Changeset 207

Timestamp:

Dec 4, 2006, 4:25:30 PM (15 years ago)

Author:

Johan Enell

Message:

Fixes #31 external id, symbol and locuslink is written to table

Location:

trunk/se/lu/onk/ZTest/src/ztest

Files:

• Reporter.java (modified) (3 diffs)
• Start.java (modified) (5 diffs)

trunk/se/lu/onk/ZTest/src/ztest/Reporter.java

@@ -27 +27 @@
 {
   
-  private int reporter;
+  private String reporter;
   private double m;
   private double p;
   private int size;
+  private String symbol;
+  private String locusLink;
   
   
-  public Reporter(String reporter)
+  public Reporter(String reporter, String symbol, String locusLink)
   {
-    this.reporter = new Integer(reporter); 
+    this.reporter = reporter;
+    this.symbol = symbol;
+    this.locusLink = locusLink;
   }
 
@@ -42 +46 @@
     this.p = p;
   }
+  
+  public double getP()
+  {
+    return p;
+  }
 
   public void setM(double m)
@@ -47 +56 @@
     this.m = m;
   }
-
-  public double getP()
+  
+  public double getM()
   {
-    return p;
+    return m;
   }
 
-  public int getReporter()
+  public String getReporter()
   {
     return reporter;
   }
+  
+  public final String getLocusLink()
+  {
+    return locusLink;
+  }
 
-  public double getM()
+  public final String getSymbol()
   {
-    return m;
+    return symbol;
   }
 

trunk/se/lu/onk/ZTest/src/ztest/Start.java

@@ -56 +56 @@
       int mCol = assayFields.indexOf("l2ratio1_2");
       int repCol = columns.indexOf("reporter");
+      int repidCol = columns.indexOf("reporterId");
+      int symCol = columns.indexOf("geneSymbol");
+      int llCol = columns.indexOf("locusLink");
       int assayDataCol = columns.indexOf("assayData");
 
-      if (mCol == -1 || repCol == -1 || assayDataCol == -1)
+      if (mCol == -1 || repCol == -1 || repidCol == -1 || symCol == -1 || llCol == -1 || assayDataCol == -1)
       {
         throw new BASEFileException("Cant find the columns l2ratio1_2, reporter or assayData");
@@ -80 +83 @@
           spots[i] = new Spot(m);
         }
-        Reporter r = new Reporter(data[repCol]);
+        Reporter r = new Reporter(data[repidCol], data[symCol], data[llCol]);
         bfss.addData(r, spots);
         data = bfr.readDataRow(dataLength);
@@ -135 +138 @@
       html.println("<table>");
       html.println("<tr><th>Reporter</th>" +
+          "<th>Gene symbol</th>" +
+          "<th>Locus Link</th>" +
           "<th>Average M</th>" +
           "<th>P</th>" +
@@ -143 +148 @@
 
       tab.println("Reporter\t" +
-          "Average M\t" +
+          "GeneSymbol\t" +
+          "LocusLink\t" +
+          "AverageM\t" +
           "P\t" +
-          "Number of values\t" +
+          "NumberOfValues\t" +
           "Rank\t" +
           "Expected\t" +
@@ -157 +164 @@
         double fdr = (expected / rank);
         
-        html.printf("<tr class=\"row"+(i%2+1)+"\">" +
-          "<td>%1$d</td>" +
-          "<td>%2$f</td>" +
-          "<td>%3$f</td>" +
-          "<td>%4$d</td>" +
-          "<td>%5$d</td>" +
-          "<td>%6$f</td>" +
-          "<td>%7$.2f</td></tr>\n",
+        if (i < 1000)
+        {
+          html.printf(
+            "<tr class=\"row" + (i % 2 + 1) + "\"><td>%s</td><td>%s</td><td>%s</td>" +
+            "<td>%f</td><td>%f</td><td>%d</td><td>%d</td><td>%f</td><td>%.2f</td></tr>\n",
+            r.getReporter(),
+            r.getSymbol(),
+            r.getLocusLink(),
+            r.getM(),
+            r.getP(),
+            r.getSize(),
+            rank,
+            expected,
+            fdr);
+        }
+        tab.printf("%s\t%s\t%s\t%f\t%f\t%d\t%d\t%f\t%f\n",
           r.getReporter(),
-          r.getM(),
-          r.getP(),
-          r.getSize(),
-          rank,
-          expected,
-          fdr);
-        
-        tab.printf("%d\t%f\t%f\t%d\t%d\t%f\t%f\n",
-          r.getReporter(),
+          r.getSymbol(),
+          r.getLocusLink(),
           r.getM(),
           r.getP(),