Andreas Tille pushed to branch master at Debian Med / proteinortho
Commits:
2249f1b3 by Andreas Tille at 2019-01-08T08:20:38Z
d/watch: Also catch letters in version number
- - - - -
6062c902 by Andreas Tille at 2019-01-08T08:20:58Z
New upstream version 5.16b+dfsg
- - - - -
f6159a9b by Andreas Tille at 2019-01-08T08:20:59Z
Update upstream source from tag 'upstream/5.16b+dfsg'
Update to upstream version '5.16b+dfsg'
with Debian dir 15c5f588b80b9659a3374de889894726cb9e2abd
- - - - -
39627755 by Andreas Tille at 2019-01-08T08:28:53Z
Make sure upstream version using appended letters is greater than without letter
- - - - -
a0ec3e07 by Andreas Tille at 2019-01-08T08:29:44Z
New upstream version 5.16.b+dfsg
- - - - -
026cdcaf by Andreas Tille at 2019-01-08T08:29:44Z
Update upstream source from tag 'upstream/5.16.b+dfsg'
Update to upstream version '5.16.b+dfsg'
with Debian dir b979a6656c297cd0faf26f248d4407f47000461b
- - - - -
52a50410 by Andreas Tille at 2019-01-08T08:29:44Z
New upstream version
- - - - -
ab43ef2c by Andreas Tille at 2019-01-08T08:31:37Z
Upload to unstable
- - - - -
5 changed files:
- Makefile
- debian/changelog
- debian/watch
- proteinortho5.pl
- proteinortho5_clustering.cpp
Changes:
=====================================
Makefile
=====================================
@@ -19,4 +19,5 @@ test: proteinortho5.pl proteinortho5_clustering
./proteinortho5.pl -project=test -synteny -singles test/*.faa
@./chk_test.pl test.proteinortho
@./chk_test.pl test.poff
+ rm test.*
@echo "Test okay"
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+proteinortho (5.16.b+dfsg-1) unstable; urgency=medium
+
+ * d/watch: Also catch letters in version number
+ * New upstream version
+
+ -- Andreas Tille <[email protected]> Tue, 08 Jan 2019 09:29:46 +0100
+
proteinortho (5.16+dfsg-2) unstable; urgency=medium
* Fix Homepage
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=3
+version=4
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- http://www.bioinf.uni-leipzig.de/Software/proteinortho/
proteinortho_v([\d.]+)\.tar\.gz
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz,uversionmangle=s/([\d.]+)([a-z])/$1.$2/"
\
+ http://www.bioinf.uni-leipzig.de/Software/proteinortho/
proteinortho_v@ANY_VERSION@@ARCHIVE_EXT@
=====================================
proteinortho5.pl
=====================================
@@ -47,7 +47,7 @@ use Thread::Queue;
##########################################################################################
# Variables
##########################################################################################
-our $version = "5.16";
+our $version = "5.16b";
our $step = 0; # 0/1/2/3 -> do all / only apply step 1 / only
apply step 2 / only apply step 3
our $verbose = 1; # 0/1 -> don't / be verbose
our $debug = 0; # 0/1 -> don't / show debug data
=====================================
proteinortho5_clustering.cpp
=====================================
@@ -3,7 +3,7 @@
* Reads edge list and splits connected components
* according to algebraic connectivity threshold
*
- * Last updated: 2017/03/20
+ * Last updated: 2017/09/20
* Author: Marcus Lechner
*/
@@ -307,7 +307,7 @@ void partition_graph() {
// Connectivity analysis
if (debug_level > 0) cerr << "[DEBUG] Calculating connectivity
of a group. " << current_group.size() << " proteins (ID: " << protein_id << ")"
<< endl;
- if (current_group.size() > 16000) cerr << "[WARN] Current
connected component conatins " << current_group.size() << " proteins. That
might be way to much for me. Try raising the e-value!" << endl;
+ if (current_group.size() > 16000) cerr << "[WARN] Current
connected component contains " << current_group.size() << " proteins. That
might be way to much for me. Try raising the e-value!" << endl;
double connectivity = getConnectivity(current_group);
if (debug_level > 0) cerr << "[DEBUG] Connectivity was " <<
connectivity << endl;
@@ -535,8 +535,8 @@ void splitGroups(vector<double>& y, vector<unsigned int>&
nodes){
// cerr << groupA.size() << " -- " << groupB.size() << endl;
// Catch error in laplacien calcs
- if (groupA.size() == 0 || groupB.size() == 0) {
- throw "Failed to partition subgraph! This might lead to an
infinit loop. Please submit the .blastgraph file to
[email protected] to help fixing this issue.";
+ if ((groupA.size() == 0 || groupB.size() == 0) && groupZero.size() ==
0) {
+ throw string("Failed to partition subgraph! This might lead to
an infinit loop. Please submit the .blastgraph file to
[email protected] to help fixing this issue.");
}
removeExternalEdges(groupZero);
@@ -621,7 +621,7 @@ void remove_edge(protein& node, const unsigned int
remove_id) {
// Search for element in edge list
vector<unsigned int>::iterator element = find(node.edges.begin(),
node.edges.end(), remove_id);
// Not found (something is wrong!)
- if (element == node.edges.end()) throw "Element could not be found in
edge list";
+ if (element == node.edges.end()) throw string("Element could not be
found in edge list");
// // Remove element
node.edges.erase(element);
}
@@ -706,7 +706,7 @@ void parse_file(string file) {
}
}
else {
- throw "Could not open file " + file;
+ throw string("Could not open file ") + file;
}
}
View it on GitLab:
https://salsa.debian.org/med-team/proteinortho/compare/6714c10b9c3ce7e53137864cadc1969e1e9e737a...ab43ef2c1b22d620b79e272446f004c60177183a
--
View it on GitLab:
https://salsa.debian.org/med-team/proteinortho/compare/6714c10b9c3ce7e53137864cadc1969e1e9e737a...ab43ef2c1b22d620b79e272446f004c60177183a
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