFromMaps( probe );
          }
       }
       setUp(); //creates the classToGene map.
 
       //      System.err.println( "Orig: GO:0019058 has probes: "
       //            + geneData.numProbesInGeneSet( "GO:0019058" ) );
       //      System.err.println( "New: GO:0019058 has probes: "
       //            + this.numProbesInGeneSet( "GO:0019058" ) );
    }
 
    /***
     * Make a new GeneAnnotations that only includes the probes in the parameter 'probes'.
     * 
     * @param stream
     * @param activeGenes Only genes in this set are left.
     * @throws IOException
     */
    public GeneAnnotations( InputStream stream, Set activeGenes,
          StatusViewer messenger ) throws IOException {
       this.messenger = messenger;
       setUpDataStructures();
       this.read( stream, activeGenes );
       setUp();
    }
 
    /***
     * @param fileName
     */
    public GeneAnnotations( String fileName, Set activeGenes,
          StatusViewer messenger ) throws IOException {
       this.messenger = messenger;
       FileInputStream fis = new FileInputStream( fileName );
       BufferedInputStream bis = new BufferedInputStream( fis );
       setUpDataStructures();
       this.read( bis, activeGenes );
       setUp();
    }
 
    /***
     * @return Map
     */
    public Map getProbeToGeneMap() {
       return probeToGeneName;
    }
 
    /***
     * @return Map
     */
    public Map getGeneToProbeList() {
       return geneToProbeList;
    }
 
    /***
     * @return Map
     */
    public Map getGeneSetToProbeMap() {
       return geneSetToProbeMap;
    }
 
    /***
     * @param id String class id
     * @return ArrayList list of probes in class
     */
    public ArrayList getClassToProbes( String id ) {
       return ( ArrayList ) geneSetToProbeMap.get( id );
    }
 
    /***
     * Sort the gene sets, filling out the sortedGeneSets. This should be called after any changes have been made to the
     * classToProbeMap. The sort is just in order of id.
     */
    public void sortGeneSets() {
 
       if ( geneSetToProbeMap.size() == 0 ) {
          throw new IllegalStateException(
                "Could not sort because there are no gene sets in the classToProbeMap" );
       }
 
       if ( sortedGeneSets == null ) {
          sortedGeneSets = new Vector();
       }
 
       Vector vec = new Vector( geneSetToProbeMap.keySet() );
       Collections.sort( vec );
       for ( Iterator iter = vec.iterator(); iter.hasNext(); ) {
          sortedGeneSets.add( iter.next() );
       }
    }
 
    /***
     * @return
     */
    public List sortGeneSetsBySize() {
 
       List sets = new Vector();
       for ( Iterator iter = getGeneSetToGeneMap().keySet().iterator(); iter
             .hasNext(); ) {
          String name = ( String ) iter.next();
          sets.add( new GeneSet( name, ( Set ) geneSetToGeneMap.get( name ) ) );
       }
 
       Collections.sort( sets, new ClassSizeComparator() );
 
       List returnVal = new Vector();
       for ( Iterator iter = sets.iterator(); iter.hasNext(); ) {
          returnVal.add( ( ( GeneSet ) iter.next() ).getName() );
       }
 
       return returnVal;
    }
 
    /***
     * @return Map
     */
    public Map getProbeToGeneSetMap() {
       return probeToGeneSetMap;
    }
 
    /***
     * @return Map
     */
    public Map geneSetToRedundantMap() {
       return geneSetToRedundantMap;
    }
 
    /***
     * Get the gene that a probe belongs to.
     * 
     * @param p String
     * @return String
     */
    public String getProbeGeneName( String p ) {
       return ( String ) probeToGeneName.get( p );
    }
 
    /***
     * Get the description for a gene.
     * 
     * @param p String
     * @return String
     */
    public String getProbeDescription( String p ) {
       return ( String ) probeToDescription.get( p );
    }
 
    /***
     * Get a list of the probes that correspond to a particular gene.
     * 
     * @param g String a gene name
     * @return ArrayList list of the probes for gene g
     */
    public ArrayList getGeneProbeList( String g ) {
       return ( ArrayList ) geneToProbeList.get( g );
    }
 
    /***
     * Get a class by an integer index i from the sorted list.
     * 
     * @param i
     * @return
     */
    public String getGeneSetByIndex( int i ) {
       return ( String ) sortedGeneSets.get( i );
    }
 
    /***
     * Returns true if the class is in the classToProbe map
     * 
     * @param id String a class id
     * @return boolean
     */
    public boolean geneSetExists( String id ) {
       return geneSetToProbeMap.containsKey( id );
    }
 
    /***
     * Get how many probes point to the same gene. This is like the old "numReplicates".
     * 
     * @param g
     * @return
     */
    public int numProbesForGene( String g ) {
       if ( !geneToProbeList.containsKey( g ) ) return 0;
       return ( ( ArrayList ) geneToProbeList.get( g ) ).size();
    }
 
    /***
     * Get the number of classes. This is computed from the sortedGeneSets.
     * 
     * @return
     */
    public int numGeneSets() {
       if ( geneSetToGeneMap == null ) {
          throw new IllegalStateException( "classToGeneMap was null" );
       }
       return geneSetToGeneMap.size();
    }
 
    /***
     * How many genes are in the file?
     */
    public int numGenes() {
       return geneToProbeList.size();
    }
 
    /***
     * Get the number of probes in a gene set, identified by id.
     * 
     * @param id String a class id
     * @return int number of probes in the class
     */
    public int numProbesInGeneSet( String id ) {
       if ( !geneSetToProbeMap.containsKey( id ) ) {
          return 0;
       }
       //      System.err.println( "GO:0019058 has probes: "
       //            + ( ( ArrayList ) classToProbeMap.get( "GO:0019058" ) ).size() );
       return ( ( ArrayList ) geneSetToProbeMap.get( id ) ).size();
    }
 
    /***
     * Get the number of genes in a gene set, identified by id.
     * 
     * @param id String a class id
     * @return int number of genes in the class
     */
    public int numGenesInGeneSet( String id ) {
       if ( !geneSetToGeneMap.containsKey( id ) ) {
          return 0;
       }
       return ( ( Set ) geneSetToGeneMap.get( id ) ).size();
    }
 
    /***
     * Add a class
     * 
     * @param id String class to be added
     * @param probesForNew ArrayList user-defined list of members.
     */
    public void addClass( String id, ArrayList probesForNew ) {
       geneSetToProbeMap.put( id, probesForNew );
 
       Iterator probe_it = probesForNew.iterator();
       while ( probe_it.hasNext() ) {
          String probe = new String( ( String ) probe_it.next() );
          ( ( ArrayList ) probeToGeneSetMap.get( probe ) ).add( id );
       }
 
       Set genes = new HashSet();
       Iterator probe_it2 = probesForNew.iterator();
       while ( probe_it2.hasNext() ) {
          genes.add( probeToGeneName.get( probe_it2.next() ) );
       }
       geneSetToGeneMap.put( id, genes );
 
       geneToGeneSetMap.put( id, probeToGeneSetMap.get( id ) );
 
       resetSelectedSets();
    }
 
    /***
     * Redefine a class.
     * 
     * @param classId String class to be modified
     * @param probesForNew ArrayList current user-defined list of members. The "real" version of the class is modified to
     *        look like this one.
     */
    public void modifyClass( String classId, ArrayList probesForNew ) {
       ArrayList orig_probes = ( ArrayList ) geneSetToProbeMap.get( classId );
       Iterator orig_probe_it = orig_probes.iterator();
       while ( orig_probe_it.hasNext() ) {
          String orig_probe = new String( ( String ) orig_probe_it.next() );
          if ( !probesForNew.contains( orig_probe ) ) {
             Set ptc = new HashSet( ( Collection ) probeToGeneSetMap
                   .get( orig_probe ) );
             ptc.remove( classId );
             probeToGeneSetMap.remove( orig_probe );
             probeToGeneSetMap.put( orig_probe, new ArrayList( ptc ) );
          }
       }
       Iterator probe_it = probesForNew.iterator();
       while ( probe_it.hasNext() ) {
          String probe = ( String ) probe_it.next();
          if ( !orig_probes.contains( probe ) ) {
             ( ( ArrayList ) probeToGeneSetMap.get( probe ) ).add( classId );
          }
       }
       geneSetToProbeMap.put( classId, probesForNew );
       resetSelectedSets();
    }
 
    /***
     * @return
     */
    public TableModel toTableModel() {
       return new AbstractTableModel() {
          private String[] columnNames = {
                "Probe", "Gene", "Description"
          };
 
          public String getColumnName( int i ) {
             return columnNames[i];
          }
 
          public int getColumnCount() {
             return 3;
          }
 
          public int getRowCount() {
             return selectedProbes.size();
          }
 
          public Object getValueAt( int i, int j ) {
 
             String probeid = ( String ) selectedProbes.get( i );
             switch ( j ) {
                case 0:
                   return probeid;
                case 1:
                   return getProbeGeneName( probeid );
                case 2:
                   return getProbeDescription( probeid );
                default:
                   return null;
             }
          }
 
       };
    }
 
    /***
     * Create a selected probes list based on a search string.
     * 
     * @param searchOn A string to be searched.
     */
    public void selectProbes( String searchOn ) {
 
       String searchOnUp = searchOn.toUpperCase();
       resetSelectedProbes();
       Set removeUs = new HashSet();
       for ( Iterator it = probeToGeneName.keySet().iterator(); it.hasNext(); ) {
          String probe = ( String ) it.next();
 
          String candidate = ( ( String ) probeToGeneName.get( ( probe ) ) )
                .toUpperCase();
 
          // look in descriptions.
          String candidateD = ( ( String ) probeToDescription.get( ( probe ) ) )
                .toUpperCase();
 
          if ( !candidate.startsWith( searchOnUp )
                && candidateD.indexOf( searchOnUp ) < 0 ) {
             removeUs.add( probe );
          }
 
       }
 
       for ( Iterator it = removeUs.iterator(); it.hasNext(); ) {
          selectedProbes.remove( it.next() );
       }
    }
 
    /***
     * Set the selected gene set to be the entire set.
     */
    public void resetSelectedProbes() {
       selectedProbes = new Vector( probeToGeneName.keySet() );
    }
 
    /***
     * @return the list of selected probes.
     */
    public List getSelectedProbes() {
       return selectedProbes;
    }
 
    /***
     * @return the number of probes currently on the 'selected' list.
     */
    public int selectedProbes() {
       return selectedProbes.size();
    }
 
    /***
     * @param searchOn
     * @param goData
     */
    public void selectSets( String searchOn, GONames goData ) {
 
       String searchOnUp = searchOn.toUpperCase();
       resetSelectedSets();
       Set removeUs = new HashSet();
       for ( Iterator it = geneSetToProbeMap.keySet().iterator(); it.hasNext(); ) {
          String candidate = ( String ) it.next();
 
          // look in the name too
          String candidateN = goData.getNameForId( candidate ).toUpperCase();
 
          if ( !candidate.toUpperCase().startsWith( searchOnUp )
                && candidateN.indexOf( searchOnUp ) < 0 ) {
             removeUs.add( candidate );
          }
       }
 
       for ( Iterator it = removeUs.iterator(); it.hasNext(); ) {
          selectedSets.remove( it.next() );
       }
    }
 
    /***
     * Set the selected gene set to be the entire set.
     */
    public void resetSelectedSets() {
       selectedSets = new Vector( geneSetToProbeMap.keySet() );
    }
 
    /***
     * @return list of selected sets.
     */
    public List getSelectedSets() {
       return selectedSets;
    }
 
    /***
     * @return the number of sets currently on the 'selected' list.
     */
    public int selectedSets() {
       return selectedSets.size();
    }
 
    /***
     * Print out the gene annotations in the same format we got them in, but if the gene sets have been modified, this
     * will be reflected.
     * 
     * @param out
     * @throws IOException
     */
    public void print( Writer out ) throws IOException {
       out.write( "Probe\tSymbol\tName\tGeneSets\n" );
       out.flush();
       for ( Iterator iter = probeToGeneName.keySet().iterator(); iter.hasNext(); ) {
          String probe = ( String ) iter.next();
          String gene = ( String ) probeToGeneName.get( probe );
          String desc = getProbeDescription( probe );
          out.write( probe + "\t" + gene + "\t" + desc + "\t" );
          List geneSets = ( ArrayList ) probeToGeneSetMap.get( probe );
 
          for ( Iterator iterator = geneSets.iterator(); iterator.hasNext(); ) {
             String element = ( String ) iterator.next();
             out.write( element + "|" );
          }
          out.write( "\n" );
       }
    }
 
    /***
     * @return Returns the classToGeneMap.
     */
    public Map getGeneSetToGeneMap() {
       return geneSetToGeneMap;
    }
 
    /***
     * @return Returns the geneToClassMap.
     */
    public Map getGeneToGeneSetMap() {
       return geneToGeneSetMap;
    }
 
    /***
     * Compute how many genes have Gene set annotations.
     * 
     * @return
     */
    public int numAnnotatedGenes() {
       int count = 0;
       for ( Iterator iter = probeToGeneSetMap.keySet().iterator(); iter
             .hasNext(); ) {
          List element = ( ArrayList ) probeToGeneSetMap.get( iter.next() );
          if ( element.size() > 0 ) {
             count++;
          }
       }
       return count;
    }
 
    /*********************************************************************************************************************
     * Private or protected methods
     *******************************************************************************************************************/
 
    /***
     * 
     */
    private void setUpDataStructures() {
       probeToGeneSetMap = new LinkedHashMap();
       geneSetToProbeMap = new LinkedHashMap();
       probeToGeneName = new HashMap();
       probeToDescription = new HashMap();
       geneToProbeList = new HashMap();
       geneToGeneSetMap = new HashMap();
       geneSetToRedundantMap = new HashMap();
    }
 
    /***
     * Initialize the gene sets and other data structures that needs special handling before use.
     */
    private void setUp() {
       this.geneSetToGeneMap = makeClassToGeneMap();
 
       GeneSetMapTools.collapseGeneSets( this, messenger );
       prune( ABSOLUTE_MINIMUM_GENESET_SIZE, PRACTICAL_MAXIMUM_GENESET_SIZE );
       resetSelectedProbes();
       resetSelectedSets();
       sortGeneSets();
    }
 
    /***
     * Remove a gene set (class) from all the maps that reference it.
     * 
     * @param id
     */
    public void removeClassFromMaps( String id ) {
       if ( geneSetToProbeMap.containsKey( id ) ) {
          for ( Iterator pit = ( ( ArrayList ) geneSetToProbeMap.get( id ) )
                .iterator(); pit.hasNext(); ) {
             String probe = ( String ) pit.next();
             if ( probeToGeneSetMap.containsKey( probe )
                   && ( ( ArrayList ) probeToGeneSetMap.get( probe ) )
                         .contains( id ) ) {
                if ( !( ( ArrayList ) probeToGeneSetMap.get( probe ) )
                      .remove( id ) ) {
                   System.err.println( "Couldn't remove " + id
                         + " from probe to class map for" + probe );
                }
             }
          }
          if ( geneSetToProbeMap.remove( id ) == null )
                System.err.println( "Couldn't remove " + id
                      + " from classToProbeMap" );
 
          if ( geneSetToGeneMap.remove( id ) == null )
                System.err.println( "Couldn't remove " + id
                      + " from classToGeneMap" );
       }
       if ( geneSetToRedundantMap.containsKey( id ) )
             geneSetToRedundantMap.remove( id );
    }
 
    /***
     * @param probe
     */
    private void removeProbeFromMaps( String probe ) {
       if ( probeToGeneName.containsKey( probe ) ) {
          String gene = ( String ) probeToGeneName.get( probe );
          probeToGeneName.remove( probe );
          if ( geneToProbeList.containsKey( gene ) ) {
             ( ( ArrayList ) geneToProbeList.get( gene ) ).remove( probe );
          }
       }
       if ( probeToGeneSetMap.containsKey( probe ) ) {
          Iterator cit = ( ( ArrayList ) probeToGeneSetMap.get( probe ) )
                .iterator();
          while ( cit.hasNext() ) {
             String geneSet = ( String ) cit.next();
             if ( geneSetToProbeMap.containsKey( geneSet ) ) {
                ( ( ArrayList ) geneSetToProbeMap.get( geneSet ) )
                      .remove( probe );
             }
          }
          if ( probeToGeneSetMap.remove( probe ) == null ) {
             System.err.println( "Could not remove " + probe
                   + " from probeToClassMap" );
          }
       }
       if ( probeToDescription.containsKey( probe ) )
             probeToDescription.remove( probe );
    }
 
    /***
     * Fill in the classToGeneMap with information from the classToProbeMap.
     * 
     * @return mapping of gene sets to genes.
     */
    private Map makeClassToGeneMap() {
       Map gsToGeneMap = new HashMap();
       for ( Iterator iter = geneSetToProbeMap.keySet().iterator(); iter
             .hasNext(); ) {
          String geneSetId = ( String ) iter.next();
          List probesInSet = ( ArrayList ) geneSetToProbeMap.get( geneSetId );
 
          Set genesInSet = new HashSet();
          for ( Iterator biter = probesInSet.iterator(); biter.hasNext(); ) {
             String probe = ( String ) biter.next();
             genesInSet.add( probeToGeneName.get( probe ) );
          }
          gsToGeneMap.put( geneSetId, genesInSet );
       }
       return gsToGeneMap;
    }
 
    private void read( InputStream bis ) throws IOException {
       this.read( bis, null );
    }
 
    private void read( InputStream bis, Set activeGenes ) throws IOException {
       if ( bis == null ) {
          throw new IOException( "Inputstream was null" );
       }
 
       BufferedReader dis = new BufferedReader( new InputStreamReader( bis ) );
       ArrayList probeIds = new ArrayList();
       String classIds = null;
 
       // loop through rows. Makes hash map of probes to go, and map of go to
       // probes.
       int n = 0;
       String line = "";
 
       while ( ( line = dis.readLine() ) != null ) {
          if ( line.startsWith( "#" ) ) continue;
          StringTokenizer st = new StringTokenizer( line, "\t" );
 
          if ( !st.hasMoreTokens() ) {
             continue; // blank line
          }
 
          String probe = st.nextToken().intern();
 
          /* read gene name */
          if ( !st.hasMoreTokens() ) {
             continue; // no gene name or anything else.
          }
 
          String group = st.nextToken().intern();
 
          if ( activeGenes != null && !activeGenes.contains( group ) ) {
             continue;
          }
 
          probeToGeneName.put( probe.intern(), group.intern() );
 
          // create the list if need be.
          if ( geneToProbeList.get( group ) == null ) {
             geneToProbeList.put( group.intern(), new ArrayList() );
          }
          ( ( ArrayList ) geneToProbeList.get( group ) ).add( probe.intern() );
 
          probeIds.add( probe );
          probeToGeneSetMap.put( probe.intern(), new ArrayList() );
          geneToGeneSetMap.put( group, probeToGeneSetMap.get( probe ) );
 
          /* read gene description */
          if ( st.hasMoreTokens() ) {
             String description = st.nextToken().intern();
             if ( !description.startsWith( "GO:" ) ) { // this happens when
                // there is no
                // desription and we
                // skip to the GO
                // terms.
                probeToDescription.put( probe.intern(), description.intern() );
             } else {
                probeToDescription.put( probe.intern(), "[No description]" );
             }
          } else {
             probeToDescription.put( probe.intern(), "[No description]" );
          }
 
          /* read GO data */
          if ( st.hasMoreTokens() ) {
             classIds = st.nextToken();
 
             //another tokenizer is required since the ClassesID's are
             // seperated by the | character
             StringTokenizer st1 = new StringTokenizer( classIds, "|" );
             while ( st1.hasMoreTokens() ) {
                String go = st1.nextToken().intern();
 
                // add this go to the probe->go map.
                ( ( ArrayList ) probeToGeneSetMap.get( probe ) ).add( go );
 
                // add this probe this go->probe map.
                if ( !geneSetToProbeMap.containsKey( go ) ) {
                   geneSetToProbeMap.put( go, new ArrayList() );
                }
                ( ( ArrayList ) geneSetToProbeMap.get( go ) ).add( probe );
 
             }
          }
          if ( messenger != null && n % 500 == 0 ) {
             messenger.setStatus( "Read " + n + " probes" );
          }
          n++;
       }
 
       /* Fill in the genegroupreader and the classmap */
       dis.close();
       resetSelectedProbes();
       
       if (probeToGeneName.size() == 0 || geneSetToProbeMap.size() == 0) {
          throw new IllegalArgumentException("The gene annotations had invalid information. Please check the format.");
       }
       
    }
 
    //read in from a file.
    private void read( String filename ) throws IOException {
 
       if ( !FileTools.testFile( filename ) ) {
          throw new IOException( "Could not read from " + filename );
       }
 
       FileInputStream fis = new FileInputStream( filename );
       BufferedInputStream bis = new BufferedInputStream( fis );
       read( bis );
    }
 
    /***
     * remove classes that have too few members todo this doesn't affect the tree representation of the genesets. todo
     * this overlaps with functionality in GeneSetMapTools
     * 
     * @param lowThreshold
     * @param highThreshold
     */
    private void prune( int lowThreshold, int highThreshold ) {
 
       Set removeUs = new HashSet();
       for ( Iterator it = geneSetToProbeMap.keySet().iterator(); it.hasNext(); ) {
          String id = ( String ) it.next();
          if ( numProbesInGeneSet( id ) < lowThreshold
                || numGenesInGeneSet( id ) < lowThreshold
                || numProbesInGeneSet( id ) > highThreshold
                || numGenesInGeneSet( id ) > highThreshold ) {
             removeUs.add( id );
          }
       }
 
       for ( Iterator it = removeUs.iterator(); it.hasNext(); ) {
          String id = ( String ) it.next();
          removeClassFromMaps( id );
       }
 
       sortGeneSets();
    }
 
 }
 
 class ClassSizeComparator implements Comparator {
 
    /*
     * (non-Javadoc)
     * 
     * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
     */
    public int compare( Object o1, Object o2 ) {
       GeneSet a = ( GeneSet ) o1;
       GeneSet b = ( GeneSet ) o2;
 
       int sizea = a.size();
       int sizeb = b.size();
 
       if ( sizea > sizeb ) {
          return 1;
       } else if ( sizeb < sizea ) {
          return -1;
       }
 
       return 0;
    }
 
    public static void main( String[] args ) {
    }
 }
 
 // used for the comparator.
 
 class GeneSet {
    private String name;
    private Set items;
 
    public GeneSet( String name, Set items ) {
       this.name = name;
       this.items = items;
    }
 
    /***
     * @return Returns the items.
     */
    public Set getItems() {
       return items;
    }
 
    /***
     * @param items The items to set.
     */
    public void setItems( Set items ) {
       this.items = items;
    }
 
    /***
     * @return Returns the name.
     */
    public String getName() {
       return name;
    }
 
    /***
     * @param name The name to set.
     */
    public void setName( String name ) {
       this.name = name;
    }
 
    public int size() {
       return items.size();
    }
 }