From 08194f467319ba954eafbcc47c07cbaff801bc3d Mon Sep 17 00:00:00 2001
From: Carsten Kemena <c.kemena@uni-muenster.de>
Date: Mon, 2 Jul 2018 16:24:13 +0200
Subject: [PATCH] fixed collapsing option, added test

---
 CHANGELOG                                     |  3 ++
 CMakeLists.txt                                |  2 +-
 src/DBAccess.cpp                              |  5 ++-
 .../results/collapse-both.txt                 | 35 +++++++++++++++++++
 .../results/collapse-none.txt                 | 35 +++++++++++++++++++
 tests/integrationTests/runTests.sh            | 12 +++++--
 6 files changed, 88 insertions(+), 4 deletions(-)
 create mode 100644 tests/integrationTests/results/collapse-both.txt
 create mode 100644 tests/integrationTests/results/collapse-none.txt

diff --git a/CHANGELOG b/CHANGELOG
index a2a8dcb..f9ffd86 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,6 @@
+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
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ce60c8d..00e176e 100644
--- a/CMakeLists.txt
+++ b/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
diff --git a/src/DBAccess.cpp b/src/DBAccess.cpp
index 32150c9..36a99bd 100644
--- a/src/DBAccess.cpp
+++ b/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();
 }
diff --git a/tests/integrationTests/results/collapse-both.txt b/tests/integrationTests/results/collapse-both.txt
new file mode 100644
index 0000000..eec37fa
--- /dev/null
+++ b/tests/integrationTests/results/collapse-both.txt
@@ -0,0 +1,35 @@
+# 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
+
diff --git a/tests/integrationTests/results/collapse-none.txt b/tests/integrationTests/results/collapse-none.txt
new file mode 100644
index 0000000..50187f3
--- /dev/null
+++ b/tests/integrationTests/results/collapse-none.txt
@@ -0,0 +1,35 @@
+# 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
+
diff --git a/tests/integrationTests/runTests.sh b/tests/integrationTests/runTests.sh
index fa6ab57..6eb68af 100755
--- a/tests/integrationTests/runTests.sh
+++ b/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
 }
 
 
-- 
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