Class SearchIO

  • All Implemented Interfaces:
    java.lang.Iterable<Result>

    public class SearchIO
    extends java.lang.Object
    implements java.lang.Iterable<Result>
    Designed by Paolo Pavan. You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. https://github.com/paolopavan
    Author:
    Paolo Pavan
    • Constructor Summary

      Constructors 
      Constructor Description
      SearchIO​(java.io.File f)
      Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.
      SearchIO​(java.io.File f, ResultFactory factory)
      Build a SearchIO reader and specify a ResultFactory object to be used for parsing
      SearchIO​(java.io.File f, ResultFactory factory, double maxEvalue)
      Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double getEvalueThreshold()  
      java.util.Iterator<Result> iterator()  
      void writeResults()
      used to write a search report using the guessed or specified factory
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator
    • Constructor Detail

      • SearchIO

        public SearchIO​(java.io.File f)
                 throws java.io.IOException,
                        java.text.ParseException
        Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.
        Parameters:
        f -
        Throws:
        java.lang.Exception
        java.io.IOException
        java.text.ParseException
      • SearchIO

        public SearchIO​(java.io.File f,
                        ResultFactory factory)
                 throws java.io.IOException,
                        java.text.ParseException
        Build a SearchIO reader and specify a ResultFactory object to be used for parsing
        Parameters:
        f -
        factory -
        Throws:
        java.io.IOException - for file access related issues
        java.text.ParseException - for file format related issues
      • SearchIO

        public SearchIO​(java.io.File f,
                        ResultFactory factory,
                        double maxEvalue)
                 throws java.io.IOException,
                        java.text.ParseException
        Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold. This usually increase parsing speed
        Parameters:
        f -
        factory -
        maxEvalue -
        Throws:
        java.io.IOException - for file access related issues
        java.text.ParseException - for file format related issues
    • Method Detail

      • writeResults

        public void writeResults()
                          throws java.io.IOException,
                                 java.text.ParseException
        used to write a search report using the guessed or specified factory
        Throws:
        java.io.IOException - for file access related issues
        java.text.ParseException - for file format related issues
      • getEvalueThreshold

        public double getEvalueThreshold()
      • iterator

        public java.util.Iterator<Result> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<Result>