[med-svn] [seaview] 01/01: Enable reading number of bootstraps from phyml runs

[Andreas Tille]

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tille pushed a commit to branch master
in repository seaview.

commit 8880102e845038eb13eb6da4251332016e4515ca
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 1 10:14:51 2017 +0100

    Enable reading number of bootstraps from phyml runs
---
 debian/changelog                                   |  6 ++++
 .../patches/evaluate_phyml_bootstrap_number.patch  | 32 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 3 files changed, 39 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index c60d310..dfcc6d0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+seaview (1:4.6.1.2-2) UNRELEASED; urgency=medium
+
+  * Enable reading number of bootstraps from phyml runs
+
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Feb 2017 08:51:09 +0100
+
 seaview (1:4.6.1.2-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/evaluate_phyml_bootstrap_number.patch b/debian/patches/evaluate_phyml_bootstrap_number.patch
new file mode 100644
index 0000000..cde00a6
--- /dev/null
+++ b/debian/patches/evaluate_phyml_bootstrap_number.patch
@@ -0,0 +1,32 @@
+Description: Enable reading number of bootstraps from phyml runs
+Author: Manolo Gouy <manolo.gouy at univ-lyon1.fr>
+        Patch extracted from Upstream version 4.6.1.3
+Last-Update: Wed, 01 Feb 2017 08:51:09 +0100
+
+--- a/trees.cxx
++++ b/trees.cxx
+@@ -1201,6 +1201,24 @@ void run_phyml_callback(Fl_Widget *ob, v
+ 	  display_tree = put_names_back_in_tree(display_tree, truenames);
+     //process bootstrap trees
+     char *bootstrap_trees = NULL;
++    if (replicates > 0) {
++      sprintf(input, "%s.phy_phyml_boot_stats.txt", base_fname);
++      in = fopen(input, "r");
++      if (!in) {
++        sprintf(input, "%s.phy_phyml_boot_stats", base_fname);
++        in = fopen(input, "r");
++      }
++      if (in) { // compute the true # of bootstrap replicates because parallelized phyML can compute a few more
++        char line[150];
++        while ((p = fgets(line, sizeof(line), in))) {
++          while (*p == ' ') p++;
++          if (*p == '#') {
++            sscanf(p+1, "%d", &replicates);
++          }
++        }
++        fclose(in);
++      }
++    }
+     if (replicates > 0 && b_keep_trees->value()) {
+       sprintf(input, "%s.phy_phyml_boot_trees.txt", base_fname);
+       in = fopen(input, "r");
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..567512c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+evaluate_phyml_bootstrap_number.patch

-- 
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