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Description: Fix broken encodings in some Java files
Strangely enough without this patch grep consideres the files in question
as "binary data files"
Bug-Debian: https://bugs.debian.org/893275
Author: Andreas Tille <tille@debian.org>
Last-Update: Sun, 18 Mar 2018 07:13:23 +0100
--- a/src/pal/distance/PairwiseDistance.java
+++ b/src/pal/distance/PairwiseDistance.java
@@ -201,7 +201,7 @@ public class PairwiseDistance implements
of.setSequences(s1, s2);
if (start > BranchLimits.MAXARC || start < BranchLimits.MINARC)
{
- // Dont use start value
+ // Don't use start value
dist = um.findMinimum(of, BranchLimits.FRACDIGITS);
}
else
--- a/src/pal/math/UnivariateMinimum.java
+++ b/src/pal/math/UnivariateMinimum.java
@@ -298,7 +298,7 @@ public class UnivariateMinimum
}
double u = b - ((b - c) * q - (b - a) * r) / 2.0 / (q - r);
u = constrain(u, searchToMax, min, max);
- double fu = 0; // Dont evaluate now
+ double fu = 0; // Don't evaluate now
boolean magnify = false;
--- a/src/pal/treesearch/UnrootedMLSearcher.java
+++ b/src/pal/treesearch/UnrootedMLSearcher.java
@@ -15,7 +15,7 @@ package pal.treesearch;
* Even given the offsourcing of code this class is rather large!
* Includes the algorithm of [1]
* </p>
- * [1] Guindon, Stphane Gascuel, Olivier (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology 52:5 pages 696 - 704 / October 2003
+ * [1] Guindon, Stephane Gascuel, Olivier (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology 52:5 pages 696 - 704 / October 2003
* @author Matthew Goode
* @version 1.0
*/
@@ -2805,4 +2805,4 @@ public class UnrootedMLSearcher implemen
public int getNumberOfStates() { return numberOfStates_; }
public int getNumberOfTransitionCategories() { return numberOfCategories_; }
}
-}
\ No newline at end of file
+}
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