From 277a26871be1ca39d01dcc888cf2fecafb0e55ca Mon Sep 17 00:00:00 2001
From: danielgeiszler <danny.geisz@gmail.com>
Date: Thu, 2 May 2024 19:56:49 +0300
Subject: [PATCH] Partial swapped AA decoy generation method

---
 .../iterativelocalization/IterativeLocalizer.java     |  4 +---
 src/edu/umich/andykong/ptmshepherd/utils/Peptide.java | 11 +++++++++++
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
index fa13715..4511c38 100644
--- a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
+++ b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
@@ -676,9 +676,7 @@ public int compareTo(SpecProbQ o) {
             qEntropyDecoyModel[i] = min;
         }
 
-
-
-
+        
         /**
         // Print to test
         for (int i = flrProb.length-1; i >= 0; i--) {
diff --git a/src/edu/umich/andykong/ptmshepherd/utils/Peptide.java b/src/edu/umich/andykong/ptmshepherd/utils/Peptide.java
index e2a2989..fbd9c06 100644
--- a/src/edu/umich/andykong/ptmshepherd/utils/Peptide.java
+++ b/src/edu/umich/andykong/ptmshepherd/utils/Peptide.java
@@ -81,6 +81,13 @@ else if (method.equals("mono-mutated"))
             return null; //TODO
     }
 
+    public Peptide generateDecoy(Random rng, String method, int pos) {
+        if (method.equals("swap"))
+            return generateSwappedDecoy(this.pepSeq, this.mods, pos, rng);
+        else
+            return null; //TODO
+    }
+
     public static Peptide generateDecoy(String pep, float[] mods, Random rng, String method) {
         if (method.equals("shuffled"))
             return generateShuffledDecoy(pep, mods, rng);
@@ -148,6 +155,10 @@ public static Peptide generateMonoMutatedDecoy(String pep, float[] mods, int mut
         return new Peptide(newPep.toString(), mods, mutSite);
     }
 
+    public static Peptide generateSwappedDecoy(String pepSeq, float[] mods, int pos, Random rng) {
+        //TODO
+        return new Peptide(pepSeq, mods);
+    }
 
     static class Site {
         char aa;