From ca65b981ea56ffbd5a6f0ae417263532f1b5cad7 Mon Sep 17 00:00:00 2001
From: "Esch, Roel van" <roel.vanesch@wur.nl>
Date: Fri, 27 Jan 2023 16:05:19 +0000
Subject: [PATCH] storing scoring matrices as resource files
---
CHANGELOG.md | 2 +
docs/source/user_guide/construct.rst | 4 +
docs/source/user_guide/phylogeny.rst | 8 +-
.../BoundedLocalSequenceAlignment.java | 2170 +----------------
.../alignment/LocalSequenceAlignment.java | 878 +------
.../nl/wur/bif/pantools/cli/AddFunctions.java | 4 +-
.../wur/bif/pantools/cli/ConsensusTree.java | 7 +
.../wur/bif/pantools/cli/CorePhylogeny.java | 9 +-
.../java/nl/wur/bif/pantools/cli/Group.java | 9 +-
.../java/nl/wur/bif/pantools/cli/MSA.java | 3 +-
.../wur/bif/pantools/cli/OptimalGrouping.java | 6 +-
.../pantools/cli/validation/Constraints.java | 17 +
.../validators/ScoringMatrixValidator.java | 28 +
.../pantools/pangenome/Classification.java | 69 +-
.../bif/pantools/pangenome/GenomeLayer.java | 4 +-
.../wur/bif/pantools/pangenome/Phylogeny.java | 8 +-
.../bif/pantools/pangenome/ProteomeLayer.java | 12 +-
.../nl/wur/bif/pantools/utils/FileUtils.java | 46 +-
.../nl/wur/bif/pantools/utils/Globals.java | 2 +-
src/main/resources/Defaults.properties | 2 +
src/main/resources/ErrorMessages.properties | 5 +
src/main/resources/MessageBundle.properties | 5 +-
src/main/resources/scoring-matrices/BLOSUM45 | 27 +
src/main/resources/scoring-matrices/BLOSUM50 | 27 +
src/main/resources/scoring-matrices/BLOSUM62 | 27 +
src/main/resources/scoring-matrices/BLOSUM80 | 27 +
src/main/resources/scoring-matrices/BLOSUM90 | 27 +
src/main/resources/scoring-matrices/NUC.4.4 | 24 +
src/main/resources/scoring-matrices/PAM250 | 27 +
src/main/resources/scoring-matrices/PAM30 | 27 +
src/main/resources/scoring-matrices/PAM70 | 27 +
.../pantools/utils/LoadScoringMatrixTest.java | 39 +
32 files changed, 457 insertions(+), 3120 deletions(-)
create mode 100644 src/main/java/nl/wur/bif/pantools/cli/validation/validators/ScoringMatrixValidator.java
create mode 100644 src/main/resources/scoring-matrices/BLOSUM45
create mode 100644 src/main/resources/scoring-matrices/BLOSUM50
create mode 100644 src/main/resources/scoring-matrices/BLOSUM62
create mode 100644 src/main/resources/scoring-matrices/BLOSUM80
create mode 100644 src/main/resources/scoring-matrices/BLOSUM90
create mode 100644 src/main/resources/scoring-matrices/NUC.4.4
create mode 100644 src/main/resources/scoring-matrices/PAM250
create mode 100644 src/main/resources/scoring-matrices/PAM30
create mode 100644 src/main/resources/scoring-matrices/PAM70
create mode 100644 src/test/java/nl/wur/bif/pantools/utils/LoadScoringMatrixTest.java
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c80d9b2a..47c57260f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,10 +5,12 @@ All notable changes to Pantools will be documented in this file.
### Added
- Added `sphinx-lint` to both pre-commit hooks and CI/CD pipeline to ensure correctness documentation (!112 !116).
- Option to add read group to alignment files produced by `pantools map` (!102).
+- Added more BLOSUM and PAM protein scoring matrix options (!123).
### Changed
- `add_functions` can now specify a directory where functional databases are stored (!117).
- parameter `-v` is now required for `change_grouping` (!124).
+- Scoring matrices are now stored in the resources directory as readable files (!123).
### Fixed
- `msa` now works correctly with 'alt_id' properties of GO nodes (!118).
diff --git a/docs/source/user_guide/construct.rst b/docs/source/user_guide/construct.rst
index bdbd27cb5..b395a59f8 100644
--- a/docs/source/user_guide/construct.rst
+++ b/docs/source/user_guide/construct.rst
@@ -355,6 +355,8 @@ Options
for genomes without an identifier.
* - ``--longest``
- Only cluster protein sequences of the longest transcript per gene.
+ * - ``--scoring-matrix``
+ - The scoring matrix used, default is BLOSUM62.
* - ``--relaxation``
- The relaxation in homology calls. Should be in range [1-8], from
strict to relaxed. This argument automatically sets
@@ -503,6 +505,8 @@ Options
compared to the previous clustering round.
* - ``--longest``
- Only cluster protein sequences of the longest transcript per gene.
+ * - ``--scoring-matrix``
+ - The scoring matrix used, default is BLOSUM62.
* - ``--relaxation``
- Only consider a selection of relaxation settings (1-8 allowed).
diff --git a/docs/source/user_guide/phylogeny.rst b/docs/source/user_guide/phylogeny.rst
index 3d3d0e416..79d8be74c 100644
--- a/docs/source/user_guide/phylogeny.rst
+++ b/docs/source/user_guide/phylogeny.rst
@@ -92,6 +92,8 @@ Options
* - ``--clustering-mode``/``-m``
- Maximum likelihood (--mode ML) or Neighbour joining (--mode NJ).
Default is ML.
+ - A BLOSUM matrix to be used for the calculation of protein similarity.
+ Allowed values are 45, 50, 62 80 and 90 (default: 62).
Example commands
~~~~~~~~~~~~~~~~
@@ -224,8 +226,10 @@ Options
homology groups. (Mutually exclusive with ``--homology-groups``.)
* - ``--homology-groups``/``-G``
- A comma separated list of homology group node identifiers. Default
- is all homology groups. (Mutually exclusive with
- ``--homology-file``.)
+ is all homology groups. (Mutually exclusive with ``--homology-file``.)
+ * - ``--blosum``
+ - A BLOSUM matrix to be used for the calculation of protein similarity.
+ Allowed values are 45, 50, 62 80 and 90 (default: 62).
* - ``--polytomies``
- Allow polytomies for ASTRAL-PRO.
diff --git a/src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java
index a40d5c995..9e88e183e 100755
--- a/src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java
+++ b/src/main/java/nl/wur/bif/pantools/alignment/BoundedLocalSequenceAlignment.java
@@ -1,5 +1,7 @@
package nl.wur.bif.pantools.alignment;
+import nl.wur.bif.pantools.utils.FileUtils;
+
import java.util.Stack;
/**
@@ -32,7 +34,7 @@ public class BoundedLocalSequenceAlignment {
private int deletions;
private int insertions;
private int BOUND;
- private char TYPE;
+ private String TYPE;
private int offset;
private int range_len;
private int mismatch_penalty, insertion_penalty;
@@ -49,7 +51,7 @@ public class BoundedLocalSequenceAlignment {
* @param clip The stringency of soft-clipping in the range [0..3]
* @param type Type of the input sequences(N for nucleotide P for peptide).
*/
- public BoundedLocalSequenceAlignment(int gap_open, int gap_ext, int max_length, int band, int clip, char type) {
+ public BoundedLocalSequenceAlignment(int gap_open, int gap_ext, int max_length, int band, int clip, String type) {
int i, j;
seq1 = new StringBuilder();
seq2 = new StringBuilder();
@@ -89,12 +91,7 @@ public class BoundedLocalSequenceAlignment {
left[0][j] = -1000;
matrix[0][j] = 0;
}
- if (TYPE == 'N')
- initialize_NUCC_matrix();
- else if (TYPE == 'P')
- initialize_BLOSUM_matrix(62);
- else
- System.out.println("Aligner type should be N or P");
+ match = FileUtils.loadScoringMatrix(TYPE);
switch (CLIPPING_STRIGENCY) {
case 1:
mismatch_penalty = -1;
@@ -110,2163 +107,6 @@ public class BoundedLocalSequenceAlignment {
break;
}
}
-
- /**
- * Initializes the NUCC.1 scoring matrix.
- */
- public final void initialize_NUCC_matrix() {
- match = new int[256][256];
-
- match['A']['A'] = 5;
- match['A']['T'] = -4;
- match['A']['G'] = -4;
- match['A']['C'] = -4;
- match['A']['S'] = -4;
- match['A']['W'] = 1;
- match['A']['R'] = 1;
- match['A']['Y'] = -4;
- match['A']['K'] = -4;
- match['A']['M'] = 1;
- match['A']['B'] = -4;
- match['A']['V'] = -1;
- match['A']['H'] = -1;
- match['A']['D'] = -1;
- match['A']['N'] = -2;
- match['T']['A'] = -4;
- match['T']['T'] = 5;
- match['T']['G'] = -4;
- match['T']['C'] = -4;
- match['T']['S'] = -4;
- match['T']['W'] = 1;
- match['T']['R'] = -4;
- match['T']['Y'] = 1;
- match['T']['K'] = 1;
- match['T']['M'] = -4;
- match['T']['B'] = -1;
- match['T']['V'] = -4;
- match['T']['H'] = -1;
- match['T']['D'] = -1;
- match['T']['N'] = -2;
- match['G']['A'] = -4;
- match['G']['T'] = -4;
- match['G']['G'] = 5;
- match['G']['C'] = -4;
- match['G']['S'] = 1;
- match['G']['W'] = -4;
- match['G']['R'] = 1;
- match['G']['Y'] = -4;
- match['G']['K'] = 1;
- match['G']['M'] = -4;
- match['G']['B'] = -1;
- match['G']['V'] = -1;
- match['G']['H'] = -4;
- match['G']['D'] = -1;
- match['G']['N'] = -2;
- match['C']['A'] = -4;
- match['C']['T'] = -4;
- match['C']['G'] = -4;
- match['C']['C'] = 5;
- match['C']['S'] = 1;
- match['C']['W'] = -4;
- match['C']['R'] = -4;
- match['C']['Y'] = 1;
- match['C']['K'] = -4;
- match['C']['M'] = 1;
- match['C']['B'] = -1;
- match['C']['V'] = -1;
- match['C']['H'] = -1;
- match['C']['D'] = -4;
- match['C']['N'] = -2;
- match['S']['A'] = -4;
- match['S']['T'] = -4;
- match['S']['G'] = 1;
- match['S']['C'] = 1;
- match['S']['S'] = -1;
- match['S']['W'] = -4;
- match['S']['R'] = -2;
- match['S']['Y'] = -2;
- match['S']['K'] = -2;
- match['S']['M'] = -2;
- match['S']['B'] = -1;
- match['S']['V'] = -1;
- match['S']['H'] = -3;
- match['S']['D'] = -3;
- match['S']['N'] = -1;
- match['W']['A'] = 1;
- match['W']['T'] = 1;
- match['W']['G'] = -4;
- match['W']['C'] = -4;
- match['W']['S'] = -4;
- match['W']['W'] = -1;
- match['W']['R'] = -2;
- match['W']['Y'] = -2;
- match['W']['K'] = -2;
- match['W']['M'] = -2;
- match['W']['B'] = -3;
- match['W']['V'] = -3;
- match['W']['H'] = -1;
- match['W']['D'] = -1;
- match['W']['N'] = -1;
- match['R']['A'] = 1;
- match['R']['T'] = -4;
- match['R']['G'] = 1;
- match['R']['C'] = -4;
- match['R']['S'] = -2;
- match['R']['W'] = -2;
- match['R']['R'] = -1;
- match['R']['Y'] = -4;
- match['R']['K'] = -2;
- match['R']['M'] = -2;
- match['R']['B'] = -3;
- match['R']['V'] = -1;
- match['R']['H'] = -3;
- match['R']['D'] = -1;
- match['R']['N'] = -1;
- match['Y']['A'] = -4;
- match['Y']['T'] = 1;
- match['Y']['G'] = -4;
- match['Y']['C'] = 1;
- match['Y']['S'] = -2;
- match['Y']['W'] = -2;
- match['Y']['R'] = -4;
- match['Y']['Y'] = -1;
- match['Y']['K'] = -2;
- match['Y']['M'] = -2;
- match['Y']['B'] = -1;
- match['Y']['V'] = -3;
- match['Y']['H'] = -1;
- match['Y']['D'] = -3;
- match['Y']['N'] = -1;
- match['K']['A'] = -4;
- match['K']['T'] = 1;
- match['K']['G'] = 1;
- match['K']['C'] = -4;
- match['K']['S'] = -2;
- match['K']['W'] = -2;
- match['K']['R'] = -2;
- match['K']['Y'] = -2;
- match['K']['K'] = -1;
- match['K']['M'] = -4;
- match['K']['B'] = -1;
- match['K']['V'] = -3;
- match['K']['H'] = -3;
- match['K']['D'] = -1;
- match['K']['N'] = -1;
- match['M']['A'] = 1;
- match['M']['T'] = -4;
- match['M']['G'] = -4;
- match['M']['C'] = 1;
- match['M']['S'] = -2;
- match['M']['W'] = -2;
- match['M']['R'] = -2;
- match['M']['Y'] = -2;
- match['M']['K'] = -4;
- match['M']['M'] = -1;
- match['M']['B'] = -3;
- match['M']['V'] = -1;
- match['M']['H'] = -1;
- match['M']['D'] = -3;
- match['M']['N'] = -1;
- match['B']['A'] = -4;
- match['B']['T'] = -1;
- match['B']['G'] = -1;
- match['B']['C'] = -1;
- match['B']['S'] = -1;
- match['B']['W'] = -3;
- match['B']['R'] = -3;
- match['B']['Y'] = -1;
- match['B']['K'] = -1;
- match['B']['M'] = -3;
- match['B']['B'] = -1;
- match['B']['V'] = -2;
- match['B']['H'] = -2;
- match['B']['D'] = -2;
- match['B']['N'] = -1;
- match['V']['A'] = -1;
- match['V']['T'] = -4;
- match['V']['G'] = -1;
- match['V']['C'] = -1;
- match['V']['S'] = -1;
- match['V']['W'] = -3;
- match['V']['R'] = -1;
- match['V']['Y'] = -3;
- match['V']['K'] = -3;
- match['V']['M'] = -1;
- match['V']['B'] = -2;
- match['V']['V'] = -1;
- match['V']['H'] = -2;
- match['V']['D'] = -2;
- match['V']['N'] = -1;
- match['H']['A'] = -1;
- match['H']['T'] = -1;
- match['H']['G'] = -4;
- match['H']['C'] = -1;
- match['H']['S'] = -3;
- match['H']['W'] = -1;
- match['H']['R'] = -3;
- match['H']['Y'] = -1;
- match['H']['K'] = -3;
- match['H']['M'] = -1;
- match['H']['B'] = -2;
- match['H']['V'] = -2;
- match['H']['H'] = -1;
- match['H']['D'] = -2;
- match['H']['N'] = -1;
- match['D']['A'] = -1;
- match['D']['T'] = -1;
- match['D']['G'] = -1;
- match['D']['C'] = -4;
- match['D']['S'] = -3;
- match['D']['W'] = -1;
- match['D']['R'] = -1;
- match['D']['Y'] = -3;
- match['D']['K'] = -1;
- match['D']['M'] = -3;
- match['D']['B'] = -2;
- match['D']['V'] = -2;
- match['D']['H'] = -2;
- match['D']['D'] = -1;
- match['D']['N'] = -1;
- match['N']['A'] = -2;
- match['N']['T'] = -2;
- match['N']['G'] = -2;
- match['N']['C'] = -2;
- match['N']['S'] = -1;
- match['N']['W'] = -1;
- match['N']['R'] = -1;
- match['N']['Y'] = -1;
- match['N']['K'] = -1;
- match['N']['M'] = -1;
- match['N']['B'] = -1;
- match['N']['V'] = -1;
- match['N']['H'] = -1;
- match['N']['D'] = -1;
- match['N']['N'] = -1;
-
- }
-
- /**
- * Initializes a BLOSUM45, BLOSUM62 or BLOSUM80 scoring matrix.
- *
- * Entries for the BLOSUM80 matrix at a scale of ln(2)/2.0.
- * Source https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM80
- *
- * Entries for the BLOSUM45 matrix at a scale of ln(2)/3.0.
- * Source https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM45
- * @param number 45, 62 or 80
- */
- public static void initialize_BLOSUM_matrix(int number) {
- if (number != 45 && number != 62 && number != 80){
- System.out.println("BLOSUM value must be 45, 62 or 80.");
- System.exit(1);
- }
- match = new int[256][256];
- if (number == 62) {
- match['A']['A'] = 4;
- match['A']['R'] = -1;
- match['A']['N'] = -2;
- match['A']['D'] = -2;
- match['A']['C'] = 0;
- match['A']['Q'] = -1;
- match['A']['E'] = -1;
- match['A']['G'] = 0;
- match['A']['H'] = -2;
- match['A']['I'] = -1;
- match['A']['L'] = -1;
- match['A']['K'] = -1;
- match['A']['M'] = -1;
- match['A']['F'] = -2;
- match['A']['P'] = -1;
- match['A']['S'] = 1;
- match['A']['T'] = 0;
- match['A']['W'] = -3;
- match['A']['Y'] = -2;
- match['A']['V'] = 0;
- match['A']['B'] = -2;
- match['A']['Z'] = -1;
- match['A']['X'] = 0;
- match['A']['*'] = -4;
-
- match['R']['A'] = -1;
- match['R']['R'] = 5;
- match['R']['N'] = 0;
- match['R']['D'] = -2;
- match['R']['C'] = -3;
- match['R']['Q'] = 1;
- match['R']['E'] = 0;
- match['R']['G'] = -2;
- match['R']['H'] = 0;
- match['R']['I'] = -3;
- match['R']['L'] = -2;
- match['R']['K'] = 2;
- match['R']['M'] = -1;
- match['R']['F'] = -3;
- match['R']['P'] = -2;
- match['R']['S'] = -1;
- match['R']['T'] = -1;
- match['R']['W'] = -3;
- match['R']['Y'] = -2;
- match['R']['V'] = -3;
- match['R']['B'] = -1;
- match['R']['Z'] = 0;
- match['R']['X'] = -1;
- match['R']['*'] = -4;
-
- match['N']['A'] = -2;
- match['N']['R'] = 0;
- match['N']['N'] = 6;
- match['N']['D'] = 1;
- match['N']['C'] = -3;
- match['N']['Q'] = 0;
- match['N']['E'] = 0;
- match['N']['G'] = 0;
- match['N']['H'] = 1;
- match['N']['I'] = -3;
- match['N']['L'] = -3;
- match['N']['K'] = 0;
- match['N']['M'] = -2;
- match['N']['F'] = -3;
- match['N']['P'] = -2;
- match['N']['S'] = 1;
- match['N']['T'] = 0;
- match['N']['W'] = -4;
- match['N']['Y'] = -2;
- match['N']['V'] = -3;
- match['N']['B'] = 3;
- match['N']['Z'] = 0;
- match['N']['X'] = -1;
- match['N']['*'] = -4;
-
- match['D']['A'] = -2;
- match['D']['R'] = -2;
- match['D']['N'] = 1;
- match['D']['D'] = 6;
- match['D']['C'] = -3;
- match['D']['Q'] = 0;
- match['D']['E'] = 2;
- match['D']['G'] = -1;
- match['D']['H'] = -1;
- match['D']['I'] = -3;
- match['D']['L'] = -4;
- match['D']['K'] = -1;
- match['D']['M'] = -3;
- match['D']['F'] = -3;
- match['D']['P'] = -1;
- match['D']['S'] = 0;
- match['D']['T'] = -1;
- match['D']['W'] = -4;
- match['D']['Y'] = -3;
- match['D']['V'] = -3;
- match['D']['B'] = 4;
- match['D']['Z'] = 1;
- match['D']['X'] = -1;
- match['D']['*'] = -4;
-
- match['C']['A'] = 0;
- match['C']['R'] = -3;
- match['C']['N'] = -3;
- match['C']['D'] = -3;
- match['C']['C'] = 9;
- match['C']['Q'] = -3;
- match['C']['E'] = -4;
- match['C']['G'] = -3;
- match['C']['H'] = -3;
- match['C']['I'] = -1;
- match['C']['L'] = -1;
- match['C']['K'] = -3;
- match['C']['M'] = -1;
- match['C']['F'] = -2;
- match['C']['P'] = -3;
- match['C']['S'] = -1;
- match['C']['T'] = -1;
- match['C']['W'] = -2;
- match['C']['Y'] = -2;
- match['C']['V'] = -1;
- match['C']['B'] = -3;
- match['C']['Z'] = -3;
- match['C']['X'] = -2;
- match['C']['*'] = -4;
-
- match['Q']['A'] = -1;
- match['Q']['R'] = 1;
- match['Q']['N'] = 0;
- match['Q']['D'] = 0;
- match['Q']['C'] = -3;
- match['Q']['Q'] = 5;
- match['Q']['E'] = 2;
- match['Q']['G'] = -2;
- match['Q']['H'] = 0;
- match['Q']['I'] = -3;
- match['Q']['L'] = -2;
- match['Q']['K'] = 1;
- match['Q']['M'] = 0;
- match['Q']['F'] = -3;
- match['Q']['P'] = -1;
- match['Q']['S'] = 0;
- match['Q']['T'] = -1;
- match['Q']['W'] = -2;
- match['Q']['Y'] = -1;
- match['Q']['V'] = -2;
- match['Q']['B'] = 0;
- match['Q']['Z'] = 3;
- match['Q']['X'] = -1;
- match['Q']['*'] = -4;
-
- match['E']['A'] = -1;
- match['E']['R'] = 0;
- match['E']['N'] = 0;
- match['E']['D'] = 2;
- match['E']['C'] = -4;
- match['E']['Q'] = 2;
- match['E']['E'] = 5;
- match['E']['G'] = -2;
- match['E']['H'] = 0;
- match['E']['I'] = -3;
- match['E']['L'] = -3;
- match['E']['K'] = 1;
- match['E']['M'] = -2;
- match['E']['F'] = -3;
- match['E']['P'] = -1;
- match['E']['S'] = 0;
- match['E']['T'] = -1;
- match['E']['W'] = -3;
- match['E']['Y'] = -2;
- match['E']['V'] = -2;
- match['E']['B'] = 1;
- match['E']['Z'] = 4;
- match['E']['X'] = -1;
- match['E']['*'] = -4;
-
- match['G']['A'] = 0;
- match['G']['R'] = -2;
- match['G']['N'] = 0;
- match['G']['D'] = -1;
- match['G']['C'] = -3;
- match['G']['Q'] = -2;
- match['G']['E'] = -2;
- match['G']['G'] = 6;
- match['G']['H'] = -2;
- match['G']['I'] = -4;
- match['G']['L'] = -4;
- match['G']['K'] = -2;
- match['G']['M'] = -3;
- match['G']['F'] = -3;
- match['G']['P'] = -2;
- match['G']['S'] = 0;
- match['G']['T'] = -2;
- match['G']['W'] = -2;
- match['G']['Y'] = -3;
- match['G']['V'] = -3;
- match['G']['B'] = -1;
- match['G']['Z'] = -2;
- match['G']['X'] = -1;
- match['G']['*'] = -4;
-
- match['H']['A'] = -2;
- match['H']['R'] = 0;
- match['H']['N'] = 1;
- match['H']['D'] = -1;
- match['H']['C'] = -3;
- match['H']['Q'] = 0;
- match['H']['E'] = 0;
- match['H']['G'] = -2;
- match['H']['H'] = 8;
- match['H']['I'] = -3;
- match['H']['L'] = -3;
- match['H']['K'] = -1;
- match['H']['M'] = -2;
- match['H']['F'] = -1;
- match['H']['P'] = -2;
- match['H']['S'] = -1;
- match['H']['T'] = -2;
- match['H']['W'] = -2;
- match['H']['Y'] = 2;
- match['H']['V'] = -3;
- match['H']['B'] = 0;
- match['H']['Z'] = 0;
- match['H']['X'] = -1;
- match['H']['*'] = -4;
-
- match['I']['A'] = -1;
- match['I']['R'] = -3;
- match['I']['N'] = -3;
- match['I']['D'] = -3;
- match['I']['C'] = -1;
- match['I']['Q'] = -3;
- match['I']['E'] = -3;
- match['I']['G'] = -4;
- match['I']['H'] = -3;
- match['I']['I'] = 4;
- match['I']['L'] = 2;
- match['I']['K'] = -3;
- match['I']['M'] = 1;
- match['I']['F'] = 0;
- match['I']['P'] = -3;
- match['I']['S'] = -2;
- match['I']['T'] = -1;
- match['I']['W'] = -3;
- match['I']['Y'] = -1;
- match['I']['V'] = 3;
- match['I']['B'] = -3;
- match['I']['Z'] = -3;
- match['I']['X'] = -1;
- match['I']['*'] = -4;
-
- match['L']['A'] = -1;
- match['L']['R'] = -2;
- match['L']['N'] = -3;
- match['L']['D'] = -4;
- match['L']['C'] = -1;
- match['L']['Q'] = -2;
- match['L']['E'] = -3;
- match['L']['G'] = -4;
- match['L']['H'] = -3;
- match['L']['I'] = 2;
- match['L']['L'] = 4;
- match['L']['K'] = -2;
- match['L']['M'] = 2;
- match['L']['F'] = 0;
- match['L']['P'] = -3;
- match['L']['S'] = -2;
- match['L']['T'] = -1;
- match['L']['W'] = -2;
- match['L']['Y'] = -1;
- match['L']['V'] = 1;
- match['L']['B'] = -4;
- match['L']['Z'] = -3;
- match['L']['X'] = -1;
- match['L']['*'] = -4;
-
- match['K']['A'] = -1;
- match['K']['R'] = 2;
- match['K']['N'] = 0;
- match['K']['D'] = -1;
- match['K']['C'] = -3;
- match['K']['Q'] = 1;
- match['K']['E'] = 1;
- match['K']['G'] = -2;
- match['K']['H'] = -1;
- match['K']['I'] = -3;
- match['K']['L'] = -2;
- match['K']['K'] = 5;
- match['K']['M'] = -1;
- match['K']['F'] = -3;
- match['K']['P'] = -1;
- match['K']['S'] = 0;
- match['K']['T'] = -1;
- match['K']['W'] = -3;
- match['K']['Y'] = -2;
- match['K']['V'] = -2;
- match['K']['B'] = 0;
- match['K']['Z'] = 1;
- match['K']['X'] = -1;
- match['K']['*'] = -4;
-
- match['M']['A'] = -1;
- match['M']['R'] = -1;
- match['M']['N'] = -2;
- match['M']['D'] = -3;
- match['M']['C'] = -1;
- match['M']['Q'] = 0;
- match['M']['E'] = -2;
- match['M']['G'] = -3;
- match['M']['H'] = -2;
- match['M']['I'] = 1;
- match['M']['L'] = 2;
- match['M']['K'] = -1;
- match['M']['M'] = 5;
- match['M']['F'] = 0;
- match['M']['P'] = -2;
- match['M']['S'] = -1;
- match['M']['T'] = -1;
- match['M']['W'] = -1;
- match['M']['Y'] = -1;
- match['M']['V'] = 1;
- match['M']['B'] = -3;
- match['M']['Z'] = -1;
- match['M']['X'] = -1;
- match['M']['*'] = -4;
-
- match['F']['A'] = -2;
- match['F']['R'] = -3;
- match['F']['N'] = -3;
- match['F']['D'] = -3;
- match['F']['C'] = -2;
- match['F']['Q'] = -3;
- match['F']['E'] = -3;
- match['F']['G'] = -3;
- match['F']['H'] = -1;
- match['F']['I'] = 0;
- match['F']['L'] = 0;
- match['F']['K'] = -3;
- match['F']['M'] = 0;
- match['F']['F'] = 6;
- match['F']['P'] = -4;
- match['F']['S'] = -2;
- match['F']['T'] = -2;
- match['F']['W'] = 1;
- match['F']['Y'] = 3;
- match['F']['V'] = -1;
- match['F']['B'] = -3;
- match['F']['Z'] = -3;
- match['F']['X'] = -1;
- match['F']['*'] = -4;
-
- match['P']['A'] = -1;
- match['P']['R'] = -2;
- match['P']['N'] = -2;
- match['P']['D'] = -1;
- match['P']['C'] = -3;
- match['P']['Q'] = -1;
- match['P']['E'] = -1;
- match['P']['G'] = -2;
- match['P']['H'] = -2;
- match['P']['I'] = -3;
- match['P']['L'] = -3;
- match['P']['K'] = -1;
- match['P']['M'] = -2;
- match['P']['F'] = -4;
- match['P']['P'] = 7;
- match['P']['S'] = -1;
- match['P']['T'] = -1;
- match['P']['W'] = -4;
- match['P']['Y'] = -3;
- match['P']['V'] = -2;
- match['P']['B'] = -2;
- match['P']['Z'] = -1;
- match['P']['X'] = -2;
- match['P']['*'] = -4;
-
- match['S']['A'] = 1;
- match['S']['R'] = -1;
- match['S']['N'] = 1;
- match['S']['D'] = 0;
- match['S']['C'] = -1;
- match['S']['Q'] = 0;
- match['S']['E'] = 0;
- match['S']['G'] = 0;
- match['S']['H'] = -1;
- match['S']['I'] = -2;
- match['S']['L'] = -2;
- match['S']['K'] = 0;
- match['S']['M'] = -1;
- match['S']['F'] = -2;
- match['S']['P'] = -1;
- match['S']['S'] = 4;
- match['S']['T'] = 1;
- match['S']['W'] = -3;
- match['S']['Y'] = -2;
- match['S']['V'] = -2;
- match['S']['B'] = 0;
- match['S']['Z'] = 0;
- match['S']['X'] = 0;
- match['S']['*'] = -4;
-
- match['T']['A'] = 0;
- match['T']['R'] = -1;
- match['T']['N'] = 0;
- match['T']['D'] = -1;
- match['T']['C'] = -1;
- match['T']['Q'] = -1;
- match['T']['E'] = -1;
- match['T']['G'] = -2;
- match['T']['H'] = -2;
- match['T']['I'] = -1;
- match['T']['L'] = -1;
- match['T']['K'] = -1;
- match['T']['M'] = -1;
- match['T']['F'] = -2;
- match['T']['P'] = -1;
- match['T']['S'] = 1;
- match['T']['T'] = 5;
- match['T']['W'] = -2;
- match['T']['Y'] = -2;
- match['T']['V'] = 0;
- match['T']['B'] = -1;
- match['T']['Z'] = -1;
- match['T']['X'] = 0;
- match['T']['*'] = -4;
-
- match['W']['A'] = -3;
- match['W']['R'] = -3;
- match['W']['N'] = -4;
- match['W']['D'] = -4;
- match['W']['C'] = -2;
- match['W']['Q'] = -2;
- match['W']['E'] = -3;
- match['W']['G'] = -2;
- match['W']['H'] = -2;
- match['W']['I'] = -3;
- match['W']['L'] = -2;
- match['W']['K'] = -3;
- match['W']['M'] = -1;
- match['W']['F'] = 1;
- match['W']['P'] = -4;
- match['W']['S'] = -3;
- match['W']['T'] = -2;
- match['W']['W'] = 11;
- match['W']['Y'] = 2;
- match['W']['V'] = -3;
- match['W']['B'] = -4;
- match['W']['Z'] = -3;
- match['W']['X'] = -2;
- match['W']['*'] = -4;
-
- match['Y']['A'] = -2;
- match['Y']['R'] = -2;
- match['Y']['N'] = -2;
- match['Y']['D'] = -3;
- match['Y']['C'] = -2;
- match['Y']['Q'] = -1;
- match['Y']['E'] = -2;
- match['Y']['G'] = -3;
- match['Y']['H'] = 2;
- match['Y']['I'] = -1;
- match['Y']['L'] = -1;
- match['Y']['K'] = -2;
- match['Y']['M'] = -1;
- match['Y']['F'] = 3;
- match['Y']['P'] = -3;
- match['Y']['S'] = -2;
- match['Y']['T'] = -2;
- match['Y']['W'] = 2;
- match['Y']['Y'] = 7;
- match['Y']['V'] = -1;
- match['Y']['B'] = -3;
- match['Y']['Z'] = -2;
- match['Y']['X'] = -1;
- match['Y']['*'] = -4;
-
- match['V']['A'] = 0;
- match['V']['R'] = -3;
- match['V']['N'] = -3;
- match['V']['D'] = -3;
- match['V']['C'] = -1;
- match['V']['Q'] = -2;
- match['V']['E'] = -2;
- match['V']['G'] = -3;
- match['V']['H'] = -3;
- match['V']['I'] = 3;
- match['V']['L'] = 1;
- match['V']['K'] = -2;
- match['V']['M'] = 1;
- match['V']['F'] = -1;
- match['V']['P'] = -2;
- match['V']['S'] = -2;
- match['V']['T'] = 0;
- match['V']['W'] = -3;
- match['V']['Y'] = -1;
- match['V']['V'] = 4;
- match['V']['B'] = -3;
- match['V']['Z'] = -2;
- match['V']['X'] = -1;
- match['V']['*'] = -4;
-
- match['B']['A'] = -2;
- match['B']['R'] = -1;
- match['B']['N'] = 3;
- match['B']['D'] = 4;
- match['B']['C'] = -3;
- match['B']['Q'] = 0;
- match['B']['E'] = 1;
- match['B']['G'] = -1;
- match['B']['H'] = 0;
- match['B']['I'] = -3;
- match['B']['L'] = -4;
- match['B']['K'] = 0;
- match['B']['M'] = -3;
- match['B']['F'] = -3;
- match['B']['P'] = -2;
- match['B']['S'] = 0;
- match['B']['T'] = -1;
- match['B']['W'] = -4;
- match['B']['Y'] = -3;
- match['B']['V'] = -3;
- match['B']['B'] = 4;
- match['B']['Z'] = 1;
- match['B']['X'] = -1;
- match['B']['*'] = -4;
-
- match['Z']['A'] = -1;
- match['Z']['R'] = 0;
- match['Z']['N'] = 0;
- match['Z']['D'] = 1;
- match['Z']['C'] = -3;
- match['Z']['Q'] = 3;
- match['Z']['E'] = 4;
- match['Z']['G'] = -2;
- match['Z']['H'] = 0;
- match['Z']['I'] = -3;
- match['Z']['L'] = -3;
- match['Z']['K'] = 1;
- match['Z']['M'] = -1;
- match['Z']['F'] = -3;
- match['Z']['P'] = -1;
- match['Z']['S'] = 0;
- match['Z']['T'] = -1;
- match['Z']['W'] = -3;
- match['Z']['Y'] = -2;
- match['Z']['V'] = -2;
- match['Z']['B'] = 1;
- match['Z']['Z'] = 4;
- match['Z']['X'] = -1;
- match['Z']['*'] = -4;
-
- match['X']['A'] = 0;
- match['X']['R'] = -1;
- match['X']['N'] = -1;
- match['X']['D'] = -1;
- match['X']['C'] = -2;
- match['X']['Q'] = -1;
- match['X']['E'] = -1;
- match['X']['G'] = -1;
- match['X']['H'] = -1;
- match['X']['I'] = -1;
- match['X']['L'] = -1;
- match['X']['K'] = -1;
- match['X']['M'] = -1;
- match['X']['F'] = -1;
- match['X']['P'] = -2;
- match['X']['S'] = 0;
- match['X']['T'] = 0;
- match['X']['W'] = -2;
- match['X']['Y'] = -1;
- match['X']['V'] = -1;
- match['X']['B'] = -1;
- match['X']['Z'] = -1;
- match['X']['X'] = -1;
- match['X']['*'] = -4;
-
- match['*']['A'] = -4;
- match['*']['R'] = -4;
- match['*']['N'] = -4;
- match['*']['D'] = -4;
- match['*']['C'] = -4;
- match['*']['Q'] = -4;
- match['*']['E'] = -4;
- match['*']['G'] = -4;
- match['*']['H'] = -4;
- match['*']['I'] = -4;
- match['*']['L'] = -4;
- match['*']['K'] = -4;
- match['*']['M'] = -4;
- match['*']['F'] = -4;
- match['*']['P'] = -4;
- match['*']['S'] = -4;
- match['*']['T'] = -4;
- match['*']['W'] = -4;
- match['*']['Y'] = -4;
- match['*']['V'] = -4;
- match['*']['B'] = -4;
- match['*']['Z'] = -4;
- match['*']['X'] = -4;
- match['*']['*'] = 1;
- }
-
- if (number == 80) {
- match['A']['A'] = 5;
- match['A']['R'] = -2;
- match['A']['N'] = -2;
- match['A']['D'] = -2;
- match['A']['C'] = -1;
- match['A']['Q'] = -1;
- match['A']['E'] = -1;
- match['A']['G'] = 0;
- match['A']['H'] = -2;
- match['A']['I'] = -2;
- match['A']['L'] = -2;
- match['A']['K'] = -1;
- match['A']['M'] = -1;
- match['A']['F'] = -3;
- match['A']['P'] = -1;
- match['A']['S'] = 1;
- match['A']['T'] = 0;
- match['A']['W'] = -3;
- match['A']['Y'] = -2;
- match['A']['V'] = 0;
- match['A']['B'] = -2;
- match['A']['J'] = -2;
- match['A']['Z'] = -1;
- match['A']['X'] = -1;
- match['A']['*'] = -6;
-
- match['R']['A'] = -2;
- match['R']['R'] = 6;
- match['R']['N'] = -1;
- match['R']['D'] = -2;
- match['R']['C'] = -4;
- match['R']['Q'] = 1;
- match['R']['E'] = -1;
- match['R']['G'] = -3;
- match['R']['H'] = 0;
- match['R']['I'] = -3;
- match['R']['L'] = -3;
- match['R']['K'] = 2;
- match['R']['M'] = -2;
- match['R']['F'] = -4;
- match['R']['P'] = -2;
- match['R']['S'] = -1;
- match['R']['T'] = -1;
- match['R']['W'] = -4;
- match['R']['Y'] = -3;
- match['R']['V'] = -3;
- match['R']['B'] = -1;
- match['R']['J'] = -3;
- match['R']['Z'] = 0;
- match['R']['X'] = -1;
- match['R']['*'] = -6;
-
- match['N']['A'] = -2;
- match['N']['R'] = -1;
- match['N']['N'] = 6;
- match['N']['D'] = 1;
- match['N']['C'] = -3;
- match['N']['Q'] = 0;
- match['N']['E'] = -1;
- match['N']['G'] = -1;
- match['N']['H'] = 0;
- match['N']['I'] = -4;
- match['N']['L'] = -4;
- match['N']['K'] = 0;
- match['N']['M'] = -3;
- match['N']['F'] = -4;
- match['N']['P'] = -3;
- match['N']['S'] = 0;
- match['N']['T'] = 0;
- match['N']['W'] = -4;
- match['N']['Y'] = -3;
- match['N']['V'] = -4;
- match['N']['B'] = 5;
- match['N']['J'] = -4;
- match['N']['Z'] = 0;
- match['N']['X'] = -1;
- match['N']['*'] = -6;
-
- match['D']['A'] = -2;
- match['D']['R'] = -2;
- match['D']['N'] = 1;
- match['D']['D'] = 6;
- match['D']['C'] = -4;
- match['D']['Q'] = -1;
- match['D']['E'] = 1;
- match['D']['G'] = -2;
- match['D']['H'] = -2;
- match['D']['I'] = -4;
- match['D']['L'] = -5;
- match['D']['K'] = -1;
- match['D']['M'] = -4;
- match['D']['F'] = -4;
- match['D']['P'] = -2;
- match['D']['S'] = -1;
- match['D']['T'] = -1;
- match['D']['W'] = -6;
- match['D']['Y'] = -4;
- match['D']['V'] = -4;
- match['D']['B'] = 5;
- match['D']['J'] = -5;
- match['D']['Z'] = 1;
- match['D']['X'] = -1;
- match['D']['*'] = -6;
-
- match['C']['A'] = -1;
- match['C']['R'] = -4;
- match['C']['N'] = -3;
- match['C']['D'] = -4;
- match['C']['C'] = 9;
- match['C']['Q'] = -4;
- match['C']['E'] = -5;
- match['C']['G'] = -4;
- match['C']['H'] = -4;
- match['C']['I'] = -2;
- match['C']['L'] = -2;
- match['C']['K'] = -4;
- match['C']['M'] = -2;
- match['C']['F'] = -3;
- match['C']['P'] = -4;
- match['C']['S'] = -2;
- match['C']['T'] = -1;
- match['C']['W'] = -3;
- match['C']['Y'] = -3 ;
- match['C']['V'] = -1;
- match['C']['B'] = -4;
- match['C']['J'] = -2 ;
- match['C']['Z'] = -4;
- match['C']['X'] = -1;
- match['C']['*'] = -6;
-
- match['Q']['A'] = -1;
- match['Q']['R'] = 1;
- match['Q']['N'] = 0;
- match['Q']['D'] = -1;
- match['Q']['C'] = -4;
- match['Q']['Q'] = 6;
- match['Q']['E'] = 2;
- match['Q']['G'] = -2;
- match['Q']['H'] = 1;
- match['Q']['I'] = -3;
- match['Q']['L'] = -3;
- match['Q']['K'] = 1;
- match['Q']['M'] = 0;
- match['Q']['F'] = -4;
- match['Q']['P'] = -2;
- match['Q']['S'] = 0;
- match['Q']['T'] = -1;
- match['Q']['W'] = -3;
- match['Q']['Y'] = -2;
- match['Q']['V'] = -3;
- match['Q']['B'] = 0;
- match['Q']['J'] = -3;
- match['Q']['Z'] = 4;
- match['Q']['X'] = -1;
- match['Q']['*'] = -6;
-
- match['E']['A'] = -1;
- match['E']['R'] = -1;
- match['E']['N'] = -1;
- match['E']['D'] = 1;
- match['E']['C'] = -5;
- match['E']['Q'] = 2;
- match['E']['E'] = 6;
- match['E']['G'] = -3;
- match['E']['H'] = 0;
- match['E']['I'] = -4;
- match['E']['L'] = -4;
- match['E']['K'] = 1;
- match['E']['M'] = -2;
- match['E']['F'] = -4;
- match['E']['P'] = -2;
- match['E']['S'] = 0;
- match['E']['T'] = -1;
- match['E']['W'] = -4 ;
- match['E']['Y'] = -3;
- match['E']['V'] = -3;
- match['E']['B'] = 1;
- match['E']['J'] = -4;
- match['E']['Z'] = 5;
- match['E']['X'] = -1;
- match['E']['*'] = -6;
-
- match['G']['A'] = 0;
- match['G']['R'] = -3;
- match['G']['N'] = -1;
- match['G']['D'] = -2;
- match['G']['C'] = -4;
- match['G']['Q'] = -2;
- match['G']['E'] = -3;
- match['G']['G'] = 6;
- match['G']['H'] = -3;
- match['G']['I'] = -5;
- match['G']['L'] = -4;
- match['G']['K'] = -2;
- match['G']['M'] = -4;
- match['G']['F'] = -4;
- match['G']['P'] = -3;
- match['G']['S'] = -1;
- match['G']['T'] = -2;
- match['G']['W'] = -4;
- match['G']['Y'] = -4;
- match['G']['V'] = -4;
- match['G']['B'] = -1;
- match['G']['J'] = -5;
- match['G']['Z'] = -3;
- match['G']['X'] = -1;
- match['G']['*'] = -6;
-
- match['H']['A'] = -2;
- match['H']['R'] = 0;
- match['H']['N'] = 0;
- match['H']['D'] = -2;
- match['H']['C'] = -4;
- match['H']['Q'] = 1;
- match['H']['E'] = 0;
- match['H']['G'] = -3;
- match['H']['H'] = 8;
- match['H']['I'] = -4;
- match['H']['L'] = -3;
- match['H']['K'] = -1;
- match['H']['M'] = -2;
- match['H']['F'] = -2;
- match['H']['P'] = -3;
- match['H']['S'] = -1;
- match['H']['T'] = -2;
- match['H']['W'] = -3;
- match['H']['Y'] = 2;
- match['H']['V'] = -4;
- match['H']['B'] = -1;
- match['H']['J'] = -4;
- match['H']['Z'] = 0;
- match['H']['X'] = -1;
- match['H']['*'] = -6;
-
- match['I']['A'] = -2;
- match['I']['R'] = -3;
- match['I']['N'] = -4;
- match['I']['D'] = -4;
- match['I']['C'] = -2;
- match['I']['Q'] = -3;
- match['I']['E'] = -4;
- match['I']['G'] = -5;
- match['I']['H'] = -4;
- match['I']['I'] = 5;
- match['I']['L'] = 1;
- match['I']['K'] = -3;
- match['I']['M'] = 1;
- match['I']['F'] = -1;
- match['I']['P'] = -4;
- match['I']['S'] = -3;
- match['I']['T'] = -1;
- match['I']['W'] = -3;
- match['I']['Y'] = -2;
- match['I']['V'] = 3;
- match['I']['B'] = -4;
- match['I']['J'] = 3;
- match['I']['Z'] = -4;
- match['I']['X'] = -1;
- match['I']['*'] = -6;
-
- match['L']['A'] = -2;
- match['L']['R'] = -3;
- match['L']['N'] = -4;
- match['L']['D'] = -5;
- match['L']['C'] = -2;
- match['L']['Q'] = -3;
- match['L']['E'] = -4;
- match['L']['G'] = -4;
- match['L']['H'] = -3;
- match['L']['I'] = 1;
- match['L']['L'] = 4;
- match['L']['K'] = -3;
- match['L']['M'] = 2;
- match['L']['F'] = 0;
- match['L']['P'] = -3;
- match['L']['S'] = -3;
- match['L']['T'] = -2;
- match['L']['W'] = -2;
- match['L']['Y'] = -2;
- match['L']['V'] = 1;
- match['L']['B'] = -4;
- match['L']['J'] = 3;
- match['L']['Z'] = -3;
- match['L']['X'] = -1;
- match['L']['*'] = -6;
-
- match['K']['A'] = -1;
- match['K']['R'] = 2;
- match['K']['N'] = 0;
- match['K']['D'] = -1;
- match['K']['C'] = -4;
- match['K']['Q'] = 1;
- match['K']['E'] = 1;
- match['K']['G'] = -2;
- match['K']['H'] = -1;
- match['K']['I'] = -3;
- match['K']['L'] = -3;
- match['K']['K'] = 5;
- match['K']['M'] = -2;
- match['K']['F'] = -4;
- match['K']['P'] = -1;
- match['K']['S'] = -1;
- match['K']['T'] = -1;
- match['K']['W'] = -4;
- match['K']['Y'] = -3;
- match['K']['V'] = -3;
- match['K']['B'] = -1;
- match['K']['J'] = -3;
- match['K']['Z'] = 1;
- match['K']['X'] = -1;
- match['K']['*'] = -6;
-
- match['M']['A'] = -1;
- match['M']['R'] = -2;
- match['M']['N'] = -3;
- match['M']['D'] = -4;
- match['M']['C'] = -2;
- match['M']['Q'] = 0;
- match['M']['E'] = -2;
- match['M']['G'] = -4;
- match['M']['H'] = -2;
- match['M']['I'] = 1;
- match['M']['L'] = 2;
- match['M']['K'] = -2;
- match['M']['M'] = 6;
- match['M']['F'] = 0;
- match['M']['P'] = -3;
- match['M']['S'] = -2;
- match['M']['T'] = -1;
- match['M']['W'] = -2;
- match['M']['Y'] = -2;
- match['M']['V'] = 1;
- match['M']['B'] = -3;
- match['M']['J'] = 2;
- match['M']['Z'] = -1;
- match['M']['X'] = -1;
- match['M']['*'] = -6;
-
- match['F']['A'] = -3;
- match['F']['R'] = -4;
- match['F']['N'] = -4;
- match['F']['D'] = -4;
- match['F']['C'] = -3;
- match['F']['Q'] = -4;
- match['F']['E'] = -4;
- match['F']['G'] = -4;
- match['F']['H'] = -2;
- match['F']['I'] = -1;
- match['F']['L'] = 0;
- match['F']['K'] = -4;
- match['F']['M'] = 0;
- match['F']['F'] = 6;
- match['F']['P'] = -4;
- match['F']['S'] = -3;
- match['F']['T'] = -2;
- match['F']['W'] = 0;
- match['F']['Y'] = 3;
- match['F']['V'] = -1;
- match['F']['B'] = -4;
- match['F']['J'] = 0;
- match['F']['Z'] = -4;
- match['F']['X'] = -1;
- match['F']['*'] = -6;
-
- match['P']['A'] = -1;
- match['P']['R'] = -2;
- match['P']['N'] = -3;
- match['P']['D'] = -2;
- match['P']['C'] = -4 ;
- match['P']['Q'] = -2;
- match['P']['E'] = -2 ;
- match['P']['G'] = -3;
- match['P']['H'] = -3;
- match['P']['I'] = -4;
- match['P']['L'] = -3 ;
- match['P']['K'] = -1;
- match['P']['M'] = -3;
- match['P']['F'] = -4 ;
- match['P']['P'] = 8;
- match['P']['S'] = -1;
- match['P']['T'] = -2;
- match['P']['W'] = -5;
- match['P']['Y'] = -4;
- match['P']['V'] = -3;
- match['P']['B'] = -2;
- match['P']['J'] = -4;
- match['P']['Z'] = -2;
- match['P']['X'] = -1;
- match['P']['*'] = -6;
-
- match['S']['A'] = 1;
- match['S']['R'] = -1;
- match['S']['N'] = 0;
- match['S']['D'] = -1;
- match['S']['C'] = -2;
- match['S']['Q'] = 0;
- match['S']['E'] = 0;
- match['S']['G'] = -1;
- match['S']['H'] = -1;
- match['S']['I'] = -3;
- match['S']['L'] = -3;
- match['S']['K'] = -1;
- match['S']['M'] = -2;
- match['S']['F'] = -3;
- match['S']['P'] = -1;
- match['S']['S'] = 5;
- match['S']['T'] = 1;
- match['S']['W'] = -4;
- match['S']['Y'] = -2;
- match['S']['V'] = -2;
- match['S']['B'] = 0;
- match['S']['J'] = -3;
- match['S']['Z'] = 0;
- match['S']['X'] = -1;
- match['S']['*'] = -6;
-
- match['T']['A'] = 0;
- match['T']['R'] = -1;
- match['T']['N'] = 0;
- match['T']['D'] = -1;
- match['T']['C'] = -1;
- match['T']['Q'] = -1;
- match['T']['E'] = -1;
- match['T']['G'] = -2;
- match['T']['H'] = -2;
- match['T']['I'] = -1;
- match['T']['L'] = -2;
- match['T']['K'] = -1 ;
- match['T']['M'] = -1;
- match['T']['F'] = -2;
- match['T']['P'] = -2;
- match['T']['S'] = 1;
- match['T']['T'] = 5;
- match['T']['W'] = -4;
- match['T']['Y'] = -2;
- match['T']['V'] = 0;
- match['T']['B'] = -1;
- match['T']['J'] = -1;
- match['T']['Z'] = -1 ;
- match['T']['X'] = -1;
- match['T']['*'] = -6;
-
- match['W']['A'] = -3;
- match['W']['R'] = -4;
- match['W']['N'] = -4;
- match['W']['D'] = -6;
- match['W']['C'] = -3;
- match['W']['Q'] = -3;
- match['W']['E'] = -4;
- match['W']['G'] = -4;
- match['W']['H'] = -3;
- match['W']['I'] = -3;
- match['W']['L'] = -2;
- match['W']['K'] = -4;
- match['W']['M'] = -2 ;
- match['W']['F'] = 0;
- match['W']['P'] = -5;
- match['W']['S'] = -4;
- match['W']['T'] = -4;
- match['W']['W'] = 11;
- match['W']['Y'] = 2;
- match['W']['V'] = -3;
- match['W']['B'] = -5;
- match['W']['J'] = -3;
- match['W']['Z'] = -3;
- match['W']['X'] = -1;
- match['W']['*'] = -6;
-
- match['Y']['A'] = -2 ;
- match['Y']['R'] = -3;
- match['Y']['N'] = -3;
- match['Y']['D'] = -4;
- match['Y']['C'] = -3;
- match['Y']['Q'] = -2;
- match['Y']['E'] = -3;
- match['Y']['G'] = -4;
- match['Y']['H'] = 2;
- match['Y']['I'] = -2;
- match['Y']['L'] = -2;
- match['Y']['K'] = -3;
- match['Y']['M'] = -2;
- match['Y']['F'] = 3;
- match['Y']['P'] = -4;
- match['Y']['S'] = -2;
- match['Y']['T'] = -2;
- match['Y']['W'] = 2;
- match['Y']['Y'] = 7;
- match['Y']['V'] = -2;
- match['Y']['B'] = -3;
- match['Y']['J'] = -2;
- match['Y']['Z'] = -3;
- match['Y']['X'] = -1;
- match['Y']['*'] = -6;
-
- match['V']['A'] = 0;
- match['V']['R'] = -3;
- match['V']['N'] = -4;
- match['V']['D'] = -4;
- match['V']['C'] = -1;
- match['V']['Q'] = -3;
- match['V']['E'] = -3;
- match['V']['G'] = -4;
- match['V']['H'] = -4;
- match['V']['I'] = 3;
- match['V']['L'] = 1;
- match['V']['K'] = -3;
- match['V']['M'] = 1;
- match['V']['F'] = -1;
- match['V']['P'] = -3;
- match['V']['S'] = -2;
- match['V']['T'] = 0;
- match['V']['W'] = -3;
- match['V']['Y'] = -2;
- match['V']['V'] = 4;
- match['V']['B'] = -4;
- match['V']['J'] = 2;
- match['V']['Z'] = -3;
- match['V']['X'] = -1;
- match['V']['*'] = -6;
-
- match['B']['A'] = -2;
- match['B']['R'] = -1;
- match['B']['N'] = 5;
- match['B']['D'] = 5;
- match['B']['C'] = -4;
- match['B']['Q'] = 0;
- match['B']['E'] = 1;
- match['B']['G'] = -1;
- match['B']['H'] = -1;
- match['B']['I'] = -4;
- match['B']['L'] = -4;
- match['B']['K'] = -1 ;
- match['B']['M'] = -3;
- match['B']['F'] = -4;
- match['B']['P'] = -2;
- match['B']['S'] = 0;
- match['B']['T'] = -1;
- match['B']['W'] = -5 ;
- match['B']['Y'] = -3 ;
- match['B']['V'] = -4;
- match['B']['B'] = 5;
- match['B']['J'] = -4;
- match['B']['Z'] = 0;
- match['B']['X'] = -1;
- match['B']['*'] = -6;
-
- match['J']['A'] = -2;
- match['J']['R'] = -3;
- match['J']['N'] = -4 ;
- match['J']['D'] = -5;
- match['J']['C'] = -2;
- match['J']['Q'] = -3;
- match['J']['E'] = -4;
- match['J']['G'] = -5;
- match['J']['H'] = -4 ;
- match['J']['I'] = 3;
- match['J']['L'] = 3;
- match['J']['K'] = -3;
- match['J']['M'] = 2;
- match['J']['F'] = 0;
- match['J']['P'] = -4;
- match['J']['S'] = -3 ;
- match['J']['T'] = -1;
- match['J']['W'] = -3;
- match['J']['Y'] = -2;
- match['J']['V'] = 2;
- match['J']['B'] = -4;
- match['J']['J'] = 3;
- match['J']['Z'] = -3;
- match['J']['X'] = -1;
- match['J']['*'] = -6;
-
- match['Z']['A'] = -1;
- match['Z']['R'] = 0;
- match['Z']['N'] = 0;
- match['Z']['D'] = 1;
- match['Z']['C'] = -4;
- match['Z']['Q'] = 4;
- match['Z']['E'] = 5;
- match['Z']['G'] = -3;
- match['Z']['H'] = 0;
- match['Z']['I'] = -4;
- match['Z']['L'] = -3;
- match['Z']['K'] = 1;
- match['Z']['M'] = -1;
- match['Z']['F'] = -4;
- match['Z']['P'] = -2;
- match['Z']['S'] = 0;
- match['Z']['T'] = -1;
- match['Z']['W'] = -3;
- match['Z']['Y'] = -3;
- match['Z']['V'] = -3;
- match['Z']['B'] = 0;
- match['Z']['J'] = -3;
- match['Z']['Z'] = 5;
- match['Z']['X'] = -1;
- match['Z']['*'] = -6;
-
- match['X']['A'] = -1;
- match['X']['R'] = -1;
- match['X']['N'] = -1;
- match['X']['D'] = -1;
- match['X']['C'] = -1;
- match['X']['Q'] = -1;
- match['X']['E'] = -1;
- match['X']['G'] = -1;
- match['X']['H'] = -1;
- match['X']['I'] = -1;
- match['X']['L'] = -1;
- match['X']['K'] = -1;
- match['X']['M'] = -1;
- match['X']['F'] = -1;
- match['X']['P'] = -1;
- match['X']['S'] = -1;
- match['X']['T'] = -1;
- match['X']['W'] = -1;
- match['X']['Y'] = -1;
- match['X']['V'] = -1;
- match['X']['B'] = -1;
- match['X']['J'] = -1;
- match['X']['Z'] = -1;
- match['X']['X'] = -1;
- match['X']['*'] = -6;
-
- match['*']['A'] = -6;
- match['*']['R'] = -6;
- match['*']['N'] = -6;
- match['*']['D'] = -6;
- match['*']['C'] = -6;
- match['*']['Q'] = -6;
- match['*']['E'] = -6;
- match['*']['G'] = -6;
- match['*']['H'] = -6;
- match['*']['I'] = -6;
- match['*']['L'] = -6;
- match['*']['K'] = -6;
- match['*']['M'] = -6;
- match['*']['F'] = -6;
- match['*']['P'] = -6;
- match['*']['S'] = -6;
- match['*']['T'] = -6;
- match['*']['W'] = -6;
- match['*']['Y'] = -6;
- match['*']['V'] = -6;
- match['*']['B'] = -6;
- match['*']['J'] = -6;
- match['*']['Z'] = -6;
- match['*']['X'] = -6;
- match['*']['*'] = 1;
- }
-
- if (number == 45) {
- match['A']['A'] = 5;
- match['A']['R'] = -2;
- match['A']['N'] = -1;
- match['A']['D'] = -2;
- match['A']['C'] = -1;
- match['A']['Q'] = -1 ;
- match['A']['E'] = -1;
- match['A']['G'] = 0;
- match['A']['H'] = -2;
- match['A']['I'] = -1;
- match['A']['L'] = -1;
- match['A']['K'] = -1;
- match['A']['M'] = -1;
- match['A']['F'] = -2;
- match['A']['P'] = -1;
- match['A']['S'] = 1;
- match['A']['T'] = 0;
- match['A']['W'] = -2;
- match['A']['Y'] = -2;
- match['A']['V'] = 0;
- match['A']['B'] = -1;
- match['A']['J'] = -1;
- match['A']['Z'] = -1;
- match['A']['X'] = -1;
- match['A']['*'] = -5;
-
- match['R']['A'] = -2;
- match['R']['R'] = 7 ;
- match['R']['N'] = 0;
- match['R']['D'] = -1;
- match['R']['C'] = -3;
- match['R']['Q'] = 1;
- match['R']['E'] = 0;
- match['R']['G'] = -2;
- match['R']['H'] = 0;
- match['R']['I'] = -3;
- match['R']['L'] = -2;
- match['R']['K'] = 3;
- match['R']['M'] = -1;
- match['R']['F'] = -2;
- match['R']['P'] = -2;
- match['R']['S'] = -1;
- match['R']['T'] = -1;
- match['R']['W'] = -2;
- match['R']['Y'] = -1;
- match['R']['V'] = -2;
- match['R']['B'] = -1;
- match['R']['J'] = -3 ;
- match['R']['Z'] = 1;
- match['R']['X'] = -1;
- match['R']['*'] = -5;
-
- match['N']['A'] = -1;
- match['N']['R'] = 0;
- match['N']['N'] = 6;
- match['N']['D'] = 2;
- match['N']['C'] = -2;
- match['N']['Q'] = 0;
- match['N']['E'] = 0;
- match['N']['G'] = 0;
- match['N']['H'] = 1;
- match['N']['I'] = -2;
- match['N']['L'] = -3;
- match['N']['K'] = 0;
- match['N']['M'] = -2;
- match['N']['F'] = -2;
- match['N']['P'] = -2;
- match['N']['S'] = 1;
- match['N']['T'] = 0;
- match['N']['W'] = -4;
- match['N']['Y'] = -2;
- match['N']['V'] = -3;
- match['N']['B'] = 5;
- match['N']['J'] = -3;
- match['N']['Z'] = 0;
- match['N']['X'] = -1;
- match['N']['*'] = -5;
-
- match['D']['A'] = -2;
- match['D']['R'] = -1;
- match['D']['N'] = 2;
- match['D']['D'] = 7;
- match['D']['C'] = -3;
- match['D']['Q'] = 0;
- match['D']['E'] = 2;
- match['D']['G'] = -1;
- match['D']['H'] = 0;
- match['D']['I'] = -4;
- match['D']['L'] = -3;
- match['D']['K'] = 0;
- match['D']['M'] = -3;
- match['D']['F'] = -4;
- match['D']['P'] = -1;
- match['D']['S'] = 0;
- match['D']['T'] = -1;
- match['D']['W'] = -4;
- match['D']['Y'] = -2;
- match['D']['V'] = -3;
- match['D']['B'] = 6;
- match['D']['J'] = -3;
- match['D']['Z'] = 1;
- match['D']['X'] = -1;
- match['D']['*'] = -5;
-
- match['C']['A'] = -1 ;
- match['C']['R'] = -3;
- match['C']['N'] = -2;
- match['C']['D'] = -3;
- match['C']['C'] = 12;
- match['C']['Q'] = -3 ;
- match['C']['E'] = -3 ;
- match['C']['G'] = -3;
- match['C']['H'] = -3;
- match['C']['I'] = -3;
- match['C']['L'] = -2 ;
- match['C']['K'] = -3;
- match['C']['M'] = -2;
- match['C']['F'] = -2;
- match['C']['P'] = -4 ;
- match['C']['S'] = -1;
- match['C']['T'] = -1;
- match['C']['W'] = -5;
- match['C']['Y'] = -3;
- match['C']['V'] = -1;
- match['C']['B'] = -2;
- match['C']['J'] = -2;
- match['C']['Z'] = -3;
- match['C']['X'] = -1;
- match['C']['*'] = -5;
-
- match['Q']['A'] = -1 ;
- match['Q']['R'] = 1;
- match['Q']['N'] = 0;
- match['Q']['D'] = 0;
- match['Q']['C'] = -3;
- match['Q']['Q'] = 6;
- match['Q']['E'] = 2;
- match['Q']['G'] = -2;
- match['Q']['H'] = 1;
- match['Q']['I'] = -2;
- match['Q']['L'] = -2 ;
- match['Q']['K'] = 1 ;
- match['Q']['M'] = 0;
- match['Q']['F'] = -4;
- match['Q']['P'] = -1;
- match['Q']['S'] = 0;
- match['Q']['T'] = -1;
- match['Q']['W'] = -2;
- match['Q']['Y'] = -1;
- match['Q']['V'] = -3;
- match['Q']['B'] = 0;
- match['Q']['J'] = -2;
- match['Q']['Z'] = 4;
- match['Q']['X'] = -1;
- match['Q']['*'] = -5;
-
- match['E']['A'] = 1;
- match['E']['R'] = 0;
- match['E']['N'] = 0;
- match['E']['D'] = 2;
- match['E']['C'] = -3;
- match['E']['Q'] = 2;
- match['E']['E'] = 6;
- match['E']['G'] = -2;
- match['E']['H'] = 0 ;
- match['E']['I'] = -3;
- match['E']['L'] = -2;
- match['E']['K'] = 1;
- match['E']['M'] = -2;
- match['E']['F'] = -3;
- match['E']['P'] = 0;
- match['E']['S'] = 0;
- match['E']['T'] = -1;
- match['E']['W'] = -3;
- match['E']['Y'] = -2;
- match['E']['V'] = -3;
- match['E']['B'] = 1;
- match['E']['J'] = -3;
- match['E']['Z'] = 5;
- match['E']['X'] = -1;
- match['E']['*'] = -5;
-
- match['G']['A'] = 0;
- match['G']['R'] = -2;
- match['G']['N'] = 0;
- match['G']['D'] = -1;
- match['G']['C'] = -3;
- match['G']['Q'] = -2;
- match['G']['E'] = -2;
- match['G']['G'] = 7;
- match['G']['H'] = -2;
- match['G']['I'] = -4;
- match['G']['L'] = -3;
- match['G']['K'] = -2;
- match['G']['M'] = -2;
- match['G']['F'] = -3;
- match['G']['P'] = -2;
- match['G']['S'] = 0;
- match['G']['T'] = -2;
- match['G']['W'] = -2;
- match['G']['Y'] = -3;
- match['G']['V'] = -3;
- match['G']['B'] = -1;
- match['G']['J'] = -4;
- match['G']['Z'] = -2;
- match['G']['X'] = -1;
- match['G']['*'] = -5;
-
- match['H']['A'] = -2 ;
- match['H']['R'] = 0;
- match['H']['N'] = 1;
- match['H']['D'] = 0;
- match['H']['C'] = -3;
- match['H']['Q'] = 1;
- match['H']['E'] = 0;
- match['H']['G'] = -2;
- match['H']['H'] = 10;
- match['H']['I'] = -3;
- match['H']['L'] = -2;
- match['H']['K'] = -1;
- match['H']['M'] = 0;
- match['H']['F'] = -2;
- match['H']['P'] = -2;
- match['H']['S'] = -1;
- match['H']['T'] = -2;
- match['H']['W'] = -3;
- match['H']['Y'] = 2;
- match['H']['V'] = -3;
- match['H']['B'] = 0;
- match['H']['J'] = -2;
- match['H']['Z'] = 0;
- match['H']['X'] = -1;
- match['H']['*'] = -5;
-
- match['I']['A'] = -1;
- match['I']['R'] = -3;
- match['I']['N'] = -2;
- match['I']['D'] = -4 ;
- match['I']['C'] = -3;
- match['I']['Q'] = -2;
- match['I']['E'] = -3;
- match['I']['G'] = -4;
- match['I']['H'] = -3;
- match['I']['I'] = 5 ;
- match['I']['L'] = 2;
- match['I']['K'] = -3 ;
- match['I']['M'] = 2;
- match['I']['F'] = 0;
- match['I']['P'] = -2 ;
- match['I']['S'] = -2;
- match['I']['T'] = -1;
- match['I']['W'] = -2;
- match['I']['Y'] = 0;
- match['I']['V'] = 3;
- match['I']['B'] = -3;
- match['I']['J'] = 4;
- match['I']['Z'] = -3;
- match['I']['X'] = -1;
- match['I']['*'] = -5;
-
- match['L']['A'] = -1;
- match['L']['R'] = -2;
- match['L']['N'] = -3;
- match['L']['D'] = -3;
- match['L']['C'] = -2 ;
- match['L']['Q'] = -2;
- match['L']['E'] = -2;
- match['L']['G'] = -3 ;
- match['L']['H'] = -2;
- match['L']['I'] = 2;
- match['L']['L'] = 5 ;
- match['L']['K'] = -3;
- match['L']['M'] = 2;
- match['L']['F'] = 1;
- match['L']['P'] = -3;
- match['L']['S'] = -3;
- match['L']['T'] = -1;
- match['L']['W'] = -2 ;
- match['L']['Y'] = 0;
- match['L']['V'] = 1;
- match['L']['B'] = -3;
- match['L']['J'] = 4;
- match['L']['Z'] = -2;
- match['L']['X'] = -1;
- match['L']['*'] = -5;
-
- match['K']['A'] = -1;
- match['K']['R'] = 3;
- match['K']['N'] = 0 ;
- match['K']['D'] = 0;
- match['K']['C'] = -3 ;
- match['K']['Q'] = 1;
- match['K']['E'] = 1;
- match['K']['G'] = -2;
- match['K']['H'] = -1 ;
- match['K']['I'] = -3;
- match['K']['L'] = -3;
- match['K']['K'] = 5;
- match['K']['M'] =-1;
- match['K']['F'] = -3 ;
- match['K']['P'] = -1 ;
- match['K']['S'] = -1;
- match['K']['T'] = -1;
- match['K']['W'] = -2 ;
- match['K']['Y'] = -1;
- match['K']['V'] = -2;
- match['K']['B'] = 0;
- match['K']['J'] = -3;
- match['K']['Z'] = 1;
- match['K']['X'] = -1;
- match['K']['*'] = -5;
-
- match['M']['A'] = -1;
- match['M']['R'] = -1;
- match['M']['N'] = -2 ;
- match['M']['D'] = -3;
- match['M']['C'] = -2;
- match['M']['Q'] = 0;
- match['M']['E'] = -2;
- match['M']['G'] = -2;
- match['M']['H'] = 0;
- match['M']['I'] = 2;
- match['M']['L'] = 2;
- match['M']['K'] = -1 ;
- match['M']['M'] = 6;
- match['M']['F'] = 0;
- match['M']['P'] = -2;
- match['M']['S'] = -2;
- match['M']['T'] = -1;
- match['M']['W'] = -2;
- match['M']['Y'] = 0;
- match['M']['V'] = 1;
- match['M']['B'] = -2;
- match['M']['J'] = 2;
- match['M']['Z'] = -1;
- match['M']['X'] = -1;
- match['M']['*'] = -5;
-
- match['F']['A'] = -2;
- match['F']['R'] = -2;
- match['F']['N'] = -2;
- match['F']['D'] = -4;
- match['F']['C'] = -2;
- match['F']['Q'] = -4;
- match['F']['E'] = -3;
- match['F']['G'] = -3;
- match['F']['H'] = -2;
- match['F']['I'] = 0;
- match['F']['L'] = 1;
- match['F']['K'] = -3;
- match['F']['M'] = 0;
- match['F']['F'] = 8;
- match['F']['P'] = -3;
- match['F']['S'] = -2;
- match['F']['T'] = -1;
- match['F']['W'] = 1;
- match['F']['Y'] = 3;
- match['F']['V'] = 0;
- match['F']['B'] = -3;
- match['F']['J'] = 1;
- match['F']['Z'] = -3;
- match['F']['X'] = -1;
- match['F']['*'] = -5;
-
- match['P']['A'] = -1;
- match['P']['R'] = -2;
- match['P']['N'] = -2 ;
- match['P']['D'] = -1;
- match['P']['C'] = -4 ;
- match['P']['Q'] = -1;
- match['P']['E'] = 0;
- match['P']['G'] = -2;
- match['P']['H'] = -2;
- match['P']['I'] = -2;
- match['P']['L'] = -3;
- match['P']['K'] = -1;
- match['P']['M'] = -2;
- match['P']['F'] = -3;
- match['P']['P'] = 9;
- match['P']['S'] = -1;
- match['P']['T'] = -1;
- match['P']['W'] = -3;
- match['P']['Y'] = -3;
- match['P']['V'] = -3;
- match['P']['B'] = -2;
- match['P']['J'] = -3;
- match['P']['Z'] = -1;
- match['P']['X'] = -1;
- match['P']['*'] = -5;
-
- match['S']['A'] = 1;
- match['S']['R'] = -1;
- match['S']['N'] = 1;
- match['S']['D'] = 0;
- match['S']['C'] = -1;
- match['S']['Q'] = 0;
- match['S']['E'] = 0;
- match['S']['G'] = 0;
- match['S']['H'] = -1;
- match['S']['I'] = -2;
- match['S']['L'] = -3;
- match['S']['K'] = -1;
- match['S']['M'] = -2;
- match['S']['F'] = -2 ;
- match['S']['P'] = -1;
- match['S']['S'] = 4;
- match['S']['T'] = 2;
- match['S']['W'] = -4;
- match['S']['Y'] = -2;
- match['S']['V'] = -1;
- match['S']['B'] = 0;
- match['S']['J'] = -2;
- match['S']['Z'] = 0;
- match['S']['X'] = -1;
- match['S']['*'] = -5;
-
- match['T']['A'] = 0;
- match['T']['R'] = -1;
- match['T']['N'] = 0;
- match['T']['D'] = -1;
- match['T']['C'] = -1;
- match['T']['Q'] = -1;
- match['T']['E'] = -1;
- match['T']['G'] = -2;
- match['T']['H'] = -2 ;
- match['T']['I'] = -1;
- match['T']['L'] = -1;
- match['T']['K'] = -1;
- match['T']['M'] = -1;
- match['T']['F'] = -1;
- match['T']['P'] = -1;
- match['T']['S'] = 2;
- match['T']['T'] = 5 ;
- match['T']['W'] = -3;
- match['T']['Y'] = -1;
- match['T']['V'] = 0;
- match['T']['B'] = 0;
- match['T']['J'] = -1;
- match['T']['Z'] = -1;
- match['T']['X'] = -1;
- match['T']['*'] = -5;
-
- match['W']['A'] = -2;
- match['W']['R'] = -2;
- match['W']['N'] = -4;
- match['W']['D'] = -4;
- match['W']['C'] = -5;
- match['W']['Q'] = -2;
- match['W']['E'] = -3;
- match['W']['G'] = -2;
- match['W']['H'] = -3;
- match['W']['I'] = -2;
- match['W']['L'] = -2;
- match['W']['K'] = -2;
- match['W']['M'] = -2;
- match['W']['F'] = 1;
- match['W']['P'] =-3 ;
- match['W']['S'] = -4;
- match['W']['T'] = -3;
- match['W']['W'] = 15;
- match['W']['Y'] = 3;
- match['W']['V'] = -3;
- match['W']['B'] = -4;
- match['W']['J'] = -2;
- match['W']['Z'] = -2;
- match['W']['X'] = -1;
- match['W']['*'] = -5;
-
- match['Y']['A'] = -2;
- match['Y']['R'] = -1;
- match['Y']['N'] = -2;
- match['Y']['D'] = -2;
- match['Y']['C'] = -3;
- match['Y']['Q'] = -1;
- match['Y']['E'] = -2;
- match['Y']['G'] = -3;
- match['Y']['H'] = 2;
- match['Y']['I'] = 0;
- match['Y']['L'] = 0;
- match['Y']['K'] = -1;
- match['Y']['M'] = 0;
- match['Y']['F'] = 3;
- match['Y']['P'] = -3;
- match['Y']['S'] = -2;
- match['Y']['T'] = -1;
- match['Y']['W'] = 3;
- match['Y']['Y'] = 8;
- match['Y']['V'] = -1;
- match['Y']['B'] = -2;
- match['Y']['J'] = 0;
- match['Y']['Z'] = -2;
- match['Y']['X'] = -1;
- match['Y']['*'] = -5;
-
- match['V']['A'] = 0;
- match['V']['R'] = -2;
- match['V']['N'] = -3;
- match['V']['D'] = -3;
- match['V']['C'] = -1;
- match['V']['Q'] = -3;
- match['V']['E'] = -3;
- match['V']['G'] = -3;
- match['V']['H'] = -3;
- match['V']['I'] = 3;
- match['V']['L'] = 1;
- match['V']['K'] = -2;
- match['V']['M'] = 1;
- match['V']['F'] = 0;
- match['V']['P'] = -3;
- match['V']['S'] = -1;
- match['V']['T'] = 0;
- match['V']['W'] = -3;
- match['V']['Y'] = -1;
- match['V']['V'] = 5;
- match['V']['B'] = -3;
- match['V']['J'] = 2;
- match['V']['Z'] = -3;
- match['V']['X'] = -1;
- match['V']['*'] = -5;
-
- match['B']['A'] = -1;
- match['B']['R'] = -1;
- match['B']['N'] = 5;
- match['B']['D'] = 6;
- match['B']['C'] = -2;
- match['B']['Q'] = 0;
- match['B']['E'] = 1;
- match['B']['G'] = -1;
- match['B']['H'] = 0;
- match['B']['I'] = -3;
- match['B']['L'] = -3;
- match['B']['K'] = 0;
- match['B']['M'] = -2;
- match['B']['F'] = -3;
- match['B']['P'] = -2;
- match['B']['S'] = 0;
- match['B']['T'] = 0;
- match['B']['W'] = -4;
- match['B']['Y'] = -2;
- match['B']['V'] = -3;
- match['B']['B'] = 5;
- match['B']['J'] = -3;
- match['B']['Z'] = 1;
- match['B']['X'] = -1;
- match['B']['*'] = -5;
-
- match['J']['A'] = -1;
- match['J']['R'] = -3;
- match['J']['N'] = -3;
- match['J']['D'] = -3;
- match['J']['C'] = -2;
- match['J']['Q'] = -2;
- match['J']['E'] = -3;
- match['J']['G'] = -4;
- match['J']['H'] = -2;
- match['J']['I'] = 4;
- match['J']['L'] = 4;
- match['J']['K'] = -3;
- match['J']['M'] = 2;
- match['J']['F'] = 1 ;
- match['J']['P'] = -3;
- match['J']['S'] = -2;
- match['J']['T'] = -1;
- match['J']['W'] = -2;
- match['J']['Y'] = 0;
- match['J']['V'] = 2 ;
- match['J']['B'] = -3 ;
- match['J']['J'] = 4;
- match['J']['Z'] = -2;
- match['J']['X'] = -1;
- match['J']['*'] = -5;
-
- match['Z']['A'] = -1;
- match['Z']['R'] = 1;
- match['Z']['N'] = 0;
- match['Z']['D'] = 1;
- match['Z']['C'] = -3;
- match['Z']['Q'] = 4;
- match['Z']['E'] = 5;
- match['Z']['G'] = -2;
- match['Z']['H'] = 0;
- match['Z']['I'] = -3;
- match['Z']['L'] = -2;
- match['Z']['K'] = 1;
- match['Z']['M'] = -1;
- match['Z']['F'] = -3;
- match['Z']['P'] = -1;
- match['Z']['S'] = 0;
- match['Z']['T'] = -1;
- match['Z']['W'] = -2 ;
- match['Z']['Y'] = -2;
- match['Z']['V'] = -3;
- match['Z']['B'] = 1;
- match['Z']['J'] = -2;
- match['Z']['Z'] = 5;
- match['Z']['X'] = -1;
- match['Z']['*'] = -5;
-
- match['X']['A'] = -1;
- match['X']['R'] = -1;
- match['X']['N'] = -1;
- match['X']['D'] = -1;
- match['X']['C'] = -1;
- match['X']['Q'] = -1;
- match['X']['E'] = -1;
- match['X']['G'] = -1;
- match['X']['H'] = -1;
- match['X']['I'] = -1;
- match['X']['L'] = -1;
- match['X']['K'] = -1;
- match['X']['M'] = -1;
- match['X']['F'] = -1;
- match['X']['P'] = -1;
- match['X']['S'] = -1;
- match['X']['T'] = -1 ;
- match['X']['W'] = -1;
- match['X']['Y'] = -1;
- match['X']['V'] = -1;
- match['X']['B'] = -1;
- match['X']['J'] = -1;
- match['X']['Z'] = -1;
- match['X']['X'] = -1;
- match['X']['*'] = -5;
-
- match['*']['A'] = -5;
- match['*']['R'] = -5;
- match['*']['N'] = -5;
- match['*']['D'] = -5;
- match['*']['C'] = -5;
- match['*']['Q'] = -5;
- match['*']['E'] = -5;
- match['*']['G'] = -5;
- match['*']['H'] = -5;
- match['*']['I'] = -5;
- match['*']['L'] = -5;
- match['*']['K'] = -5;
- match['*']['M'] = -5;
- match['*']['F'] = -5;
- match['*']['P'] = -5;
- match['*']['S'] = -5;
- match['*']['T'] = -5;
- match['*']['W'] = -5;
- match['*']['Y'] = -5;
- match['*']['V'] = -5;
- match['*']['B'] = -5;
- match['*']['J'] = -5;
- match['*']['Z'] = -5;
- match['*']['X'] = -5;
- match['*']['*'] = 1;
- }
- }
/**
* Fills the the similarity and direction matrixes of the two input sequences.
diff --git a/src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java
index b0925a587..ef0485f47 100755
--- a/src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java
+++ b/src/main/java/nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java
@@ -1,5 +1,7 @@
package nl.wur.bif.pantools.alignment;
+import nl.wur.bif.pantools.utils.FileUtils;
+
import java.util.Stack;
/**
@@ -30,7 +32,7 @@ public class LocalSequenceAlignment {
private int insertions;
private int similarity;
private double identity;
- private char TYPE;
+ private String TYPE;
private int offset;
private int range_len;
private int[] score_array;
@@ -47,7 +49,7 @@ public class LocalSequenceAlignment {
* @param clip The stringency of soft-clipping in the range [0..3]
* @param type Type of the input sequences(N for nucleotide P for peptide).
*/
- public LocalSequenceAlignment(int gap_open, int gap_ext, int max_length, int clip, char type) {
+ public LocalSequenceAlignment(int gap_open, int gap_ext, int max_length, int clip, String type) {
int i, j;
seq1 = new StringBuilder();
seq2 = new StringBuilder();
@@ -79,13 +81,8 @@ public class LocalSequenceAlignment {
left[0][j] = -1000;
matrix[0][j] = 0;
direction[0][j] = 'D';
- }
- if (TYPE == 'N')
- initialize_NUCC_matrix();
- else if (TYPE == 'P')
- initialize_BLOSUM_matrix();
- else
- System.out.println("Aligner type should be N or P");
+ }
+ match = FileUtils.loadScoringMatrix(TYPE);
switch (CLIPPING_STRIGENCY) {
case 1:
mismatch_penalty = -1;
@@ -101,869 +98,6 @@ public class LocalSequenceAlignment {
break;
}
}
-
- /**
- * Initializes the NUCC.1 scoring matrix.
- */
- public final void initialize_NUCC_matrix() {
- match = new int[256][256];
-
- match['A']['A'] = 5;
- match['A']['T'] = -4;
- match['A']['G'] = -4;
- match['A']['C'] = -4;
- match['A']['S'] = -4;
- match['A']['W'] = 1;
- match['A']['R'] = 1;
- match['A']['Y'] = -4;
- match['A']['K'] = -4;
- match['A']['M'] = 1;
- match['A']['B'] = -4;
- match['A']['V'] = -1;
- match['A']['H'] = -1;
- match['A']['D'] = -1;
- match['A']['N'] = -2;
- match['T']['A'] = -4;
- match['T']['T'] = 5;
- match['T']['G'] = -4;
- match['T']['C'] = -4;
- match['T']['S'] = -4;
- match['T']['W'] = 1;
- match['T']['R'] = -4;
- match['T']['Y'] = 1;
- match['T']['K'] = 1;
- match['T']['M'] = -4;
- match['T']['B'] = -1;
- match['T']['V'] = -4;
- match['T']['H'] = -1;
- match['T']['D'] = -1;
- match['T']['N'] = -2;
- match['G']['A'] = -4;
- match['G']['T'] = -4;
- match['G']['G'] = 5;
- match['G']['C'] = -4;
- match['G']['S'] = 1;
- match['G']['W'] = -4;
- match['G']['R'] = 1;
- match['G']['Y'] = -4;
- match['G']['K'] = 1;
- match['G']['M'] = -4;
- match['G']['B'] = -1;
- match['G']['V'] = -1;
- match['G']['H'] = -4;
- match['G']['D'] = -1;
- match['G']['N'] = -2;
- match['C']['A'] = -4;
- match['C']['T'] = -4;
- match['C']['G'] = -4;
- match['C']['C'] = 5;
- match['C']['S'] = 1;
- match['C']['W'] = -4;
- match['C']['R'] = -4;
- match['C']['Y'] = 1;
- match['C']['K'] = -4;
- match['C']['M'] = 1;
- match['C']['B'] = -1;
- match['C']['V'] = -1;
- match['C']['H'] = -1;
- match['C']['D'] = -4;
- match['C']['N'] = -2;
- match['S']['A'] = -4;
- match['S']['T'] = -4;
- match['S']['G'] = 1;
- match['S']['C'] = 1;
- match['S']['S'] = -1;
- match['S']['W'] = -4;
- match['S']['R'] = -2;
- match['S']['Y'] = -2;
- match['S']['K'] = -2;
- match['S']['M'] = -2;
- match['S']['B'] = -1;
- match['S']['V'] = -1;
- match['S']['H'] = -3;
- match['S']['D'] = -3;
- match['S']['N'] = -1;
- match['W']['A'] = 1;
- match['W']['T'] = 1;
- match['W']['G'] = -4;
- match['W']['C'] = -4;
- match['W']['S'] = -4;
- match['W']['W'] = -1;
- match['W']['R'] = -2;
- match['W']['Y'] = -2;
- match['W']['K'] = -2;
- match['W']['M'] = -2;
- match['W']['B'] = -3;
- match['W']['V'] = -3;
- match['W']['H'] = -1;
- match['W']['D'] = -1;
- match['W']['N'] = -1;
- match['R']['A'] = 1;
- match['R']['T'] = -4;
- match['R']['G'] = 1;
- match['R']['C'] = -4;
- match['R']['S'] = -2;
- match['R']['W'] = -2;
- match['R']['R'] = -1;
- match['R']['Y'] = -4;
- match['R']['K'] = -2;
- match['R']['M'] = -2;
- match['R']['B'] = -3;
- match['R']['V'] = -1;
- match['R']['H'] = -3;
- match['R']['D'] = -1;
- match['R']['N'] = -1;
- match['Y']['A'] = -4;
- match['Y']['T'] = 1;
- match['Y']['G'] = -4;
- match['Y']['C'] = 1;
- match['Y']['S'] = -2;
- match['Y']['W'] = -2;
- match['Y']['R'] = -4;
- match['Y']['Y'] = -1;
- match['Y']['K'] = -2;
- match['Y']['M'] = -2;
- match['Y']['B'] = -1;
- match['Y']['V'] = -3;
- match['Y']['H'] = -1;
- match['Y']['D'] = -3;
- match['Y']['N'] = -1;
- match['K']['A'] = -4;
- match['K']['T'] = 1;
- match['K']['G'] = 1;
- match['K']['C'] = -4;
- match['K']['S'] = -2;
- match['K']['W'] = -2;
- match['K']['R'] = -2;
- match['K']['Y'] = -2;
- match['K']['K'] = -1;
- match['K']['M'] = -4;
- match['K']['B'] = -1;
- match['K']['V'] = -3;
- match['K']['H'] = -3;
- match['K']['D'] = -1;
- match['K']['N'] = -1;
- match['M']['A'] = 1;
- match['M']['T'] = -4;
- match['M']['G'] = -4;
- match['M']['C'] = 1;
- match['M']['S'] = -2;
- match['M']['W'] = -2;
- match['M']['R'] = -2;
- match['M']['Y'] = -2;
- match['M']['K'] = -4;
- match['M']['M'] = -1;
- match['M']['B'] = -3;
- match['M']['V'] = -1;
- match['M']['H'] = -1;
- match['M']['D'] = -3;
- match['M']['N'] = -1;
- match['B']['A'] = -4;
- match['B']['T'] = -1;
- match['B']['G'] = -1;
- match['B']['C'] = -1;
- match['B']['S'] = -1;
- match['B']['W'] = -3;
- match['B']['R'] = -3;
- match['B']['Y'] = -1;
- match['B']['K'] = -1;
- match['B']['M'] = -3;
- match['B']['B'] = -1;
- match['B']['V'] = -2;
- match['B']['H'] = -2;
- match['B']['D'] = -2;
- match['B']['N'] = -1;
- match['V']['A'] = -1;
- match['V']['T'] = -4;
- match['V']['G'] = -1;
- match['V']['C'] = -1;
- match['V']['S'] = -1;
- match['V']['W'] = -3;
- match['V']['R'] = -1;
- match['V']['Y'] = -3;
- match['V']['K'] = -3;
- match['V']['M'] = -1;
- match['V']['B'] = -2;
- match['V']['V'] = -1;
- match['V']['H'] = -2;
- match['V']['D'] = -2;
- match['V']['N'] = -1;
- match['H']['A'] = -1;
- match['H']['T'] = -1;
- match['H']['G'] = -4;
- match['H']['C'] = -1;
- match['H']['S'] = -3;
- match['H']['W'] = -1;
- match['H']['R'] = -3;
- match['H']['Y'] = -1;
- match['H']['K'] = -3;
- match['H']['M'] = -1;
- match['H']['B'] = -2;
- match['H']['V'] = -2;
- match['H']['H'] = -1;
- match['H']['D'] = -2;
- match['H']['N'] = -1;
- match['D']['A'] = -1;
- match['D']['T'] = -1;
- match['D']['G'] = -1;
- match['D']['C'] = -4;
- match['D']['S'] = -3;
- match['D']['W'] = -1;
- match['D']['R'] = -1;
- match['D']['Y'] = -3;
- match['D']['K'] = -1;
- match['D']['M'] = -3;
- match['D']['B'] = -2;
- match['D']['V'] = -2;
- match['D']['H'] = -2;
- match['D']['D'] = -1;
- match['D']['N'] = -1;
- match['N']['A'] = -2;
- match['N']['T'] = -2;
- match['N']['G'] = -2;
- match['N']['C'] = -2;
- match['N']['S'] = -1;
- match['N']['W'] = -1;
- match['N']['R'] = -1;
- match['N']['Y'] = -1;
- match['N']['K'] = -1;
- match['N']['M'] = -1;
- match['N']['B'] = -1;
- match['N']['V'] = -1;
- match['N']['H'] = -1;
- match['N']['D'] = -1;
- match['N']['N'] = -1;
-
- }
-
- /**
- * Initializes the BLOSUM62 scoring matrix.
- */
- public final void initialize_BLOSUM_matrix() {
- match = new int[256][256];
- match['A']['A'] = 4;
- match['A']['R'] = -1;
- match['A']['N'] = -2;
- match['A']['D'] = -2;
- match['A']['C'] = 0;
- match['A']['Q'] = -1;
- match['A']['E'] = -1;
- match['A']['G'] = 0;
- match['A']['H'] = -2;
- match['A']['I'] = -1;
- match['A']['L'] = -1;
- match['A']['K'] = -1;
- match['A']['M'] = -1;
- match['A']['F'] = -2;
- match['A']['P'] = -1;
- match['A']['S'] = 1;
- match['A']['T'] = 0;
- match['A']['W'] = -3;
- match['A']['Y'] = -2;
- match['A']['V'] = 0;
- match['A']['B'] = -2;
- match['A']['Z'] = -1;
- match['A']['X'] = 0;
- match['A']['*'] = -4;
-
-
- match['R']['A'] = -1;
- match['R']['R'] = 5;
- match['R']['N'] = 0;
- match['R']['D'] = -2;
- match['R']['C'] = -3;
- match['R']['Q'] = 1;
- match['R']['E'] = 0;
- match['R']['G'] = -2;
- match['R']['H'] = 0;
- match['R']['I'] = -3;
- match['R']['L'] = -2;
- match['R']['K'] = 2;
- match['R']['M'] = -1;
- match['R']['F'] = -3;
- match['R']['P'] = -2;
- match['R']['S'] = -1;
- match['R']['T'] = -1;
- match['R']['W'] = -3;
- match['R']['Y'] = -2;
- match['R']['V'] = -3;
- match['R']['B'] = -1;
- match['R']['Z'] = 0;
- match['R']['X'] = -1;
- match['R']['*'] = -4;
-
-
- match['N']['A'] = -2;
- match['N']['R'] = 0;
- match['N']['N'] = 6;
- match['N']['D'] = 1;
- match['N']['C'] = -3;
- match['N']['Q'] = 0;
- match['N']['E'] = 0;
- match['N']['G'] = 0;
- match['N']['H'] = 1;
- match['N']['I'] = -3;
- match['N']['L'] = -3;
- match['N']['K'] = 0;
- match['N']['M'] = -2;
- match['N']['F'] = -3;
- match['N']['P'] = -2;
- match['N']['S'] = 1;
- match['N']['T'] = 0;
- match['N']['W'] = -4;
- match['N']['Y'] = -2;
- match['N']['V'] = -3;
- match['N']['B'] = 3;
- match['N']['Z'] = 0;
- match['N']['X'] = -1;
- match['N']['*'] = -4;
-
-
- match['D']['A'] = -2;
- match['D']['R'] = -2;
- match['D']['N'] = 1;
- match['D']['D'] = 6;
- match['D']['C'] = -3;
- match['D']['Q'] = 0;
- match['D']['E'] = 2;
- match['D']['G'] = -1;
- match['D']['H'] = -1;
- match['D']['I'] = -3;
- match['D']['L'] = -4;
- match['D']['K'] = -1;
- match['D']['M'] = -3;
- match['D']['F'] = -3;
- match['D']['P'] = -1;
- match['D']['S'] = 0;
- match['D']['T'] = -1;
- match['D']['W'] = -4;
- match['D']['Y'] = -3;
- match['D']['V'] = -3;
- match['D']['B'] = 4;
- match['D']['Z'] = 1;
- match['D']['X'] = -1;
- match['D']['*'] = -4;
-
-
- match['C']['A'] = 0;
- match['C']['R'] = -3;
- match['C']['N'] = -3;
- match['C']['D'] = -3;
- match['C']['C'] = 9;
- match['C']['Q'] = -3;
- match['C']['E'] = -4;
- match['C']['G'] = -3;
- match['C']['H'] = -3;
- match['C']['I'] = -1;
- match['C']['L'] = -1;
- match['C']['K'] = -3;
- match['C']['M'] = -1;
- match['C']['F'] = -2;
- match['C']['P'] = -3;
- match['C']['S'] = -1;
- match['C']['T'] = -1;
- match['C']['W'] = -2;
- match['C']['Y'] = -2;
- match['C']['V'] = -1;
- match['C']['B'] = -3;
- match['C']['Z'] = -3;
- match['C']['X'] = -2;
- match['C']['*'] = -4;
-
-
- match['Q']['A'] = -1;
- match['Q']['R'] = 1;
- match['Q']['N'] = 0;
- match['Q']['D'] = 0;
- match['Q']['C'] = -3;
- match['Q']['Q'] = 5;
- match['Q']['E'] = 2;
- match['Q']['G'] = -2;
- match['Q']['H'] = 0;
- match['Q']['I'] = -3;
- match['Q']['L'] = -2;
- match['Q']['K'] = 1;
- match['Q']['M'] = 0;
- match['Q']['F'] = -3;
- match['Q']['P'] = -1;
- match['Q']['S'] = 0;
- match['Q']['T'] = -1;
- match['Q']['W'] = -2;
- match['Q']['Y'] = -1;
- match['Q']['V'] = -2;
- match['Q']['B'] = 0;
- match['Q']['Z'] = 3;
- match['Q']['X'] = -1;
- match['Q']['*'] = -4;
-
-
- match['E']['A'] = -1;
- match['E']['R'] = 0;
- match['E']['N'] = 0;
- match['E']['D'] = 2;
- match['E']['C'] = -4;
- match['E']['Q'] = 2;
- match['E']['E'] = 5;
- match['E']['G'] = -2;
- match['E']['H'] = 0;
- match['E']['I'] = -3;
- match['E']['L'] = -3;
- match['E']['K'] = 1;
- match['E']['M'] = -2;
- match['E']['F'] = -3;
- match['E']['P'] = -1;
- match['E']['S'] = 0;
- match['E']['T'] = -1;
- match['E']['W'] = -3;
- match['E']['Y'] = -2;
- match['E']['V'] = -2;
- match['E']['B'] = 1;
- match['E']['Z'] = 4;
- match['E']['X'] = -1;
- match['E']['*'] = -4;
-
-
- match['G']['A'] = 0;
- match['G']['R'] = -2;
- match['G']['N'] = 0;
- match['G']['D'] = -1;
- match['G']['C'] = -3;
- match['G']['Q'] = -2;
- match['G']['E'] = -2;
- match['G']['G'] = 6;
- match['G']['H'] = -2;
- match['G']['I'] = -4;
- match['G']['L'] = -4;
- match['G']['K'] = -2;
- match['G']['M'] = -3;
- match['G']['F'] = -3;
- match['G']['P'] = -2;
- match['G']['S'] = 0;
- match['G']['T'] = -2;
- match['G']['W'] = -2;
- match['G']['Y'] = -3;
- match['G']['V'] = -3;
- match['G']['B'] = -1;
- match['G']['Z'] = -2;
- match['G']['X'] = -1;
- match['G']['*'] = -4;
-
-
- match['H']['A'] = -2;
- match['H']['R'] = 0;
- match['H']['N'] = 1;
- match['H']['D'] = -1;
- match['H']['C'] = -3;
- match['H']['Q'] = 0;
- match['H']['E'] = 0;
- match['H']['G'] = -2;
- match['H']['H'] = 8;
- match['H']['I'] = -3;
- match['H']['L'] = -3;
- match['H']['K'] = -1;
- match['H']['M'] = -2;
- match['H']['F'] = -1;
- match['H']['P'] = -2;
- match['H']['S'] = -1;
- match['H']['T'] = -2;
- match['H']['W'] = -2;
- match['H']['Y'] = 2;
- match['H']['V'] = -3;
- match['H']['B'] = 0;
- match['H']['Z'] = 0;
- match['H']['X'] = -1;
- match['H']['*'] = -4;
-
-
- match['I']['A'] = -1;
- match['I']['R'] = -3;
- match['I']['N'] = -3;
- match['I']['D'] = -3;
- match['I']['C'] = -1;
- match['I']['Q'] = -3;
- match['I']['E'] = -3;
- match['I']['G'] = -4;
- match['I']['H'] = -3;
- match['I']['I'] = 4;
- match['I']['L'] = 2;
- match['I']['K'] = -3;
- match['I']['M'] = 1;
- match['I']['F'] = 0;
- match['I']['P'] = -3;
- match['I']['S'] = -2;
- match['I']['T'] = -1;
- match['I']['W'] = -3;
- match['I']['Y'] = -1;
- match['I']['V'] = 3;
- match['I']['B'] = -3;
- match['I']['Z'] = -3;
- match['I']['X'] = -1;
- match['I']['*'] = -4;
-
-
- match['L']['A'] = -1;
- match['L']['R'] = -2;
- match['L']['N'] = -3;
- match['L']['D'] = -4;
- match['L']['C'] = -1;
- match['L']['Q'] = -2;
- match['L']['E'] = -3;
- match['L']['G'] = -4;
- match['L']['H'] = -3;
- match['L']['I'] = 2;
- match['L']['L'] = 4;
- match['L']['K'] = -2;
- match['L']['M'] = 2;
- match['L']['F'] = 0;
- match['L']['P'] = -3;
- match['L']['S'] = -2;
- match['L']['T'] = -1;
- match['L']['W'] = -2;
- match['L']['Y'] = -1;
- match['L']['V'] = 1;
- match['L']['B'] = -4;
- match['L']['Z'] = -3;
- match['L']['X'] = -1;
- match['L']['*'] = -4;
-
-
- match['K']['A'] = -1;
- match['K']['R'] = 2;
- match['K']['N'] = 0;
- match['K']['D'] = -1;
- match['K']['C'] = -3;
- match['K']['Q'] = 1;
- match['K']['E'] = 1;
- match['K']['G'] = -2;
- match['K']['H'] = -1;
- match['K']['I'] = -3;
- match['K']['L'] = -2;
- match['K']['K'] = 5;
- match['K']['M'] = -1;
- match['K']['F'] = -3;
- match['K']['P'] = -1;
- match['K']['S'] = 0;
- match['K']['T'] = -1;
- match['K']['W'] = -3;
- match['K']['Y'] = -2;
- match['K']['V'] = -2;
- match['K']['B'] = 0;
- match['K']['Z'] = 1;
- match['K']['X'] = -1;
- match['K']['*'] = -4;
-
-
- match['M']['A'] = -1;
- match['M']['R'] = -1;
- match['M']['N'] = -2;
- match['M']['D'] = -3;
- match['M']['C'] = -1;
- match['M']['Q'] = 0;
- match['M']['E'] = -2;
- match['M']['G'] = -3;
- match['M']['H'] = -2;
- match['M']['I'] = 1;
- match['M']['L'] = 2;
- match['M']['K'] = -1;
- match['M']['M'] = 5;
- match['M']['F'] = 0;
- match['M']['P'] = -2;
- match['M']['S'] = -1;
- match['M']['T'] = -1;
- match['M']['W'] = -1;
- match['M']['Y'] = -1;
- match['M']['V'] = 1;
- match['M']['B'] = -3;
- match['M']['Z'] = -1;
- match['M']['X'] = -1;
- match['M']['*'] = -4;
-
-
- match['F']['A'] = -2;
- match['F']['R'] = -3;
- match['F']['N'] = -3;
- match['F']['D'] = -3;
- match['F']['C'] = -2;
- match['F']['Q'] = -3;
- match['F']['E'] = -3;
- match['F']['G'] = -3;
- match['F']['H'] = -1;
- match['F']['I'] = 0;
- match['F']['L'] = 0;
- match['F']['K'] = -3;
- match['F']['M'] = 0;
- match['F']['F'] = 6;
- match['F']['P'] = -4;
- match['F']['S'] = -2;
- match['F']['T'] = -2;
- match['F']['W'] = 1;
- match['F']['Y'] = 3;
- match['F']['V'] = -1;
- match['F']['B'] = -3;
- match['F']['Z'] = -3;
- match['F']['X'] = -1;
- match['F']['*'] = -4;
-
-
- match['P']['A'] = -1;
- match['P']['R'] = -2;
- match['P']['N'] = -2;
- match['P']['D'] = -1;
- match['P']['C'] = -3;
- match['P']['Q'] = -1;
- match['P']['E'] = -1;
- match['P']['G'] = -2;
- match['P']['H'] = -2;
- match['P']['I'] = -3;
- match['P']['L'] = -3;
- match['P']['K'] = -1;
- match['P']['M'] = -2;
- match['P']['F'] = -4;
- match['P']['P'] = 7;
- match['P']['S'] = -1;
- match['P']['T'] = -1;
- match['P']['W'] = -4;
- match['P']['Y'] = -3;
- match['P']['V'] = -2;
- match['P']['B'] = -2;
- match['P']['Z'] = -1;
- match['P']['X'] = -2;
- match['P']['*'] = -4;
-
-
- match['S']['A'] = 1;
- match['S']['R'] = -1;
- match['S']['N'] = 1;
- match['S']['D'] = 0;
- match['S']['C'] = -1;
- match['S']['Q'] = 0;
- match['S']['E'] = 0;
- match['S']['G'] = 0;
- match['S']['H'] = -1;
- match['S']['I'] = -2;
- match['S']['L'] = -2;
- match['S']['K'] = 0;
- match['S']['M'] = -1;
- match['S']['F'] = -2;
- match['S']['P'] = -1;
- match['S']['S'] = 4;
- match['S']['T'] = 1;
- match['S']['W'] = -3;
- match['S']['Y'] = -2;
- match['S']['V'] = -2;
- match['S']['B'] = 0;
- match['S']['Z'] = 0;
- match['S']['X'] = 0;
- match['S']['*'] = -4;
-
-
- match['T']['A'] = 0;
- match['T']['R'] = -1;
- match['T']['N'] = 0;
- match['T']['D'] = -1;
- match['T']['C'] = -1;
- match['T']['Q'] = -1;
- match['T']['E'] = -1;
- match['T']['G'] = -2;
- match['T']['H'] = -2;
- match['T']['I'] = -1;
- match['T']['L'] = -1;
- match['T']['K'] = -1;
- match['T']['M'] = -1;
- match['T']['F'] = -2;
- match['T']['P'] = -1;
- match['T']['S'] = 1;
- match['T']['T'] = 5;
- match['T']['W'] = -2;
- match['T']['Y'] = -2;
- match['T']['V'] = 0;
- match['T']['B'] = -1;
- match['T']['Z'] = -1;
- match['T']['X'] = 0;
- match['T']['*'] = -4;
-
-
- match['W']['A'] = -3;
- match['W']['R'] = -3;
- match['W']['N'] = -4;
- match['W']['D'] = -4;
- match['W']['C'] = -2;
- match['W']['Q'] = -2;
- match['W']['E'] = -3;
- match['W']['G'] = -2;
- match['W']['H'] = -2;
- match['W']['I'] = -3;
- match['W']['L'] = -2;
- match['W']['K'] = -3;
- match['W']['M'] = -1;
- match['W']['F'] = 1;
- match['W']['P'] = -4;
- match['W']['S'] = -3;
- match['W']['T'] = -2;
- match['W']['W'] = 11;
- match['W']['Y'] = 2;
- match['W']['V'] = -3;
- match['W']['B'] = -4;
- match['W']['Z'] = -3;
- match['W']['X'] = -2;
- match['W']['*'] = -4;
-
-
- match['Y']['A'] = -2;
- match['Y']['R'] = -2;
- match['Y']['N'] = -2;
- match['Y']['D'] = -3;
- match['Y']['C'] = -2;
- match['Y']['Q'] = -1;
- match['Y']['E'] = -2;
- match['Y']['G'] = -3;
- match['Y']['H'] = 2;
- match['Y']['I'] = -1;
- match['Y']['L'] = -1;
- match['Y']['K'] = -2;
- match['Y']['M'] = -1;
- match['Y']['F'] = 3;
- match['Y']['P'] = -3;
- match['Y']['S'] = -2;
- match['Y']['T'] = -2;
- match['Y']['W'] = 2;
- match['Y']['Y'] = 7;
- match['Y']['V'] = -1;
- match['Y']['B'] = -3;
- match['Y']['Z'] = -2;
- match['Y']['X'] = -1;
- match['Y']['*'] = -4;
-
-
- match['V']['A'] = 0;
- match['V']['R'] = -3;
- match['V']['N'] = -3;
- match['V']['D'] = -3;
- match['V']['C'] = -1;
- match['V']['Q'] = -2;
- match['V']['E'] = -2;
- match['V']['G'] = -3;
- match['V']['H'] = -3;
- match['V']['I'] = 3;
- match['V']['L'] = 1;
- match['V']['K'] = -2;
- match['V']['M'] = 1;
- match['V']['F'] = -1;
- match['V']['P'] = -2;
- match['V']['S'] = -2;
- match['V']['T'] = 0;
- match['V']['W'] = -3;
- match['V']['Y'] = -1;
- match['V']['V'] = 4;
- match['V']['B'] = -3;
- match['V']['Z'] = -2;
- match['V']['X'] = -1;
- match['V']['*'] = -4;
-
-
- match['B']['A'] = -2;
- match['B']['R'] = -1;
- match['B']['N'] = 3;
- match['B']['D'] = 4;
- match['B']['C'] = -3;
- match['B']['Q'] = 0;
- match['B']['E'] = 1;
- match['B']['G'] = -1;
- match['B']['H'] = 0;
- match['B']['I'] = -3;
- match['B']['L'] = -4;
- match['B']['K'] = 0;
- match['B']['M'] = -3;
- match['B']['F'] = -3;
- match['B']['P'] = -2;
- match['B']['S'] = 0;
- match['B']['T'] = -1;
- match['B']['W'] = -4;
- match['B']['Y'] = -3;
- match['B']['V'] = -3;
- match['B']['B'] = 4;
- match['B']['Z'] = 1;
- match['B']['X'] = -1;
- match['B']['*'] = -4;
-
-
- match['Z']['A'] = -1;
- match['Z']['R'] = 0;
- match['Z']['N'] = 0;
- match['Z']['D'] = 1;
- match['Z']['C'] = -3;
- match['Z']['Q'] = 3;
- match['Z']['E'] = 4;
- match['Z']['G'] = -2;
- match['Z']['H'] = 0;
- match['Z']['I'] = -3;
- match['Z']['L'] = -3;
- match['Z']['K'] = 1;
- match['Z']['M'] = -1;
- match['Z']['F'] = -3;
- match['Z']['P'] = -1;
- match['Z']['S'] = 0;
- match['Z']['T'] = -1;
- match['Z']['W'] = -3;
- match['Z']['Y'] = -2;
- match['Z']['V'] = -2;
- match['Z']['B'] = 1;
- match['Z']['Z'] = 4;
- match['Z']['X'] = -1;
- match['Z']['*'] = -4;
-
-
- match['X']['A'] = 0;
- match['X']['R'] = -1;
- match['X']['N'] = -1;
- match['X']['D'] = -1;
- match['X']['C'] = -2;
- match['X']['Q'] = -1;
- match['X']['E'] = -1;
- match['X']['G'] = -1;
- match['X']['H'] = -1;
- match['X']['I'] = -1;
- match['X']['L'] = -1;
- match['X']['K'] = -1;
- match['X']['M'] = -1;
- match['X']['F'] = -1;
- match['X']['P'] = -2;
- match['X']['S'] = 0;
- match['X']['T'] = 0;
- match['X']['W'] = -2;
- match['X']['Y'] = -1;
- match['X']['V'] = -1;
- match['X']['B'] = -1;
- match['X']['Z'] = -1;
- match['X']['X'] = -1;
- match['X']['*'] = -4;
-
-
- match['*']['A'] = -4;
- match['*']['R'] = -4;
- match['*']['N'] = -4;
- match['*']['D'] = -4;
- match['*']['C'] = -4;
- match['*']['Q'] = -4;
- match['*']['E'] = -4;
- match['*']['G'] = -4;
- match['*']['H'] = -4;
- match['*']['I'] = -4;
- match['*']['L'] = -4;
- match['*']['K'] = -4;
- match['*']['M'] = -4;
- match['*']['F'] = -4;
- match['*']['P'] = -4;
- match['*']['S'] = -4;
- match['*']['T'] = -4;
- match['*']['W'] = -4;
- match['*']['Y'] = -4;
- match['*']['V'] = -4;
- match['*']['B'] = -4;
- match['*']['Z'] = -4;
- match['*']['X'] = -4;
- match['*']['*'] = 1;
- }
/**
* Fills the the similarity and direction matrixes of the two input sequences.
diff --git a/src/main/java/nl/wur/bif/pantools/cli/AddFunctions.java b/src/main/java/nl/wur/bif/pantools/cli/AddFunctions.java
index cc323a0e9..8731f7075 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/AddFunctions.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/AddFunctions.java
@@ -28,11 +28,11 @@ public class AddFunctions implements Callable<Integer> {
private Pantools pantools;
@Parameters(descriptionKey = "functions-file", index = "0+")
- @InputFile(message = "file.functions")
+ @InputFile(message = "{file.functions}")
Path functionsFile;
@Option(names = {"-A", "--annotations-file"})
- @InputFile(message = "{file.functions}")
+ @InputFile(message = "{file.annotations}")
Path annotationsFile;
@Option(names = "--function")
diff --git a/src/main/java/nl/wur/bif/pantools/cli/ConsensusTree.java b/src/main/java/nl/wur/bif/pantools/cli/ConsensusTree.java
index 48bf4217b..bcf5a7abf 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/ConsensusTree.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/ConsensusTree.java
@@ -3,6 +3,8 @@ package nl.wur.bif.pantools.cli;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.cli.mixins.ThreadNumber;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
+import nl.wur.bif.pantools.cli.validation.Constraints;
+import nl.wur.bif.pantools.cli.validation.Constraints.MatchInteger;
import nl.wur.bif.pantools.pantools.Pantools;
import picocli.CommandLine.Model.CommandSpec;
@@ -32,6 +34,10 @@ public class ConsensusTree implements Callable<Integer> {
@Option(names = {"-l", "--log"}, hidden = true)
boolean log;
+ @Option(names = "--blosum")
+ @MatchInteger(value = {45, 50, 62, 80, 90}, message = "match.blosum")
+ int blosum;
+
@Option(names = {"--polytomies"})
boolean polytomies;
@@ -47,6 +53,7 @@ public class ConsensusTree implements Callable<Integer> {
private void setGlobalParameters() {
THREADS = threadNumber.getnThreads();
+ BLOSUM = blosum;
LOG = log;
ALLOW_POLYTOMIES = polytomies;
}
diff --git a/src/main/java/nl/wur/bif/pantools/cli/CorePhylogeny.java b/src/main/java/nl/wur/bif/pantools/cli/CorePhylogeny.java
index 38e1a0367..ca0e66fe6 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/CorePhylogeny.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/CorePhylogeny.java
@@ -5,6 +5,8 @@ import nl.wur.bif.pantools.cli.mixins.SelectGenomes;
import nl.wur.bif.pantools.cli.mixins.SelectHmGroups;
import nl.wur.bif.pantools.cli.mixins.ThreadNumber;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
+import nl.wur.bif.pantools.cli.validation.Constraints;
+import nl.wur.bif.pantools.cli.validation.Constraints.MatchInteger;
import nl.wur.bif.pantools.pantools.Pantools;
import picocli.CommandLine.Model.CommandSpec;
@@ -40,9 +42,13 @@ public class CorePhylogeny implements Callable<Integer> {
String phenotype;
@Option(names = {"-m", "--clustering-mode"})
- @Pattern(regexp = "ML|NJ", flags = CASE_INSENSITIVE, message = "pattern.clustering-mode")
+ @Pattern(regexp = "ML|NJ", flags = CASE_INSENSITIVE, message = "{pattern.clustering-mode}")
String mode;
+ @Option(names = "--blosum")
+ @MatchInteger(value = {45, 50, 62, 80, 90}, message = "match.blosum")
+ int blosum;
+
@Override
public Integer call() throws IOException {
pantools.createLogger(spec);
@@ -56,6 +62,7 @@ public class CorePhylogeny implements Callable<Integer> {
private void setGlobalParameters() {
setGenomeSelectionOptions(selectGenomes);
THREADS = threadNumber.getnThreads();
+ BLOSUM = blosum;
PHENOTYPE = phenotype;
CLUSTERING_METHOD = mode;
if (protein) Mode = "PROTEIN";
diff --git a/src/main/java/nl/wur/bif/pantools/cli/Group.java b/src/main/java/nl/wur/bif/pantools/cli/Group.java
index e7686e535..a5b5a6476 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/Group.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/Group.java
@@ -7,6 +7,7 @@ import jakarta.validation.constraints.Min;
import nl.wur.bif.pantools.cli.mixins.SelectGenomes;
import nl.wur.bif.pantools.cli.mixins.ThreadNumber;
import nl.wur.bif.pantools.cli.validation.BeanValidation;
+import nl.wur.bif.pantools.cli.validation.Constraints.ScoringMatrix;
import nl.wur.bif.pantools.pantools.Pantools;
import java.nio.file.Path;
@@ -57,7 +58,11 @@ public class Group implements Callable<Integer> {
@DecimalMax(value = "10", message = "{max.contrast}")
static double contrast;
- @ArgGroup(multiplicity = "1") RelaxationSettings relaxationSettings;
+ @Option(names = "--scoring-matrix")
+ @ScoringMatrix(message = "{scoring_matrix}")
+ String scoringMatrix;
+
+ @ArgGroup RelaxationSettings relaxationSettings;
private static class RelaxationSettings {
@Option(names = {"--relaxation"})
void setParams(int value) {
@@ -96,7 +101,7 @@ public class Group implements Callable<Integer> {
pantools.setPangenomeGraph();
setGlobalParameters(); //TODO: use local parameters instead
- proLayer.group();
+ proLayer.group(scoringMatrix);
return 0;
}
diff --git a/src/main/java/nl/wur/bif/pantools/cli/MSA.java b/src/main/java/nl/wur/bif/pantools/cli/MSA.java
index 258eff7bb..3177ce05b 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/MSA.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/MSA.java
@@ -69,7 +69,7 @@ public class MSA implements Callable<Integer> {
String phenotype;
@Option(names = "--blosum")
- @MatchInteger(value = {45, 62, 80}, message = "match.blosum")
+ @MatchInteger(value = {45, 50, 62, 80, 90}, message = "match.blosum")
int blosum;
@Option(names = "--phenotype-threshold")
@@ -108,6 +108,7 @@ public class MSA implements Callable<Integer> {
if (regionsFile != null) PATH_TO_THE_REGIONS_FILE = regionsFile.toString();
if (functions != null) SELECTED_NAME = functions.toString().replaceAll("[\\[\\]]", "");
THREADS = threadNumber.getnThreads();
+ BLOSUM = blosum;
phenotype_threshold = phenotypeThreshold;
Mode = (mode == null) ? "0" : mode.toUpperCase();
PHENOTYPE = phenotype;
diff --git a/src/main/java/nl/wur/bif/pantools/cli/OptimalGrouping.java b/src/main/java/nl/wur/bif/pantools/cli/OptimalGrouping.java
index 4db8aaa33..d567077bc 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/OptimalGrouping.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/OptimalGrouping.java
@@ -59,6 +59,10 @@ public class OptimalGrouping implements Callable<Integer> {
@Size(min = 1, message = "{size.empty.relaxation}")
List<Integer> relaxation;
+ @Option(names = "--scoring-matrix")
+ @ScoringMatrix(message = "{scoring_matrix}")
+ String scoringMatrix;
+
@Override
public Integer call() {
pantools.createLogger(spec);
@@ -67,7 +71,7 @@ public class OptimalGrouping implements Callable<Integer> {
pantools.setPangenomeGraph();
setGlobalParameters(); //TODO: use local parameters instead
- proLayer.optimal_grouping();
+ proLayer.optimal_grouping(scoringMatrix);
return 0;
}
diff --git a/src/main/java/nl/wur/bif/pantools/cli/validation/Constraints.java b/src/main/java/nl/wur/bif/pantools/cli/validation/Constraints.java
index 3f2d5180c..e855e6b5a 100644
--- a/src/main/java/nl/wur/bif/pantools/cli/validation/Constraints.java
+++ b/src/main/java/nl/wur/bif/pantools/cli/validation/Constraints.java
@@ -84,6 +84,23 @@ public class Constraints {
Class<? extends Payload>[] payload() default {};
}
+ /**
+ * Validate whether the scoring matrix exist in resources/scoring-matrices.
+ * Usage: @ScoringMatrix String matrixName
+ */
+ @Documented
+ @Target({METHOD, FIELD, ANNOTATION_TYPE, CONSTRUCTOR, PARAMETER, TYPE_USE})
+ @Retention(RUNTIME)
+ @Constraint(validatedBy = ScoringMatrixValidator.class)
+ public @interface ScoringMatrix {
+
+ String message() default "Matrix does not exist: (${validatedValue})";
+
+ Class<?>[] groups() default {};
+
+ Class<? extends Payload>[] payload() default {};
+ }
+
/**
* Validate an optional integer that has a minimum, bus is 0 when unassigned.
* Usage: @MinOrZero(value=x) int integer
diff --git a/src/main/java/nl/wur/bif/pantools/cli/validation/validators/ScoringMatrixValidator.java b/src/main/java/nl/wur/bif/pantools/cli/validation/validators/ScoringMatrixValidator.java
new file mode 100644
index 000000000..bac019b44
--- /dev/null
+++ b/src/main/java/nl/wur/bif/pantools/cli/validation/validators/ScoringMatrixValidator.java
@@ -0,0 +1,28 @@
+package nl.wur.bif.pantools.cli.validation.validators;
+
+import jakarta.validation.ConstraintValidator;
+import jakarta.validation.ConstraintValidatorContext;
+import nl.wur.bif.pantools.cli.validation.Constraints.ScoringMatrix;
+
+import java.io.InputStream;
+import java.nio.file.Paths;
+
+import static org.apache.logging.log4j.core.util.Loader.getClassLoader;
+
+
+public class ScoringMatrixValidator implements ConstraintValidator<ScoringMatrix, String> {
+
+ @Override
+ public void initialize(ScoringMatrix constraintAnnotation) {
+ }
+
+ @Override
+ public boolean isValid(String matrixName, ConstraintValidatorContext context) {
+ if (matrixName == null) return true;
+
+ // get matrix files from the resources/scoring-matrices directory
+ final String resourceLocation = Paths.get("scoring-matrices").resolve(matrixName).toString();
+ final InputStream inputStream = getClassLoader().getResourceAsStream(resourceLocation);
+ return inputStream != null;
+ }
+}
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/Classification.java b/src/main/java/nl/wur/bif/pantools/pangenome/Classification.java
index cbb3227f2..abdf0fc6f 100644
--- a/src/main/java/nl/wur/bif/pantools/pangenome/Classification.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/Classification.java
@@ -6,66 +6,33 @@
package nl.wur.bif.pantools.pangenome;
-import java.util.Arrays;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-
import cern.jet.math.Arithmetic;
import nl.wur.bif.pantools.cli.RemoveFunctions;
import nl.wur.bif.pantools.index.IndexDatabase;
+import nl.wur.bif.pantools.index.IndexPointer;
+import nl.wur.bif.pantools.index.IndexScanner;
import nl.wur.bif.pantools.pantools.Pantools;
import nl.wur.bif.pantools.sequence.SequenceDatabase;
+import nl.wur.bif.pantools.sequence.SequenceScanner;
+import nl.wur.bif.pantools.utils.FileUtils;
import nl.wur.bif.pantools.utils.Utils;
-import org.neo4j.graphdb.Label;
-import java.util.Scanner;
-import java.util.stream.Collectors;
-import java.util.Map;
import org.apache.commons.lang.ArrayUtils;
-import nl.wur.bif.pantools.index.IndexPointer;
-import org.neo4j.graphdb.Node;
-import org.neo4j.graphdb.Relationship;
-import org.neo4j.graphdb.RelationshipType;
-import org.neo4j.graphdb.ResourceIterator;
-import org.neo4j.graphdb.Transaction;
-import org.neo4j.graphdb.Direction;
-import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.match;
-import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.initialize_BLOSUM_matrix;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import org.neo4j.graphdb.NotFoundException;
-
-import java.io.File;
+import org.neo4j.graphdb.*;
+
+import java.io.*;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.text.DecimalFormat;
-import java.util.HashSet;
-import java.util.Set;
-import org.neo4j.graphdb.ResourceIterable;
-import nl.wur.bif.pantools.sequence.SequenceScanner;
-import nl.wur.bif.pantools.index.IndexScanner;
-import java.util.Collections;
-import java.util.Random;
-import java.util.TreeSet;
+import java.util.*;
+import java.util.concurrent.*;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
-import java.util.concurrent.ConcurrentHashMap;
-
-import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
-
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeUnit;
+import java.util.stream.Collectors;
+import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.match;
import static nl.wur.bif.pantools.pangenome.FunctionalAnnotations.function_overview_per_group;
-
+import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
import static nl.wur.bif.pantools.utils.Globals.*;
import static nl.wur.bif.pantools.utils.Utils.*;
@@ -9155,7 +9122,7 @@ public class Classification {
public static void create_write_msa_trimmed_output(ArrayList<String> msaNames, String outdirMsa) {
Pantools.logger.info("Reading alignments from {} for calculating variable/informative positions.", outdirMsa);
ArrayList<String> nuc_or_prot_list = prepare_type_list_for_msa(); // list can contain "protein", "nucleotide" or both
- initialize_BLOSUM();
+ match = FileUtils.loadScoringMatrix("BLOSUM" + BLOSUM);
delete_file_full_path(outdirMsa + "/groups_with_phenotype_specific_changes.txt");
for (String nuc_or_prot : nuc_or_prot_list) {
@@ -9680,14 +9647,6 @@ public class Classification {
System.exit(1);
}
}
-
- public static void initialize_BLOSUM() {
- if (BLOSUM != 45 && BLOSUM != 62 && BLOSUM != 80) {
- System.out.println("BLOSUM value must be 45, 62 or 80. Using BLOSUM62");
- BLOSUM = 62;
- }
- initialize_BLOSUM_matrix(BLOSUM);
- }
/**
*
@@ -9697,7 +9656,7 @@ public class Classification {
public static void create_write_msa_no_trimming_output(ArrayList<String> msaNames, String outdirMsa) {
Pantools.logger.info("Reading alignments from {} for calculating variable/informative positions.", outdirMsa);
ArrayList<String> nuc_or_prot_list = prepare_type_list_for_msa(); // list can contain "protein", "nucleotide" or both
- initialize_BLOSUM();
+ match = FileUtils.loadScoringMatrix("BLOSUM" + BLOSUM);
delete_file_full_path(outdirMsa + "/groups_with_phenotype_specific_changes.txt");
for (String nuc_or_prot : nuc_or_prot_list) {
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java b/src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java
index b9c4caa74..988f0a2d5 100755
--- a/src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java
@@ -450,8 +450,8 @@ public class GenomeLayer {
}
pointer = new IndexPointer();
reference = new StringBuilder();
- bounded_aligner = new BoundedLocalSequenceAlignment(GAP_OPEN, GAP_EXT, MAX_ALIGNMENT_LENGTH, ALIGNMENT_BOUND, CLIPPING_STRINGENCY, 'N');
- aligner = new LocalSequenceAlignment(GAP_OPEN, GAP_EXT, MAX_ALIGNMENT_LENGTH, CLIPPING_STRINGENCY, 'N');
+ bounded_aligner = new BoundedLocalSequenceAlignment(GAP_OPEN, GAP_EXT, MAX_ALIGNMENT_LENGTH, ALIGNMENT_BOUND, CLIPPING_STRINGENCY, "NUC.4.4");
+ aligner = new LocalSequenceAlignment(GAP_OPEN, GAP_EXT, MAX_ALIGNMENT_LENGTH, CLIPPING_STRINGENCY, "NUC.4.4");
int_pair_comp = new IntPairComparator();
hit_counts = new ArrayList();
rand = new Random(1);
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
index 0a341c34a..4b789bc08 100644
--- a/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java
@@ -8,6 +8,7 @@ package nl.wur.bif.pantools.pangenome;
import nl.wur.bif.pantools.index.IndexScanner;
import nl.wur.bif.pantools.pantools.Pantools;
import nl.wur.bif.pantools.sequence.SequenceScanner;
+import nl.wur.bif.pantools.utils.FileUtils;
import nl.wur.bif.pantools.utils.Utils;
import org.apache.commons.lang.ArrayUtils;
import org.neo4j.graphdb.*;
@@ -21,7 +22,7 @@ import java.util.concurrent.*;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLong;
-import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.initialize_BLOSUM_matrix;
+import static nl.wur.bif.pantools.alignment.BoundedLocalSequenceAlignment.match;
import static nl.wur.bif.pantools.pangenome.Classification.*;
import static nl.wur.bif.pantools.pangenome.create_skip_arrays.create_skip_arrays;
import static nl.wur.bif.pantools.utils.Globals.*;
@@ -485,7 +486,8 @@ public class Phylogeny {
*/
public String[] concatenate_pre_alignment(String[] gene_names) {
String new_gene_names = ""; // exclude the genes that cannot be used
- initialize_BLOSUM_matrix(62);
+
+ match = FileUtils.loadScoringMatrix("BLOSUM62");
System.out.println("\rGene name: Maximum bases trimmed from START/END of nucleotide sequences -> " +
"Parsimony informative sites in trimmed nucleotide alignment");
@@ -2293,7 +2295,7 @@ public class Phylogeny {
msa.alignSequences(true, false); //NB: I do not check for alignment_phylogeny_mode.contains("nucleotide") currently tho
ArrayList<String> updatedMsaNames = msa.getMsaNames(); //get msaNames, since this list is updated with trimming results
- initialize_BLOSUM_matrix(BLOSUM);
+ match = FileUtils.loadScoringMatrix("BLOSUM" + BLOSUM);
HashMap<String, String> groupInfoMap = gatherInfoCorePhylogenyLog(hmNodeList, updatedMsaNames);
GRAPH_DB.shutdown();
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java b/src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java
index ac3a3722c..f7ff8fe06 100644
--- a/src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java
@@ -413,8 +413,8 @@ public class ProteomeLayer {
StringBuilder query;
StringBuilder subject;
LocalSequenceAlignment aligner;
- public Find_similarities() {
- aligner = new LocalSequenceAlignment(GAP_OPEN, GAP_EXT,MAX_ALIGNMENT_LENGTH, 0, 'P');
+ public Find_similarities(String scoringMatrix) {
+ aligner = new LocalSequenceAlignment(GAP_OPEN, GAP_EXT,MAX_ALIGNMENT_LENGTH, 0, scoringMatrix);
query = new StringBuilder();
subject = new StringBuilder();
}
@@ -1080,7 +1080,7 @@ public class ProteomeLayer {
D7 - similarity: 35%, mcl_inflation: 3.6, intersection: 0.02, contrast: 2
D8 - similarity: 25%, mcl_inflation: 2.4, intersection: 0.01, contrast: 1
*/
- public void optimal_grouping() {
+ public void optimal_grouping(String scoringMatrix) {
if (Mode.contains("FAST")) {
FAST = true; // check if the F1 score dropped compared to the previous grouping, stop when this is the case
}
@@ -1109,7 +1109,7 @@ public class ProteomeLayer {
}
System.out.println("Grouping " + (i+1) + ", similarity = " + MIN_NORMALIZED_SIMILARITY);
first_generate_proteins = true;
- group();
+ group(scoringMatrix);
/*append_string_to_file_full_path(date + "\npantools optimal_grouping\nRuntime after grouping relaxation: " + (i+1) + "\n",
WORKING_DIRECTORY + "/log/used_commands");
print_runtime(false, true);*/
@@ -2793,7 +2793,7 @@ public class ProteomeLayer {
/**
* Groups similar proteins into homology groups.
*/
- public void group() {
+ public void group(String scoringMatrix) {
MAX_TRANSACTION_SIZE = 1000;
progress = "";
System.out.println("\nClustering protein sequences\n");
@@ -2891,7 +2891,7 @@ public class ProteomeLayer {
es.execute(new Generate_proteins());
es.execute(new Find_intersections(num_proteins));
for(int i = 1; i <= THREADS - 2; i++) {
- es.execute(new Find_similarities());
+ es.execute(new Find_similarities(scoringMatrix));
}
es.execute(new Write_similarities());
es.shutdown();
diff --git a/src/main/java/nl/wur/bif/pantools/utils/FileUtils.java b/src/main/java/nl/wur/bif/pantools/utils/FileUtils.java
index 022829af8..793b6f2f5 100644
--- a/src/main/java/nl/wur/bif/pantools/utils/FileUtils.java
+++ b/src/main/java/nl/wur/bif/pantools/utils/FileUtils.java
@@ -9,14 +9,50 @@ import org.apache.commons.io.IOUtils;
import java.io.*;
import java.nio.file.Files;
import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Scanner;
import java.util.zip.GZIPInputStream;
-/**
- * Class for pantools file utility functions.
- *
- * @author Roel van Esch, Bioinformatics group, Wageningen University, the Netherlands
- */
+import static org.apache.logging.log4j.core.util.Loader.getClassLoader;
+
public class FileUtils {
+ /**
+ * Load a matrix file from the project resources.
+ * @param matrixName name of the scoring matrix file
+ * @return scoring matrix that can be indexed by char values
+ */
+ public static int[][] loadScoringMatrix(String matrixName) {
+ // initialize empty matrix and column headers
+ final int[][] scoringMatrix = new int[256][256];
+ char[] headers = null;
+
+ // load matrix file from project resources
+ final String resourceLocation = Paths.get("scoring-matrices").resolve(matrixName).toString();
+ final InputStream inputStream = getClassLoader().getResourceAsStream(resourceLocation);
+ assert inputStream != null;
+ final Scanner matrixFile = new Scanner(inputStream);
+
+ // scan the matrix
+ while (matrixFile.hasNextLine()) {
+ final String line = matrixFile.nextLine();
+ if (line.length() == 0 || line.startsWith("#")) continue;
+ if (headers == null) {
+ // set header char values
+ headers = line.replaceAll("\\s+", "").toCharArray();
+ continue;
+ }
+ // add values to matrix using char col/row headers as indices
+ final String[] values = line.split("\\s+");
+ final char a = values[0].charAt(0);
+ for (int i = 1; i < values.length; i++) {
+ final char b = headers[i - 1];
+ scoringMatrix[a][b] = Integer.parseInt(values[i]);
+ }
+ }
+ matrixFile.close();
+ return scoringMatrix;
+ }
+
/**
* Add a shutdown hook to a temporary directory to remove it on system exit.
* @param directory path of temporary directory
diff --git a/src/main/java/nl/wur/bif/pantools/utils/Globals.java b/src/main/java/nl/wur/bif/pantools/utils/Globals.java
index ac07d4332..5a537880c 100644
--- a/src/main/java/nl/wur/bif/pantools/utils/Globals.java
+++ b/src/main/java/nl/wur/bif/pantools/utils/Globals.java
@@ -175,7 +175,7 @@ public class Globals {
public static boolean ALLOW_POLYTOMIES = false;
public static boolean TRIMMING = true;
public static String msaMethod = "per_group";
- public static int BLOSUM = 62;
+ public static int BLOSUM;
public static HashMap<String, Integer> phenotype_threshold_map;
public static HashMap<Integer, String> geno_pheno_map; // genome number is coupled to its phenotype
diff --git a/src/main/resources/Defaults.properties b/src/main/resources/Defaults.properties
index 57343d848..fa34afbe2 100644
--- a/src/main/resources/Defaults.properties
+++ b/src/main/resources/Defaults.properties
@@ -4,6 +4,8 @@ threads = 0
core-threshold = 100
phenotype-threshold = 100
unique-threshold = 0
+scoring-matrix = BLOSUM62
+blosum = 62
# subcommands
# add_phenotypes
diff --git a/src/main/resources/ErrorMessages.properties b/src/main/resources/ErrorMessages.properties
index f7957befc..188f50f0b 100644
--- a/src/main/resources/ErrorMessages.properties
+++ b/src/main/resources/ErrorMessages.properties
@@ -26,6 +26,8 @@ file.short-read = Short-read file(s) not found
file.tree = Phylogenetic tree file not found (${validatedValue})
match.blosum = --blosum should be 45, 62 or 80
+no-protein = Protein scoring matrices are not allowed for this command, choose a nucleotide matrix like NUC.4.4
+no-nuc = Nucleotide scoring matrices are not allowed for this command, choose a protein matrix like BLOSUM62
max.alignment-band = --alignment-band must be less than or equal to {value}
max.contrast = --contrast must be less than or equal to {value}
@@ -94,6 +96,9 @@ positive.threads = --threads must be greater than 0
range.clipping-stringency = '--clipping-stringency' must be in range [0..3]
range.ir = --intersection-rate must be in range [0.001,0.1]
+scoring_matrix = Invalid scoring matrix, choose between BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, \
+ PAM30, PAM70 and PAM250.
+
size.empty.exclude = --exclude should consist of comma separated integers or ranges for genomes \
(example: --exclude 1,2,5-10)
size.empty.include = --include should consist of comma separated integers or ranges for genomes \
diff --git a/src/main/resources/MessageBundle.properties b/src/main/resources/MessageBundle.properties
index 1191a8ee3..5b55fa997 100644
--- a/src/main/resources/MessageBundle.properties
+++ b/src/main/resources/MessageBundle.properties
@@ -151,6 +151,8 @@ pantools.export_pangenome.usage.description = Export a pangenome built with buil
# Options
annotations-file = A text file with the identifiers of annotations to be included.
+blosum = A BLOSUM matrix to be used for the calculation of protein similarity. Allowed values are 45, 50, 62 80 and 90 \
+ (default: ${DEFAULT-VALUE}).
core-threshold = Threshold (%%) for (soft) core genes. Default is ${DEFAULT-VALUE}%% of genomes.
database-path = Path to the database root directory.
exclude = Exclude a selection of genomes.
@@ -175,6 +177,7 @@ regions-file = A text file containing genome locations with on each line: a geno
end position, separated by a space.
threads = Number of parallel working threads, default is the number of cores or 8, whichever is lower.
unique-threshold = Threshold (%%) for unique/cloud genes. Default is a single genome, not a percentage.
+scoring-matrix = The scoring matrix used (default: ${DEFAULT-VALUE}).
# Subcommand options
# AddAnnotations
@@ -328,8 +331,6 @@ pantools.mlsa_concatenate.threads = Number of threads for MAFFT, \
pantools.mlsa_find_genes.include = Only search for genes in a selection of genomes.
pantools.mlsa_find_genes.exclude = Do not search for genes in this selection of genomes.
# MSA
-pantools.msa.blosum = A BLOSUM matrix to be used for the calculation of protein similarity. Allowed values are 45, 62 \
- and 80 (default: ${DEFAULT-VALUE}).
pantools.msa.no-fasttree = Run FastTree (default: ${DEFAULT-VALUE}).
pantools.msa.functions = For specifying one or multiple functional domains \
(Only used when @|fg(yellow) --method=functions|@).
diff --git a/src/main/resources/scoring-matrices/BLOSUM45 b/src/main/resources/scoring-matrices/BLOSUM45
new file mode 100644
index 000000000..80ba30f56
--- /dev/null
+++ b/src/main/resources/scoring-matrices/BLOSUM45
@@ -0,0 +1,27 @@
+# Entries for the BLOSUM45 matrix at a scale of ln(2)/3.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 -1 -1 -5
+R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 -3 1 -1 -5
+N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 5 -3 0 -1 -5
+D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 6 -3 1 -1 -5
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -2 -3 -1 -5
+Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 -2 4 -1 -5
+E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 -3 5 -1 -5
+G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -4 -2 -1 -5
+H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 -2 0 -1 -5
+I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 4 -3 -1 -5
+L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 4 -2 -1 -5
+K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 -3 1 -1 -5
+M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 2 -1 -1 -5
+F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 1 -3 -1 -5
+P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -3 -1 -1 -5
+S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 -2 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 -1 -1 -5
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -1 -5
+Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 0 -2 -1 -5
+V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 2 -3 -1 -5
+B -1 -1 5 6 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 5 -3 1 -1 -5
+J -1 -3 -3 -3 -2 -2 -3 -4 -2 4 4 -3 2 1 -3 -2 -1 -2 0 2 -3 4 -2 -1 -5
+Z -1 1 0 1 -3 4 5 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 1 -2 5 -1 -5
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/BLOSUM50 b/src/main/resources/scoring-matrices/BLOSUM50
new file mode 100644
index 000000000..fce0f81b5
--- /dev/null
+++ b/src/main/resources/scoring-matrices/BLOSUM50
@@ -0,0 +1,27 @@
+# Entries for the BLOSUM50 matrix at a scale of ln(2)/3.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -2 -1 -1 -5
+R -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 -3 0 -1 -5
+N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 5 -4 0 -1 -5
+D -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 6 -4 1 -1 -5
+C -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -2 -3 -1 -5
+Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 -3 4 -1 -5
+E -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 -3 5 -1 -5
+G 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -4 -2 -1 -5
+H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 -3 0 -1 -5
+I -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 4 -3 -1 -5
+L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 4 -3 -1 -5
+K -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 -3 1 -1 -5
+M -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 2 -1 -1 -5
+F -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 1 -4 -1 -5
+P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -3 -1 -1 -5
+S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 -3 0 -1 -5
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 -1 -1 -5
+W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -2 -1 -5
+Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -1 -2 -1 -5
+V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -3 2 -3 -1 -5
+B -2 -1 5 6 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -3 6 -4 1 -1 -5
+J -2 -3 -4 -4 -2 -3 -3 -4 -3 4 4 -3 2 1 -3 -3 -1 -2 -1 2 -4 4 -3 -1 -5
+Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 1 -3 5 -1 -5
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -5
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/BLOSUM62 b/src/main/resources/scoring-matrices/BLOSUM62
new file mode 100644
index 000000000..0d184f05c
--- /dev/null
+++ b/src/main/resources/scoring-matrices/BLOSUM62
@@ -0,0 +1,27 @@
+# Entries for the BLOSUM62 matrix at a scale of ln(2)/2.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -1 -4
+R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2 0 -1 -4
+N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 -3 0 -1 -4
+D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 -3 1 -1 -4
+C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4
+Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 -2 4 -1 -4
+E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 -3 4 -1 -4
+G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -4 -2 -1 -4
+H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 -3 0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 3 -3 -1 -4
+K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 -3 1 -1 -4
+M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 2 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 0 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -3 -1 -1 -4
+S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 -2 0 -1 -4
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 -1 -1 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -2 -2 -1 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -1 -2 -1 -4
+V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 2 -2 -1 -4
+B -2 -1 4 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 -3 0 -1 -4
+J -1 -2 -3 -3 -1 -2 -3 -4 -3 3 3 -3 2 0 -3 -2 -1 -2 -1 2 -3 3 -3 -1 -4
+Z -1 0 0 1 -3 4 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -2 -2 -2 0 -3 4 -1 -4
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/BLOSUM80 b/src/main/resources/scoring-matrices/BLOSUM80
new file mode 100644
index 000000000..970f9287f
--- /dev/null
+++ b/src/main/resources/scoring-matrices/BLOSUM80
@@ -0,0 +1,27 @@
+# Entries for the BLOSUM80 matrix at a scale of ln(2)/2.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -2 -1 -1 -6
+R -2 6 -1 -2 -4 1 -1 -3 0 -3 -3 2 -2 -4 -2 -1 -1 -4 -3 -3 -1 -3 0 -1 -6
+N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -4 5 -4 0 -1 -6
+D -2 -2 1 6 -4 -1 1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4 5 -5 1 -1 -6
+C -1 -4 -3 -4 9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1 -4 -2 -4 -1 -6
+Q -1 1 0 -1 -4 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -3 -2 -3 0 -3 4 -1 -6
+E -1 -1 -1 1 -5 2 6 -3 0 -4 -4 1 -2 -4 -2 0 -1 -4 -3 -3 1 -4 5 -1 -6
+G 0 -3 -1 -2 -4 -2 -3 6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4 -1 -5 -3 -1 -6
+H -2 0 0 -2 -4 1 0 -3 8 -4 -3 -1 -2 -2 -3 -1 -2 -3 2 -4 -1 -4 0 -1 -6
+I -2 -3 -4 -4 -2 -3 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -4 3 -4 -1 -6
+L -2 -3 -4 -5 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -2 1 -4 3 -3 -1 -6
+K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 -1 -1 -4 -3 -3 -1 -3 1 -1 -6
+M -1 -2 -3 -4 -2 0 -2 -4 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 2 -1 -1 -6
+F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 0 6 -4 -3 -2 0 3 -1 -4 0 -4 -1 -6
+P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4 8 -1 -2 -5 -4 -3 -2 -4 -2 -1 -6
+S 1 -1 0 -1 -2 0 0 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -3 0 -1 -6
+T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2 1 5 -4 -2 0 -1 -1 -1 -1 -6
+W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2 0 -5 -4 -4 11 2 -3 -5 -3 -3 -1 -6
+Y -2 -3 -3 -4 -3 -2 -3 -4 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -3 -2 -3 -1 -6
+V 0 -3 -4 -4 -1 -3 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 2 -3 -1 -6
+B -2 -1 5 5 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 5 -4 0 -1 -6
+J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 3 -3 2 0 -4 -3 -1 -3 -2 2 -4 3 -3 -1 -6
+Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -1 -4 -2 0 -1 -3 -3 -3 0 -3 5 -1 -6
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/BLOSUM90 b/src/main/resources/scoring-matrices/BLOSUM90
new file mode 100644
index 000000000..066def786
--- /dev/null
+++ b/src/main/resources/scoring-matrices/BLOSUM90
@@ -0,0 +1,27 @@
+# Entries for the BLOSUM90 matrix at a scale of ln(2)/2.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -2 -2 -1 -1 -6
+R -2 6 -1 -3 -5 1 -1 -3 0 -4 -3 2 -2 -4 -3 -1 -2 -4 -3 -3 -2 -3 0 -1 -6
+N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 5 -4 -1 -1 -6
+D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 5 -5 1 -1 -6
+C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -2 -5 -1 -6
+Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 -3 5 -1 -6
+E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 1 -4 5 -1 -6
+G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -5 -3 -1 -6
+H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 -4 0 -1 -6
+I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 3 -4 -1 -6
+L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 4 -4 -1 -6
+K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 -3 1 -1 -6
+M -2 -2 -3 -4 -2 0 -3 -4 -3 1 2 -2 7 -1 -3 -2 -1 -2 -2 0 -4 2 -2 -1 -6
+F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 0 -4 -1 -6
+P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -4 -2 -1 -6
+S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -3 -1 -1 -6
+T 0 -2 0 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -3 -2 1 6 -4 -2 -1 -1 -2 -1 -1 -6
+W -4 -4 -5 -6 -4 -3 -5 -4 -3 -4 -3 -5 -2 0 -5 -4 -4 11 2 -3 -6 -3 -4 -1 -6
+Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -2 -3 -1 -6
+V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 1 -3 -1 -6
+B -2 -2 5 5 -4 -1 1 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 5 -5 0 -1 -6
+J -2 -3 -4 -5 -2 -3 -4 -5 -4 3 4 -3 2 0 -4 -3 -2 -3 -2 1 -5 4 -4 -1 -6
+Z -1 0 -1 1 -5 5 5 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 -4 5 -1 -6
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -6
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/NUC.4.4 b/src/main/resources/scoring-matrices/NUC.4.4
new file mode 100644
index 000000000..c7ba6c68b
--- /dev/null
+++ b/src/main/resources/scoring-matrices/NUC.4.4
@@ -0,0 +1,24 @@
+#
+# This matrix was created by Todd Lowe 12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+# nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+ A T G C S W R Y K M B V H D N
+A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2
+T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2
+G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2
+C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2
+S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1
+W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1
+R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1
+Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1
+K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1
+M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1
+B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1
+V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1
+H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1
+D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1
+N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/PAM250 b/src/main/resources/scoring-matrices/PAM250
new file mode 100644
index 000000000..9644ee494
--- /dev/null
+++ b/src/main/resources/scoring-matrices/PAM250
@@ -0,0 +1,27 @@
+# Entries for the PAM250 matrix at a scale of ln(2)/3.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 -1 0 -1 -8
+R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 -3 0 -1 -8
+N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 -3 1 -1 -8
+D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 -3 3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -5 -1 -8
+Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 -2 3 -1 -8
+E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 -3 3 -1 -8
+G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 -4 0 -1 -8
+H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 -2 2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 3 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 5 -3 -1 -8
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 -3 0 -1 -8
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 3 -2 -1 -8
+F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 2 -5 -1 -8
+P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 -2 0 -1 -8
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 -2 0 -1 -8
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 -1 -1 -8
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -3 -6 -1 -8
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -1 -4 -1 -8
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 2 -2 -1 -8
+B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 -3 2 -1 -8
+J -1 -3 -3 -3 -5 -2 -3 -4 -2 3 5 -3 3 2 -2 -2 -1 -3 -1 2 -3 5 -2 -1 -8
+Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 -2 3 -1 -8
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/PAM30 b/src/main/resources/scoring-matrices/PAM30
new file mode 100644
index 000000000..55d8a6554
--- /dev/null
+++ b/src/main/resources/scoring-matrices/PAM30
@@ -0,0 +1,27 @@
+# Entries for the PAM30 matrix at a scale of ln(2)/2.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -6 -3 -1 -17
+R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -7 -4 -1 -17
+N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -6 -3 -1 -17
+D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 -10 1 -1 -17
+C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -9 -14 -1 -17
+Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 -5 6 -1 -17
+E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 -7 6 -1 -17
+G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -10 -5 -1 -17
+H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -7 -1 -1 -17
+I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 5 -6 -1 -17
+L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 6 -7 -1 -17
+K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -7 -4 -1 -17
+M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 0 -5 -1 -17
+F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -2 -13 -1 -17
+P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -7 -4 -1 -17
+S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -8 -5 -1 -17
+T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -5 -6 -1 -17
+W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -7 -14 -1 -17
+Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -7 -9 -1 -17
+V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 0 -6 -1 -17
+B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 -8 0 -1 -17
+J -6 -7 -6 -10 -9 -5 -7 -10 -7 5 6 -7 0 -2 -7 -8 -5 -7 -7 0 -8 6 -6 -1 -17
+Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 -6 6 -1 -17
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -17
+* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
\ No newline at end of file
diff --git a/src/main/resources/scoring-matrices/PAM70 b/src/main/resources/scoring-matrices/PAM70
new file mode 100644
index 000000000..d287d225a
--- /dev/null
+++ b/src/main/resources/scoring-matrices/PAM70
@@ -0,0 +1,27 @@
+# Entries for the PAM70 matrix at a scale of ln(2)/2.0.
+ A R N D C Q E G H I L K M F P S T W Y V B J Z X *
+A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -3 -1 -1 -11
+R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -5 -2 -1 -11
+N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -4 -1 -1 -11
+D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 -7 2 -1 -11
+C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -7 -9 -1 -11
+Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 -3 5 -1 -11
+E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 -5 5 -1 -11
+G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -7 -3 -1 -11
+H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 -4 1 -1 -11
+I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 4 -4 -1 -11
+L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 5 -4 -1 -11
+K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -5 -2 -1 -11
+M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 2 -3 -1 -11
+F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -1 -9 -1 -11
+P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -5 -2 -1 -11
+S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -5 -2 -1 -11
+T 1 -4 0 -2 -5 -3 -3 -3 -4 -1 -4 -1 -2 -6 -2 2 6 -8 -4 -1 -1 -3 -3 -1 -11
+W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -5 -10 -1 -11
+Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -4 -7 -1 -11
+V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 1 -4 -1 -11
+B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 -5 1 -1 -11
+J -3 -5 -4 -7 -7 -3 -5 -7 -4 4 5 -5 2 -1 -5 -5 -3 -5 -4 1 -5 5 -4 -1 -11
+Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 -4 5 -1 -11
+X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 1
\ No newline at end of file
diff --git a/src/test/java/nl/wur/bif/pantools/utils/LoadScoringMatrixTest.java b/src/test/java/nl/wur/bif/pantools/utils/LoadScoringMatrixTest.java
new file mode 100644
index 000000000..8aa1ed44c
--- /dev/null
+++ b/src/test/java/nl/wur/bif/pantools/utils/LoadScoringMatrixTest.java
@@ -0,0 +1,39 @@
+package nl.wur.bif.pantools.utils;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+/**
+ * Sample tests for the FileUtils.loadScoringMatrix() functions for each of the available matrices.
+ */
+class LoadScoringMatrixTest {
+ @Test
+ void loadBlosum45Test() {
+ final int[][] blosum = FileUtils.loadScoringMatrix("BLOSUM45");
+ assertAll(
+ () -> assertEquals(blosum['F']['G'], -3),
+ () -> assertEquals(blosum['W']['W'], 15),
+ () -> assertEquals(blosum['V']['Q'], -3)
+ );
+ }
+ @Test
+ void loadBlosum62Test() {
+ final int[][] blosum = FileUtils.loadScoringMatrix("BLOSUM62");
+ assertAll(
+ () -> assertEquals(blosum['F']['G'], -3),
+ () -> assertEquals(blosum['W']['W'], 11),
+ () -> assertEquals(blosum['V']['Q'], -2)
+ );
+ }
+
+ @Test
+ void LoadNucTest() {
+ final int[][] blosum = FileUtils.loadScoringMatrix("NUC.4.4");
+ assertAll(
+ () -> assertEquals(blosum['G']['W'], -4),
+ () -> assertEquals(blosum['G']['W'], -4),
+ () -> assertEquals(blosum['G']['W'], -4)
+ );
+ }
+}
\ No newline at end of file
--
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