[med-svn] [Git][med-team/proteinortho][upstream] 2 commits: New upstream version 5.16b+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / proteinortho


Commits:
6062c902 by Andreas Tille at 2019-01-08T08:20:58Z
New upstream version 5.16b+dfsg
- - - - -
a0ec3e07 by Andreas Tille at 2019-01-08T08:29:44Z
New upstream version 5.16.b+dfsg
- - - - -


3 changed files:

- Makefile
- 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"


=====================================
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 lechner at staff.uni-marburg.de 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 lechner at staff.uni-marburg.de 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/6ecf7dce0bb2fb4706bc16e7989b138f814daab2...a0ec3e070fc4b2b1df5954f67d9b64f3069f42cb

-- 
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/compare/6ecf7dce0bb2fb4706bc16e7989b138f814daab2...a0ec3e070fc4b2b1df5954f67d9b64f3069f42cb
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