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

java/src/org/broadinstitute/sting/gatk/report/GATKReport.java

@@ -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
      *