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java.lang.Objectedu.cmu.cs.sb.chromviewer.BiomartAccess
public class BiomartAccess
Class responsible for downloading gene locations from Biomart
Constructor Summary | |
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BiomartAccess(java.lang.String fname)
Constructor, sets m_file to a File handle on fname |
Method Summary | |
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int |
executeCountQuery(java.lang.String xmlMessage)
Executes the BioMart query in xmlMessage that counts the number of records satisfying query. |
void |
executeQuery(java.io.BufferedOutputStream bos,
java.lang.String xmlMessage,
int[] npercentdone,
int nstatusfield,
java.lang.Object lockpd)
ExecuteQuery. |
java.util.HashSet |
getValidAttributes(java.lang.String szdataset)
Gets a HashSet of valid attributes for the gene location |
void |
updateGeneFile(java.lang.String species,
java.lang.String szoutfile,
int[] npercentdone,
int nstatusfield,
java.lang.Object lockpd)
Species is the name of the species to download the locations for. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public BiomartAccess(java.lang.String fname)
Method Detail |
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public int executeCountQuery(java.lang.String xmlMessage) throws java.io.IOException
java.io.IOException
public void executeQuery(java.io.BufferedOutputStream bos, java.lang.String xmlMessage, int[] npercentdone, int nstatusfield, java.lang.Object lockpd) throws java.io.IOException
java.io.IOException
public java.util.HashSet getValidAttributes(java.lang.String szdataset) throws java.io.IOException
java.io.IOException
public void updateGeneFile(java.lang.String species, java.lang.String szoutfile, int[] npercentdone, int nstatusfield, java.lang.Object lockpd) throws java.io.IOException
java.io.IOException
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