Changeset 255

Timestamp:

Apr 13, 2007, 11:03:14 AM (15 years ago)

Author:

Johan Enell

Message:

made some changes in the printing methods

Location:

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct

Files:

• RankProduct.java (modified) (9 diffs)
• Start.java (modified) (2 diffs)

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct/RankProduct.java

@@ -38 +38 @@
 public class RankProduct
 {
-  private final File dataFolder;
-  
   private final BASEFile<Reporter, Spot> basefile;
 
@@ -52 +50 @@
   public RankProduct(BASEFile<Reporter, Spot> basefile) throws BASEFileException
   {
-    dataFolder = new File("lib");
-    dataFolder.mkdir();
-    
     this.basefile = basefile;
     readAssaySection();
@@ -61 +56 @@
     
     this.basefileOut = new BASEFile<ReporterOut, SpotOut>(new File("stdout.txt"), "rw");
-    BASEFileSpotSection<Reporter, Spot> bfss = this.basefile.getSpotSection();
     BASEFileAssaySection bfas = new BASEFileAssaySection();
     bfas.setAnnotationColumns("");
@@ -135 +129 @@
     }
   }
-
-  public void printTab() throws BASEFileException
+  
+  public void print(File dataFolder) throws BASEFileException
   {
     bfss.sortReporter(new Comparator<Reporter>()
@@ -145 +139 @@
       }
     });
-
-    writeTabFile(basefileOut.getSpotSection(0), new File(dataFolder, "resultUP.csv"));
-    writeTabFile(basefileOut.getSpotSection(1), new File(dataFolder, "resultDOWN.csv"));
-  }
-  
-  private void writeTabFile(BASEFileSpotSection<ReporterOut, SpotOut> bfss, File file) throws BASEFileException
+    
+    printTab(0, new File(dataFolder, "resultUP.csv"));
+    printTab(1, new File(dataFolder, "resultDOWN.csv"));
+    printHTML(0, new File(dataFolder, "resultUP.html"));
+    printHTML(1, new File(dataFolder, "resultDOWN.html"));
+    printBASE();
+  }
+
+  private void printTab(int section, File file) throws BASEFileException
   {
     try
@@ -173 +170 @@
       }
       tab.println(formatArray("", "", "\t", tableRow));
-      
+
+      BASEFileSpotSection<ReporterOut, SpotOut> bfss = basefileOut.getSpotSection(section);
       for (int i = 0; i < bfss.getHeight(); i++)
       {
@@ -202 +200 @@
   }
 
-  public void printHTML() throws BASEFileException
-  {
-    bfss.sortReporter(new Comparator<Reporter>()
-    {
-      public int compare(Reporter r1, Reporter r2)
-      {
-        return Double.compare(r1.getRankProduct(), r2.getRankProduct());
-      }
-    });
-    
-    writeHTMLFile(basefileOut.getSpotSection(0), new File(dataFolder, "resultUP.html"));
-    writeHTMLFile(basefileOut.getSpotSection(1), new File(dataFolder, "resultDOWN.html"));
-  }
-  
-  private void writeHTMLFile(BASEFileSpotSection<ReporterOut, SpotOut> bfss, File file) throws BASEFileException
+  public void printHTML(int section, File file) throws BASEFileException
   {
     try
@@ -229 +213 @@
       
       String[] tableRow = new String[8];
-      tableRow[0] = "Reporter"; 
-      tableRow[1] = "GeneSymbol"; 
+      tableRow[0] = "Reporter";
+      tableRow[1] = "GeneSymbol";
       tableRow[2] = "LocusLink";
       tableRow[3] = "AverageM";
       tableRow[4] = "up/down";
       tableRow[5] = "Rank";
-      tableRow[6] = "Rank product"; 
+      tableRow[6] = "Rank product";
       tableRow[7] = "NumberOfValues";
       html.println("<tr>" + formatArray("<th>", "</th>", "", tableRow) + "</tr>");
 
       DecimalFormat df = new DecimalFormat("#&nbsp;##0.000");
+      BASEFileSpotSection<ReporterOut, SpotOut> bfss = basefileOut.getSpotSection(section);
       for (int i = 0; i < 1000 && i < bfss.getHeight(); i++)
       {
@@ -316 +301 @@
   {   
     //Read spot section
-    BASEFileSpotSection<Reporter, Spot> bfss = basefile.getSpotSection();
-
     int mCol = bfss.getAssayFieldsColIndex("l2ratio1_2");
     int aCol = bfss.getAssayFieldsColIndex("l10intgmean1_2");

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct/Start.java

@@ -39 +39 @@
     try
     {
+      File dataFolder = new File("lib");
+      dataFolder.mkdir();
+      
       BASEFile<Reporter, Spot> basefile;
       basefile = new BASEFile<Reporter, Spot>(new File(args.length == 1 ? args[0] : "stdin.txt"), "r");
@@ -44 +47 @@
       RankProduct rankproduct = new RankProduct(basefile);
       rankproduct.calculate();
-      rankproduct.printTab();
-      rankproduct.printHTML();
-      rankproduct.printBASE();
-    
+      rankproduct.print(dataFolder);
     }
     catch (BASEFileException e)