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chore: Updated patch files to not need whitespace fixing #12

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12 changes: 7 additions & 5 deletions LinearFold-E.patch
View file
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Original file line number Diff line number Diff line change
@@ -1,22 +1,24 @@
diff --git a/Makefile b/Makefile
index 2c10c80..2b5ffa7 100644
index 2c10c80..ecfe992 100644
--- a/Makefile
+++ b/Makefile
@@ -6,16 +6,17 @@
################################

CC=g++
-DEPS=src/LinearFoldEval.cpp src/LinearFold.h src/Utils/energy_parameter.h src/Utils/feature_weight.h src/Utils/intl11.h src/Utils/intl21.h src/Utils/intl22.h src/Utils/utility_v.h src/Utils/utility.h
-DEPS=src/LinearFoldEval.cpp src/LinearFold.h src/Utils/energy_parameter.h src/Utils/feature_weight.h src/Utils/intl11.h src/Utils/intl21.h src/Utils/intl22.h src/Utils/utility_v.h src/Utils/utility.h
+DEPS=src/LinearFoldEval.cpp src/LinearFold.h src/Utils/energy_parameter.h src/Utils/feature_weight.h src/Utils/feature_weight_e.h src/Utils/intl11.h src/Utils/intl21.h src/Utils/intl22.h src/Utils/utility_v.h src/Utils/utility.h
CFLAGS=-std=c++11 -O3
.PHONY : clean linearfold
-objects=bin/linearfold_v bin/linearfold_c
+objects=bin/linearfold_v bin/linearfold_c bin/linearfold_e

linearfold: src/LinearFold.cpp $(DEPS)
-linearfold: src/LinearFold.cpp $(DEPS)
+linearfold: src/LinearFold.cpp $(DEPS)
chmod +x linearfold draw_circular_plot
mkdir -p bin
$(CC) src/LinearFold.cpp $(CFLAGS) -Dlv -Dis_cube_pruning -Dis_candidate_list -o bin/linearfold_v
- $(CC) src/LinearFold.cpp $(CFLAGS) -Dlv -Dis_cube_pruning -Dis_candidate_list -o bin/linearfold_v
+ $(CC) src/LinearFold.cpp $(CFLAGS) -Dlv -Dis_cube_pruning -Dis_candidate_list -o bin/linearfold_v
$(CC) src/LinearFold.cpp $(CFLAGS) -Dis_cube_pruning -Dis_candidate_list -o bin/linearfold_c
+ $(CC) src/LinearFold.cpp $(CFLAGS) -Dlpe -Dis_cube_pruning -Dis_candidate_list -o bin/linearfold_e

Expand All @@ -25,7 +27,7 @@ index 2c10c80..2b5ffa7 100644
\ No newline at end of file
diff --git a/src/Utils/feature_weight_e.h b/src/Utils/feature_weight_e.h
new file mode 100644
index 0000000..5bbb480
index 0000000..2cf420b
--- /dev/null
+++ b/src/Utils/feature_weight_e.h
@@ -0,0 +1,36 @@
Expand Down
12 changes: 7 additions & 5 deletions LinearPartition-E.patch
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
diff --git a/Makefile b/Makefile
index 49a7aca..a4c6e20 100755
index 49a7aca..720f4bb 100755
--- a/Makefile
+++ b/Makefile
@@ -6,16 +6,17 @@
Expand All @@ -13,10 +13,12 @@ index 49a7aca..a4c6e20 100755
-objects=bin/linearpartition_v bin/linearpartition_c
+objects=bin/linearpartition_v bin/linearpartition_c bin/linearpartition_e

linearpartition: src/LinearPartition.cpp $(DEPS)
-linearpartition: src/LinearPartition.cpp $(DEPS)
+linearpartition: src/LinearPartition.cpp $(DEPS)
chmod +x linearpartition draw_bpp_plot draw_heatmap
mkdir -p bin
$(CC) src/LinearPartition.cpp $(CFLAGS) -Dlpv -o bin/linearpartition_v
- $(CC) src/LinearPartition.cpp $(CFLAGS) -Dlpv -o bin/linearpartition_v
+ $(CC) src/LinearPartition.cpp $(CFLAGS) -Dlpv -o bin/linearpartition_v
$(CC) src/LinearPartition.cpp $(CFLAGS) -o bin/linearpartition_c
+ $(CC) src/LinearPartition.cpp $(CFLAGS) -Dlpe -o bin/linearpartition_e

Expand All @@ -25,7 +27,7 @@ index 49a7aca..a4c6e20 100755
\ No newline at end of file
diff --git a/src/Utils/feature_weight_e.h b/src/Utils/feature_weight_e.h
new file mode 100644
index 0000000..5bbb480
index 0000000..2cf420b
--- /dev/null
+++ b/src/Utils/feature_weight_e.h
@@ -0,0 +1,36 @@
Expand Down Expand Up @@ -67,7 +69,7 @@ index 0000000..5bbb480
+#endif
\ No newline at end of file
diff --git a/src/Utils/utility.h b/src/Utils/utility.h
index 0601a4d..a5866b1 100755
index 0601a4d..5c96a39 100755
--- a/src/Utils/utility.h
+++ b/src/Utils/utility.h
@@ -13,7 +13,11 @@
Expand Down
4 changes: 2 additions & 2 deletions README_LinearFold-E_patch.md
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ git reset --hard ae6507f3053573decd2e4bdae60d5a96eac87783

```
cd LinearFold
git apply --whitespace=fix /PATH/TO/ETERNAFOLD/LinearFold-E.patch
git apply /PATH/TO/ETERNAFOLD/LinearFold-E.patch
make
cd ..
```
Expand All @@ -38,7 +38,7 @@ cd ..

```
cd LinearPartition
git apply --whitespace=fix /PATH/TO/ETERNAFOLD/LinearPartition-E.patch
git apply /PATH/TO/ETERNAFOLD/LinearPartition-E.patch
make
cd ..
```
Expand Down