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Added ability to load a GATKReport from disk. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5134 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-31 05:31:49 +00:00
parent 5e7a5cf924
commit 83dcca7e82
1 changed files with 81 additions and 1 deletions
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82
java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
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@ -1,6 +1,8 @@
package org.broadinstitute.sting.gatk.report;
import java.io.PrintStream;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.*;
import java.util.TreeMap;
/**
@ -9,10 +11,88 @@ import java.util.TreeMap;
public class GATKReport {
private TreeMap<String, GATKReportTable> tables;
/**
* Create a new, empty GATKReport.
*/
public GATKReport() {
tables = new TreeMap<String, GATKReportTable>();
}
/**
* Create a new GATKReport with the contents of a GATKReport on disk.
* @param filename the path to the file to load
*/
public GATKReport(String filename) {
loadReport(new File(filename));
}
/**
* Create a new GATKReport with the contents of a GATKReport on disk.
* @param file the file to load
*/
public GATKReport(File file) {
tables = new TreeMap<String, GATKReportTable>();
loadReport(file);
}
/**
* Load a GATKReport file from disk
* @param file the file to load
*/
private void loadReport(File file) {
try {
BufferedReader reader = new BufferedReader(new FileReader(file));
GATKReportTable table = null;
String[] header = null;
int id = 0;
String line;
while ( (line = reader.readLine()) != null ) {
if (line.startsWith("##:GATKReport.v0.1 ")) {
line = line.replaceFirst("##:GATKReport.v0.1 ", "");
String[] pieces = line.split(" : ");
String tableName = pieces[0];
String tableDesc = pieces[1];
addTable(tableName, tableDesc);
table = getTable(tableName);
header = null;
} else if ( line.isEmpty() ) {
// do nothing
} else {
if (table != null) {
if (header == null) {
header = line.split("\\s+");
table.addPrimaryKey("id", false);
for ( String columnName : header ) {
table.addColumn(columnName, "");
}
id = 0;
} else {
String[] entries = line.split("\\s+");
for (int columnIndex = 0; columnIndex < header.length; columnIndex++) {
table.set(id, header[columnIndex], entries[columnIndex]);
}
id++;
}
}
}
}
} catch (FileNotFoundException e) {
throw new StingException("Cannot read GATKReport: " + e);
} catch (IOException e) {
throw new StingException("Cannot read GATKReport: " + e);
}
}
/**
* Add a new table to the collection
*