edu.mssm.crover.webapps.dimlib.util
Class ExportAln

java.lang.Object
  |
  +--edu.mssm.crover.webapps.dimlib.util.ExportAln

public class ExportAln
extends java.lang.Object


Field Summary
protected  javax.jdo.PersistenceManager pm
           
 
Constructor Summary
ExportAln()
          Used when running it as administrator to download all alignments.
ExportAln(javax.jdo.PersistenceManager session_pm)
          Used when running it to download a selected alignment.
 
Method Summary
 void exportAllAln()
          Exports all alignments in the database to a file.
 java.lang.String exportSelectedAln(ArcadiaAlignment a)
          Converts the selected alignment to a String, which can be downloaded (as a MultiLineOutput) from the website.
 java.lang.String exportSelectedAln(ArcadiaAlignment a, java.lang.String[] chosSeqs)
           
static void main(java.lang.String[] args)
           
 java.lang.String writeAln(ArcadiaAlignment aln)
           
 java.lang.String writeAln(ArcadiaAlignment aln, java.util.HashSet seqsHash)
           
 java.lang.String writeClustalwAln(ArcadiaAlignment aln)
          Returns the alignment in ClustalW format.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

pm

protected javax.jdo.PersistenceManager pm
Constructor Detail

ExportAln

public ExportAln()
Used when running it as administrator to download all alignments.


ExportAln

public ExportAln(javax.jdo.PersistenceManager session_pm)
Used when running it to download a selected alignment.

Method Detail

exportSelectedAln

public java.lang.String exportSelectedAln(ArcadiaAlignment a)
Converts the selected alignment to a String, which can be downloaded (as a MultiLineOutput) from the website.


exportSelectedAln

public java.lang.String exportSelectedAln(ArcadiaAlignment a,
                                          java.lang.String[] chosSeqs)

exportAllAln

public void exportAllAln()
                  throws java.io.IOException
Exports all alignments in the database to a file.

java.io.IOException

writeAln

public java.lang.String writeAln(ArcadiaAlignment aln)

writeAln

public java.lang.String writeAln(ArcadiaAlignment aln,
                                 java.util.HashSet seqsHash)

writeClustalwAln

public java.lang.String writeClustalwAln(ArcadiaAlignment aln)
Returns the alignment in ClustalW format.


main

public static void main(java.lang.String[] args)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.