To compile a program using these libraries:
---------------------------------------------

setenv SEQHOUND $BIRCH/java/seqhound
setenv SHJARPATH "$SEQHOUND/seqhound.jar:$SEQHOUND/commons-httpclient-2.0.jar:$SEQHOUND/commons-mpfogging-api.jar"

setenv CLASSPATH "$SHJARPATH":.
setenv CLASSPATH "$SHJARPATH":$BIRCH/java/Leash/Leash.jar:.

javac leashw.java


Note: the classes and .jar files used by SeqHound 1.5 were different,
so leash won't work with SeqHound 1.5

To run a program using these libraries:
---------------------------------------

You need to have .shoundremrc in the directory in which the
program is launched. Probably we should re-write seqhoundlib/SeqHound.java
to look for this file in $HOME, or in a location specified
by an environment variable.

java leashw -mn

java leashw -mn SHoundTaxIDFromGiList -mpf small.flat -of small.taxid.flat
java leashw -e .acc -mn SHoundAccFromGiList -mpf ex1.flat -of ex1.acc.flat

java leashw -mn SHound3DExists -mpi 4534 
java leashw -mn SHoundIsNRFirst -mpi 4534
java leashw -mn SHoundExists -mpi 41629670
java leashw -mn SHoundProteinFromDNA -mpi 4646

java leashw -mn SHoundAllGenomes -of outfile
java leashw -mn SHoundProteinFromDNA -mpi 6598330 -of prot.gi

// a short seq.
java leashw -mn SHoundGetGenBankff -mpi 4646 -of outfile

// A bac clone, AC002329
leash -mn SHoundGetGenBankff -mpi 14595407 -of 14595407.gen
leash -mn SHoundGetGenBankff -mpi 21541293 -of 21541293.gen
leash -mn SHoundGetGenBankffList -mpi 14595407,21541293 -of both.gen
leash -mn SHoundGetFastaList -mpi 14595407,21541293 -of both.fsa

// Possible error isn SeqHound 2.5
leash SHoundGetGenBankff -mpi 6598330 -of outfile




// Yeast chromosomes II (>800kb), III (>315kb) and IV (>1500kb)
java leashw -mn SHoundFindAcc -mpi NC_001134 
java leashw -mn SHoundGetGenBankff -mpi 41629670 -of NC_001134.gen

java leashw -mn SHoundFindAcc -mpi NC_001135 
java  leashw -mn SHoundGetGenBankff -mpi 42759850 -of NC_001135.gen

java leashw -mn SHoundFindAcc -mpi NC_001136 
java  leashw SHoundGetGenBankff -mpi 42742056 -of NC_001136.gen
Exception in thread "main" java.lang.NullPointerException
        at leash.WriteStr(leash.java:171)
        at leash.LSHoundGetGenBankff(leash.java:231)
        at leash.main(leash.java:276)
Fetch also fails to retrieve this seq. 

java leashw -mn SHoundGetGenBankff -mpi 16127994 -of NC_000913.gen
java  leashw -mn SHoundGetFastaList -mpf gilist outfile.fsa

java  leashw -mn SHoundGetGenBankffList -mpf gilist -of outfile.gen


java leashw -mn SHoundFindAccList -mpf acclist -of gilist
java leashw -mn SHoundFindAcc -mpi CAA28783 
java leashw -mn SHoundFindAcc -mpi AC002329 

java leashw -mn SHoundAccFromGi -mpi 6598330 
java leashw -mn SHoundFindAcc -mpi XXXXXXX 
java leashw -mn SHoundFindAccList -mpf acclist 

java leashw -1 -s -e .acc -mn SHoundAccFromGiList -mpf gilist -of /dev/tty

java leashw -mn SHoundFindAcc -mpi CAA28783 

java leashw -mn SHoundGetTaxLineageFromTaxID -mpi 170187 -f SHoundGetTaxLineage_FULL  
java leashw -mn SHoundGetTaxNameFromTaxID -mpi 170187 
java leashw -mn SHoundSequenceLength -mpi 41629670 


// Methods that return a Hashtable
java leashw -mn SHoundGetFastaKeyedList -mpf gilist -of hashtable
java leashw -mn SHoundGetFastaKeyedList -mpf prot.gi -of hashtable