[Gmod-apollo-cmts] SF.net SVN: gmod:[24072] apollo/trunk/src/java/apollo

[<gk...@us...>]

Revision: 24072
          http://gmod.svn.sourceforge.net/gmod/?rev=24072&view=rev
Author:   gk_fan
Date:     2010-11-01 18:49:16 +0000 (Mon, 01 Nov 2010)

Log Message:
-----------
Added configurable option for allowing partial ORFs to be calculated.

Modified Paths:
--------------
    apollo/trunk/src/java/apollo/config/Style.java
    apollo/trunk/src/java/apollo/datamodel/FeatureSet.java

Modified: apollo/trunk/src/java/apollo/config/Style.java
===================================================================
--- apollo/trunk/src/java/apollo/config/Style.java	2010-11-01 16:23:16 UTC (rev 24071)
+++ apollo/trunk/src/java/apollo/config/Style.java	2010-11-01 18:49:16 UTC (rev 24072)
@@ -203,6 +203,8 @@
   protected Hashtable parameters = null;
   
   private String overlapDefinition;
+  
+  private boolean allowPartialORFs = true;
 
   public Style(String styleFileString) {
     logger.debug("Creating new style "+styleFileString);
@@ -627,6 +629,8 @@
               }
               geneticCodeNumber = num;
             }
+          } else if (key.equalsIgnoreCase("AllowPartialORFs")) {
+            this.allowPartialORFs = getBoolean(value);
           } else {
             // Stick it in as a generic parameter
             logger.debug("saved unknown parameter from " + styleFile + ": " + key + "=" + value);
@@ -2104,5 +2108,13 @@
       parameters = new Hashtable(1, 1.0F);
     return parameters;
   }
+  
+  /** Gets whether partial ORFs are allowed when calculating longest ORF
+   * 
+   * @return whether partial ORFs are allowed
+   */
+  public boolean isPartialORFsAllowed() {
+    return allowPartialORFs;
+  }
 
 }

Modified: apollo/trunk/src/java/apollo/datamodel/FeatureSet.java
===================================================================
--- apollo/trunk/src/java/apollo/datamodel/FeatureSet.java	2010-11-01 16:23:16 UTC (rev 24071)
+++ apollo/trunk/src/java/apollo/datamodel/FeatureSet.java	2010-11-01 18:49:16 UTC (rev 24072)
@@ -4,6 +4,7 @@
 import java.util.*;
 import javax.swing.JOptionPane;
 
+import apollo.config.Config;
 import apollo.util.SeqFeatureUtil;
 import apollo.util.FeatureList;
 import apollo.util.QuickSort;
@@ -829,16 +830,19 @@
       /* just in case the 5 prime end is missing see if
          a longer translation can be obtained without looking
          for the ATG */
-      start_index = 0;
-      while (start_index < 3) {
-        String orf = get_ORF(the_mRNA, start_index, -1);
-        String aa = getTrimmedAA(orf, start_index);
-        if (aa.length() > longest_peptide.length()) {
-          setMissing5prime(true);
-          longest_peptide = aa;
-          best_start_index = start_index;
+      // only do this if Apollo is configured to allow partial ORFs
+      if (Config.getStyle().isPartialORFsAllowed()) {
+        start_index = 0;
+        while (start_index < 3) {
+          String orf = get_ORF(the_mRNA, start_index, -1);
+          String aa = getTrimmedAA(orf, start_index);
+          if (aa.length() > longest_peptide.length()) {
+            setMissing5prime(true);
+            longest_peptide = aa;
+            best_start_index = start_index;
+          }
+          start_index++;
         }
-        start_index++;
       }
     }
     


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.