From 365d18a32780f5e6113b4374456d12ca38e2a9cf Mon Sep 17 00:00:00 2001
From: Michael Coleman <tutufan@gmail.com>
Date: Thu, 3 May 2007 00:10:00 -0500
Subject: [PATCH] zap a bit of dead code; cleanups; update TODO list

---
 TODO         | 10 +++++-----
 cgreylag.hpp | 12 +-----------
 cgreylag.i   |  4 ----
 3 files changed, 6 insertions(+), 20 deletions(-)

diff --git a/TODO b/TODO
index 074494a..a5b43c3 100644
--- a/TODO
+++ b/TODO
@@ -37,10 +37,12 @@ TASK QUEUE
 * MINI-GOAL: basic greylag-process usable on our cluster (no mods)
 
 
-* Demo runs! (vs SEQUEST)
-** observe memory use!
+* save .git backup
+* reinitialize git mirror on research
+
+* Demo runs! (vs SEQUEST)  [DTASelect -t 0, Contrast]
 ** no mod
-** one mod
+** one mod??
 ** ASFP (multiple mods)
 ** vs myrimatch, if run completes
 
@@ -81,8 +83,6 @@ TASK QUEUE
 
 
 
-* do a cg-admin-rewritehist before publishing git archive?
-
 * calculate Ion%?
 
 
diff --git a/cgreylag.hpp b/cgreylag.hpp
index efe1fc4..40ef92a 100644
--- a/cgreylag.hpp
+++ b/cgreylag.hpp
@@ -120,12 +120,6 @@ public:
 };
 
 
-enum ion { ION_MIN, ION_Y=ION_MIN, ION_B, ION_MAX }; // NB: [ION_MIN, ION_MAX)
-
-inline void operator++(ion &i) { i = ion(i + 1); }
-inline void operator++(ion &i, int) { i = ion(i + 1); }
-
-
 class peak {
 public:
   double mz;
@@ -139,10 +133,7 @@ public:
   char *__repr__() const;
 
   static bool less_mz(peak x, peak y) { return x.mz < y.mz; }
-  // FIX: delete one of these
-  static bool less_intensity(peak x, peak y) {
-    return x.intensity < y.intensity;
-  }
+
   static bool greater_intensity(peak x, peak y) {
     return x.intensity > y.intensity;
   }
@@ -298,7 +289,6 @@ struct mass_trace_item {
 
 // This is everything we want to remember about a match, so that we can report
 // it later.
-// FIX: Are any of these fields unneeded?
 class match {
 public:
   double score;
diff --git a/cgreylag.i b/cgreylag.i
index d0b8b64..3598a8b 100644
--- a/cgreylag.i
+++ b/cgreylag.i
@@ -40,10 +40,6 @@
     }
 }
 
-// not sure these are useful--just avoiding SWIG warning
-%rename(ion_increment) operator++(ion &);
-%rename(ion_post_increment) operator++(ion &, int);
-
 
 %include std_string.i
 %apply const std::string & { std::string *name };
-- 
2.11.4.GIT