Merge branch 'develop' into 'master'

fixed collapsing option, added test

See merge request !3

CHANGELOG

+v. 2.3.2
+- fixed: query was uncollapsed for next target if collapse was activated
+
 v. 2.3.1
 - fixed: query was always collapse independently of parameter
 

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 2.6)
 project (RADS C CXX)
 SET(MAJOR_VERSION 2)
 SET(MINOR_VERSION 3)
-SET(PATCH_VERSION 1)
+SET(PATCH_VERSION 2)
 
 
 SET(CMAKE_CXX_FLAGS_COVERAGE

src/DBAccess.cpp

@@ -158,7 +158,10 @@ DBAccess::search(BSDL::AlignmentMatrix<int, BSDL::DSM> &matrix, bool all, bool c
 		// add all sequences having the same domain arrangement
 		readSequences_(results.targets.back().targetSequences, domains);
 
-		queryDA.reconstruct();
 	}
+
+	if (collapse)
+		queryDA.reconstruct();
+
 	results.sort();
 }

tests/integrationTests/results/collapse-both.txt

+# RADS version 2.3.1
+# RADS Output v1
+# run at Mon Jul  2 16:19:24 2018
+#
+# query file: -
+# database: /local/home/ckeme_01/projects/domainWorld/RADS/tests/integrationTests/annotation
+# gap open penalty -50
+# gap extension penalty -10
+# matrix: /local/home/ckeme_01/.domainWorld/dsm/pfam-31.dsm
+# all: false
+# collapse: true
+# ******************************************************************
+
+# -------------------------------------------------------------------
+Results for: manual entered query
+Domain arrangement: PF02543 PF02543 PF16861
+
+# score | normalized | SeqID | sequence length | domain arrangement | aln
+# -------------------------------------------------------------------
+200	1.00	A0A010	530	PF02543 10 63 PF16861 362 524	1
+200	1.00	A0A009	530	PF02543 10 63 PF02543 104 312 PF16861 362 524	2
+
+
+# -------------------------------------------------------------------
+List of alignments:
+# -------------------------------------------------------------------
+
+1)
+ Query DA: PF02543 PF16861
+Target DA: PF02543 PF16861
+
+2)
+ Query DA: PF02543 PF16861
+Target DA: PF02543 PF16861
+

tests/integrationTests/results/collapse-none.txt

+# RADS version 2.3.1
+# RADS Output v1
+# run at Mon Jul  2 16:20:43 2018
+#
+# query file: -
+# database: /local/home/ckeme_01/projects/domainWorld/RADS/tests/integrationTests/annotation
+# gap open penalty -50
+# gap extension penalty -10
+# matrix: /local/home/ckeme_01/.domainWorld/dsm/pfam-31.dsm
+# all: false
+# collapse: false
+# ******************************************************************
+
+# -------------------------------------------------------------------
+Results for: manual entered query
+Domain arrangement: PF02543 PF02543 PF16861
+
+# score | normalized | SeqID | sequence length | domain arrangement | aln
+# -------------------------------------------------------------------
+300	1.00	A0A009	530	PF02543 10 63 PF02543 104 312 PF16861 362 524	1
+190	0.69	A0A010	530	PF02543 10 63 PF16861 362 524	2
+
+
+# -------------------------------------------------------------------
+List of alignments:
+# -------------------------------------------------------------------
+
+1)
+ Query DA: PF02543 PF02543 PF16861
+Target DA: PF02543 PF02543 PF16861
+
+2)
+ Query DA: PF02543 PF02543 PF16861
+Target DA: ******* PF02543 PF16861
+

tests/integrationTests/runTests.sh

@@ -81,11 +81,19 @@
 	[ "$output" == $'Number of sequences included: 9\nNumber of distinct arrangements 8' ]
 
 	run ../../build/rads -D  PF02543 PF16861 -m pfam-31.dsm -d annotation -o test-col-aln.txt -c -l
-	
 	run diff <(grep -v '#' test-col-aln.txt) <(grep -v '#' results/test-col-aln.txt)
 	[ $status == 0 ]
+	
 
-	rm annotation.db annotation.da test-col-aln.txt
+	run ../../build/rads -D  PF02543 PF02543 PF16861 -m pfam-31.dsm -d annotation  -l -c -o collapse-both.txt
+    run diff <(grep -v '#' collapse-both.txt) <(grep -v '#' results/collapse-both.txt)
+    [ $status == 0 ]
+	
+    run ../../build/rads -D  PF02543 PF02543 PF16861 -m pfam-31.dsm -d annotation  -l -o collapse-none.txt
+	run diff <(grep -v '#' collapse-none.txt) <(grep -v '#' results/collapse-none.txt)
+	[ $status == 0 ]
+	
+	rm annotation.db annotation.da test-col-aln.txt collapse-both.txt collapse-none.txt
 }