[med-svn] [trinityrnaseq] 02/04: Imported Upstream version 2.0.4+dfsg
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 07:10:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit a0eedbeae8505cb73c9c1b6445bd93a69176e7dd
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 00:51:21 2015 -0500
Imported Upstream version 2.0.4+dfsg
---
Analysis/DifferentialExpression/run_DE_analysis.pl | 11 +-
Butterfly/Butterfly.jar | Bin 1427334 -> 0 bytes
Butterfly/prev_vers/Butterfly_r2013_08_14.jar | Bin 1150829 -> 0 bytes
Butterfly/src/src/jaligner/Alignment.java | 692 ---
Butterfly/src/src/jaligner/Cell.java | 98 -
Butterfly/src/src/jaligner/Directions.java | 44 -
Butterfly/src/src/jaligner/Markups.java | 47 -
Butterfly/src/src/jaligner/NeedlemanWunsch.java | 304 --
.../src/src/jaligner/NeedlemanWunschGotoh.java | 432 --
Butterfly/src/src/jaligner/Sequence.java | 250 --
Butterfly/src/src/jaligner/SmithWatermanGotoh.java | 388 --
Butterfly/src/src/jaligner/TracebackNode.java | 99 -
.../jaligner/example/NeedlemanWunschExample.java | 74 -
.../example/NeedlemanWunschGotohExample.java | 76 -
.../example/SmithWatermanGotohExample.java | 112 -
Butterfly/src/src/jaligner/example/package.html | 8 -
.../src/jaligner/example/sequences/p53_human.fasta | 7 -
.../src/jaligner/example/sequences/p53_mouse.fasta | 8 -
Butterfly/src/src/jaligner/formats/CLUSTAL.java | 121 -
Butterfly/src/src/jaligner/formats/FASTA.java | 79 -
Butterfly/src/src/jaligner/formats/Format.java | 59 -
.../src/src/jaligner/formats/FormatFactory.java | 84 -
Butterfly/src/src/jaligner/formats/Pair.java | 191 -
Butterfly/src/src/jaligner/formats/package.html | 8 -
.../src/src/jaligner/matrix/MatricesCompartor.java | 68 -
Butterfly/src/src/jaligner/matrix/Matrix.java | 80 -
.../src/src/jaligner/matrix/MatrixGenerator.java | 61 -
.../src/src/jaligner/matrix/MatrixLoader.java | 243 -
.../src/jaligner/matrix/MatrixLoaderException.java | 39 -
.../src/src/jaligner/matrix/matrices/BLOSUM100 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM30 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM35 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM40 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM45 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM50 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM55 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM60 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM62 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM65 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM70 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM75 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM80 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM85 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM90 | 31 -
Butterfly/src/src/jaligner/matrix/matrices/BLOSUMN | 31 -
Butterfly/src/src/jaligner/matrix/matrices/DAYHOFF | 32 -
.../src/src/jaligner/matrix/matrices/EDNAFULL | 25 -
Butterfly/src/src/jaligner/matrix/matrices/GONNET | 26 -
.../src/src/jaligner/matrix/matrices/IDENTITY | 25 -
Butterfly/src/src/jaligner/matrix/matrices/MATCH | 25 -
Butterfly/src/src/jaligner/matrix/matrices/PAM10 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM100 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM110 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM120 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM130 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM140 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM150 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM160 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM170 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM180 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM190 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM20 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM200 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM210 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM220 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM230 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM240 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM250 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM260 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM270 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM280 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM290 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM30 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM300 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM310 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM320 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM330 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM340 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM350 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM360 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM370 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM380 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM390 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM40 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM400 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM410 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM420 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM430 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM440 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM450 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM460 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM470 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM480 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM490 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM50 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM500 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM60 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM70 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM80 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM90 | 34 -
Butterfly/src/src/jaligner/matrix/package.html | 8 -
Butterfly/src/src/jaligner/package.html | 8 -
.../jaligner/test/NeedlemanWunschGotohTester.java | 131 -
.../src/jaligner/test/NeedlemanWunschTester.java | 129 -
.../src/jaligner/test/RandomSequenceGenerator.java | 77 -
.../jaligner/test/SmithWatermanGotohTester.java | 131 -
Butterfly/src/src/jaligner/test/package.html | 8 -
.../jaligner/ui/filechooser/NamedInputStream.java | 67 -
Butterfly/src/src/jaligner/util/Commons.java | 222 -
.../src/src/jaligner/util/SequenceParser.java | 215 -
.../src/jaligner/util/SequenceParserException.java | 38 -
Butterfly/src/src/jaligner/util/package.html | 8 -
Makefile | 4 +-
Release.Notes | 10 +-
Trinity | 72 +-
sample_data/test_Trinity_Assembly/Makefile | 10 +-
.../__test_runMe_with_jaccard_clip.sh | 6 -
sample_data/test_Trinity_Assembly/cleanme.pl | 2 +
.../misc_run_tests/__runMe_with_qual_trimming.sh | 2 +-
...__runMe_with_qual_trimming_and_normalization.sh | 2 +-
.../__test_runMe_include_normalization.sh | 2 +-
.../__test_runMe_with_jaccard_clip.sh | 2 +-
trinity-plugins/GAL_0.2.1/README | 6 -
trinity-plugins/GAL_0.2.1/fasta_tool | 1053 -----
trinity-plugins/Makefile | 4 +-
trinity-plugins/TransDecoder_r20140704.tar.gz | Bin 21189681 -> 0 bytes
trinity-plugins/Trimmomatic-0.32/LICENSE | 674 ---
.../Trimmomatic-0.32/adapters/NexteraPE-PE.fa | 12 -
.../Trimmomatic-0.32/adapters/TruSeq2-PE.fa | 16 -
.../Trimmomatic-0.32/adapters/TruSeq2-SE.fa | 6 -
.../Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa | 12 -
.../Trimmomatic-0.32/adapters/TruSeq3-PE.fa | 4 -
.../Trimmomatic-0.32/adapters/TruSeq3-SE.fa | 4 -
.../Trimmomatic-0.32/trimmomatic-0.32.jar | Bin 118310 -> 0 bytes
trinity-plugins/Trimmomatic-0.32/trimmomatic.jar | 1 -
trinity-plugins/collectl/Tests.py | 117 -
trinity-plugins/collectl/build_collectl.sh | 53 -
trinity-plugins/collectl/collectl-3.6.9.src.tar.gz | Bin 467637 -> 0 bytes
trinity-plugins/collectl/collectl-3.7.4.src.tar.gz | Bin 462752 -> 0 bytes
trinity-plugins/collectl/make_data_files.py | 181 -
trinity-plugins/collectl/plot.py | 176 -
trinity-plugins/collectl/timetable.py | 33 -
trinity-plugins/parafly-code/LICENSE | 17 -
trinity-plugins/parafly-code/Makefile.am | 1 -
trinity-plugins/parafly-code/Makefile.in | 671 ---
trinity-plugins/parafly-code/aclocal.m4 | 951 ----
trinity-plugins/parafly-code/config.h | 23 -
trinity-plugins/parafly-code/config.h.in | 22 -
trinity-plugins/parafly-code/configure | 4685 --------------------
trinity-plugins/parafly-code/configure.ac | 15 -
trinity-plugins/parafly-code/depcomp | 688 ---
trinity-plugins/parafly-code/install-sh | 527 ---
trinity-plugins/parafly-code/missing | 331 --
trinity-plugins/parafly-code/src/Makefile.am | 6 -
trinity-plugins/parafly-code/src/Makefile.in | 449 --
trinity-plugins/parafly-code/src/ParaFly.cpp | 268 --
trinity-plugins/parafly-code/src/argProcessor.cpp | 61 -
trinity-plugins/parafly-code/src/argProcessor.hpp | 31 -
trinity-plugins/parafly-code/stamp-h1 | 1 -
trinity-plugins/rsem-1.2.19.tar.gz | Bin 9367568 -> 0 bytes
util/align_and_estimate_abundance.pl | 8 +-
.../process_GMAP_alignments_gff3_chimeras_ok.pl | 3 +-
util/misc/run_GSNAP.pl | 51 +-
util/support_scripts/tests.py | 40 +-
164 files changed, 152 insertions(+), 18215 deletions(-)
diff --git a/Analysis/DifferentialExpression/run_DE_analysis.pl b/Analysis/DifferentialExpression/run_DE_analysis.pl
index a514d92..10b1cff 100755
--- a/Analysis/DifferentialExpression/run_DE_analysis.pl
+++ b/Analysis/DifferentialExpression/run_DE_analysis.pl
@@ -92,6 +92,8 @@ my $contrasts_file;
my $reference_sample;
+my $make_tar_gz_file = 0;
+
my ($DESEQ_method, $DESEQ_sharingMode, $DESEQ_fitType);
@@ -111,6 +113,7 @@ my ($DESEQ_method, $DESEQ_sharingMode, $DESEQ_fitType);
'DESEQ_sharingMode=s' => \$DESEQ_sharingMode,
'DESEQ_fitType=s' => \$DESEQ_fitType,
+ 'tar_gz_outdir' => \$make_tar_gz_file,
);
@@ -263,7 +266,13 @@ main: {
}
}
-
+
+ if ($make_tar_gz_file) {
+ chdir $workdir or die "Error, cannot cd to $workdir";
+ my $cmd = "tar -zcvf $output_dir.tar.gz $output_dir";
+ &process_cmd($cmd);
+ }
+
exit(0);
}
diff --git a/Butterfly/Butterfly.jar b/Butterfly/Butterfly.jar
deleted file mode 100644
index 21e2d54..0000000
Binary files a/Butterfly/Butterfly.jar and /dev/null differ
diff --git a/Butterfly/prev_vers/Butterfly_r2013_08_14.jar b/Butterfly/prev_vers/Butterfly_r2013_08_14.jar
deleted file mode 100644
index 4767a2c..0000000
Binary files a/Butterfly/prev_vers/Butterfly_r2013_08_14.jar and /dev/null differ
diff --git a/Butterfly/src/src/jaligner/Alignment.java b/Butterfly/src/src/jaligner/Alignment.java
deleted file mode 100644
index f279e72..0000000
--- a/Butterfly/src/src/jaligner/Alignment.java
+++ /dev/null
@@ -1,692 +0,0 @@
-/*
- * $Id: Alignment.java,v 1.11 2006/08/19 00:42:35 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import jaligner.matrix.Matrix;
-import jaligner.util.Commons;
-
-import java.text.DecimalFormat;
-
-/**
- * Holds the output of a pairwise sequences alignment.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public final class Alignment {
-
- /**
- * Gap character
- */
- public static final char GAP = '-';
-
- /**
- * Default name for sequence #1
- */
- private static final String SEQUENCE1 = "jaligner_1";
-
- /**
- * Default name for sequence #2
- */
- private static final String SEQUENCE2 = "jaligner_2";
-
- /**
- * Scoring matrix
- */
- private Matrix matrix;
-
- /**
- * Gap open cost
- */
- private float open;
-
- /**
- * Gap extend cost
- */
- private float extend;
-
- /**
- * Alignment score
- */
- private float score;
-
- /**
- * Aligned sequence #1
- */
- private char[] sequence1;
-
- /**
- * Name of sequence #1
- */
- private String name1;
-
- /**
- * Alignment start location in sequence #1
- */
- private int start1;
-
- /**
- * Aligned sequence #2
- */
- private char[] sequence2;
-
- /**
- * Name of sequence #2
- */
- private String name2;
-
- /**
- * Alignment start location in sequence #2
- */
- private int start2;
-
- /**
- * Markup line
- */
- private char[] markupLine;
-
- /**
- * Count of identical locations
- */
- private int identity;
-
- /**
- * Count of similar locations
- */
- private int similarity;
-
- /**
- * Count of gap locations
- */
- private int gaps;
-
- private Sequence originalSequence1;
-
- private Sequence originalSequence2;
-
- /**
- * Constructor for Alignment
- */
-
- public Alignment() {
- super();
- }
-
- /**
- * @return Returns the extend.
- */
- public float getExtend() {
- return extend;
- }
-
- /**
- * @param extend
- * The extend to set.
- */
- public void setExtend(float extend) {
- this.extend = extend;
- }
-
- /**
- * @return Returns the matrix.
- */
- public Matrix getMatrix() {
- return matrix;
- }
-
- /**
- * @param matrix
- * The matrix to set.
- */
- public void setMatrix(Matrix matrix) {
- this.matrix = matrix;
- }
-
- /**
- * @return Returns the name1.
- */
- public String getName1() {
- return name1 == null || name1.trim().length() == 0 ? SEQUENCE1 : name1;
- }
-
- /**
- * @param name1
- * The name1 to set.
- */
- public void setName1(String name1) {
- this.name1 = name1;
- }
-
- /**
- * @return Returns the name2.
- */
- public String getName2() {
- return name2 == null || name2.trim().length() == 0 ? SEQUENCE2 : name2;
- }
-
- /**
- * @param name2
- * The name2 to set.
- */
- public void setName2(String name2) {
- this.name2 = name2;
- }
-
- /**
- * @return Returns the open.
- */
- public float getOpen() {
- return open;
- }
-
- /**
- * @param open
- * The open to set.
- */
- public void setOpen(float open) {
- this.open = open;
- }
-
- /**
- * @return Returns the score.
- */
- public float getScore() {
- return score;
- }
-
- /**
- * @param score
- * The score to set.
- */
- public void setScore(float score) {
- this.score = score;
- }
-
- /**
- * Returns the length of the alignment
- *
- * @return Alignment length
- */
- public int getLength() {
- return this.sequence1.length;
- }
-
- /**
- * @return Returns the sequence1.
- */
- public char[] getSequence1() {
- return sequence1;
- }
-
- /**
- * @param sequence1
- * The sequence1 to set.
- */
- public void setSequence1(char[] sequence1) {
- this.sequence1 = sequence1;
- }
-
- /**
- * @return Returns the sequence2.
- */
- public char[] getSequence2() {
- return sequence2;
- }
-
- /**
- * @param sequence2
- * The sequence2 to set.
- */
- public void setSequence2(char[] sequence2) {
- this.sequence2 = sequence2;
- }
-
- /**
- * @return Returns the start1.
- */
- public int getStart1() {
- return start1;
- }
-
- /**
- * @param start1
- * The start1 to set.
- */
- public void setStart1(int start1) {
- this.start1 = start1;
- }
-
- /**
- * @return Returns the start2.
- */
- public int getStart2() {
- return start2;
- }
-
- /**
- * @param start2
- * The start2 to set.
- */
- public void setStart2(int start2) {
- this.start2 = start2;
- }
-
- /**
- * @return Returns the gaps.
- */
- public int getGaps() {
- return gaps;
- }
-
- /**
- * @param gaps
- * The gaps to set.
- */
- public void setGaps(int gaps) {
- this.gaps = gaps;
- }
-
- /**
- * @return Returns the identity.
- */
- public int getIdentity() {
- return identity;
- }
-
- /**
- * @param identity
- * The identity to set.
- */
- public void setIdentity(int identity) {
- this.identity = identity;
- }
-
- /**
- * @return Returns the markupLine.
- */
- public char[] getMarkupLine() {
- return markupLine;
- }
-
- /**
- * @param markupLine
- * The markupLine to set.
- */
- public void setMarkupLine(char[] markupLine) {
- this.markupLine = markupLine;
- }
-
- /**
- * @return Returns the similarity.
- */
- public int getSimilarity() {
- return similarity;
- }
-
- /**
- * @param similarity
- * The similarity to set.
- */
- public void setSimilarity(int similarity) {
- this.similarity = similarity;
- }
-
- /**
- * Returns a summary for alignment
- *
- * @return {@link String} alignment summary
- */
- public String getSummary() {
- StringBuffer buffer = new StringBuffer();
- DecimalFormat f1 = new DecimalFormat("0.00");
- DecimalFormat f2 = new DecimalFormat("0.00%");
-
- int length = getSequence1().length;
-
- buffer.append("Sequence #1: " + getName1());
- buffer.append(Commons.getLineSeparator());
- buffer.append("Sequence #2: " + getName2());
- buffer.append(Commons.getLineSeparator());
- buffer.append("Length #1: " + getOriginalSequence1().length());
- buffer.append(Commons.getLineSeparator());
- buffer.append("Length #2: " + getOriginalSequence2().length());
- buffer.append(Commons.getLineSeparator());
- buffer.append("Matrix: "
- + (matrix.getId() == null ? "" : matrix.getId()));
- buffer.append(Commons.getLineSeparator());
- buffer.append("Gap open: " + open);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Gap extend: " + extend);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Length: " + length);
- buffer.append(Commons.getLineSeparator());
- buffer.append("Identity: " + identity + "/" + length + " ("
- + f2.format(identity / (float) length) + ")");
- buffer.append(Commons.getLineSeparator());
- buffer.append("Similarity: " + similarity + "/" + length + " ("
- + f2.format(similarity / (float) length) + ")");
- buffer.append(Commons.getLineSeparator());
- buffer.append("Gaps: " + gaps + "/" + length + " ("
- + f2.format(gaps / (float) length) + ")");
- buffer.append(Commons.getLineSeparator());
- buffer.append("Score: " + f1.format(score));
- buffer.append(Commons.getLineSeparator());
-
- return buffer.toString();
- }
-
- /**
- * Calculate the score of the alignment, not using the score field (the
- * function only uses sequence1, sequence2, matrix and gap penalties).
- *
- * @return the calculated score (By: Bram Minnaert)
- */
- public float calculateScore() {
- // The calculated score
- float calcScore = 0;
-
- // In the previous step there was a gap in the first sequence
- boolean previous1wasGap = false;
-
- // In the previous step there was a gap in the second sequence
- boolean previous2wasGap = false;
-
- int start = 0;
- int end = sequence1.length - 1;
-
- char c1, c2; // the next character
- for (int i = start; i <= end; i++) {
- c1 = sequence1[i];
- c2 = sequence2[i];
- // the next character in the first sequence is a gap
- if (c1 == GAP) {
- if (previous1wasGap) {
- calcScore -= extend;
- } else {
- calcScore -= open;
- }
- previous1wasGap = true;
- previous2wasGap = false;
- }
- // the next character in the second sequence is a gap
- else if (c2 == GAP) {
- if (previous2wasGap) {
- calcScore -= extend;
- } else {
- calcScore -= open;
- }
- previous1wasGap = false;
- previous2wasGap = true;
- }
- // the next characters in boths sequences are not gaps
- else {
- calcScore += matrix.getScore(c1, c2);
- previous1wasGap = false;
- previous2wasGap = false;
- }
- }
- return calcScore;
- }
-
- /**
- * Calculate the score of the alignment without the terminal gaps.
- *
- */
- public float getScoreWithNoTerminalGaps() {
- // The calculated score
- float calcScore = 0;
-
- // In the previous step there was a gap in the first sequence
- boolean previous1wasGap = false;
-
- // In the previous step there was a gap in the second sequence
- boolean previous2wasGap = false;
-
- int start = 0;
- int end = sequence1.length - 1;
-
- if (sequence1[start] == GAP) {
- while (sequence1[start] == GAP) {
- start++;
- }
- } else if (sequence2[start] == GAP) {
- while (sequence2[start] == GAP) {
- start++;
- }
- }
-
- if (sequence1[end] == GAP) {
- while (sequence1[end] == GAP) {
- end--;
- }
- } else if (sequence2[end] == GAP) {
- while (sequence2[end] == GAP) {
- end--;
- }
- }
-
- char c1, c2; // the next character
- for (int i = start; i <= end; i++) {
- c1 = sequence1[i];
- c2 = sequence2[i];
- // the next character in the first sequence is a gap
- if (c1 == GAP) {
- if (previous1wasGap) {
- calcScore -= extend;
- } else {
- calcScore -= open;
- }
- previous1wasGap = true;
- previous2wasGap = false;
- }
- // the next character in the second sequence is a gap
- else if (c2 == GAP) {
- if (previous2wasGap) {
- calcScore -= extend;
- } else {
- calcScore -= open;
- }
- previous1wasGap = false;
- previous2wasGap = true;
- }
- // the next characters in boths sequences are not gaps
- else {
- calcScore += matrix.getScore(c1, c2);
- previous1wasGap = false;
- previous2wasGap = false;
- }
- }
- return calcScore;
- }
-
- /**
- * Check if the calculated score matches the field score.
- *
- * @return true if equal, else false. (By: Bram Minnaert)
- */
- public boolean checkScore() {
- if (calculateScore() == score) {
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Returns original {@link Sequence} #1
- *
- * @return original {@link Sequence} #1
- */
- public Sequence getOriginalSequence1() {
- return originalSequence1;
- }
-
- /**
- *
- * @param originalSequence1
- */
- public void setOriginalSequence1(Sequence originalSequence1) {
- this.originalSequence1 = originalSequence1;
- }
-
- /**
- * Returns original {@link Sequence} #2
- *
- * @return original {@link Sequence} #2
- */
- public Sequence getOriginalSequence2() {
- return originalSequence2;
- }
-
- /**
- *
- * @param originalSequence2
- */
- public void setOriginalSequence2(Sequence originalSequence2) {
- this.originalSequence2 = originalSequence2;
- }
-
- /**
- * Returns the number of gaps of the aligned sequence #1
- *
- * @return the number of gaps of the aligned sequence #1
- */
- public int getGaps1() {
- int count = 0;
- for (int i = 0, n = sequence1.length; i < n; i++) {
- if (sequence1[i] == Alignment.GAP) {
- count++;
- }
- }
- return count;
- }
-
- /**
- * Returns the number of gaps of the aligned sequence #2
- *
- * @return the number of gaps of the aligned sequence #2
- */
- public int getGaps2() {
- int count = 0;
- for (int i = 0, n = sequence2.length; i < n; i++) {
- if (sequence2[i] == Alignment.GAP) {
- count++;
- }
- }
- return count;
- }
-
- /**
- * Adds this alignment to another alignment, the order is important.
- *
- * @param a1
- * The 1st alignment
- * @param a2
- * The 2nd alignment
- * @return the sum of two alignment
- */
- public static Alignment add(Alignment a1, Alignment a2) {
-
- if (a1 == null) {
- if (a2 == null) {
- return null;
- } else {
- return copy(a2);
- }
- } else {
- if (a2 == null) {
- return copy(a1);
- } else {
- Alignment sum = new Alignment();
-
- StringBuffer buffer = new StringBuffer();
-
- buffer.append(a1.getOriginalSequence1());
- buffer.append(a2.getOriginalSequence1());
-
- sum.setOriginalSequence1(new Sequence(buffer.toString()));
-
- buffer = new StringBuffer();
-
- buffer.append(a1.getOriginalSequence2());
- buffer.append(a2.getOriginalSequence2());
-
- sum.setOriginalSequence2(new Sequence(buffer.toString()));
-
- buffer = new StringBuffer();
-
- buffer.append(a1.getSequence1());
- buffer.append(a2.getSequence1());
-
- sum.setSequence1(buffer.toString().toCharArray());
-
- buffer = new StringBuffer();
-
- buffer.append(a1.getSequence2());
- buffer.append(a2.getSequence2());
-
- sum.setSequence2(buffer.toString().toCharArray());
-
- buffer = new StringBuffer();
-
- buffer.append(a1.getMarkupLine());
- buffer.append(a2.getMarkupLine());
-
- sum.setMarkupLine(buffer.toString().toCharArray());
-
- sum.setScore(a1.getScore() + a2.getScore());
- sum.setGaps(a1.getGaps() + a2.getGaps());
-
- sum.setStart1(a1.getStart1());
- sum.setStart2(a1.getStart2());
- sum.setExtend(a1.getExtend());
- sum.setOpen(a1.getOpen());
- sum.setMatrix(a1.getMatrix());
-
- return sum;
- }
- }
- }
-
- /**
- * Copies an alignment to another alignment.
- *
- * @param alignment
- * Alignment
- */
- public static Alignment copy(Alignment alignment) {
-
- Alignment copy = new Alignment();
-
- copy.setSequence1(alignment.getSequence1());
- copy.setSequence2(alignment.getSequence2());
- copy.setMarkupLine(alignment.getMarkupLine());
- copy.setScore(alignment.getScore());
- copy.setGaps(alignment.getGaps());
- copy.setStart1(alignment.getStart1());
- copy.setStart2(alignment.getStart2());
- copy.setExtend(alignment.getExtend());
- copy.setOpen(alignment.getOpen());
- copy.setMatrix(alignment.getMatrix());
- copy.setOriginalSequence1(alignment.getOriginalSequence1());
- copy.setOriginalSequence2(alignment.getOriginalSequence2());
-
- return copy;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/Cell.java b/Butterfly/src/src/jaligner/Cell.java
deleted file mode 100644
index 165ce69..0000000
--- a/Butterfly/src/src/jaligner/Cell.java
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * $Id: Cell.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * A cell in a similarity matrix, to hold row, column and score.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class Cell {
- /**
- * Row of the cell
- */
- private int row;
- /**
- * Column of the cell
- */
- private int col;
- /**
- * Alignment score at this cell
- */
- private float score;
-
- /**
- * Constructor
- */
- public Cell() {
- super();
- this.row = 0;
- this.col = 0;
- this.score = Float.NEGATIVE_INFINITY;
- }
- /**
- * @return Returns the col.
- */
- public int getCol() {
- return this.col;
- }
- /**
- * @param col The col to set.
- */
- public void setCol(int col) {
- this.col = col;
- }
- /**
- * @return Returns the row.
- */
- public int getRow() {
- return this.row;
- }
- /**
- * @param row The row to set.
- */
- public void setRow(int row) {
- this.row = row;
- }
- /**
- * @return Returns the score.
- */
- public float getScore() {
- return this.score;
- }
- /**
- * @param score The score to set.
- */
- public void setScore(float score) {
- this.score = score;
- }
-
- /**
- * Sets the row, column and score of the cell.
- * @param row The row to set.
- * @param col The col to set.
- * @param score The score to set.
- */
- public void set(int row, int col, float score) {
- this.row = row;
- this.col = col;
- this.score = score;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/Directions.java b/Butterfly/src/src/jaligner/Directions.java
deleted file mode 100644
index 2bd067f..0000000
--- a/Butterfly/src/src/jaligner/Directions.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * $Id: Directions.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * Traceback directions.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public abstract class Directions {
- /**
- * Traceback direction stop
- */
- public static final byte STOP = 0;
- /**
- * Traceback direction left
- */
- public static final byte LEFT = 1;
- /**
- * Traceback direction diagonal
- */
- public static final byte DIAGONAL = 2;
- /**
- * Traceback direction up
- */
- public static final byte UP = 3;
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/Markups.java b/Butterfly/src/src/jaligner/Markups.java
deleted file mode 100644
index 61599fa..0000000
--- a/Butterfly/src/src/jaligner/Markups.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * $Id: Markups.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * Markups line characters.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public abstract class Markups {
- /**
- * Markup line identity character
- */
- public static final char IDENTITY = '|';
-
- /**
- * Markup line similarity character
- */
- public static final char SIMILARITY = ':';
-
- /**
- * Markup line gap character
- */
- public static final char GAP = ' ';
-
- /**
- * Markup line mismatch character
- */
- public static final char MISMATCH = '.';
-}
diff --git a/Butterfly/src/src/jaligner/NeedlemanWunsch.java b/Butterfly/src/src/jaligner/NeedlemanWunsch.java
deleted file mode 100644
index 8e072b1..0000000
--- a/Butterfly/src/src/jaligner/NeedlemanWunsch.java
+++ /dev/null
@@ -1,304 +0,0 @@
-/*
- * $Id: NeedlemanWunsch.java,v 1.4 2006/02/09 12:23:24 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import jaligner.matrix.Matrix;
-
-/**
- * An implementation of the Needleman-Wunsch algorithm for biological global
- * pairwise sequence alignment.
- *
- * <br>
- * Reference: <a
- * href="http://www.sbc.su.se/~per/molbioinfo2001/dynprog/adv_dynamic.html">Advanced
- * Dynamic Programming Tutorial</a>.
- *
- *
- * @author <a href="ahmed at users.sf.net">Ahmed Moustafa</a>
- */
-
-public final class NeedlemanWunsch {
- /**
- * Hidden constructor
- */
- private NeedlemanWunsch() {
- super();
- }
-
- /**
- * Aligns two sequences by Needleman-Wunsch (global)
- *
- * @param s1
- * sequene #1 ({@link Sequence})
- * @param s2
- * sequene #2 ({@link Sequence})
- * @param matrix
- * scoring matrix ({@link Matrix})
- * @param gap
- * open gap penalty
- * @return alignment object contains the two aligned sequences, the
- * alignment score and alignment statistics
- * @see Sequence
- * @see Matrix
- */
- public static Alignment align(Sequence s1, Sequence s2, Matrix matrix,
- float gap) {
- float[][] scores = matrix.getScores();
-
- int m = s1.length() + 1;
- int n = s2.length() + 1;
-
- byte[][] pointers = new byte[m][n];
-
- // Initializes the element (0,0) of the traceback matrix to STOP.
- pointers[0][0] = Directions.STOP;
-
- // Initializes the boundaries of the traceback matrix.
- for (int i = 1; i < m; i++) {
- pointers[i][0] = Directions.UP;
- }
- for (int j = 1; j < n; j++) {
- pointers[0][j] = Directions.LEFT;
- }
-
- Cell cell = construct(s1, s2, scores, gap, pointers);
- Alignment alignment = traceback(s1, s2, matrix, pointers, cell);
-
- alignment.setOriginalSequence1(s1);
- alignment.setOriginalSequence2(s2);
- alignment.setMatrix(matrix);
- alignment.setOpen(gap);
- alignment.setExtend(gap);
-
- if (s1.getId() != null) {
- alignment.setName1(s1.getId());
- }
- if (s2.getId() != null) {
- alignment.setName2(s2.getId());
- }
-
- return alignment;
- }
-
- /**
- * Constructs directions matrix for the traceback.
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param matrix
- * scoring matrix
- * @param gap
- * gap penalty
- * @param pointers
- * traceback matrix
- *
- * @return The cell where the traceback starts.
- */
- private static Cell construct(Sequence s1, Sequence s2, float[][] matrix,
- float gap, byte[][] pointers) {
-
- Cell cell = new Cell();
-
- char[] a1 = s1.toArray();
- char[] a2 = s2.toArray();
-
- int m = s1.length() + 1; // number of rows in similarity matrix
- int n = s2.length() + 1; // number of columns in similarity matrix
-
- // float[] v = new float[n]; // optimal alignment
- float[] v = new float[n];
-
- // Initialization of v
- for (int j = 1; j < n; j++) {
- v[j] = j * -gap;
- }
- v[0] = 0;
-
- float x, y, z;
- float vOld = 0;
-
- // Fill the matrices
- for (int i = 1; i < m; i++) { // for all rows
- v[0] = i * -gap;
-
- for (int j = 1; j < n; j++) { // for all columns
-
- x = v[j] - gap;
- y = v[j - 1] - gap;
- z = vOld + matrix[a1[i - 1]][a2[j - 1]];
-
- vOld = v[j];
- v[j] = maximum(x, y, z);
-
- // Determine the traceback direction
- if (v[j] == x) {
- pointers[i][j] = Directions.UP;
- } else if (v[j] == y) {
- pointers[i][j] = Directions.LEFT;
- } else {
- pointers[i][j] = Directions.DIAGONAL;
- }
-
- } // loop columns
-
- vOld = i * -gap;
- } // loop rows
-
- // cell contains the row number, the column number
- // and the score of the cell with the maximum score
-
- // Set the traceback start at the last cell m, n
- // because we are doing global alignment
- cell.set(m - 1, n - 1, v[n - 1]);
- return cell;
- }
-
- /**
- * Returns the alignment of two sequences based on the passed array of
- * pointers
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param m
- * scoring matrix
- * @param pointers
- * traceback matrix
- * @param cell
- * The cell where the traceback starts.
- * @return {@link Alignment} with the two aligned sequences and alignment
- * score.
- * @see Cell
- * @see Alignment
- */
- private static Alignment traceback(Sequence s1, Sequence s2, Matrix m,
- byte[][] pointers, Cell cell) {
- char[] array1 = s1.toArray();
- char[] array2 = s2.toArray();
- float[][] scores = m.getScores();
-
- Alignment alignment = new Alignment();
- alignment.setScore(cell.getScore());
-
- // maximum length after the aligned sequences
- int maxlen = s1.length() + s2.length();
-
- char[] reversed1 = new char[maxlen]; // reversed sequence #1
- char[] reversed2 = new char[maxlen]; // reversed sequence #2
- char[] reversed3 = new char[maxlen]; // reversed markup
-
- int len1 = 0; // length of sequence #1 after alignment
- int len2 = 0; // length of sequence #2 after alignment
- int len3 = 0; // length of the markup line
-
- int identity = 0; // count of identitcal pairs
- int similarity = 0; // count of similar pairs
- int gaps = 0; // count of gaps
-
- char c1, c2;
-
- int i = cell.getRow(); // traceback start row
- int j = cell.getCol(); // traceback start col
-
- // Traceback flag, where true => continue and false => stop
- boolean stillGoing = true;
- while (stillGoing) {
- switch (pointers[i][j]) {
- case Directions.UP:
- reversed1[len1++] = array1[--i];
- reversed2[len2++] = Alignment.GAP;
- reversed3[len3++] = Markups.GAP;
- gaps++;
- break;
- case Directions.DIAGONAL:
- c1 = array1[--i];
- c2 = array2[--j];
- reversed1[len1++] = c1;
- reversed2[len2++] = c2;
- if (c1 == c2) {
- reversed3[len3++] = Markups.IDENTITY;
- identity++;
- similarity++;
- } else if (scores[c1][c2] > 0) {
- reversed3[len3++] = Markups.SIMILARITY;
- similarity++;
- } else {
- reversed3[len3++] = Markups.MISMATCH;
- }
- break;
- case Directions.LEFT:
- reversed1[len1++] = Alignment.GAP;
- reversed2[len2++] = array2[--j];
- reversed3[len3++] = Markups.GAP;
- gaps++;
- break;
- case Directions.STOP:
- stillGoing = false;
- }
- }
-
- alignment.setSequence1(reverse(reversed1, len1));
- alignment.setStart1(i);
- alignment.setSequence2(reverse(reversed2, len2));
- alignment.setStart2(j);
- alignment.setMarkupLine(reverse(reversed3, len3));
- alignment.setIdentity(identity);
- alignment.setGaps(gaps);
- alignment.setSimilarity(similarity);
-
- return alignment;
- }
-
- /**
- * Returns the maximum of two float numbers.
- *
- * @param a
- * float #1
- * @param b
- * float #2
- * @param c
- * float #3
- * @return the maximum of a and b
- */
- private static float maximum(float a, float b, float c) {
- if (a > b) {
- return a > c ? a : c;
- } else {
- return b > c ? b : c;
- }
- }
-
- /**
- * Reverses an array of chars
- *
- * @param a
- * @param len
- * @return the input array of char reserved
- */
- private static char[] reverse(char[] a, int len) {
- char[] b = new char[len];
- for (int i = len - 1, j = 0; i >= 0; i--, j++) {
- b[j] = a[i];
- }
- return b;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/NeedlemanWunschGotoh.java b/Butterfly/src/src/jaligner/NeedlemanWunschGotoh.java
deleted file mode 100644
index f321d37..0000000
--- a/Butterfly/src/src/jaligner/NeedlemanWunschGotoh.java
+++ /dev/null
@@ -1,432 +0,0 @@
-/*
- * $Id: NeedlemanWunschGotoh.java,v 1.12 2006/04/05 00:18:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-package jaligner;
-
-import jaligner.matrix.Matrix;
-
-import java.util.logging.Logger;
-
-/**
- * An implementation of the Needleman-Wunsch algorithm with Gotoh's improvement
- * for biological global pairwise sequence alignment.
- *
- * Modified to use int[[] for lengths array for deal with long sequences by Josh Bowden, CSIRO
- *
- * @author Ahmed Moustafa
- * @author Bram Minnaert
- * @version $Revision: 1.12 $
- */
-
-public final class NeedlemanWunschGotoh {
-
- /**
- * Logger
- */
- private static final Logger logger = Logger
- .getLogger(NeedlemanWunschGotoh.class.getSimpleName());
-
- /**
- * Hidden constructor
- */
- private NeedlemanWunschGotoh() {
- super();
- }
-
- /**
- * Aligns two sequences by Needleman-Wunsch (global)
- *
- * @param s1
- * sequene #1 ({@link Read})
- * @param s2
- * sequene #2 ({@link Read})
- * @param matrix
- * scoring matrix ({@link Matrix})
- * @param o
- * open gap penalty
- * @param e
- * extend gap penalty
- * @return alignment object contains the two aligned sequences, the
- * alignment score and alignment statistics
- * @see Read
- * @see Matrix
- */
- public static Alignment align(Sequence s1, Sequence s2, Matrix matrix,
- float o, float e) {
-
- float[][] scores = matrix.getScores();
-
- Sequence _s1;
- Sequence _s2;
-
- if (s1.length() < s2.length()) {
- _s1 = s2;
- _s2 = s1;
- } else {
- _s1 = s1;
- _s2 = s2;
- }
-
- int m = _s1.length() + 1;
- int n = _s2.length() + 1;
-
- byte[] pointers = new byte[m * n];
-
- int[] lengths = new int[m * n]; // was short
-
- // Initializes the element (0,0) of the traceback matrix to STOP.
- pointers[0] = Directions.STOP;
-
- // Initializes the boundaries of the traceback matrix.
- for (int i = 1, k = n; i < m; i++, k += n) {
- pointers[k] = Directions.UP;
- lengths[k] = (int) i; // was short
- }
- for (int j = 1; j < n; j++) {
- pointers[j] = Directions.LEFT;
- lengths[j] = (int) j; // was short
- }
-
- Cell cell = construct(_s1, _s2, scores, o, e, pointers, lengths);
-
- Alignment alignment = traceback(_s1, _s2, matrix, pointers, cell,
- lengths);
-
- alignment.setMatrix(matrix);
- alignment.setOpen(o);
- alignment.setExtend(e);
- alignment.setName1(_s1.getId());
- alignment.setName2(_s2.getId());
- alignment.setOriginalSequence1(_s1);
- alignment.setOriginalSequence2(_s2);
-
- return alignment;
- }
-
- /**
- * Constructs directions matrix for the traceback.
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param matrix
- * scoring matrix
- * @param o
- * open gap penalty
- * @param e
- * extend gap penalty
- * @param pointers
- * traceback matrix
- *
- * @return The cell where the traceback starts.
- */
- private static Cell construct(Sequence s1, Sequence s2, float[][] matrix,
- float o, float e, byte[] pointers, int[] lengths) { // was short[] lengths
-
- //logger.info("Started...");
-
- char[] a1 = s1.toArray();
- char[] a2 = s2.toArray();
-
- int m = s1.length() + 1; // number of rows in similarity matrix
- int n = s2.length() + 1; // number of columns in similarity matrix
-
- float[] v = new float[n];
- float vDiagonal = 0;// Float.NEGATIVE_INFINITY; // best score in cell
- float f = Float.NEGATIVE_INFINITY; // score from diagonal
- float h = Float.NEGATIVE_INFINITY; // best score ending with gap from
- // left
- float[] g = new float[n]; // best score ending with gap from above
-
- // Initialization of v and g
- g[0] = Float.NEGATIVE_INFINITY;
- for (int j = 1; j < n; j++) {
- v[j] = 0;// -o - (j - 1) * e;
- g[j] = Float.NEGATIVE_INFINITY;
- }
-
- int lengthOfHorizontalGap = 0;
- int[] lengthOfVerticalGap = new int[n];
-
- float similarityScore;
- float maximumScore = Float.NEGATIVE_INFINITY;
- int maxi = 0;
- int maxj = 0;
-
- // Fill the matrices
- for (int i = 1, k = n; i < m; i++, k += n) { // for all rows
- v[0] = -o - (i - 1) * e;
- for (int j = 1, l = k + 1; j < n; j++, l++) { // for all columns
-
- similarityScore = matrix[a1[i - 1]][a2[j - 1]];
-
- f = vDiagonal + similarityScore;// from diagonal
-
- // Which cell from the left?
- if (h - e >= v[j - 1] - o) {
- h -= e;
- lengthOfHorizontalGap++;
- } else {
- h = v[j - 1] - o;
- lengthOfHorizontalGap = 1;
- }
-
- // Which cell from above?
- if (g[j] - e >= v[j] - o) {
- g[j] = g[j] - e;
- lengthOfVerticalGap[j] = lengthOfVerticalGap[j] + 1;
- } else {
- g[j] = v[j] - o;
- lengthOfVerticalGap[j] = 1;
- }
-
- vDiagonal = v[j];
- v[j] = maximum(f, g[j], h); // best one
- if (v[j] > maximumScore) {
- maximumScore = v[j];
- maxi = i;
- maxj = j;
- }
-
- // Determine the traceback direction
- if (v[j] == f) {
- pointers[l] = Directions.DIAGONAL;
- } else if (v[j] == g[j]) {
- pointers[l] = Directions.UP;
- lengths[l] = (int) lengthOfVerticalGap[j]; // was short
- } else if (v[j] == h) {
- pointers[l] = Directions.LEFT;
- lengths[l] = (int) lengthOfHorizontalGap; // was short
- }
-
- } // loop columns
-
- // Reset
- h = Float.NEGATIVE_INFINITY;
- vDiagonal = 0;// -o - (i - 1) * e;
-
- lengthOfHorizontalGap = 0;
-
- } // loop rows
-
- Cell cell = new Cell();
- cell.set(maxi, maxj, v[n - 1]);
-
- //logger.info("Finished.");
-
- return cell;
- }
-
- /**
- * Returns the alignment of two sequences based on the passed array of
- * pointers
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param m
- * scoring matrix
- * @param pointers
- * traceback matrix
- * @param cell
- * The cell where the traceback starts.
- * @return {@link Alignment} with the two aligned sequences and alignment
- * score.
- * @see Cell
- * @see Alignment
- */
- private static Alignment traceback(Sequence s1, Sequence s2, Matrix m,
- byte[] pointers, Cell cell, int[] lengths) { // was short[] lengths
- //logger.info("Started...");
-
- char[] array1 = s1.toArray();
- char[] array2 = s2.toArray();
- float[][] scores = m.getScores();
-
- Alignment alignment = new Alignment();
- alignment.setScore(cell.getScore());
-
- // maximum length after the aligned sequences
- int maxlen = s1.length() + s2.length();
-
- char[] reversed1 = new char[maxlen]; // reversed sequence #1
- char[] reversed2 = new char[maxlen]; // reversed sequence #2
- char[] reversed3 = new char[maxlen]; // reversed markup
-
- int len1 = 0; // length of sequence #1 after alignment
- int len2 = 0; // length of sequence #2 after alignment
- int len3 = 0; // length of the markup line
-
- int identity = 0; // count of identitcal pairs
- int similarity = 0; // count of similar pairs
- int gaps = 0; // count of gaps
-
- char c1, c2;
-
- int i = cell.getRow(); // traceback start row
- int j = cell.getCol(); // traceback start col
- int n = s2.length() + 1;
- int row = i * n;
-
- int a = s1.length() - 1;
- int b = s2.length() - 1;
- if (a - i > b - j) {
- for (; a - i > b - j; a--) {
- reversed1[len1++] = array1[a];
- reversed2[len2++] = Alignment.GAP;
- reversed3[len3++] = Markups.GAP;
- gaps++;
- }
- for (; b > j - 1; a--, b--) {
- c1 = array1[a];
- c2 = array2[b];
-
- reversed1[len1++] = c1;
- reversed2[len2++] = c2;
-
- if (c1 == c2) {
- reversed3[len3++] = Markups.IDENTITY;
- identity++;
- similarity++;
- } else if (scores[c1][c2] > 0) {
- reversed3[len3++] = Markups.SIMILARITY;
- similarity++;
- } else {
- reversed3[len3++] = Markups.MISMATCH;
- }
- }
- } else {
- for (; b - j > a - i; b--) {
- reversed1[len1++] = Alignment.GAP;
- reversed2[len2++] = array2[b];
- reversed3[len3++] = Markups.GAP;
- gaps++;
- }
- for (; a > i - 1; a--, b--) {
- c1 = array1[a];
- c2 = array2[b];
-
- reversed1[len1++] = c1;
- reversed2[len2++] = c2;
-
- if (c1 == c2) {
- reversed3[len3++] = Markups.IDENTITY;
- identity++;
- similarity++;
- } else if (scores[c1][c2] > 0) {
- reversed3[len3++] = Markups.SIMILARITY;
- similarity++;
- } else {
- reversed3[len3++] = Markups.MISMATCH;
- }
- }
- }
-
- // Traceback flag, where true => continue and false => stop
- boolean stillGoing = true;
- while (stillGoing) {
- int l = row + j;
- switch (pointers[l]) {
- case Directions.UP:
- for (int k = 0, len = lengths[l]; k < len; k++) {
- reversed1[len1++] = array1[--i];
- reversed2[len2++] = Alignment.GAP;
- reversed3[len3++] = Markups.GAP;
- row -= n;
- gaps++;
- }
- break;
- case Directions.DIAGONAL:
- c1 = array1[--i];
- c2 = array2[--j];
- reversed1[len1++] = c1;
- reversed2[len2++] = c2;
- row -= n;
- if (c1 == c2) {
- reversed3[len3++] = Markups.IDENTITY;
- identity++;
- similarity++;
- } else if (scores[c1][c2] > 0) {
- reversed3[len3++] = Markups.SIMILARITY;
- similarity++;
- } else {
- reversed3[len3++] = Markups.MISMATCH;
- }
- break;
- case Directions.LEFT:
- for (int k = 0, len = lengths[l]; k < len; k++) {
- reversed1[len1++] = Alignment.GAP;
- reversed2[len2++] = array2[--j];
- reversed3[len3++] = Markups.GAP;
- gaps++;
- }
- break;
- case Directions.STOP:
- stillGoing = false;
- }
- }
-
- alignment.setSequence1(reverse(reversed1, len1));
- alignment.setStart1(i);
- alignment.setSequence2(reverse(reversed2, len2));
- alignment.setStart2(j);
- alignment.setMarkupLine(reverse(reversed3, len3));
- alignment.setIdentity(identity);
- alignment.setGaps(gaps);
- alignment.setSimilarity(similarity);
-
- //logger.info("Finished.");
-
- return alignment;
- }
-
- /**
- * Returns the maximum of two float numbers.
- *
- * @param a
- * float #1
- * @param b
- * float #2
- * @param c
- * float #3
- * @return the maximum of a and b
- */
- private static float maximum(float a, float b, float c) {
- if (a > b) {
- return a > c ? a : c;
- } else {
- return b > c ? b : c;
- }
- }
-
- /**
- * Reverses an array of chars
- *
- * @param a
- * @param len
- * @return the input array of char reserved
- */
- private static char[] reverse(char[] a, int len) {
- char[] b = new char[len];
- for (int i = len - 1, j = 0; i >= 0; i--, j++) {
- b[j] = a[i];
- }
- return b;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/Sequence.java b/Butterfly/src/src/jaligner/Sequence.java
deleted file mode 100644
index d05f3c4..0000000
--- a/Butterfly/src/src/jaligner/Sequence.java
+++ /dev/null
@@ -1,250 +0,0 @@
-/*
- * $Id: Sequence.java,v 1.6 2006/07/27 16:28:24 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import jaligner.util.Commons;
-
-import java.io.Serializable;
-
-/**
- * A basic (nucleic or protein) sequence. It's a wrapper to
- * {@link java.lang.String}.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class Sequence implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 3256721801357898297L;
-
- /**
- * Sequence type nucleic.
- */
- public static final int NUCLEIC = 0;
-
- /**
- * Sequence type protein.
- */
- public static final int PROTEIN = 1;
-
- /**
- * Sequence
- */
- private String sequence;
-
- /**
- * Sequence id.
- */
- private String id = null;
-
- /**
- * Sequence description.
- */
- private String description = null;
-
- /**
- * Sequence type.
- */
- private int type = PROTEIN;
-
- /**
- * Constructor
- */
- public Sequence() {
- super();
- }
-
- /**
- * Constructor
- *
- * @param sequence
- */
- public Sequence(String sequence) {
- super();
- this.sequence = sequence;
- }
-
- /**
- * Constructor
- *
- * @param name
- * @param sequence
- */
- public Sequence(String name, char[] sequence) {
- super();
- this.id = name;
- this.sequence = new String(sequence);
- }
-
- /**
- * Constructor
- *
- * @param name
- * @param sequence
- */
- public Sequence(String name, String sequence) {
- super();
- this.id = name;
- this.sequence = sequence;
- }
-
- /**
- * Constructor
- *
- * @param sequence
- * @param id
- * @param description
- * @param type
- */
- public Sequence(String sequence, String id, String description, int type) {
- super();
- this.sequence = sequence;
- this.id = id;
- this.description = description;
- this.type = type;
- }
-
- /**
- * Returns the sequence string
- *
- * @return Returns the sequence
- */
- public String getSequence() {
- return sequence;
- }
-
- /**
- * Sets the sequence string
- *
- * @param sequence
- * The sequence to set
- */
- public void setSequence(String sequence) {
- this.sequence = sequence;
- }
-
- /**
- * Returns the sequence id
- *
- * @return Returns the id
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the sequence id
- *
- * @param id
- * The id to set
- */
- public void setId(String id) {
- this.id = id;
- }
-
- /**
- * Returns the sequence description
- *
- * @return Returns the description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the sequence description
- *
- * @param description
- * The description to set
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * Returns the sequence type (nucleic or protein)
- *
- * @return Returns the type
- */
- public int getType() {
- return type;
- }
-
- /**
- * Sets the sequence type (nucleic or protein)
- *
- * @param type
- * The type to set
- */
- public void setType(int type) {
- this.type = type;
- }
-
- /**
- * Returns the length of the sequence
- *
- * @return sequence length
- */
- public int length() {
- return this.sequence.length();
- }
-
- /**
- * Returns a subsequence
- *
- * @param index
- * start index
- * @param length
- * length of subsequence
- * @return subsequence
- */
- public String subsequence(int index, int length) {
- return this.sequence.substring(index, index + length);
- }
-
- /**
- * Returns the acid at specific location in the sequence
- *
- * @param index
- * @return acid at index
- */
- public char acidAt(int index) {
- return this.sequence.charAt(index);
- }
-
- /**
- * Returns the sequence as an array of characters.
- *
- * @return array of chars.
- */
- public char[] toArray() {
- return this.sequence.toCharArray();
- }
-
- /**
- * Returns the sequence id and the sequence string
- *
- * @return Returns the sequence id and the sequence string
- */
- public String toString() {
- return id + Commons.TAB + sequence;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/SmithWatermanGotoh.java b/Butterfly/src/src/jaligner/SmithWatermanGotoh.java
deleted file mode 100644
index 695a283..0000000
--- a/Butterfly/src/src/jaligner/SmithWatermanGotoh.java
+++ /dev/null
@@ -1,388 +0,0 @@
-/*
- * $Id: SmithWatermanGotoh.java,v 1.10 2006/02/09 13:27:36 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-import jaligner.matrix.Matrix;
-
-import java.util.logging.Logger;
-
-/**
- * An implementation of the Smith-Waterman algorithm with Gotoh's improvement
- * for biological local pairwise sequence alignment.
- *
- * <strong>Recursive definition:</strong>
- * <ul>
- * <li>
- * <strong>Base conditions:</strong>
- * <ul>
- * <li><code>V(0, 0) = 0</code></li>
- * <li><code>V(i, 0) = E(i, 0) = W<sub>g</sub> + iW<sub>s</sub></code></li>
- * <li><code>V(0, j) = F(0, j) = W<sub>g</sub> + jW<sub>s</sub></code></li>
- * </ul>
- * </li>
- * <li>
- * <strong>Recurrence relation:</strong>
- * <ul>
- * <li><code>V(i, j) = max{E(i, j), F(i, j), G(i, j)}</code>, where:</li>
- * <li><code>G(i, j) = V(i - 1, j - 1) + similarity(S<sub>i</sub>, T<sub>j</sub>)</code></li>
- * <li><code>E(i, j) = max{E(i, j - 1) + W<sub>s</sub>, V(i, j - 1) + W<sub>g</sub> + W<sub>s</sub>}</code></li>
- * <li><code>F(i, j) = max{F(i - 1, j) + W<sub>s</sub>, V(i - 1, j) + W<sub>g</sub> + W<sub>s</sub>}</code></li>
- * </ul>
- * </ul>
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public final class SmithWatermanGotoh {
- /**
- * Hidden constructor
- */
- private SmithWatermanGotoh() {
- super();
- }
-
- /**
- * Logger
- */
- private static final Logger logger = Logger
- .getLogger(SmithWatermanGotoh.class.getName());
-
- /**
- * Aligns two sequences by Smith-Waterman (local)
- *
- * @param s1
- * sequene #1 ({@link Sequence})
- * @param s2
- * sequene #2 ({@link Sequence})
- * @param matrix
- * scoring matrix ({@link Matrix})
- * @param o
- * open gap penalty
- * @param e
- * extend gap penalty
- * @return alignment object contains the two aligned sequences, the
- * alignment score and alignment statistics
- * @see Sequence
- * @see Matrix
- */
- public static Alignment align(Sequence s1, Sequence s2, Matrix matrix,
- float o, float e) {
- //logger.info("Started...");
- long start = System.currentTimeMillis();
- float[][] scores = matrix.getScores();
-
- int m = s1.length() + 1;
- int n = s2.length() + 1;
-
- byte[] pointers = new byte[m * n];
-
- // Initializes the boundaries of the traceback matrix to STOP.
- for (int i = 0, k = 0; i < m; i++, k += n) {
- pointers[k] = Directions.STOP;
- }
- for (int j = 1; j < n; j++) {
- pointers[j] = Directions.STOP;
- }
-
- short[] sizesOfVerticalGaps = new short[m * n];
- short[] sizesOfHorizontalGaps = new short[m * n];
- for (int i = 0, k = 0; i < m; i++, k += n) {
- for (int j = 0; j < n; j++) {
- sizesOfVerticalGaps[k + j] = sizesOfHorizontalGaps[k + j] = 1;
- }
- }
-
- Cell cell = SmithWatermanGotoh.construct(s1, s2, scores, o, e,
- pointers, sizesOfVerticalGaps, sizesOfHorizontalGaps);
- Alignment alignment = SmithWatermanGotoh.traceback(s1, s2, matrix,
- pointers, cell, sizesOfVerticalGaps, sizesOfHorizontalGaps);
- alignment.setOriginalSequence1(s1);
- alignment.setOriginalSequence2(s2);
- alignment.setMatrix(matrix);
- alignment.setOpen(o);
- alignment.setExtend(e);
- if (s1.getId() != null) {
- alignment.setName1(s1.getId());
- }
- if (s2.getId() != null) {
- alignment.setName2(s2.getId());
- }
- /*logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");
- */
-
- return alignment;
- }
-
- /**
- * Constructs directions matrix for the traceback
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param matrix
- * scoring matrix
- * @param o
- * open gap penalty
- * @param e
- * extend gap penalty
- * @return The cell where the traceback starts.
- */
- private static Cell construct(Sequence s1, Sequence s2, float[][] matrix,
- float o, float e, byte[] pointers, short[] sizesOfVerticalGaps,
- short[] sizesOfHorizontalGaps) {
- //logger.info("Started...");
- long start = System.currentTimeMillis();
-
- char[] a1 = s1.toArray();
- char[] a2 = s2.toArray();
-
- int m = s1.length() + 1;
- int n = s2.length() + 1;
-
- float f; // score of alignment x1...xi to y1...yi if xi aligns to yi
- float[] g = new float[n]; // score if xi aligns to a gap after yi
- float h; // score if yi aligns to a gap after xi
- float[] v = new float[n]; // best score of alignment x1...xi to
- // y1...yi
- float vDiagonal;
-
- g[0] = Float.NEGATIVE_INFINITY;
- h = Float.NEGATIVE_INFINITY;
- v[0] = 0;
-
- for (int j = 1; j < n; j++) {
- g[j] = Float.NEGATIVE_INFINITY;
- v[j] = 0;
- }
-
- float similarityScore, g1, g2, h1, h2;
-
- Cell cell = new Cell();
-
- for (int i = 1, k = n; i < m; i++, k += n) {
- h = Float.NEGATIVE_INFINITY;
- vDiagonal = v[0];
- for (int j = 1, l = k + 1; j < n; j++, l++) {
- similarityScore = matrix[a1[i - 1]][a2[j - 1]];
-
- // Fill the matrices
- f = vDiagonal + similarityScore;
-
- g1 = g[j] - e;
- g2 = v[j] - o;
- if (g1 > g2) {
- g[j] = g1;
- sizesOfVerticalGaps[l] = (short) (sizesOfVerticalGaps[l - n] + 1);
- } else {
- g[j] = g2;
- }
-
- h1 = h - e;
- h2 = v[j - 1] - o;
- if (h1 > h2) {
- h = h1;
- sizesOfHorizontalGaps[l] = (short) (sizesOfHorizontalGaps[l - 1] + 1);
- } else {
- h = h2;
- }
-
- vDiagonal = v[j];
- v[j] = maximum(f, g[j], h, 0);
-
- // Determine the traceback direction
- if (v[j] == 0) {
- pointers[l] = Directions.STOP;
- } else if (v[j] == f) {
- pointers[l] = Directions.DIAGONAL;
- } else if (v[j] == g[j]) {
- pointers[l] = Directions.UP;
- } else {
- pointers[l] = Directions.LEFT;
- }
-
- // Set the traceback start at the current cell i, j and score
- if (v[j] > cell.getScore()) {
- cell.set(i, j, v[j]);
- }
- }
- }
- /*logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");
- */
- return cell;
- }
-
- /**
- * Returns the alignment of two sequences based on the passed array of
- * pointers
- *
- * @param s1
- * sequence #1
- * @param s2
- * sequence #2
- * @param m
- * scoring matrix
- * @param cell
- * The cell where the traceback starts.
- * @return {@link Alignment}with the two aligned sequences and alignment
- * score.
- * @see Cell
- * @see Alignment
- */
- private static Alignment traceback(Sequence s1, Sequence s2, Matrix m,
- byte[] pointers, Cell cell, short[] sizesOfVerticalGaps,
- short[] sizesOfHorizontalGaps) {
- //logger.info("Started...");
- long start = System.currentTimeMillis();
-
- char[] a1 = s1.toArray();
- char[] a2 = s2.toArray();
-
- float[][] scores = m.getScores();
-
- int n = s2.length() + 1;
-
- Alignment alignment = new Alignment();
- alignment.setScore(cell.getScore());
-
- int maxlen = s1.length() + s2.length(); // maximum length after the
- // aligned sequences
-
- char[] reversed1 = new char[maxlen]; // reversed sequence #1
- char[] reversed2 = new char[maxlen]; // reversed sequence #2
- char[] reversed3 = new char[maxlen]; // reversed markup
-
- int len1 = 0; // length of sequence #1 after alignment
- int len2 = 0; // length of sequence #2 after alignment
- int len3 = 0; // length of the markup line
-
- int identity = 0; // count of identitcal pairs
- int similarity = 0; // count of similar pairs
- int gaps = 0; // count of gaps
-
- char c1, c2;
-
- int i = cell.getRow(); // traceback start row
- int j = cell.getCol(); // traceback start col
- int k = i * n;
-
- boolean stillGoing = true; // traceback flag: true -> continue & false
- // -> stop
-
- while (stillGoing) {
- switch (pointers[k + j]) {
- case Directions.UP:
- for (int l = 0, len = sizesOfVerticalGaps[k + j]; l < len; l++) {
- reversed1[len1++] = a1[--i];
- reversed2[len2++] = Alignment.GAP;
- reversed3[len3++] = Markups.GAP;
- k -= n;
- gaps++;
- }
- break;
- case Directions.DIAGONAL:
- c1 = a1[--i];
- c2 = a2[--j];
- k -= n;
- reversed1[len1++] = c1;
- reversed2[len2++] = c2;
- if (c1 == c2) {
- reversed3[len3++] = Markups.IDENTITY;
- identity++;
- similarity++;
- } else if (scores[c1][c2] > 0) {
- reversed3[len3++] = Markups.SIMILARITY;
- similarity++;
- } else {
- reversed3[len3++] = Markups.MISMATCH;
- }
- break;
- case Directions.LEFT:
- for (int l = 0, len = sizesOfHorizontalGaps[k + j]; l < len; l++) {
- reversed1[len1++] = Alignment.GAP;
- reversed2[len2++] = a2[--j];
- reversed3[len3++] = Markups.GAP;
- gaps++;
- }
- break;
- case Directions.STOP:
- stillGoing = false;
- }
- }
-
- alignment.setSequence1(reverse(reversed1, len1));
- alignment.setStart1(i);
- alignment.setSequence2(reverse(reversed2, len2));
- alignment.setStart2(j);
- alignment.setMarkupLine(reverse(reversed3, len3));
- alignment.setIdentity(identity);
- alignment.setGaps(gaps);
- alignment.setSimilarity(similarity);
-
- /*logger.info("Finished in " + (System.currentTimeMillis() - start)
- + " milliseconds");
- */
-
- return alignment;
- }
-
- /**
- * Returns the maximum of 4 float numbers.
- *
- * @param a
- * float #1
- * @param b
- * float #2
- * @param c
- * float #3
- * @param d
- * float #4
- * @return The maximum of a, b, c and d.
- */
- private static float maximum(float a, float b, float c, float d) {
- if (a > b) {
- if (a > c) {
- return a > d ? a : d;
- } else {
- return c > d ? c : d;
- }
- } else if (b > c) {
- return b > d ? b : d;
- } else {
- return c > d ? c : d;
- }
- }
-
- /**
- * Reverses an array of chars
- *
- * @param a
- * @param len
- * @return the input array of char reserved
- */
- private static char[] reverse(char[] a, int len) {
- char[] b = new char[len];
- for (int i = len - 1, j = 0; i >= 0; i--, j++) {
- b[j] = a[i];
- }
- return b;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/TracebackNode.java b/Butterfly/src/src/jaligner/TracebackNode.java
deleted file mode 100644
index 701b96c..0000000
--- a/Butterfly/src/src/jaligner/TracebackNode.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * $Id: TracebackNode.java,v 1.1 2006/01/18 20:12:04 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner;
-
-/**
- * Traceback node
- *
- * @author Bram Minnaert
- * @author Ahmed Moustafa
- */
-
-public final class TracebackNode {
-
- /**
- * Direction
- */
- private byte direction;
-
- /**
- * Length of gap (for up and left directions)
- */
- private int length;
-
- /**
- * Constructor
- */
- public TracebackNode() {
- super();
- }
-
- /**
- * Sets the direction to diagonal
- *
- */
- public void setDiagonal() {
- direction = Directions.DIAGONAL;
- length = 0;
- }
-
- /**
- * Sets the direction to up
- *
- * @param length
- * length of gap
- */
- public void setUp(int length) {
- direction = Directions.UP;
- this.length = length;
- }
-
- /**
- * Sets the direction to left
- *
- * @param length
- * length of gap
- */
- public void setLeft(int length) {
- direction = Directions.LEFT;
- this.length = length;
- }
-
- /**
- * Sets the direction to stop
- */
- public void setStop() {
- direction = Directions.STOP;
- length = 0;
- }
-
- /**
- * @return Returns the direction.
- */
- public byte getDirection() {
- return direction;
- }
-
- /**
- * @return Returns the length.
- */
- public int getLength() {
- return length;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/example/NeedlemanWunschExample.java b/Butterfly/src/src/jaligner/example/NeedlemanWunschExample.java
deleted file mode 100644
index ad5f33c..0000000
--- a/Butterfly/src/src/jaligner/example/NeedlemanWunschExample.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * $Id: NeedlemanWunschExample.java,v 1.2 2006/02/03 05:00:22 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.example;
-
-import jaligner.Alignment;
-import jaligner.NeedlemanWunsch;
-import jaligner.Sequence;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixGenerator;
-import jaligner.util.SequenceParser;
-
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Example of using JAligner API to perform global pairwise sequence alignment
- * with Needleman-Wunsch algorithm {@link jaligner.NeedlemanWunsch}.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class NeedlemanWunschExample {
-
- /**
- * Logger
- */
- private static final Logger logger = Logger
- .getLogger(NeedlemanWunschExample.class.getName());
-
- /**
- *
- * @param args
- */
- public static void main(String[] args) {
- try {
- logger.info("Running example...");
-
- Sequence s1 = SequenceParser.parse("GAATTCAGTTA");
- Sequence s2 = SequenceParser.parse("GGATCGA");
-
- float match = 2;
- float mismatch = -1;
- Matrix matrix = MatrixGenerator.generate(match, mismatch);
- float gap = 2;
-
- Alignment alignment = NeedlemanWunsch.align(s1, s2, matrix, gap);
-
- System.out.println(alignment.getSummary());
- System.out.println(new Pair().format(alignment));
-
- logger.info("Finished running example");
- } catch (Exception e) {
- logger.log(Level.SEVERE, "Failed running example: "
- + e.getMessage(), e);
- }
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/example/NeedlemanWunschGotohExample.java b/Butterfly/src/src/jaligner/example/NeedlemanWunschGotohExample.java
deleted file mode 100644
index bbca0e7..0000000
--- a/Butterfly/src/src/jaligner/example/NeedlemanWunschGotohExample.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*
- * $Id: NeedlemanWunschGotohExample.java,v 1.1 2006/02/03 05:00:23 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.example;
-
-import jaligner.Alignment;
-import jaligner.NeedlemanWunschGotoh;
-import jaligner.Sequence;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixGenerator;
-import jaligner.util.SequenceParser;
-
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Example of using JAligner API to perform global pairwise sequence alignment
- * with {@link jaligner.NeedlemanWunschGotoh}.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class NeedlemanWunschGotohExample {
-
- /**
- * Logger
- */
- private static final Logger logger = Logger
- .getLogger(NeedlemanWunschGotohExample.class.getName());
-
- /**
- *
- * @param args
- */
- public static void main(String[] args) {
- try {
- logger.info("Running example...");
-
- Sequence s1 = SequenceParser.parse("GAATTCAGTTA");
- Sequence s2 = SequenceParser.parse("GGATCGA");
-
- float match = 2;
- float mismatch = -1;
- Matrix matrix = MatrixGenerator.generate(match, mismatch);
- float open = 2;
- float extend = 2;
-
- Alignment alignment = NeedlemanWunschGotoh.align(s1, s2, matrix,
- open, extend);
-
- System.out.println(alignment.getSummary());
- System.out.println(new Pair().format(alignment));
-
- logger.info("Finished running example");
- } catch (Exception e) {
- logger.log(Level.SEVERE, "Failed running example: "
- + e.getMessage(), e);
- }
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/example/SmithWatermanGotohExample.java b/Butterfly/src/src/jaligner/example/SmithWatermanGotohExample.java
deleted file mode 100644
index 1e6cb6b..0000000
--- a/Butterfly/src/src/jaligner/example/SmithWatermanGotohExample.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
- * $Id: SmithWatermanGotohExample.java,v 1.1 2006/02/03 03:46:18 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.example;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-import jaligner.SmithWatermanGotoh;
-import jaligner.formats.Pair;
-import jaligner.matrix.MatrixLoader;
-import jaligner.util.SequenceParser;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Example of using JAligner API to align P53 human aganist
- * P53 mouse using Smith-Waterman-Gotoh algorithm.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class SmithWatermanGotohExample {
-
- /**
- *
- */
- private static final String SAMPLE_SEQUENCE_P35_HUMAN = "jaligner/example/sequences/p53_human.fasta";
-
- /**
- *
- */
- private static final String SAMPLE_SEQUENCE_P35_MOUSE = "jaligner/example/sequences/p53_mouse.fasta";
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(SmithWatermanGotohExample.class.getName());
-
- /**
- *
- * @param args
- */
- public static void main(String[] args) {
- try {
- logger.info("Running example...");
-
- Sequence s1 = SequenceParser.parse(loadP53Human());
- Sequence s2 = SequenceParser.parse(loadP53Mouse());
-
- Alignment alignment = SmithWatermanGotoh.align(s1, s2, MatrixLoader.load("BLOSUM62"), 10f, 0.5f);
-
- System.out.println ( alignment.getSummary() );
- System.out.println ( new Pair().format(alignment) );
-
- logger.info("Finished running example");
- } catch (Exception e) {
- logger.log(Level.SEVERE, "Failed running example: " + e.getMessage(), e);
- }
- }
-
- /**
- *
- * @param path location of the sequence
- * @return sequence string
- * @throws IOException
- */
- private static String loadSampleSequence(String path) throws IOException {
- InputStream inputStream = NeedlemanWunschExample.class.getClassLoader().getResourceAsStream(path);
- StringBuffer buffer = new StringBuffer();
- int ch;
- while ((ch = inputStream.read()) != -1) {
- buffer.append((char)ch);
- }
- return buffer.toString();
- }
-
- /**
- *
- * @return sequence string
- * @throws IOException
- */
- public static String loadP53Human( ) throws IOException {
- return loadSampleSequence(SAMPLE_SEQUENCE_P35_HUMAN);
- }
-
- /**
- *
- * @return sequence string
- * @throws IOException
- */
- public static String loadP53Mouse( ) throws IOException {
- return loadSampleSequence(SAMPLE_SEQUENCE_P35_MOUSE);
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/example/package.html b/Butterfly/src/src/jaligner/example/package.html
deleted file mode 100644
index 266497b..0000000
--- a/Butterfly/src/src/jaligner/example/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head><!--$Id: package.html,v 1.1 2005/05/25 19:56:30 ahmed Exp $--></head>
-<body bgcolor="white">
-Example for using API of JAligner to perform pairwise sequence alignment.
- at author Ahmed Moustafa (ahmed at users.sf.net)
-</body>
-</html>
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/example/sequences/p53_human.fasta b/Butterfly/src/src/jaligner/example/sequences/p53_human.fasta
deleted file mode 100644
index 1591a95..0000000
--- a/Butterfly/src/src/jaligner/example/sequences/p53_human.fasta
+++ /dev/null
@@ -1,7 +0,0 @@
->p53_human
-MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
-PRVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
-CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
-TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACAGR
-DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
-KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/example/sequences/p53_mouse.fasta b/Butterfly/src/src/jaligner/example/sequences/p53_mouse.fasta
deleted file mode 100644
index 9b011cd..0000000
--- a/Butterfly/src/src/jaligner/example/sequences/p53_mouse.fasta
+++ /dev/null
@@ -1,8 +0,0 @@
->p53_mouse
-MTAMEESQSDISLELPLSQETFSGLWKLLPPEDILPSPHCMDDLLLPQDVEEFFEGPSEA
-LRVSGAPAAQDPVTETPGPAAPAPATPWPLSSFVPSQKTYQGNYGFHLGFLQSGTAKSVM
-CTYSPPLNKLFCQLAKTCPVQLWVSATPPAGSRVRAMAIYKKSQHMTEVVRRCPHHERCS
-DGDGLAPPQHLIRVEGNLYPEYLEDRQTFRHSVVVPYEPPEAGSEYTTIHYKYMCNSSCM
-GGMNRRPILTIITLEDSSGNLLGRDSFEVRVCACPGRDRRTEEENFRKKEVLCPELPPGS
-AKRALPTCTSASPPQKKKPLDGEYFTLKIRGRKRFEMFRELNEALELKDAHATEESGDSR
-AHSSYLKTKKGQSTSRHKKTMVKKVGPDSD
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/formats/CLUSTAL.java b/Butterfly/src/src/jaligner/formats/CLUSTAL.java
deleted file mode 100644
index 3d2533e..0000000
--- a/Butterfly/src/src/jaligner/formats/CLUSTAL.java
+++ /dev/null
@@ -1,121 +0,0 @@
-/*
- * $Id: CLUSTAL.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-
-/**
- * CLUSTAL format.
- * Example:
- * <pre>
- * <small>
- * CLUSTAL_FORMAT W(1.60) multiple sequence alignment
- *
- *
- * JC2395 NVSDVNLNK---YIWRTAEKMK---ICDAKKFARQHKIPESKIDEIEHNSPQDAAE----
- * KPEL_DROME MAIRLLPLPVRAQLCAHLDAL-----DVWQQLATAVKLYPDQVEQISSQKQRGRS-----
- * FASA_MOUSE NASNLSLSK---YIPRIAEDMT---IQEAKKFARENNIKEGKIDEIMHDSIQDTAE----
- *
- *
- * JC2395 -------------------------QKIQLLQCWYQSHGKT--GACQALIQGLRKANRCD
- * KPEL_DROME -------------------------ASNEFLNIWGGQYN----HTVQTLFALFKKLKLHN
- * FASA_MOUSE -------------------------QKVQLLLCWYQSHGKS--DAYQDLIKGLKKAECRR
- *
- *
- * JC2395 IAEEIQAM
- * KPEL_DROME AMRLIKDY
- * FASA_MOUSE TLDKFQDM
- * </small>
- * </pre>
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class CLUSTAL extends Format {
-
- /**
- * Name width
- */
- private static final int NAME_WIDTH = 36;
-
- /**
- * Sequence width
- */
- private static final int SEQUENCE_WIDTH = 50;
-
- /**
- * CLUSTAL header
- */
- private static final String HEADER = "CLUSTAL_FORMAT W(1.60) multiple sequence alignment\n\n";
-
- /**
- * Constructor
- */
- public CLUSTAL() {
- super( );
- setId("CLUSTAL");
- }
-
- /**
- * Returns CLUSTAL format
- * @param names array of the names of the sequences.
- * @param sequences array of the sequences
- */
- public String format(String[] names, String[] sequences) {
- StringBuffer buffer = new StringBuffer (HEADER);
- int maxSequenceLength = 0;
- for (int i = 0; i < sequences.length; i++) {
- if (sequences[i].length() > maxSequenceLength) {
- maxSequenceLength = sequences[i].length();
- }
- }
-
- for (int i = 0; i * SEQUENCE_WIDTH < maxSequenceLength; i++) {
-
- for (int j = 0; j < sequences.length; j++) {
- buffer.append( NAME_WIDTH <= names[j].length() ? names[j].substring(0, NAME_WIDTH - 1) : names[j] );
- for (int k = names[j].length(); k < NAME_WIDTH; k++) {
- buffer.append(" ");
- }
- if (names[j].length() >= NAME_WIDTH) {
- buffer.append(" ");
- }
- buffer.append(sequences[j].substring(i * SEQUENCE_WIDTH, ((i + 1) * SEQUENCE_WIDTH) < sequences[j].length() ? (i + 1) * SEQUENCE_WIDTH: sequences[j].length()));
- if (j < sequences.length) {
- buffer.append("\n");
- }
- }
- if ((i + 1) * SEQUENCE_WIDTH < maxSequenceLength) {
- buffer.append("\n\n");
- }
- }
- return buffer.toString();
- }
-
- /**
- * Returns CLUSTAL format of the alignment
- * @param alignment ({@link Alignment})
- * @return CLUSTAL format of the alignment
- */
- public String format (Alignment alignment) {
- String[] sequences = {new String(alignment.getSequence1()), new String(alignment.getSequence2())};
- String[] names = {alignment.getName1(), alignment.getName2()};
- return format (names, sequences);
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/formats/FASTA.java b/Butterfly/src/src/jaligner/formats/FASTA.java
deleted file mode 100644
index 0aab4e1..0000000
--- a/Butterfly/src/src/jaligner/formats/FASTA.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * $Id: FASTA.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-
-/**
- * <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class FASTA extends Format {
-
- /**
- * Number of characters per line
- */
- private static final int LINE_WIDTH = 60;
-
- /**
- * Constructor for FASTA.
- */
- public FASTA() {
- super( );
- setId("FASTA");
- }
-
- /**
- * Returns the name, description and sequence combined in one string.
- * The length of each line in the sequence is FASTA.LINE_LENGTH
- *
- * @return String
- */
- public String format (Sequence sequence) {
- StringBuffer buffer = new StringBuffer (">");
- buffer.append(sequence.getId() == null ? "" : sequence.getId());
- buffer.append("\n");
- for (int i = 0, n = sequence.length(); i * LINE_WIDTH < n; i++) {
- for (int j = i * LINE_WIDTH, m = (i + 1) * LINE_WIDTH < n ? (i + 1) * LINE_WIDTH: n; j < m; j++) {
- buffer.append(sequence.subsequence(j, 1));
- }
- buffer.append("\n");
- }
- return buffer.toString( );
- }
-
- /**
- *
- * @param alignment
- * @return FASTA format of the input alignment
- */
- public String format (Alignment alignment) {
- StringBuffer buffer = new StringBuffer();
- StringBuffer s1 = new StringBuffer();
- StringBuffer s2 = new StringBuffer();
- s1.append(alignment.getSequence1());
- s2.append(alignment.getSequence2());
- buffer.append(format(new Sequence(s1.toString(), alignment.getName1(), "", Sequence.PROTEIN)));
- buffer.append(format(new Sequence(s2.toString(), alignment.getName2(), "", Sequence.PROTEIN)));
- return buffer.toString();
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/formats/Format.java b/Butterfly/src/src/jaligner/formats/Format.java
deleted file mode 100644
index d2aedb6..0000000
--- a/Butterfly/src/src/jaligner/formats/Format.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * $Id: Format.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-
-/**
- * Abstract format
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public abstract class Format {
-
- /**
- * Format id
- */
- private String id = null;
-
- /**
- * Formats alignment
- * @param alignment
- * @return formatted alignment
- * @see Alignment
- */
- public abstract String format(Alignment alignment);
-
- /**
- * Sets format id
- * @param id to set
- */
- public void setId (String id) {
- this.id = id;
- }
-
- /**
- * Returns format id
- * @return id
- */
- public String getId ( ) {
- return this.id == null ? this.getClass().getName() : this.id;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/formats/FormatFactory.java b/Butterfly/src/src/jaligner/formats/FormatFactory.java
deleted file mode 100644
index 53d1b8a..0000000
--- a/Butterfly/src/src/jaligner/formats/FormatFactory.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/*
- * $Id: FormatFactory.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import java.util.Collection;
-import java.util.HashMap;
-
-/**
- * Formats factory.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class FormatFactory {
- /**
- * Instance of {@link FormatFactory}
- */
- private static FormatFactory instance = null;
-
- /**
- * {@link HashMap} of {@link Format}
- */
- private HashMap formats = new HashMap();
-
- /**
- * Hidden constructor
- *
- */
- private FormatFactory ( ) {
- super();
- }
-
- /**
- * Returns an instance for {@link FormatFactory}.
- * @return {@link FormatFactory}
- */
- public static FormatFactory getInstance() {
- if (instance == null) {
- instance = new FormatFactory();
- }
- return instance;
- }
-
- /**
- * Registers format.
- * @param format instance of format
- */
- public void registerFormat(Format format) {
- formats.put(format.getId(), format);
- }
-
- /**
- * Returns an instance of {@link Format}.
- * @param id format id
- * @return {@link Format} or null if id not found
- */
- public Format getFormat(String id) {
- return (Format) formats.get(id);
- }
-
- /**
- * Returns a list of registered formats
- * @return {@link Collection}
- */
- public Collection getFormats( ) {
- return formats.keySet();
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/formats/Pair.java b/Butterfly/src/src/jaligner/formats/Pair.java
deleted file mode 100644
index dc89158..0000000
--- a/Butterfly/src/src/jaligner/formats/Pair.java
+++ /dev/null
@@ -1,191 +0,0 @@
-/*
- * $Id: Pair.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.formats;
-
-import jaligner.Alignment;
-import jaligner.util.Commons;
-
-/**
- * <a href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Themes/AlignExamples/align.pair">Pair</a> format.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class Pair extends Format {
-
- /**
- * Name width
- */
- private static final int NAME_WIDTH = 13;
-
- /**
- * Position width
- */
- private static final int POSITION_WIDTH = 6;
-
- /**
- * Sequence width
- */
- private static final int SEQUENCE_WIDTH = 50;
-
- /**
- * Space
- */
- private static final String BLANK = " ";
-
- /**
- * Constructor
- *
- */
- public Pair( ) {
- super();
- setId("Pair");
- }
-
- /**
- * Formats an alignment object to the Pair_FORMAT format
- * @param alignment alignment object to be formated
- * @return string of the alignment pair-formatted
- */
- public String format(Alignment alignment) {
- char[] sequence1 = alignment.getSequence1();
- char[] sequence2 = alignment.getSequence2();
- char[] markup = alignment.getMarkupLine();
-
- int length = sequence1.length > sequence2.length ? sequence2.length : sequence1.length;
-
- String name1 = adjustName(alignment.getName1());
- String name2 = adjustName(alignment.getName2());
-
- StringBuffer buffer = new StringBuffer ( );
-
- StringBuffer preMarkup = new StringBuffer ( );
- for (int j = 0; j < NAME_WIDTH + 1 + POSITION_WIDTH + 1; j++) {
- preMarkup.append(BLANK);
- }
-
- int oldPosition1, position1 = 1 + alignment.getStart1();
- int oldPosition2, position2 = 1 + alignment.getStart2();
-
- char[] subsequence1;
- char[] subsequence2;
- char[] submarkup;
- int line;
-
- char c1, c2;
-
- for (int i = 0; i * SEQUENCE_WIDTH < length; i++) {
-
- oldPosition1 = position1;
- oldPosition2 = position2;
-
- line = ((i + 1) * SEQUENCE_WIDTH) < length ? (i + 1) * SEQUENCE_WIDTH: length;
-
- subsequence1 = new char[line - i * SEQUENCE_WIDTH];
- subsequence2 = new char[line - i * SEQUENCE_WIDTH];
- submarkup = new char[line - i * SEQUENCE_WIDTH];
-
- for (int j = i * SEQUENCE_WIDTH, k = 0; j < line; j++, k++) {
- subsequence1[k] = sequence1[j];
- subsequence2[k] = sequence2[j];
- submarkup[k] = markup[j];
- c1 = subsequence1[k];
- c2 = subsequence2[k];
- if (c1 == c2) {
- position1++;
- position2++;
- } else if (c1 == Alignment.GAP) {
- position2++;
- } else if (c2 == Alignment.GAP) {
- position1++;
- } else {
- position1++;
- position2++;
- }
- }
-
- buffer.append(name1);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(oldPosition1).toString()));
- buffer.append(BLANK);
- buffer.append(subsequence1);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(position1 - 1).toString()));
- buffer.append(Commons.getLineSeparator());
-
- buffer.append(preMarkup);
- buffer.append(submarkup);
- buffer.append(Commons.getLineSeparator());
-
- buffer.append(name2);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(oldPosition2).toString()));
- buffer.append(BLANK);
- buffer.append(subsequence2);
- buffer.append(BLANK);
- buffer.append(adjustPosition(new Integer(position2 - 1).toString()));
- buffer.append(Commons.getLineSeparator());
-
- buffer.append(Commons.getLineSeparator());
- }
- return buffer.toString();
- }
-
- /**
- *
- * @param name name to adjusted
- * @return adjusted name
- */
- private String adjustName(String name) {
- StringBuffer buffer = new StringBuffer ( );
-
- if (name.length() > NAME_WIDTH) {
- buffer.append(name.substring(0, NAME_WIDTH));
- } else {
- buffer.append(name);
- for (int j = buffer.length(); j < NAME_WIDTH; j++) {
- buffer.append (BLANK);
- }
- }
- return buffer.toString();
- }
-
- /**
- *
- * @param position
- * @return string
- */
- private String adjustPosition(String position) {
- StringBuffer buffer1 = new StringBuffer( );
- StringBuffer buffer2 = new StringBuffer( );
-
- if (position.length() > POSITION_WIDTH) {
- buffer1.append(position.substring(position.length() - POSITION_WIDTH, position.length()));
- } else {
- buffer1.append(position);
- }
-
- for (int j = 0, n = POSITION_WIDTH - buffer1.length(); j < n; j++) {
- buffer2.append(BLANK);
- }
-
- buffer2.append(buffer1.toString());
- return buffer2.toString();
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/formats/package.html b/Butterfly/src/src/jaligner/formats/package.html
deleted file mode 100644
index cf19168..0000000
--- a/Butterfly/src/src/jaligner/formats/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head><!--$Id: package.html,v 1.1 2005/05/25 19:56:30 ahmed Exp $--></head>
-<body bgcolor="white">
-Group of formats for output alignments.
- at author Ahmed Moustafa (ahmed at users.sf.net)
-</body>
-</html>
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/matrix/MatricesCompartor.java b/Butterfly/src/src/jaligner/matrix/MatricesCompartor.java
deleted file mode 100644
index 516ae5b..0000000
--- a/Butterfly/src/src/jaligner/matrix/MatricesCompartor.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * $Id: MatricesCompartor.java,v 1.1 2005/05/25 19:56:30 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-import java.util.Comparator;
-
-/**
- * Comparator to sort the scoring matrices by their names.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class MatricesCompartor implements Comparator {
-
- /* (non-Javadoc)
- * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
- */
- public int compare(Object o1, Object o2) {
- String s1 = (String) o1;
- String s2 = (String) o2;
-
- int index1 = firstDigitIndex(s1);
- int index2 = firstDigitIndex(s2);
-
- if (index1 == -1 || index2 == -1) {
- return s1.compareToIgnoreCase(s2);
- } else {
- String s3 = s1.substring(0, index1);
- String s4 = s2.substring(0, index2);
- if (s3.equalsIgnoreCase(s4)) {
- return new Integer(s1.substring(index1)).compareTo(new Integer(s2.substring(index2)));
- } else {
- return s1.compareToIgnoreCase(s2);
- }
- }
- }
-
- /**
- * Returns the index of the first digit in a String.
- * If there are no digits, returns -1.
- * @param s String to be searched for the digits in
- * @return int
- */
- private int firstDigitIndex (String s) {
- for (int i = 0; i < s.length(); i++) {
- if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
- return i;
- }
- }
- return -1;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/matrix/Matrix.java b/Butterfly/src/src/jaligner/matrix/Matrix.java
deleted file mode 100644
index 71389f1..0000000
--- a/Butterfly/src/src/jaligner/matrix/Matrix.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * $Id: Matrix.java,v 1.2 2006/01/18 20:16:37 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-import java.io.Serializable;
-
-/**
- * Scoring matrix.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class Matrix implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 3833742170619524400L;
-
- /**
- * The size of the scoring matrix. It is the number of the characters in the
- * ASCII table. It is more than the 20 amino acids just to save the
- * processing time of the mapping.
- */
- public static final int SIZE = 127;
-
- /**
- * Matrix id (or name)
- */
- private final String id;
-
- /**
- * Scores
- */
- private final float[][] scores;
-
- public Matrix(String id, float[][] scores) {
- this.id = id;
- this.scores = scores;
- }
-
- /**
- * @return Returns the id.
- */
- public String getId() {
- return this.id;
- }
-
- /**
- * @return Returns the scores.
- */
- public float[][] getScores() {
- return this.scores;
- }
-
- /**
- *
- * @param a
- * @param b
- * @return score
- */
- public float getScore(char a, char b) {
- return this.scores[a][b];
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/matrix/MatrixGenerator.java b/Butterfly/src/src/jaligner/matrix/MatrixGenerator.java
deleted file mode 100644
index f1b94b1..0000000
--- a/Butterfly/src/src/jaligner/matrix/MatrixGenerator.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * $Id: MatrixGenerator.java,v 1.3 2006/02/26 20:26:41 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-/**
- * A utility class to generate a scoring matrix from a fixed match and mismatch
- * scoring scheme.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public final class MatrixGenerator {
-
- /**
- * Returns scoring matrix from a fixed match/mismatch scoring scheme.
- *
- * @param match
- * match score
- * @param mismatch
- * mistmatch score
- *
- * @return scoring matrix
- */
- public static Matrix generate(float match, float mismatch) {
- float[][] scores = new float[Matrix.SIZE][Matrix.SIZE];
-
- // Fill the matrix with the scores
- for (int i = 0; i < Matrix.SIZE; i++) {
- for (int j = 0; j < Matrix.SIZE; j++) {
- if (i == j || i == 'N' || j == 'N') {
- scores[i][j] = match;
- } else {
- scores[i][j] = mismatch;
- }
- }
- }
-
- // Generate some id for the matrix (hopefully to be somehow unique)
- String id = new Long(System.currentTimeMillis()).toString();
-
- Matrix matrix = new Matrix(id, scores);
-
- return matrix;
- }
-}
diff --git a/Butterfly/src/src/jaligner/matrix/MatrixLoader.java b/Butterfly/src/src/jaligner/matrix/MatrixLoader.java
deleted file mode 100644
index c206090..0000000
--- a/Butterfly/src/src/jaligner/matrix/MatrixLoader.java
+++ /dev/null
@@ -1,243 +0,0 @@
-/*
- * $Id: MatrixLoader.java,v 1.3 2006/01/18 20:16:37 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-import jaligner.ui.filechooser.NamedInputStream;
-import jaligner.util.Commons;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.JarURLConnection;
-import java.net.URL;
-import java.net.URLDecoder;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.StringTokenizer;
-import java.util.jar.JarEntry;
-import java.util.jar.JarFile;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Scoring matrices loader from a jar file or a file system.
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class MatrixLoader {
- /**
- * The starter character of a comment line.
- */
- private static final char COMMENT_STARTER = '#';
-
- /**
- * The path to the matrices within the package.
- */
- private static final String MATRICES_HOME = "jaligner/matrix/matrices/";
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(MatrixLoader.class
- .getName());
-
- /**
- * Loads scoring matrix from Jar file or file system.
- *
- * @param matrix
- * to load
- * @return loaded matrix
- * @throws MatrixLoaderException
- * @see Matrix
- */
- public static Matrix load(String matrix) throws MatrixLoaderException {
- InputStream is = null;
-
- if (new StringTokenizer(matrix, Commons.getFileSeparator())
- .countTokens() == 1) {
- // Matrix does not include the path
- // Load the matrix from matrices.jar
- is = MatrixLoader.class.getClassLoader().getResourceAsStream(
- MATRICES_HOME + matrix);
- } else {
- // Matrix includes the path information
- // Load the matrix from the file system
- try {
- is = new FileInputStream(matrix);
- } catch (Exception e) {
- String message = "Failed opening input stream: "
- + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException(message);
- }
- }
-
- return load(new NamedInputStream(matrix, is));
- }
-
- /**
- * Loads scoring matrix from {@link InputStream}
- *
- * @param nis
- * named input stream
- * @return loaded matrix
- * @throws MatrixLoaderException
- * @see Matrix
- * @see NamedInputStream
- */
- public static Matrix load(NamedInputStream nis)
- throws MatrixLoaderException {
- logger.info("Loading scoring matrix...");
- char[] acids = new char[Matrix.SIZE];
-
- // Initialize the acids array to null values (ascii = 0)
- for (int i = 0; i < Matrix.SIZE; i++) {
- acids[i] = 0;
- }
-
- float[][] scores = new float[Matrix.SIZE][Matrix.SIZE];
-
- BufferedReader reader = new BufferedReader(new InputStreamReader(nis
- .getInputStream()));
-
- String line;
-
- try {
- // Skip the comment lines
- while ((line = reader.readLine()) != null
- && line.trim().charAt(0) == COMMENT_STARTER)
- ;
- } catch (Exception e) {
- String message = "Failed reading from input stream: "
- + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException(message);
- }
-
- // Read the headers line (the letters of the acids)
- StringTokenizer tokenizer;
- tokenizer = new StringTokenizer(line.trim());
- for (int j = 0; tokenizer.hasMoreTokens(); j++) {
- acids[j] = tokenizer.nextToken().charAt(0);
- }
-
- try {
- // Read the scores
- while ((line = reader.readLine()) != null) {
- tokenizer = new StringTokenizer(line.trim());
- char acid = tokenizer.nextToken().charAt(0);
- for (int i = 0; i < Matrix.SIZE; i++) {
- if (acids[i] != 0) {
- scores[acid][acids[i]] = Float.parseFloat(tokenizer
- .nextToken());
- }
- }
- }
- } catch (Exception e) {
- String message = "Failed reading from input stream: "
- + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException(message);
- }
- logger.info("Finished loading scoring matrix");
- return new Matrix(nis.getName(), scores);
- }
-
- /**
- * Returns a list of the scoring matrices in the matrices home directory
- *
- * @param sort
- * flag to sort the list or not
- * @return sorted array of scoring matrices
- * @throws MatrixLoaderException
- */
- public static Collection list(boolean sort) throws MatrixLoaderException {
- logger.info("Loading list of scoring matrices...");
- ArrayList matrices = new ArrayList();
- URL url = MatrixLoader.class.getClassLoader()
- .getResource(MATRICES_HOME);
- if (url.getFile().toString().indexOf("!") != -1) {
- // Load from Jar
- JarURLConnection connection = null;
- JarFile jar = null;
- try {
- connection = (JarURLConnection) url.openConnection();
- jar = connection.getJarFile();
- } catch (Exception e) {
- String message = "Failed opening a connection to jar: "
- + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException(message);
- }
- Enumeration entries = jar.entries();
- JarEntry entry;
- String entryName;
- int length = MATRICES_HOME.length();
- while (entries.hasMoreElements()) {
- entry = (JarEntry) entries.nextElement();
- if (!entry.isDirectory()) {
- entryName = entry.getName();
- if (entryName.startsWith(MATRICES_HOME)) {
- matrices.add(entryName.substring(length));
- }
- }
- }
- } else {
- // Load from file system
- String home = null;
- try {
- home = URLDecoder.decode(url.getFile(), "UTF-8");
- } catch (Exception e) {
- String message = "Failed decoding matrices url: "
- + e.getMessage();
- logger.log(Level.SEVERE, message, e);
- throw new MatrixLoaderException(message);
- }
- File dir = new File(home);
- String files[] = dir.list();
- File file;
- for (int i = 0, n = files.length; i < n; i++) {
- file = new File(home + files[i]);
- if (file.isFile() && file.canRead()) {
- matrices.add(file.getName());
- }
- }
- }
- if (sort) {
- Collections.sort(matrices, new MatricesCompartor());
- }
- logger.info("Finished loading list of scoring matrices");
- return matrices;
- }
-
- /**
- * Returns a list of the scoring matrices in the matrices home directory
- *
- * @return sorted array of scoring matrices
- * @throws MatrixLoaderException
- */
- public static Collection list() throws MatrixLoaderException {
- return list(false);
- }
-}
diff --git a/Butterfly/src/src/jaligner/matrix/MatrixLoaderException.java b/Butterfly/src/src/jaligner/matrix/MatrixLoaderException.java
deleted file mode 100644
index a62783b..0000000
--- a/Butterfly/src/src/jaligner/matrix/MatrixLoaderException.java
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.matrix;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class MatrixLoaderException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 3906364935142586680L;
-
- /**
- * @param message
- */
- public MatrixLoaderException(String message) {
- super(message);
- }
-}
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM100 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM100
deleted file mode 100644
index 46e9e85..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM100
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum100_3.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 100
-# Entropy = 1.4516, Expected = -1.0948
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10
-R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10
-N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10
-D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10
-C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10
-Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10
-E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10
-G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10
-H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10
-I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10
-L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10
-K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10
-M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10
-F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10
-P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10
-S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10
-T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10
-W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10
-Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10
-V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10
-B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10
-Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10
-X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM30 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM30
deleted file mode 100644
index 81ebd98..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM30
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum30.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/5 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 30
-# Entropy = 0.1424, Expected = -0.1074
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 0 0 -3 1 0 0 -2 0 -1 0 1 -2 -1 1 1 -5 -4 1 0 0 0 -7
-R -1 8 -2 -1 -2 3 -1 -2 -1 -3 -2 1 0 -1 -1 -1 -3 0 0 -1 -2 0 -1 -7
-N 0 -2 8 1 -1 -1 -1 0 -1 0 -2 0 0 -1 -3 0 1 -7 -4 -2 4 -1 0 -7
-D 0 -1 1 9 -3 -1 1 -1 -2 -4 -1 0 -3 -5 -1 0 -1 -4 -1 -2 5 0 -1 -7
-C -3 -2 -1 -3 17 -2 1 -4 -5 -2 0 -3 -2 -3 -3 -2 -2 -2 -6 -2 -2 0 -2 -7
-Q 1 3 -1 -1 -2 8 2 -2 0 -2 -2 0 -1 -3 0 -1 0 -1 -1 -3 -1 4 0 -7
-E 0 -1 -1 1 1 2 6 -2 0 -3 -1 2 -1 -4 1 0 -2 -1 -2 -3 0 5 -1 -7
-G 0 -2 0 -1 -4 -2 -2 8 -3 -1 -2 -1 -2 -3 -1 0 -2 1 -3 -3 0 -2 -1 -7
-H -2 -1 -1 -2 -5 0 0 -3 14 -2 -1 -2 2 -3 1 -1 -2 -5 0 -3 -2 0 -1 -7
-I 0 -3 0 -4 -2 -2 -3 -1 -2 6 2 -2 1 0 -3 -1 0 -3 -1 4 -2 -3 0 -7
-L -1 -2 -2 -1 0 -2 -1 -2 -1 2 4 -2 2 2 -3 -2 0 -2 3 1 -1 -1 0 -7
-K 0 1 0 0 -3 0 2 -1 -2 -2 -2 4 2 -1 1 0 -1 -2 -1 -2 0 1 0 -7
-M 1 0 0 -3 -2 -1 -1 -2 2 1 2 2 6 -2 -4 -2 0 -3 -1 0 -2 -1 0 -7
-F -2 -1 -1 -5 -3 -3 -4 -3 -3 0 2 -1 -2 10 -4 -1 -2 1 3 1 -3 -4 -1 -7
-P -1 -1 -3 -1 -3 0 1 -1 1 -3 -3 1 -4 -4 11 -1 0 -3 -2 -4 -2 0 -1 -7
-S 1 -1 0 0 -2 -1 0 0 -1 -1 -2 0 -2 -1 -1 4 2 -3 -2 -1 0 -1 0 -7
-T 1 -3 1 -1 -2 0 -2 -2 -2 0 0 -1 0 -2 0 2 5 -5 -1 1 0 -1 0 -7
-W -5 0 -7 -4 -2 -1 -1 1 -5 -3 -2 -2 -3 1 -3 -3 -5 20 5 -3 -5 -1 -2 -7
-Y -4 0 -4 -1 -6 -1 -2 -3 0 -1 3 -1 -1 3 -2 -2 -1 5 9 1 -3 -2 -1 -7
-V 1 -1 -2 -2 -2 -3 -3 -3 -3 4 1 -2 0 1 -4 -1 1 -3 1 5 -2 -3 0 -7
-B 0 -2 4 5 -2 -1 0 0 -2 -2 -1 0 -2 -3 -2 0 0 -5 -3 -2 5 0 -1 -7
-Z 0 0 -1 0 0 4 5 -2 0 -3 -1 1 -1 -4 0 -1 -1 -1 -2 -3 0 4 0 -7
-X 0 -1 0 -1 -2 0 -1 -1 -1 0 0 0 0 -1 -1 0 0 -2 -1 0 -1 0 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM35 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM35
deleted file mode 100644
index a6d99f5..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM35
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum35.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 35
-# Entropy = 0.2111, Expected = -0.1550
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5
-R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5
-N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5
-D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5
-C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5
-Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5
-E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5
-G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5
-H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5
-I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5
-L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5
-K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5
-M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5
-F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5
-P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5
-S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5
-T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5
-W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5
-Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5
-V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5
-B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5
-Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5
-X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM40 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM40
deleted file mode 100644
index 1a4baa2..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM40
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum40.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/4 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 40
-# Entropy = 0.2851, Expected = -0.2090
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6
-R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6
-N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6
-D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6
-C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6
-Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6
-E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6
-G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6
-H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6
-I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6
-L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6
-K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6
-M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6
-F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6
-P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6
-S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6
-T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6
-W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6
-Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6
-V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6
-B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 2 -1 -6
-Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 2 5 -1 -6
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM45 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM45
deleted file mode 100644
index 18c3323..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM45
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum45.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 45
-# Entropy = 0.3795, Expected = -0.2789
- A R N D C Q E G H I L K M F P S T W Y V B 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 0 -5
-R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
-N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
-D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 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 -3 -2 -5
-Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 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 4 -1 -5
-G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -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 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 -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 -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 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 -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 -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 -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 0 0 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -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 -5
-Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -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 -3 -1 -5
-B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
-Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM50 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM50
deleted file mode 100644
index 3f62e3c..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM50
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum50.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 50
-# Entropy = 0.4808, Expected = -0.3573
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -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 0 -1 -5
-N -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 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 5 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 -3 -2 -5
-Q -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 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 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 -2 -2 -5
-H -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 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 -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 -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 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 -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 -4 -2 -5
-P -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5
-S 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 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 0 -5
-W -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5
-Y -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5
-V 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5
-B -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 2 -1 -5
-Z -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 2 5 -1 -5
-X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM55 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM55
deleted file mode 100644
index c0cf3ff..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM55
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum55.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 55
-# Entropy = 0.5637, Expected = -0.4179
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -2 -2 0 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -2 0 -2 -1 -1 -5
-R -2 8 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 -1 8 2 -3 0 0 0 1 -4 -4 0 -3 -4 -2 1 0 -5 -2 -4 4 0 -1 -5
-D -2 -2 2 8 -4 0 2 -2 -1 -4 -5 -1 -4 -5 -2 0 -1 -5 -3 -4 5 1 -2 -5
-C 0 -4 -3 -4 13 -4 -4 -3 -4 -2 -2 -4 -2 -3 -3 -1 -1 -4 -3 -1 -4 -4 -2 -5
-Q -1 1 0 0 -4 7 2 -2 1 -4 -3 2 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
-E -1 0 0 2 -4 2 7 -3 -1 -4 -4 1 -3 -4 -1 0 -1 -3 -2 -3 1 5 -1 -5
-G 0 -3 0 -2 -3 -2 -3 8 -2 -5 -5 -2 -3 -4 -3 0 -2 -3 -4 -4 -1 -3 -2 -5
-H -2 0 1 -1 -4 1 -1 -2 11 -4 -3 0 -2 -1 -3 -1 -2 -3 2 -4 0 0 -1 -5
-I -2 -4 -4 -4 -2 -4 -4 -5 -4 6 2 -4 2 0 -3 -3 -1 -3 -1 4 -4 -4 -1 -5
-L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 6 -3 3 1 -4 -3 -2 -3 -1 1 -4 -3 -1 -5
-K -1 3 0 -1 -4 2 1 -2 0 -4 -3 6 -2 -4 -1 0 -1 -4 -2 -3 0 1 -1 -5
-M -1 -2 -3 -4 -2 0 -3 -3 -2 2 3 -2 8 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
-F -3 -3 -4 -5 -3 -4 -4 -4 -1 0 1 -4 0 9 -5 -3 -3 2 4 -1 -5 -4 -2 -5
-P -1 -3 -2 -2 -3 -1 -1 -3 -3 -3 -4 -1 -3 -5 10 -1 -1 -5 -4 -3 -2 -1 -2 -5
-S 2 -1 1 0 -1 0 0 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -3 -1 2 6 -3 -2 0 -1 -1 -1 -5
-W -4 -3 -5 -5 -4 -2 -3 -3 -3 -3 -3 -4 -2 2 -5 -4 -3 15 3 -4 -5 -3 -3 -5
-Y -2 -2 -2 -3 -3 -1 -2 -4 2 -1 -1 -2 -1 4 -4 -2 -2 3 9 -2 -3 -2 -1 -5
-V 0 -3 -4 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -4 -2 5 -4 -3 -1 -5
-B -2 -1 4 5 -4 0 1 -1 0 -4 -4 0 -3 -5 -2 0 -1 -5 -3 -4 5 2 -1 -5
-Z -1 0 0 1 -4 4 5 -3 0 -4 -3 1 -2 -4 -1 0 -1 -3 -2 -3 2 5 -1 -5
-X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM60 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM60
deleted file mode 100644
index 4fd1943..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM60
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum60.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 60
-# Entropy = 0.6603, Expected = -0.4917
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 -1 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
-R -1 5 0 -1 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -2 -1 0 -1 -4
-N -1 0 6 1 -2 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4
-D -2 -1 1 6 -3 0 2 -1 -1 -3 -3 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4
-C 0 -3 -2 -3 9 -3 -3 -2 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
-Q -1 1 0 0 -3 5 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
-E -1 0 0 2 -3 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
-G 0 -2 0 -1 -2 -2 -2 6 -2 -3 -4 -1 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4
-H -2 0 1 -1 -3 1 0 -2 7 -3 -3 -1 -1 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4
-I -1 -3 -3 -3 -1 -3 -3 -3 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -4
-L -1 -2 -3 -3 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -4
-K -1 2 0 -1 -3 1 1 -1 -1 -3 -2 4 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4
-M -1 -1 -2 -3 -1 0 -2 -2 -1 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -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 -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 -1 -2 -4
-S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 4 -2 -2 0 0 -1 0 -4
-W -3 -3 -4 -4 -2 -2 -3 -2 -2 -2 -2 -3 -1 1 -4 -3 -2 10 2 -3 -4 -2 -2 -4
-Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 6 -1 -2 -2 -1 -4
-V 0 -2 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4
-B -2 -1 3 4 -3 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -2 -3 4 1 -1 -4
-Z -1 0 0 1 -3 3 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -2 1 3 -1 -4
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM62 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM62
deleted file mode 100644
index 205f139..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM62
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum62.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 62
-# Entropy = 0.6979, Expected = -0.5209
- A R N D C Q E G H I L K M F P S T W Y V B 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 0 -4
-R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
-N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 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 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 -3 -2 -4
-Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4
-E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 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 -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 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 -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 -1 -4
-K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 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 -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 -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 -1 -2 -4
-S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4
-W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
-Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -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 -1 -4
-B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4
-Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4
-X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM65 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM65
deleted file mode 100644
index 1eacd14..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM65
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum65.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 65
-# Entropy = 0.7576, Expected = -0.5675
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -1 6 0 -2 -4 1 0 -2 0 -3 -2 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 0 6 1 -3 0 0 -1 1 -3 -4 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -5
-D -2 -2 1 6 -4 0 2 -1 -1 -3 -4 -1 -3 -4 -2 0 -1 -5 -3 -3 4 1 -1 -5
-C 0 -4 -3 -4 9 -3 -4 -3 -3 -1 -1 -3 -2 -2 -3 -1 -1 -2 -2 -1 -3 -4 -2 -5
-Q -1 1 0 0 -3 6 2 -2 1 -3 -2 1 0 -3 -1 0 -1 -2 -2 -2 0 3 -1 -5
-E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -3 1 4 -1 -5
-G 0 -2 -1 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -3 -3 -3 -1 -2 -2 -5
-H -2 0 1 -1 -3 1 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -5
-I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -2 -1 3 -3 -3 -1 -5
-L -2 -2 -4 -4 -1 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -1 -2 -1 1 -4 -3 -1 -5
-K -1 2 0 -1 -3 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -2 0 1 -1 -5
-M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
-F -2 -3 -3 -4 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -2 -5
-P -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -2 -2 -1 -2 -5
-S 1 -1 1 0 -1 0 0 0 -1 -2 -3 0 -2 -2 -1 4 1 -3 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
-W -3 -3 -4 -5 -2 -2 -3 -3 -2 -2 -2 -3 -2 1 -4 -3 -3 10 2 -3 -4 -3 -2 -5
-Y -2 -2 -2 -3 -2 -2 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -5
-V 0 -3 -3 -3 -1 -2 -3 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -5
-B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -5
-Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -5
-X -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM70 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM70
deleted file mode 100644
index 3e4093f..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM70
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum70.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 70
-# Entropy = 0.8391, Expected = -0.6313
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 -1 6 1 -3 0 0 -1 0 -4 -4 0 -2 -3 -2 0 0 -4 -2 -3 3 0 -1 -5
-D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -4 -4 4 1 -2 -5
-C -1 -4 -3 -4 9 -3 -4 -3 -4 -1 -2 -4 -2 -2 -3 -1 -1 -3 -3 -1 -4 -4 -2 -5
-Q -1 1 0 -1 -3 6 2 -2 1 -3 -2 1 0 -3 -2 0 -1 -2 -2 -2 0 3 -1 -5
-E -1 0 0 1 -4 2 5 -2 0 -4 -3 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
-G 0 -3 -1 -2 -3 -2 -2 6 -2 -4 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
-H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 -1 0 -1 -5
-I -2 -3 -4 -4 -1 -3 -4 -4 -4 4 2 -3 1 0 -3 -3 -1 -3 -1 3 -4 -3 -1 -5
-L -2 -3 -4 -4 -2 -2 -3 -4 -3 2 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
-K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -3 -1 0 -1 -3 -2 -3 -1 1 -1 -5
-M -1 -2 -2 -3 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -1 1 -3 -2 -1 -5
-F -2 -3 -3 -4 -2 -3 -4 -4 -1 0 0 -3 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
-P -1 -2 -2 -2 -3 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -4 -3 -3 -2 -1 -2 -5
-S 1 -1 0 0 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 4 1 -3 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
-W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -3 -2 1 -4 -3 -3 11 2 -3 -4 -3 -3 -5
-Y -2 -2 -2 -4 -3 -2 -3 -4 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -2 -3 -2 -2 -5
-V 0 -3 -3 -4 -1 -2 -3 -4 -3 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -3 -3 -1 -5
-B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -4 -3 -3 4 0 -1 -5
-Z -1 0 0 1 -4 3 4 -2 0 -3 -3 1 -2 -4 -1 0 -1 -3 -2 -3 0 4 -1 -5
-X -1 -1 -1 -2 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 -1 -3 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM75 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM75
deleted file mode 100644
index 98964be..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM75
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum75.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 75
-# Entropy = 0.9077, Expected = -0.6845
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5
-R -2 6 -1 -2 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -5
-N -2 -1 6 1 -3 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -4 -3 -3 3 0 -1 -5
-D -2 -2 1 6 -4 -1 1 -2 -1 -4 -4 -1 -4 -4 -2 -1 -1 -5 -4 -4 4 1 -2 -5
-C -1 -4 -3 -4 9 -3 -5 -3 -4 -1 -2 -4 -2 -2 -4 -1 -1 -3 -3 -1 -4 -4 -2 -5
-Q -1 1 0 -1 -3 6 2 -2 1 -3 -3 1 0 -4 -2 0 -1 -2 -2 -2 0 3 -1 -5
-E -1 0 -1 1 -5 2 5 -3 0 -4 -4 1 -2 -4 -1 0 -1 -4 -3 -3 1 4 -1 -5
-G 0 -3 -1 -2 -3 -2 -3 6 -2 -5 -4 -2 -3 -4 -3 -1 -2 -3 -4 -4 -1 -2 -2 -5
-H -2 0 0 -1 -4 1 0 -2 8 -4 -3 -1 -2 -2 -2 -1 -2 -2 2 -4 -1 0 -1 -5
-I -2 -3 -4 -4 -1 -3 -4 -5 -4 4 1 -3 1 0 -3 -3 -1 -3 -2 3 -4 -4 -2 -5
-L -2 -3 -4 -4 -2 -3 -4 -4 -3 1 4 -3 2 0 -3 -3 -2 -2 -1 1 -4 -3 -1 -5
-K -1 2 0 -1 -4 1 1 -2 -1 -3 -3 5 -2 -4 -1 0 -1 -4 -2 -3 -1 1 -1 -5
-M -1 -2 -3 -4 -2 0 -2 -3 -2 1 2 -2 6 0 -3 -2 -1 -2 -2 1 -3 -2 -1 -5
-F -3 -3 -4 -4 -2 -4 -4 -4 -2 0 0 -4 0 6 -4 -3 -2 1 3 -1 -4 -4 -2 -5
-P -1 -2 -3 -2 -4 -2 -1 -3 -2 -3 -3 -1 -3 -4 8 -1 -1 -5 -4 -3 -2 -2 -2 -5
-S 1 -1 0 -1 -1 0 0 -1 -1 -3 -3 0 -2 -3 -1 5 1 -3 -2 -2 0 0 -1 -5
-T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -1 1 5 -3 -2 0 -1 -1 -1 -5
-W -3 -3 -4 -5 -3 -2 -4 -3 -2 -3 -2 -4 -2 1 -5 -3 -3 11 2 -3 -5 -3 -3 -5
-Y -2 -2 -3 -4 -3 -2 -3 -4 2 -2 -1 -2 -2 3 -4 -2 -2 2 7 -2 -3 -3 -2 -5
-V 0 -3 -3 -4 -1 -2 -3 -4 -4 3 1 -3 1 -1 -3 -2 0 -3 -2 4 -4 -3 -1 -5
-B -2 -1 3 4 -4 0 1 -1 -1 -4 -4 -1 -3 -4 -2 0 -1 -5 -3 -4 4 0 -2 -5
-Z -1 0 0 1 -4 3 4 -2 0 -4 -3 1 -2 -4 -2 0 -1 -3 -3 -3 0 4 -1 -5
-X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -1 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM80 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM80
deleted file mode 100644
index 78172a3..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM80
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum80_3.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 80
-# Entropy = 0.9868, Expected = -0.7442
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8
-R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8
-N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8
-D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8
-C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8
-Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8
-E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8
-G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8
-H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8
-I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8
-L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8
-K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8
-M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8
-F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8
-P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8
-S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8
-T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8
-W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8
-Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8
-V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8
-B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8
-Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8
-X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM85 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM85
deleted file mode 100644
index cb47fd2..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM85
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum85.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 85
-# Entropy = 1.0805, Expected = -0.8153
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -2 -2 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -3 -3 -1 -2 -1 -1 -6
-R -2 6 -1 -2 -4 1 -1 -3 0 -4 -3 2 -2 -4 -2 -1 -2 -4 -3 -3 -2 0 -2 -6
-N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
-D -2 -2 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -4 -2 -1 -2 -6 -4 -4 4 1 -2 -6
-C -1 -4 -4 -5 9 -4 -5 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -3 -1 -4 -5 -3 -6
-Q -1 1 0 -1 -4 6 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -2 -3 -1 4 -1 -6
-E -1 -1 -1 1 -5 2 6 -3 -1 -4 -4 0 -3 -4 -2 -1 -1 -4 -4 -3 0 4 -1 -6
-G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -4 -3 -1 -2 -4 -5 -4 -1 -3 -2 -6
-H -2 0 0 -2 -5 1 -1 -3 8 -4 -3 -1 -3 -2 -3 -1 -2 -3 2 -4 -1 0 -2 -6
-I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -3 1 -1 -4 -3 -1 -3 -2 3 -5 -4 -2 -6
-L -2 -3 -4 -5 -2 -3 -4 -5 -3 1 4 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
-K -1 2 0 -1 -4 1 0 -2 -1 -3 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 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 -1 -6
-F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -1 -4 -4 -2 -6
-P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -1 -2 -5 -4 -3 -3 -2 -2 -6
-S 1 -1 0 -1 -2 -1 -1 -1 -1 -3 -3 -1 -2 -3 -1 5 1 -4 -2 -2 0 -1 -1 -6
-T 0 -2 0 -2 -2 -1 -1 -2 -2 -1 -2 -1 -1 -3 -2 1 5 -4 -2 0 -1 -1 -1 -6
-W -3 -4 -5 -6 -4 -3 -4 -4 -3 -3 -3 -5 -2 0 -5 -4 -4 11 2 -3 -5 -4 -3 -6
-Y -3 -3 -3 -4 -3 -2 -4 -5 2 -2 -2 -3 -2 3 -4 -2 -2 2 7 -2 -4 -3 -2 -6
-V -1 -3 -4 -4 -1 -3 -3 -4 -4 3 0 -3 0 -1 -3 -2 0 -3 -2 5 -4 -3 -1 -6
-B -2 -2 4 4 -4 -1 0 -1 -1 -5 -5 -1 -4 -4 -3 0 -1 -5 -4 -4 4 0 -2 -6
-Z -1 0 -1 1 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
-X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM90 b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM90
deleted file mode 100644
index 71441b5..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUM90
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosum90.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= 90
-# Entropy = 1.1806, Expected = -0.8887
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -2 -3 -1 1 0 -4 -3 -1 -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 0 -2 -6
-N -2 -1 7 1 -4 0 -1 -1 0 -4 -4 0 -3 -4 -3 0 0 -5 -3 -4 4 -1 -2 -6
-D -3 -3 1 7 -5 -1 1 -2 -2 -5 -5 -1 -4 -5 -3 -1 -2 -6 -4 -5 4 0 -2 -6
-C -1 -5 -4 -5 9 -4 -6 -4 -5 -2 -2 -4 -2 -3 -4 -2 -2 -4 -4 -2 -4 -5 -3 -6
-Q -1 1 0 -1 -4 7 2 -3 1 -4 -3 1 0 -4 -2 -1 -1 -3 -3 -3 -1 4 -1 -6
-E -1 -1 -1 1 -6 2 6 -3 -1 -4 -4 0 -3 -5 -2 -1 -1 -5 -4 -3 0 4 -2 -6
-G 0 -3 -1 -2 -4 -3 -3 6 -3 -5 -5 -2 -4 -5 -3 -1 -3 -4 -5 -5 -2 -3 -2 -6
-H -2 0 0 -2 -5 1 -1 -3 8 -4 -4 -1 -3 -2 -3 -2 -2 -3 1 -4 -1 0 -2 -6
-I -2 -4 -4 -5 -2 -4 -4 -5 -4 5 1 -4 1 -1 -4 -3 -1 -4 -2 3 -5 -4 -2 -6
-L -2 -3 -4 -5 -2 -3 -4 -5 -4 1 5 -3 2 0 -4 -3 -2 -3 -2 0 -5 -4 -2 -6
-K -1 2 0 -1 -4 1 0 -2 -1 -4 -3 6 -2 -4 -2 -1 -1 -5 -3 -3 -1 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 -1 -6
-F -3 -4 -4 -5 -3 -4 -5 -5 -2 -1 0 -4 -1 7 -4 -3 -3 0 3 -2 -4 -4 -2 -6
-P -1 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -3 -4 8 -2 -2 -5 -4 -3 -3 -2 -2 -6
-S 1 -1 0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2 5 1 -4 -3 -2 0 -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 -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 -4 -3 -6
-Y -3 -3 -3 -4 -4 -3 -4 -5 1 -2 -2 -3 -2 3 -4 -3 -2 2 8 -3 -4 -3 -2 -6
-V -1 -3 -4 -5 -2 -3 -3 -5 -4 3 0 -3 0 -2 -3 -2 -1 -3 -3 5 -4 -3 -2 -6
-B -2 -2 4 4 -4 -1 0 -2 -1 -5 -5 -1 -4 -4 -3 0 -1 -6 -4 -4 4 0 -2 -6
-Z -1 0 -1 0 -5 4 4 -3 0 -4 -4 1 -2 -4 -2 -1 -1 -4 -3 -3 0 4 -1 -6
-X -1 -2 -2 -2 -3 -1 -2 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUMN b/Butterfly/src/src/jaligner/matrix/matrices/BLOSUMN
deleted file mode 100644
index df064c8..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/BLOSUMN
+++ /dev/null
@@ -1,31 +0,0 @@
-# Matrix made by matblas from blosumn.iij
-# * column uses minimum score
-# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
-# Blocks Database = /data/blocks_5.0/blocks.dat
-# Cluster Percentage: >= -2
-# Entropy = 1.5172, Expected = -1.1484
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -2 -2 -3 -2 -1 -2 -1 -3 -3 -3 -2 -2 -4 -1 1 -1 -4 -4 -1 -3 -2 -1 -7
-R -2 7 -1 -3 -6 0 -2 -4 -1 -5 -4 2 -3 -4 -3 -2 -2 -5 -4 -4 -2 -1 -2 -7
-N -2 -1 7 1 -4 -1 -1 -2 0 -5 -5 -1 -4 -5 -4 0 -1 -6 -4 -4 4 -1 -2 -7
-D -3 -3 1 7 -6 -2 1 -3 -2 -6 -6 -2 -5 -5 -3 -2 -2 -7 -5 -5 4 0 -3 -7
-C -2 -6 -4 -6 9 -5 -7 -5 -6 -2 -3 -5 -3 -3 -5 -2 -2 -5 -4 -2 -5 -6 -4 -7
-Q -1 0 -1 -2 -5 7 1 -4 0 -4 -3 1 -1 -4 -2 -1 -2 -4 -3 -4 -1 4 -2 -7
-E -2 -2 -1 1 -7 1 6 -4 -1 -5 -5 0 -4 -5 -3 -1 -2 -5 -4 -4 0 5 -2 -7
-G -1 -4 -2 -3 -5 -4 -4 6 -4 -6 -6 -3 -5 -5 -4 -1 -3 -5 -6 -5 -2 -4 -3 -7
-H -3 -1 0 -2 -6 0 -1 -4 9 -5 -4 -2 -3 -3 -4 -2 -3 -4 1 -5 -1 -1 -3 -7
-I -3 -5 -5 -6 -2 -4 -5 -6 -5 6 1 -4 1 -1 -5 -4 -2 -4 -3 2 -5 -5 -2 -7
-L -3 -4 -5 -6 -3 -3 -5 -6 -4 1 5 -4 2 0 -5 -4 -3 -4 -3 0 -5 -4 -2 -7
-K -2 2 -1 -2 -5 1 0 -3 -2 -4 -4 6 -2 -4 -2 -1 -2 -6 -4 -4 -1 0 -2 -7
-M -2 -3 -4 -5 -3 -1 -4 -5 -3 1 2 -2 8 -1 -4 -3 -2 -2 -3 0 -5 -3 -2 -7
-F -4 -4 -5 -5 -3 -4 -5 -5 -3 -1 0 -4 -1 7 -5 -4 -3 0 3 -2 -5 -5 -3 -7
-P -1 -3 -4 -3 -5 -2 -3 -4 -4 -5 -5 -2 -4 -5 8 -2 -3 -5 -5 -4 -4 -3 -3 -7
-S 1 -2 0 -2 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 6 1 -4 -3 -3 -1 -1 -1 -7
-T -1 -2 -1 -2 -2 -2 -2 -3 -3 -2 -3 -2 -2 -3 -3 1 6 -5 -3 -1 -2 -2 -1 -7
-W -4 -5 -6 -7 -5 -4 -5 -5 -4 -4 -4 -6 -2 0 -5 -4 -5 11 1 -3 -6 -4 -4 -7
-Y -4 -4 -4 -5 -4 -3 -4 -6 1 -3 -3 -4 -3 3 -5 -3 -3 1 8 -3 -4 -4 -3 -7
-V -1 -4 -4 -5 -2 -4 -4 -5 -5 2 0 -4 0 -2 -4 -3 -1 -3 -3 5 -5 -4 -2 -7
-B -3 -2 4 4 -5 -1 0 -2 -1 -5 -5 -1 -5 -5 -4 -1 -2 -6 -4 -5 4 1 -2 -7
-Z -2 -1 -1 0 -6 4 5 -4 -1 -5 -4 0 -3 -5 -3 -1 -2 -4 -4 -4 1 4 -2 -7
-X -1 -2 -2 -3 -4 -2 -2 -3 -3 -2 -2 -2 -2 -3 -3 -1 -1 -4 -3 -2 -2 -2 -2 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/DAYHOFF b/Butterfly/src/src/jaligner/matrix/matrices/DAYHOFF
deleted file mode 100644
index e287ed0..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/DAYHOFF
+++ /dev/null
@@ -1,32 +0,0 @@
-#Date: Wed, 18 Sep 91 17:36:51 EDT
-#From: altschul at ray.nlm.nih.gov (Stephen Altschul)
-#To: gish at ray.nlm.nih.gov
-#Subject: Vanilla-flavored PAM-250
-#
-# substitution scores for B, Z, X, and * were obtained with "pam" version 1.0.5
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -3 0 0 0 0 -8
-R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 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 -3 -8
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 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 -1 -8
-G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 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 -1 -8
-I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -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 -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 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 -2 -1 -8
-F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 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 0 0 -8
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -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 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 3 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/EDNAFULL b/Butterfly/src/src/jaligner/matrix/matrices/EDNAFULL
deleted file mode 100644
index bfec6d9..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/EDNAFULL
+++ /dev/null
@@ -1,25 +0,0 @@
-#
-# 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 U
-A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 -4
-T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
-G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 -4
-C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 -4
-S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 -4
-W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 1
-R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 -4
-Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 1
-K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 1
-M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 -4
-B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 -1
-V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 -4
-H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 -1
-D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 -1
-N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2
-U -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 5
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/GONNET b/Butterfly/src/src/jaligner/matrix/matrices/GONNET
deleted file mode 100644
index d7bd4f4..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/GONNET
+++ /dev/null
@@ -1,26 +0,0 @@
-# PAM 250 matrix recommended by Gonnet, Cohen & Benner
-# Science June 5, 1992.
-# Values rounded to nearest integer
- C S T P A G N D E Q H R K M I L V F Y W X *
-C 12 0 0 -3 0 -2 -2 -3 -3 -2 -1 -2 -3 -1 -1 -2 0 -1 0 -1 -3 -8
-S 0 2 2 0 1 0 1 0 0 0 0 0 0 -1 -2 -2 -1 -3 -2 -3 0 -8
-T 0 2 2 0 1 -1 0 0 0 0 0 0 0 -1 -1 -1 0 -2 -2 -4 0 -8
-P -3 0 0 8 0 -2 -1 -1 0 0 -1 -1 -1 -2 -3 -2 -2 -4 -3 -5 -1 -8
-A 0 1 1 0 2 0 0 0 0 0 -1 -1 0 -1 -1 -1 0 -2 -2 -4 0 -8
-G -2 0 -1 -2 0 7 0 0 -1 -1 -1 -1 -1 -4 -4 -4 -3 -5 -4 -4 -1 -8
-N -2 1 0 -1 0 0 4 2 1 1 1 0 1 -2 -3 -3 -2 -3 -1 -4 0 -8
-D -3 0 0 -1 0 0 2 5 3 1 0 0 0 -3 -4 -4 -3 -4 -3 -5 -1 -8
-E -3 0 0 0 0 -1 1 3 4 2 0 0 1 -2 -3 -3 -2 -4 -3 -4 -1 -8
-Q -2 0 0 0 0 -1 1 1 2 3 1 2 2 -1 -2 -2 -2 -3 -2 -3 -1 -8
-H -1 0 0 -1 -1 -1 1 0 0 1 6 1 1 -1 -2 -2 -2 0 2 -1 -1 -8
-R -2 0 0 -1 -1 -1 0 0 0 2 1 5 3 -2 -2 -2 -2 -3 -2 -2 -1 -8
-K -3 0 0 -1 0 -1 1 0 1 2 1 3 3 -1 -2 -2 -2 -3 -2 -4 -1 -8
-M -1 -1 -1 -2 -1 -4 -2 -3 -2 -1 -1 -2 -1 4 2 3 2 2 0 -1 -1 -8
-I -1 -2 -1 -3 -1 -4 -3 -4 -3 -2 -2 -2 -2 2 4 3 3 1 -1 -2 -1 -8
-L -2 -2 -1 -2 -1 -4 -3 -4 -3 -2 -2 -2 -2 3 3 4 2 2 0 -1 -1 -8
-V 0 -1 0 -2 0 -3 -2 -3 -2 -2 -2 -2 -2 2 3 2 3 0 -1 -3 -1 -8
-F -1 -3 -2 -4 -2 -5 -3 -4 -4 -3 0 -3 -3 2 1 2 0 7 5 4 -2 -8
-Y 0 -2 -2 -3 -2 -4 -1 -3 -3 -2 2 -2 -2 0 -1 0 -1 5 8 4 -2 -8
-W -1 -3 -4 -5 -4 -4 -4 -5 -4 -3 -1 -2 -4 -1 -2 -1 -3 4 4 14 -4 -8
-X -3 0 0 -1 0 -1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -2 -4 -1 -8
-* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/IDENTITY b/Butterfly/src/src/jaligner/matrix/matrices/IDENTITY
deleted file mode 100644
index 63913d5..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/IDENTITY
+++ /dev/null
@@ -1,25 +0,0 @@
- A R N B D C Q Z E G H I L K M F P S T W Y V X *
-A 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-R -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-N -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-B -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-D -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-C -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-Q -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-Z -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-E -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-G -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-H -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-I -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-L -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-K -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-M -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-F -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-P -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000 -10000
-S -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000 -10000
-T -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000 -10000
-W -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000 -10000
-Y -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000 -10000
-V -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 1 -10000 -10000
-X -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0 -10000
-* -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 -10000 0
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/MATCH b/Butterfly/src/src/jaligner/matrix/matrices/MATCH
deleted file mode 100644
index cda9e49..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/MATCH
+++ /dev/null
@@ -1,25 +0,0 @@
- A R N B D C Q Z E G H I L K M F P S T W Y V X *
-A 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-R -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-N -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-B -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-D -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-C -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-Q -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-Z -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-E -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-G -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-H -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-I -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-L -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-K -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1
-F -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1 -1
-P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1 -1
-S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1 -1
-T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1 -1
-W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1 -1
-Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1 -1
-V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 -1 -1
-X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 -1
-* -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM10 b/Butterfly/src/src/jaligner/matrix/matrices/PAM10
deleted file mode 100644
index c164b06..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM10
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 10 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -8.27, Entropy = 3.43 bits
-#
-# Lowest score = -23, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 7 -10 -7 -6 -10 -7 -5 -4 -11 -8 -9 -10 -8 -12 -4 -3 -3 -20 -11 -5 -6 -6 -6 -23
-R -10 9 -9 -17 -11 -4 -15 -13 -4 -8 -12 -2 -7 -12 -7 -6 -10 -5 -14 -11 -11 -7 -9 -23
-N -7 -9 9 -1 -17 -7 -5 -6 -2 -8 -10 -4 -15 -12 -9 -2 -5 -11 -7 -12 7 -6 -6 -23
-D -6 -17 -1 8 -21 -6 0 -6 -7 -11 -19 -8 -17 -21 -12 -7 -8 -21 -17 -11 7 -1 -9 -23
-C -10 -11 -17 -21 10 -20 -20 -13 -10 -9 -21 -20 -20 -19 -11 -6 -11 -22 -7 -9 -18 -20 -13 -23
-Q -7 -4 -7 -6 -20 9 -1 -10 -2 -11 -8 -6 -7 -19 -6 -8 -9 -19 -18 -10 -6 7 -8 -23
-E -5 -15 -5 0 -20 -1 8 -7 -9 -8 -13 -7 -10 -20 -9 -7 -9 -23 -11 -10 -1 7 -8 -23
-G -4 -13 -6 -6 -13 -10 -7 7 -13 -17 -14 -10 -12 -12 -10 -4 -10 -21 -20 -9 -6 -8 -8 -23
-H -11 -4 -2 -7 -10 -2 -9 -13 10 -13 -9 -10 -17 -9 -7 -9 -11 -10 -6 -9 -4 -4 -8 -23
-I -8 -8 -8 -11 -9 -11 -8 -17 -13 9 -4 -9 -3 -5 -12 -10 -5 -20 -9 -1 -9 -9 -8 -23
-L -9 -12 -10 -19 -21 -8 -13 -14 -9 -4 7 -11 -2 -5 -10 -12 -10 -9 -10 -5 -12 -10 -9 -23
-K -10 -2 -4 -8 -20 -6 -7 -10 -10 -9 -11 7 -4 -20 -10 -7 -6 -18 -12 -13 -5 -6 -8 -23
-M -8 -7 -15 -17 -20 -7 -10 -12 -17 -3 -2 -4 12 -7 -11 -8 -7 -19 -17 -4 -16 -8 -9 -23
-F -12 -12 -12 -21 -19 -19 -20 -12 -9 -5 -5 -20 -7 9 -13 -9 -12 -7 -1 -12 -14 -20 -12 -23
-P -4 -7 -9 -12 -11 -6 -9 -10 -7 -12 -10 -10 -11 -13 8 -4 -7 -20 -20 -9 -10 -7 -8 -23
-S -3 -6 -2 -7 -6 -8 -7 -4 -9 -10 -12 -7 -8 -9 -4 7 -2 -8 -10 -10 -4 -8 -6 -23
-T -3 -10 -5 -8 -11 -9 -9 -10 -11 -5 -10 -6 -7 -12 -7 -2 8 -19 -9 -6 -6 -9 -7 -23
-W -20 -5 -11 -21 -22 -19 -23 -21 -10 -20 -9 -18 -19 -7 -20 -8 -19 13 -8 -22 -13 -21 -16 -23
-Y -11 -14 -7 -17 -7 -18 -11 -20 -6 -9 -10 -12 -17 -1 -20 -10 -9 -8 10 -10 -9 -13 -11 -23
-V -5 -11 -12 -11 -9 -10 -10 -9 -9 -1 -5 -13 -4 -12 -9 -10 -6 -22 -10 8 -11 -10 -8 -23
-B -6 -11 7 7 -18 -6 -1 -6 -4 -9 -12 -5 -16 -14 -10 -4 -6 -13 -9 -11 7 -3 -8 -23
-Z -6 -7 -6 -1 -20 7 7 -8 -4 -9 -10 -6 -8 -20 -7 -8 -9 -21 -13 -10 -3 7 -8 -23
-X -6 -9 -6 -9 -13 -8 -8 -8 -8 -8 -9 -8 -9 -12 -8 -6 -7 -16 -11 -8 -8 -8 -8 -23
-* -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 -23 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM100 b/Butterfly/src/src/jaligner/matrix/matrices/PAM100
deleted file mode 100644
index 2e33dd3..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM100
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 100 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.99, Entropy = 1.18 bits
-#
-# Lowest score = -9, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -3 -1 -1 -3 -2 0 1 -3 -2 -3 -3 -2 -5 1 1 1 -7 -4 0 -1 -1 -1 -9
-R -3 7 -2 -4 -5 1 -3 -5 1 -3 -5 2 -1 -6 -1 -1 -3 1 -6 -4 -3 -1 -2 -9
-N -1 -2 5 3 -5 -1 1 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -3 4 0 -1 -9
-D -1 -4 3 5 -7 0 4 -1 -1 -4 -6 -1 -5 -8 -3 -1 -2 -9 -6 -4 4 3 -2 -9
-C -3 -5 -5 -7 9 -8 -8 -5 -4 -3 -8 -8 -7 -7 -4 -1 -4 -9 -1 -3 -6 -8 -5 -9
-Q -2 1 -1 0 -8 6 2 -3 3 -4 -2 0 -2 -7 -1 -2 -2 -7 -6 -3 0 5 -2 -9
-E 0 -3 1 4 -8 2 5 -1 -1 -3 -5 -1 -4 -8 -2 -1 -2 -9 -5 -3 3 4 -2 -9
-G 1 -5 -1 -1 -5 -3 -1 5 -4 -5 -6 -3 -4 -6 -2 0 -2 -9 -7 -3 -1 -2 -2 -9
-H -3 1 2 -1 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
-I -2 -3 -3 -4 -3 -4 -3 -5 -4 6 1 -3 1 0 -4 -3 0 -7 -3 3 -3 -3 -2 -9
-L -3 -5 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 0 -5 -4 -3 -9
-K -3 2 1 -1 -8 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -6 -6 -4 0 -1 -2 -9
-M -2 -1 -4 -5 -7 -2 -4 -4 -4 1 3 0 9 -1 -4 -3 -1 -6 -5 1 -4 -2 -2 -9
-F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -7 -1 8 -6 -4 -5 -1 4 -3 -6 -7 -4 -9
-P 1 -1 -2 -3 -4 -1 -2 -2 -1 -4 -4 -3 -4 -6 7 0 -1 -7 -7 -3 -3 -1 -2 -9
-S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -3 -4 0 4 2 -3 -4 -2 0 -2 -1 -9
-T 1 -3 0 -2 -4 -2 -2 -2 -3 0 -3 -1 -1 -5 -1 2 5 -7 -4 0 -1 -2 -1 -9
-W -7 1 -5 -9 -9 -7 -9 -9 -4 -7 -3 -6 -6 -1 -7 -3 -7 12 -2 -9 -6 -8 -6 -9
-Y -4 -6 -2 -6 -1 -6 -5 -7 -1 -3 -3 -6 -5 4 -7 -4 -4 -2 9 -4 -4 -6 -4 -9
-V 0 -4 -3 -4 -3 -3 -3 -3 -3 3 0 -4 1 -3 -3 -2 0 -9 -4 5 -4 -3 -2 -9
-B -1 -3 4 4 -6 0 3 -1 1 -3 -5 0 -4 -6 -3 0 -1 -6 -4 -4 4 2 -2 -9
-Z -1 -1 0 3 -8 5 4 -2 1 -3 -4 -1 -2 -7 -1 -2 -2 -8 -6 -3 2 5 -2 -9
-X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM110 b/Butterfly/src/src/jaligner/matrix/matrices/PAM110
deleted file mode 100644
index 25b2c01..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM110
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 110 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.81, Entropy = 1.07 bits
-#
-# Lowest score = -9, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 -1 -1 -3 -1 0 1 -3 -1 -3 -3 -2 -4 1 1 1 -7 -4 0 -1 -1 -1 -9
-R -3 7 -1 -4 -4 1 -3 -4 1 -3 -4 2 -1 -5 -1 -1 -2 1 -5 -4 -2 -1 -2 -9
-N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -5 -2 -3 3 0 -1 -9
-D -1 -4 2 5 -7 1 4 0 0 -3 -6 -1 -5 -7 -3 -1 -1 -8 -5 -4 4 3 -2 -9
-C -3 -4 -5 -7 9 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 -1 -3 -9 -1 -3 -6 -7 -4 -9
-Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -6 -3 0 4 -1 -9
-E 0 -3 1 4 -7 2 5 -1 -1 -3 -5 -1 -3 -7 -2 -1 -2 -9 -5 -3 3 4 -2 -9
-G 1 -4 0 0 -5 -3 -1 5 -4 -4 -6 -3 -4 -5 -2 0 -2 -8 -7 -2 0 -2 -2 -9
-H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -4 -1 -3 1 1 -2 -9
-I -1 -3 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -4 -3 0 -7 -2 3 -3 -3 -2 -9
-L -3 -4 -4 -6 -8 -2 -5 -6 -3 1 6 -4 3 0 -4 -4 -3 -3 -3 1 -5 -3 -2 -9
-K -3 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -3 -1 -1 -5 -5 -4 0 -1 -2 -9
-M -2 -1 -3 -5 -7 -1 -3 -4 -4 1 3 0 8 -1 -4 -2 -1 -6 -5 1 -4 -2 -2 -9
-F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -6 -4 -4 -1 4 -3 -6 -7 -4 -9
-P 1 -1 -2 -3 -4 0 -2 -2 -1 -4 -4 -3 -4 -6 6 0 -1 -7 -7 -2 -2 -1 -2 -9
-S 1 -1 1 -1 -1 -2 -1 0 -2 -3 -4 -1 -2 -4 0 3 2 -3 -3 -2 0 -1 -1 -9
-T 1 -2 0 -1 -3 -2 -2 -2 -3 0 -3 -1 -1 -4 -1 2 5 -6 -3 0 -1 -2 -1 -9
-W -7 1 -5 -8 -9 -6 -9 -8 -4 -7 -3 -5 -6 -1 -7 -3 -6 12 -2 -8 -6 -7 -5 -9
-Y -4 -5 -2 -5 -1 -6 -5 -7 -1 -2 -3 -5 -5 4 -7 -3 -3 -2 8 -4 -3 -5 -3 -9
-V 0 -4 -3 -4 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -4 5 -3 -3 -2 -9
-B -1 -2 3 4 -6 0 3 0 1 -3 -5 0 -4 -6 -2 0 -1 -6 -3 -3 4 2 -1 -9
-Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -7 -1 -1 -2 -7 -5 -3 2 4 -2 -9
-X -1 -2 -1 -2 -4 -1 -2 -2 -2 -2 -2 -2 -2 -4 -2 -1 -1 -5 -3 -2 -1 -2 -2 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM120 b/Butterfly/src/src/jaligner/matrix/matrices/PAM120
deleted file mode 100644
index 3cbb04b..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM120
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.64, Entropy = 0.979 bits
-#
-# Lowest score = -8, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 -8
-R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
-N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 -8
-D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 -8
-C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 -8
-Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 -8
-E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 -8
-G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 -8
-H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 -8
-I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
-L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 -8
-K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 -8
-M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 -8
-F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 -8
-P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 -8
-S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
-T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
-W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 -8
-Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 -8
-V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 -8
-B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 -8
-Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
-X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM130 b/Butterfly/src/src/jaligner/matrix/matrices/PAM130
deleted file mode 100644
index 0b47a5d..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM130
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 130 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.48, Entropy = 0.895 bits
-#
-# Lowest score = -8, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
-R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 -8
-N 0 -1 4 2 -4 0 1 0 2 -2 -3 1 -3 -4 -1 1 0 -4 -2 -3 3 0 -1 -8
-D 0 -3 2 5 -6 1 3 0 0 -3 -5 -1 -4 -7 -2 0 -1 -7 -5 -3 4 3 -1 -8
-C -3 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
-Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -6 0 -1 -2 -6 -5 -3 0 4 -1 -8
-E 0 -3 1 3 -6 2 5 -1 0 -2 -4 -1 -3 -6 -2 -1 -1 -8 -5 -3 2 4 -1 -8
-G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -4 -5 -2 1 -1 -7 -6 -2 0 -1 -2 -8
-H -2 1 2 0 -4 3 0 -3 7 -3 -3 -1 -3 -2 -1 -2 -2 -3 0 -3 1 1 -1 -8
-I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -3 -3 -1 -8
-L -3 -4 -3 -5 -7 -2 -4 -5 -3 1 5 -4 3 1 -3 -4 -2 -2 -2 1 -4 -3 -2 -8
-K -2 2 1 -1 -6 0 -1 -3 -1 -2 -4 5 0 -6 -2 -1 0 -5 -5 -4 0 0 -1 -8
-M -2 -1 -3 -4 -6 -1 -3 -4 -3 2 3 0 8 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
-F -4 -5 -4 -7 -5 -6 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
-P 1 -1 -1 -2 -3 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -6 -6 -2 -2 -1 -1 -8
-S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 -8
-T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 -8
-W -6 1 -4 -7 -8 -6 -8 -7 -3 -6 -2 -5 -5 -1 -6 -2 -6 12 -1 -7 -5 -7 -5 -8
-Y -4 -5 -2 -5 -1 -5 -5 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -5 -3 -8
-V 0 -3 -3 -3 -2 -3 -3 -2 -3 3 1 -4 1 -2 -2 -2 0 -7 -3 5 -3 -3 -1 -8
-B 0 -2 3 4 -5 0 2 0 1 -3 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
-Z 0 -1 0 3 -6 4 4 -1 1 -3 -3 0 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 -8
-X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 -1 -1 -5 -3 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM140 b/Butterfly/src/src/jaligner/matrix/matrices/PAM140
deleted file mode 100644
index 022c61b..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM140
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 140 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.35, Entropy = 0.820 bits
-#
-# Lowest score = -8, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -6 -4 0 0 0 -1 -8
-R -2 6 -1 -3 -4 1 -2 -4 1 -2 -4 3 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -1 -8
-N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -8
-D 0 -3 2 4 -6 1 3 0 0 -3 -5 -1 -4 -6 -2 0 -1 -7 -5 -3 4 3 -1 -8
-C -2 -4 -4 -6 9 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 -1 -2 -5 -6 -4 -8
-Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -2 -5 -5 -2 1 4 -1 -8
-E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -3 -6 -1 -1 -1 -8 -4 -2 2 4 -1 -8
-G 1 -4 0 0 -4 -2 -1 5 -3 -4 -5 -3 -3 -5 -1 1 -1 -7 -6 -2 0 -1 -1 -8
-H -2 1 2 0 -4 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -8
-I -1 -2 -2 -3 -3 -3 -2 -4 -3 5 1 -2 2 0 -3 -2 0 -6 -2 3 -2 -2 -1 -8
-L -2 -4 -3 -5 -7 -2 -4 -5 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -8
-K -2 3 1 -1 -6 0 -1 -3 -1 -2 -3 5 0 -6 -2 -1 0 -4 -5 -3 0 0 -1 -8
-M -2 -1 -2 -4 -6 -1 -3 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -4 1 -3 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -4 -1 4 -2 -5 -6 -3 -8
-P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -6 -2 -2 -1 -1 -8
-S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 0 -8
-T 1 -2 0 -1 -3 -2 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -5 -3 0 0 -1 -1 -8
-W -6 1 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 -1 -6 -2 -5 12 -1 -7 -5 -6 -5 -8
-Y -4 -5 -2 -5 -1 -5 -4 -6 0 -2 -2 -5 -4 4 -6 -3 -3 -1 8 -3 -3 -4 -3 -8
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -2 0 -7 -3 5 -3 -2 -1 -8
-B 0 -2 3 4 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -3 3 2 -1 -8
-Z 0 -1 1 3 -6 4 4 -1 1 -2 -3 0 -2 -6 -1 -1 -1 -6 -4 -2 2 4 -1 -8
-X -1 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -5 -3 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM150 b/Butterfly/src/src/jaligner/matrix/matrices/PAM150
deleted file mode 100644
index c010eef..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM150
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 150 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.25, Entropy = 0.754 bits
-#
-# Lowest score = -7, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -6 -3 0 0 0 -1 -7
-R -2 6 -1 -2 -4 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -2 1 -4 -3 -2 0 -1 -7
-N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 3 1 -1 -7
-D 0 -2 2 4 -6 1 3 0 0 -3 -5 -1 -3 -6 -2 0 -1 -7 -4 -3 3 2 -1 -7
-C -2 -4 -4 -6 9 -6 -6 -4 -3 -2 -6 -6 -5 -5 -3 0 -3 -7 0 -2 -5 -6 -3 -7
-Q -1 1 0 1 -6 5 2 -2 3 -3 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -7
-E 0 -2 1 3 -6 2 4 -1 0 -2 -4 -1 -2 -6 -1 -1 -1 -7 -4 -2 2 4 -1 -7
-G 1 -3 0 0 -4 -2 -1 4 -3 -3 -4 -2 -3 -5 -1 1 -1 -7 -5 -2 0 -1 -1 -7
-H -2 1 2 0 -3 3 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -3 1 1 -1 -7
-I -1 -2 -2 -3 -2 -3 -2 -3 -3 5 1 -2 2 0 -3 -2 0 -5 -2 3 -2 -2 -1 -7
-L -2 -3 -3 -5 -6 -2 -4 -4 -2 1 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
-K -2 3 1 -1 -6 0 -1 -2 -1 -2 -3 4 0 -6 -2 -1 0 -4 -4 -3 0 0 -1 -7
-M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 -1 -3 -2 -1 -5 -3 1 -3 -2 -1 -7
-F -4 -4 -4 -6 -5 -5 -6 -5 -2 0 1 -6 -1 7 -5 -3 -3 -1 5 -2 -5 -5 -3 -7
-P 1 -1 -1 -2 -3 0 -1 -1 -1 -3 -3 -2 -3 -5 6 1 0 -6 -5 -2 -2 -1 -1 -7
-S 1 -1 1 0 0 -1 -1 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
-T 1 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 4 -5 -3 0 0 -1 -1 -7
-W -6 1 -4 -7 -7 -5 -7 -7 -3 -5 -2 -4 -5 -1 -6 -2 -5 12 -1 -6 -5 -6 -4 -7
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
-B 0 -2 3 3 -5 1 2 0 1 -2 -4 0 -3 -5 -2 0 0 -5 -3 -2 3 2 -1 -7
-Z 0 0 1 2 -6 4 4 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 4 -1 -7
-X -1 -1 -1 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 -1 -4 -3 -1 -1 -1 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM160 b/Butterfly/src/src/jaligner/matrix/matrices/PAM160
deleted file mode 100644
index f30d717..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM160
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 160 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -1.14, Entropy = 0.694 bits
-#
-# Lowest score = -7, Highest score = 12
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -3 1 1 1 -5 -3 0 0 0 0 -7
-R -2 6 -1 -2 -3 1 -2 -3 1 -2 -3 3 -1 -4 -1 -1 -1 1 -4 -3 -1 0 -1 -7
-N 0 -1 3 2 -4 0 1 0 2 -2 -3 1 -2 -3 -1 1 0 -4 -2 -2 2 1 0 -7
-D 0 -2 2 4 -5 1 3 0 0 -3 -4 0 -3 -6 -2 0 -1 -6 -4 -3 3 2 -1 -7
-C -2 -3 -4 -5 9 -5 -5 -3 -3 -2 -6 -5 -5 -5 -3 0 -2 -7 0 -2 -4 -5 -3 -7
-Q -1 1 0 1 -5 5 2 -2 2 -2 -2 0 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -7
-E 0 -2 1 3 -5 2 4 0 0 -2 -3 -1 -2 -5 -1 0 -1 -7 -4 -2 2 3 -1 -7
-G 1 -3 0 0 -3 -2 0 4 -3 -3 -4 -2 -3 -4 -1 1 -1 -7 -5 -2 0 -1 -1 -7
-H -2 1 2 0 -3 2 0 -3 6 -3 -2 -1 -3 -2 -1 -1 -2 -3 0 -2 1 1 -1 -7
-I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 0 -2 -2 0 -5 -2 3 -2 -2 -1 -7
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 5 -3 3 1 -3 -3 -2 -2 -2 1 -4 -3 -2 -7
-K -2 3 1 0 -5 0 -1 -2 -1 -2 -3 4 0 -5 -2 -1 0 -4 -4 -3 0 0 -1 -7
-M -1 -1 -2 -3 -5 -1 -2 -3 -3 2 3 0 7 0 -2 -2 -1 -4 -3 1 -3 -2 -1 -7
-F -3 -4 -3 -6 -5 -5 -5 -4 -2 0 1 -5 0 7 -4 -3 -3 -1 5 -2 -4 -5 -3 -7
-P 1 -1 -1 -2 -3 0 -1 -1 -1 -2 -3 -2 -2 -4 5 1 0 -5 -5 -2 -1 -1 -1 -7
-S 1 -1 1 0 0 -1 0 1 -1 -2 -3 -1 -2 -3 1 2 1 -2 -3 -1 0 -1 0 -7
-T 1 -1 0 -1 -2 -1 -1 -1 -2 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -7
-W -5 1 -4 -6 -7 -5 -7 -7 -3 -5 -2 -4 -4 -1 -5 -2 -5 12 -1 -6 -5 -6 -4 -7
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -2 -2 -4 -3 5 -5 -3 -3 -1 8 -3 -3 -4 -3 -7
-V 0 -3 -2 -3 -2 -2 -2 -2 -2 3 1 -3 1 -2 -2 -1 0 -6 -3 4 -2 -2 -1 -7
-B 0 -1 2 3 -4 1 2 0 1 -2 -4 0 -3 -4 -1 0 0 -5 -3 -2 3 2 -1 -7
-Z 0 0 1 2 -5 3 3 -1 1 -2 -3 0 -2 -5 -1 -1 -1 -6 -4 -2 2 3 -1 -7
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -1 -1 -1 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM170 b/Butterfly/src/src/jaligner/matrix/matrices/PAM170
deleted file mode 100644
index ca090d6..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM170
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 170 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.57, Entropy = 0.640 bits
-#
-# Lowest score = -10, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 0 0 -3 -1 0 1 -3 -1 -3 -2 -2 -5 1 2 2 -8 -5 0 0 0 -1 -10
-R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
-N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -3 -3 3 1 -1 -10
-D 0 -3 3 6 -7 2 5 0 0 -4 -6 -1 -4 -8 -2 0 -1 -9 -6 -4 5 4 -1 -10
-C -3 -5 -5 -7 13 -8 -8 -5 -5 -3 -9 -8 -7 -6 -4 0 -3 -10 0 -3 -6 -8 -4 -10
-Q -1 1 0 2 -8 6 3 -2 4 -3 -2 0 -1 -7 0 -1 -2 -7 -6 -3 1 5 -1 -10
-E 0 -2 2 5 -8 3 6 0 0 -3 -5 -1 -3 -8 -1 -1 -1 -10 -6 -3 3 5 -1 -10
-G 1 -4 0 0 -5 -2 0 6 -4 -4 -6 -3 -4 -6 -2 1 -1 -9 -7 -2 0 -1 -2 -10
-H -3 2 2 0 -5 4 0 -4 9 -4 -3 -1 -4 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
-I -1 -3 -3 -4 -3 -3 -3 -4 -4 7 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
-L -3 -4 -4 -6 -9 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -4 -2 -10
-K -2 4 1 -1 -8 0 -1 -3 -1 -3 -4 6 1 -8 -2 -1 0 -5 -6 -4 0 0 -2 -10
-M -2 -1 -3 -4 -7 -1 -3 -4 -4 2 4 1 10 0 -3 -2 -1 -6 -4 2 -4 -2 -1 -10
-F -5 -6 -5 -8 -6 -7 -8 -6 -3 1 1 -8 0 10 -6 -4 -5 -1 7 -2 -6 -7 -4 -10
-P 1 -1 -1 -2 -4 0 -1 -2 -1 -3 -4 -2 -3 -6 8 1 0 -8 -7 -2 -2 -1 -1 -10
-S 2 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
-T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -5 0 2 5 -7 -4 0 0 -1 -1 -10
-W -8 2 -5 -9 -10 -7 -10 -9 -4 -7 -3 -5 -6 -1 -8 -3 -7 18 -1 -9 -7 -8 -6 -10
-Y -5 -6 -3 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 12 -4 -4 -6 -4 -10
-V 0 -4 -3 -4 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -9 -4 6 -3 -3 -1 -10
-B 0 -2 3 5 -6 1 3 0 1 -3 -5 0 -4 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
-Z 0 0 1 4 -8 5 5 -1 2 -3 -4 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
-X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -2 -1 -4 -1 0 -1 -6 -4 -1 -1 -1 -2 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM180 b/Butterfly/src/src/jaligner/matrix/matrices/PAM180
deleted file mode 100644
index 84addeb..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM180
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 180 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.51, Entropy = 0.591 bits
-#
-# Lowest score = -10, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -3 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -8 -5 0 0 0 -1 -10
-R -3 8 -1 -3 -5 1 -2 -4 2 -3 -4 4 -1 -6 -1 -1 -2 2 -6 -4 -2 0 -2 -10
-N 0 -1 4 3 -5 0 2 0 2 -3 -4 1 -3 -5 -1 1 0 -5 -2 -3 3 1 -1 -10
-D 0 -3 3 5 -7 2 4 0 0 -3 -6 0 -4 -8 -2 0 -1 -9 -6 -3 4 3 -1 -10
-C -3 -5 -5 -7 13 -7 -7 -5 -4 -3 -8 -7 -7 -6 -4 0 -3 -10 0 -3 -6 -7 -4 -10
-Q -1 1 0 2 -7 6 3 -2 4 -3 -2 0 -1 -6 0 -1 -2 -6 -6 -3 1 5 -1 -10
-E 0 -2 2 4 -7 3 5 0 0 -3 -5 -1 -3 -7 -1 -1 -1 -9 -6 -3 3 5 -1 -10
-G 1 -4 0 0 -5 -2 0 6 -3 -4 -6 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -2 -10
-H -2 2 2 0 -4 4 0 -3 8 -4 -3 -1 -3 -3 -1 -2 -2 -4 0 -3 1 2 -1 -10
-I -1 -3 -3 -3 -3 -3 -3 -4 -4 6 2 -3 2 1 -3 -2 0 -7 -2 5 -3 -3 -1 -10
-L -3 -4 -4 -6 -8 -2 -5 -6 -3 2 7 -4 4 1 -4 -4 -3 -3 -2 2 -5 -3 -2 -10
-K -2 4 1 0 -7 0 -1 -3 -1 -3 -4 6 1 -7 -2 -1 0 -5 -6 -4 0 0 -1 -10
-M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -10
-F -5 -6 -5 -8 -6 -6 -7 -6 -3 1 1 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -10
-P 1 -1 -1 -2 -4 0 -1 -1 -1 -3 -4 -2 -3 -6 8 1 0 -7 -7 -2 -2 -1 -1 -10
-S 1 -1 1 0 0 -1 -1 1 -2 -2 -4 -1 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -10
-T 2 -2 0 -1 -3 -2 -1 -1 -2 0 -3 0 -1 -4 0 2 4 -7 -4 0 0 -1 -1 -10
-W -8 2 -5 -9 -10 -6 -9 -9 -4 -7 -3 -5 -6 0 -7 -3 -7 18 -1 -8 -7 -8 -6 -10
-Y -5 -6 -2 -6 0 -6 -6 -7 0 -2 -2 -6 -4 7 -7 -4 -4 -1 11 -4 -4 -6 -3 -10
-V 0 -4 -3 -3 -3 -3 -3 -2 -3 5 2 -4 2 -2 -2 -2 0 -8 -4 6 -3 -3 -1 -10
-B 0 -2 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -2 1 0 -7 -4 -3 4 3 -1 -10
-Z 0 0 1 3 -7 5 5 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -8 -6 -3 3 5 -1 -10
-X -1 -2 -1 -1 -4 -1 -1 -2 -1 -1 -2 -1 -1 -3 -1 0 -1 -6 -3 -1 -1 -1 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM190 b/Butterfly/src/src/jaligner/matrix/matrices/PAM190
deleted file mode 100644
index 6840cc4..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM190
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 190 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.35, Entropy = 0.547 bits
-#
-# Lowest score = -9, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -3 -1 0 1 -2 -1 -3 -2 -2 -5 1 1 2 -7 -4 0 0 0 0 -9
-R -2 8 -1 -2 -5 1 -2 -4 2 -3 -4 4 -1 -6 0 -1 -2 2 -5 -3 -1 0 -1 -9
-N 0 -1 3 3 -5 1 2 0 2 -2 -4 1 -3 -4 -1 1 0 -5 -2 -3 3 1 -1 -9
-D 0 -2 3 5 -7 2 4 0 0 -3 -5 0 -4 -7 -2 0 -1 -8 -5 -3 4 3 -1 -9
-C -3 -5 -5 -7 13 -7 -7 -4 -4 -3 -8 -7 -7 -6 -4 0 -3 -9 0 -3 -6 -7 -4 -9
-Q -1 1 1 2 -7 6 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
-E 0 -2 2 4 -7 3 5 0 0 -3 -4 -1 -3 -7 -1 0 -1 -9 -5 -3 3 4 -1 -9
-G 1 -4 0 0 -4 -2 0 6 -3 -4 -5 -3 -4 -6 -1 1 -1 -9 -7 -2 0 -1 -1 -9
-H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
-I -1 -3 -2 -3 -3 -3 -3 -4 -3 6 2 -3 2 1 -3 -2 0 -7 -2 4 -3 -3 -1 -9
-L -3 -4 -4 -5 -8 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -3 -2 2 -5 -3 -2 -9
-K -2 4 1 0 -7 1 -1 -3 -1 -3 -4 6 1 -7 -2 0 0 -5 -6 -3 0 0 -1 -9
-M -2 -1 -3 -4 -7 -1 -3 -4 -3 2 4 1 9 0 -3 -2 -1 -6 -4 2 -3 -2 -1 -9
-F -5 -6 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -7 -3 -9
-P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
-S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 3 2 -3 -4 -2 1 -1 0 -9
-T 2 -2 0 -1 -3 -1 -1 -1 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
-W -7 2 -5 -8 -9 -6 -9 -9 -3 -7 -3 -5 -6 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
-Y -4 -5 -2 -5 0 -5 -5 -7 0 -2 -2 -6 -4 7 -6 -4 -3 -1 11 -3 -4 -5 -3 -9
-V 0 -3 -3 -3 -3 -3 -3 -2 -3 4 2 -3 2 -2 -2 -2 0 -8 -3 6 -3 -3 -1 -9
-B 0 -1 3 4 -6 1 3 0 1 -3 -5 0 -3 -6 -1 1 0 -6 -4 -3 4 2 -1 -9
-Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -7 -1 -1 -1 -7 -5 -3 2 4 -1 -9
-X 0 -1 -1 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM20 b/Butterfly/src/src/jaligner/matrix/matrices/PAM20
deleted file mode 100644
index 58cc98c..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM20
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 20 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -6.18, Entropy = 2.95 bits
-#
-# Lowest score = -19, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -8 -5 -4 -8 -5 -3 -3 -8 -6 -7 -8 -6 -9 -2 -1 -1 -16 -9 -3 -5 -4 -4 -19
-R -8 9 -7 -12 -9 -2 -11 -11 -3 -6 -10 -1 -5 -10 -5 -4 -8 -3 -11 -9 -9 -5 -7 -19
-N -5 -7 8 1 -13 -5 -3 -4 -1 -6 -8 -2 -11 -10 -7 -1 -3 -9 -5 -9 6 -4 -4 -19
-D -4 -12 1 8 -16 -4 2 -4 -5 -9 -15 -6 -13 -17 -9 -5 -6 -17 -13 -9 6 0 -7 -19
-C -8 -9 -13 -16 10 -16 -16 -11 -8 -7 -17 -16 -16 -15 -9 -4 -9 -18 -5 -7 -14 -16 -11 -19
-Q -5 -2 -5 -4 -16 9 0 -8 0 -9 -6 -4 -5 -15 -4 -6 -7 -15 -14 -8 -4 7 -6 -19
-E -3 -11 -3 2 -16 0 8 -5 -6 -6 -10 -5 -8 -16 -7 -5 -7 -19 -9 -8 0 6 -6 -19
-G -3 -11 -4 -4 -11 -8 -5 7 -10 -13 -12 -8 -10 -10 -7 -3 -7 -17 -16 -7 -4 -6 -6 -19
-H -8 -3 -1 -5 -8 0 -6 -10 9 -11 -7 -8 -13 -7 -5 -7 -8 -8 -4 -7 -2 -2 -6 -19
-I -6 -6 -6 -9 -7 -9 -6 -13 -11 9 -2 -7 -2 -3 -10 -8 -3 -16 -7 1 -7 -7 -6 -19
-L -7 -10 -8 -15 -17 -6 -10 -12 -7 -2 7 -9 0 -4 -8 -9 -8 -7 -8 -3 -10 -8 -7 -19
-K -8 -1 -2 -6 -16 -4 -5 -8 -8 -7 -9 7 -3 -16 -8 -5 -4 -14 -10 -10 -3 -5 -6 -19
-M -6 -5 -11 -13 -16 -5 -8 -10 -13 -2 0 -3 11 -5 -9 -6 -5 -15 -13 -2 -12 -6 -6 -19
-F -9 -10 -10 -17 -15 -15 -16 -10 -7 -3 -4 -16 -5 9 -11 -7 -10 -6 1 -9 -12 -16 -9 -19
-P -2 -5 -7 -9 -9 -4 -7 -7 -5 -10 -8 -8 -9 -11 8 -3 -5 -16 -16 -7 -8 -5 -6 -19
-S -1 -4 -1 -5 -4 -6 -5 -3 -7 -8 -9 -5 -6 -7 -3 7 0 -6 -8 -8 -2 -6 -4 -19
-T -1 -8 -3 -6 -9 -7 -7 -7 -8 -3 -8 -4 -5 -10 -5 0 7 -15 -7 -4 -4 -7 -5 -19
-W -16 -3 -9 -17 -18 -15 -19 -17 -8 -16 -7 -14 -15 -6 -16 -6 -15 13 -6 -18 -11 -17 -13 -19
-Y -9 -11 -5 -13 -5 -14 -9 -16 -4 -7 -8 -10 -13 1 -16 -8 -7 -6 10 -8 -7 -11 -9 -19
-V -3 -9 -9 -9 -7 -8 -8 -7 -7 1 -3 -10 -2 -9 -7 -8 -4 -18 -8 7 -9 -8 -6 -19
-B -5 -9 6 6 -14 -4 0 -4 -2 -7 -10 -3 -12 -12 -8 -2 -4 -11 -7 -9 6 -1 -6 -19
-Z -4 -5 -4 0 -16 7 6 -6 -2 -7 -8 -5 -6 -16 -5 -6 -7 -17 -11 -8 -1 6 -6 -19
-X -4 -7 -4 -7 -11 -6 -6 -6 -6 -6 -7 -6 -6 -9 -6 -4 -5 -13 -9 -6 -6 -6 -6 -19
-* -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 -19 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM200 b/Butterfly/src/src/jaligner/matrix/matrices/PAM200
deleted file mode 100644
index d4edff2..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM200
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 200 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.23, Entropy = 0.507 bits
-#
-# Lowest score = -9, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 3 -2 0 0 -3 -1 0 1 -2 -1 -2 -2 -2 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -2 -4 1 -2 -4 2 -2 -4 4 -1 -5 0 -1 -1 2 -5 -3 -1 0 -1 -9
-N 0 0 3 3 -5 1 2 0 2 -2 -4 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
-D 0 -2 3 5 -6 2 4 0 0 -3 -5 0 -4 -7 -2 0 0 -8 -5 -3 4 3 -1 -9
-C -3 -4 -5 -6 12 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -9 0 -2 -5 -7 -4 -9
-Q -1 1 1 2 -7 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -3 1 4 -1 -9
-E 0 -2 2 4 -7 3 5 0 0 -3 -4 0 -3 -7 -1 0 -1 -9 -5 -2 3 4 -1 -9
-G 1 -4 0 0 -4 -2 0 6 -3 -3 -5 -2 -4 -6 -1 1 0 -8 -6 -2 0 -1 -1 -9
-H -2 2 2 0 -4 3 0 -3 8 -3 -3 -1 -3 -2 -1 -1 -2 -3 0 -3 1 2 -1 -9
-I -1 -2 -2 -3 -3 -3 -3 -3 -3 6 2 -2 2 1 -3 -2 0 -6 -2 4 -3 -3 -1 -9
-L -2 -4 -4 -5 -7 -2 -4 -5 -3 2 7 -4 4 2 -3 -4 -2 -2 -2 2 -4 -3 -2 -9
-K -2 4 1 0 -7 1 0 -2 -1 -2 -4 6 1 -7 -2 0 0 -4 -5 -3 0 0 -1 -9
-M -2 -1 -2 -4 -6 -1 -3 -4 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
-F -4 -5 -4 -7 -6 -6 -7 -6 -2 1 2 -7 0 10 -6 -4 -4 0 7 -2 -6 -6 -3 -9
-P 1 0 -1 -2 -4 0 -1 -1 -1 -3 -3 -2 -3 -6 7 1 0 -7 -6 -2 -1 -1 -1 -9
-S 1 -1 1 0 0 -1 0 1 -1 -2 -4 0 -2 -4 1 2 2 -3 -3 -1 1 -1 0 -9
-T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 4 -6 -3 0 0 -1 0 -9
-W -7 2 -5 -8 -9 -6 -9 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -8 -6 -7 -5 -9
-Y -4 -5 -2 -5 0 -5 -5 -6 0 -2 -2 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
-V 0 -3 -2 -3 -2 -3 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -8 -3 5 -3 -2 -1 -9
-B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -6 -1 1 0 -6 -4 -3 3 2 -1 -9
-Z 0 0 1 3 -7 4 4 -1 2 -3 -3 0 -2 -6 -1 -1 -1 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM210 b/Butterfly/src/src/jaligner/matrix/matrices/PAM210
deleted file mode 100644
index 0b49af5..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM210
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 210 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.12, Entropy = 0.470 bits
-#
-# Lowest score = -9, Highest score = 18
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -2 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -2 -4 1 -2 -3 2 -2 -4 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -9
-N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -5 -2 -2 3 1 0 -9
-D 0 -2 2 5 -6 2 4 0 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -9
-C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 0 -2 -5 -6 -4 -9
-Q -1 1 1 2 -6 5 3 -2 3 -3 -2 1 -1 -6 0 -1 -1 -6 -5 -2 1 4 -1 -9
-E 0 -2 2 4 -6 3 5 0 0 -2 -4 0 -3 -6 -1 0 -1 -8 -5 -2 3 4 -1 -9
-G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -9
-H -2 2 2 1 -4 3 0 -3 8 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -9
-I -1 -2 -2 -3 -3 -3 -2 -3 -3 5 2 -2 2 1 -3 -2 0 -6 -1 4 -3 -3 -1 -9
-L -2 -4 -3 -5 -7 -2 -4 -5 -2 2 7 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -9
-K -2 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -2 0 0 -4 -5 -3 0 0 -1 -9
-M -1 -1 -2 -3 -6 -1 -3 -3 -3 2 4 1 8 0 -3 -2 -1 -5 -3 2 -3 -2 -1 -9
-F -4 -5 -4 -7 -5 -6 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -9
-P 1 0 -1 -1 -3 0 -1 -1 0 -3 -3 -2 -3 -5 7 1 0 -7 -6 -2 -1 0 -1 -9
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 1 0 0 -9
-T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -9
-W -7 2 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 0 -7 -3 -6 18 -1 -7 -6 -7 -5 -9
-Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 -1 11 -3 -4 -5 -3 -9
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -2 -1 0 -7 -3 5 -2 -2 -1 -9
-B 0 -1 3 4 -5 1 3 0 1 -3 -4 0 -3 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
-Z 0 0 1 3 -6 4 4 -1 2 -3 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM220 b/Butterfly/src/src/jaligner/matrix/matrices/PAM220
deleted file mode 100644
index 0834a92..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM220
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 220 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -1.06, Entropy = 0.437 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
-N 0 0 3 2 -4 1 2 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -2 2 4 -6 2 4 0 1 -3 -5 0 -3 -6 -1 0 0 -8 -5 -3 4 3 -1 -8
-C -2 -4 -4 -6 12 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -8 0 -2 -5 -6 -3 -8
-Q -1 1 1 2 -6 5 3 -2 3 -2 -2 1 -1 -5 0 -1 -1 -5 -5 -2 1 4 -1 -8
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
-G 1 -3 0 0 -4 -2 0 5 -3 -3 -5 -2 -3 -5 -1 1 0 -8 -6 -2 0 -1 -1 -8
-H -2 2 2 1 -4 3 1 -3 7 -3 -2 0 -3 -2 0 -1 -2 -3 0 -3 1 2 -1 -8
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -5 -7 -2 -4 -5 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 1 -6 -1 0 0 -4 -5 -3 0 0 -1 -8
-M -1 -1 -2 -3 -6 -1 -2 -3 -3 2 4 1 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 10 -5 -4 -4 0 7 -2 -5 -6 -3 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 7 1 0 -6 -6 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -3 -1 0 0 0 -8
-T 1 -1 0 0 -3 -1 -1 0 -2 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -8
-W -6 2 -4 -8 -8 -5 -8 -8 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -7 -5 -8
-Y -4 -5 -2 -5 0 -5 -5 -6 0 -1 -1 -5 -3 7 -6 -3 -3 0 11 -3 -3 -5 -3 -8
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 4 2 -3 2 -2 -1 -1 0 -7 -3 5 -2 -2 -1 -8
-B 0 -1 2 4 -5 1 3 0 1 -2 -4 0 -3 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 2 4 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM230 b/Butterfly/src/src/jaligner/matrix/matrices/PAM230
deleted file mode 100644
index c9ff6db..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM230
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 230 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.991, Entropy = 0.407 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 -1 0 1 -2 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -2 7 0 -2 -4 1 -1 -3 2 -2 -3 4 -1 -5 0 0 -1 2 -5 -3 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -2 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -8
-C -2 -4 -4 -6 12 -6 -6 -4 -4 -2 -7 -6 -6 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
-Q -1 1 1 2 -6 5 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 4 -1 -8
-E 0 -1 1 4 -6 3 4 0 1 -2 -4 0 -2 -6 -1 0 -1 -8 -5 -2 3 4 -1 -8
-G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -6 -2 0 -1 -1 -8
-H -2 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -2 -3 0 -2 1 2 -1 -8
-I -1 -2 -2 -3 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -2 0 -6 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -8
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -8
-M -1 -1 -2 -3 -6 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -6 0 9 -5 -3 -3 0 7 -1 -5 -6 -3 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -3 1 2 2 -3 -3 -1 0 0 0 -8
-T 1 -1 0 0 -2 -1 -1 0 -2 0 -2 0 -1 -3 0 2 3 -6 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -8 -7 -3 -6 -2 -4 -5 0 -6 -3 -6 17 0 -7 -6 -6 -4 -8
-Y -4 -5 -2 -5 0 -4 -5 -6 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -5 -3 -8
-V 0 -3 -2 -2 -2 -2 -2 -2 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -8
-B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -6 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -6 4 4 -1 2 -2 -3 0 -2 -6 0 0 -1 -6 -5 -2 2 4 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -4 -3 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM240 b/Butterfly/src/src/jaligner/matrix/matrices/PAM240
deleted file mode 100644
index c17cdf8..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM240
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 240 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.923, Entropy = 0.379 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -5 0 0 -1 2 -4 -3 -1 0 -1 -8
-N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -4 -1 1 0 -4 -2 -2 2 1 0 -8
-D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
-C -2 -4 -4 -5 12 -6 -6 -4 -4 -2 -6 -6 -5 -5 -3 0 -2 -8 0 -2 -5 -6 -3 -8
-Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 -8
-E 0 -1 1 4 -6 3 4 0 1 -2 -3 0 -2 -6 -1 0 0 -7 -4 -2 3 3 -1 -8
-G 1 -3 0 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 -1 1 0 -7 -5 -1 0 0 -1 -8
-H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -8
-I -1 -2 -2 -2 -2 -2 -2 -3 -3 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -8
-K -1 3 1 0 -6 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -4 -5 -3 1 0 -1 -8
-M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 7 0 -2 -2 -1 -4 -3 2 -2 -2 -1 -8
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -5 -5 -2 -8
-P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 -8
-S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -3 -3 -1 0 0 0 -8
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -4 -4 0 -6 -3 -5 17 0 -6 -5 -6 -4 -8
-Y -4 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -5 -3 7 -5 -3 -3 0 10 -3 -3 -4 -2 -8
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -6 -3 4 -2 -2 -1 -8
-B 0 -1 2 3 -5 1 3 0 1 -2 -4 1 -2 -5 -1 0 0 -5 -3 -2 3 2 -1 -8
-Z 0 0 1 3 -6 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM250 b/Butterfly/src/src/jaligner/matrix/matrices/PAM250
deleted file mode 100644
index 17e9e60..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM250
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.844, Entropy = 0.354 bits
-#
-# Lowest score = -8, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
-R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 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 1 0 -8
-D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 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 -3 -8
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 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 -1 -8
-G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 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 -1 -8
-I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -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 -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 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 -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 -5 -2 -8
-P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 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 0 0 -8
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 -8
-W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -8
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -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 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 3 -1 -8
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM260 b/Butterfly/src/src/jaligner/matrix/matrices/PAM260
deleted file mode 100644
index 5098eb4..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM260
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 260 substitution matrix, scale = ln(2)/3 = 0.231049
-#
-# Expected score = -0.794, Entropy = 0.330 bits
-#
-# Lowest score = -7, Highest score = 17
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -7
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 -7
-N 0 0 2 2 -3 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 -7
-D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -5 -1 0 0 -6 -4 -2 3 3 -1 -7
-C -2 -4 -3 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -7 0 -2 -4 -5 -3 -7
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -4 0 0 -1 -5 -4 -2 1 3 0 -7
-E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 3 3 -1 -7
-G 1 -2 0 1 -3 -1 0 5 -2 -2 -4 -2 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -7
-H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -7
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 -7
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -2 -3 -2 -2 -1 2 -3 -2 -1 -7
-K -1 3 1 0 -5 1 0 -2 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 0 -1 -7
-M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -1 -1 -4 -2 2 -2 -2 -1 -7
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 2 -5 0 9 -4 -3 -3 0 7 -1 -4 -5 -2 -7
-P 1 0 0 -1 -3 0 0 0 0 -2 -2 -1 -2 -4 6 1 0 -5 -5 -1 -1 0 -1 -7
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -2 -3 -1 0 0 0 -7
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 2 -5 -3 0 0 0 0 -7
-W -6 2 -4 -6 -7 -5 -7 -7 -3 -5 -2 -3 -4 0 -5 -2 -5 17 0 -6 -5 -6 -4 -7
-Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 -7
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 -7
-B 0 -1 2 3 -4 1 3 1 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 0 -7
-Z 0 0 1 3 -5 3 3 0 2 -2 -2 0 -2 -5 0 0 0 -6 -4 -2 2 3 -1 -7
-X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 0 -1 -1 -7
-* -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 -7 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM270 b/Butterfly/src/src/jaligner/matrix/matrices/PAM270
deleted file mode 100644
index 322fcdb..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM270
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 270 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.969, Entropy = 0.309 bits
-#
-# Lowest score = -10, Highest score = 23
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 2 -2 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -10
-R -2 8 0 -1 -5 2 -1 -3 2 -2 -4 4 -1 -5 0 0 -1 3 -5 -3 -1 0 -1 -10
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
-D 0 -1 2 5 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -3 4 3 -1 -10
-C -2 -5 -4 -6 16 -7 -6 -4 -4 -3 -7 -7 -6 -5 -3 0 -3 -10 1 -2 -5 -7 -4 -10
-Q 0 2 1 2 -7 5 3 -1 4 -2 -2 1 -1 -6 0 -1 -1 -6 -5 -2 2 4 -1 -10
-E 0 -1 2 4 -6 3 5 0 1 -2 -4 0 -3 -7 -1 0 0 -9 -5 -2 3 4 -1 -10
-G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -9 -6 -2 1 0 -1 -10
-H -2 2 2 1 -4 4 1 -2 8 -3 -3 0 -3 -2 0 -1 -1 -3 0 -3 1 2 -1 -10
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 5 -3 -2 -1 -10
-L -2 -4 -3 -5 -7 -2 -4 -5 -3 3 8 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -2 -10
-K -1 4 1 0 -7 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 0 -1 -10
-M -1 -1 -2 -3 -6 -1 -3 -3 -3 3 5 0 8 0 -2 -2 -1 -5 -3 2 -3 -2 -1 -10
-F -4 -5 -4 -7 -5 -6 -7 -6 -2 1 2 -6 0 12 -6 -4 -4 1 9 -1 -6 -6 -3 -10
-P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -6 7 1 0 -7 -6 -1 -1 0 -1 -10
-S 1 0 1 0 0 -1 0 1 -1 -2 -3 0 -2 -4 1 2 2 -3 -4 -1 1 0 0 -10
-T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 0 2 3 -6 -3 0 0 -1 0 -10
-W -7 3 -5 -8 -10 -6 -9 -9 -3 -6 -2 -4 -5 1 -7 -3 -6 23 0 -8 -7 -7 -5 -10
-Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -4 -3 0 13 -3 -4 -5 -3 -10
-V 0 -3 -2 -3 -2 -2 -2 -2 -3 5 2 -3 2 -1 -1 -1 0 -8 -3 5 -2 -2 -1 -10
-B 0 -1 2 4 -5 2 3 1 1 -3 -4 1 -3 -6 -1 1 0 -7 -4 -2 3 3 -1 -10
-Z 0 0 2 3 -7 4 4 0 2 -2 -3 0 -2 -6 0 0 -1 -7 -5 -2 3 4 -1 -10
-X 0 -1 0 -1 -4 -1 -1 -1 -1 -1 -2 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM280 b/Butterfly/src/src/jaligner/matrix/matrices/PAM280
deleted file mode 100644
index 2b09bca..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM280
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 280 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.916, Entropy = 0.289 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 -1 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
-D 0 -1 2 4 -6 2 4 1 1 -3 -5 0 -3 -7 -1 0 0 -8 -5 -2 4 3 -1 -9
-C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -3 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -6 -5 -2 2 4 -1 -9
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
-G 2 -3 1 1 -4 -1 0 6 -2 -3 -5 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 8 -3 -2 0 -2 -2 0 -1 -1 -3 0 -3 1 2 -1 -9
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -2 0 -6 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -5 -7 -2 -4 -5 -2 3 7 -3 5 2 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 6 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -3 2 -2 -2 -1 -9
-F -4 -5 -4 -7 -5 -5 -6 -6 -2 1 2 -6 0 11 -5 -4 -4 1 9 -1 -5 -6 -3 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -7 -6 -1 -1 0 -1 -9
-S 1 0 1 0 0 0 0 1 -1 -2 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
-T 1 -1 1 0 -3 -1 0 0 -1 0 -2 0 -1 -4 1 1 3 -6 -3 0 0 0 0 -9
-W -7 3 -5 -8 -9 -6 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 22 0 -7 -6 -7 -5 -9
-Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -3 9 -6 -3 -3 0 13 -3 -4 -5 -3 -9
-V 0 -3 -2 -2 -2 -2 -2 -1 -3 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
-B 0 -1 2 4 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 -1 -9
-Z 0 0 1 3 -6 4 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -3 -1 -1 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM290 b/Butterfly/src/src/jaligner/matrix/matrices/PAM290
deleted file mode 100644
index 6852c6a..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM290
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 290 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.877, Entropy = 0.271 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -2 0 0 -2 0 0 2 -1 -1 -2 -1 -1 -4 1 1 1 -7 -4 0 0 0 0 -9
-R -2 7 0 -1 -4 2 -1 -3 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 1 0 -9
-D 0 -1 2 4 -6 2 4 1 1 -3 -4 0 -3 -6 -1 0 0 -8 -5 -2 3 3 -1 -9
-C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -5 -2 2 3 0 -9
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 4 -1 -9
-G 2 -3 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -6 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -3 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 -9
-I -1 -2 -2 -3 -3 -2 -2 -3 -3 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 -1 2 -4 -3 -1 -9
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -3 1 1 -1 -9
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 7 0 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
-F -4 -5 -4 -6 -5 -5 -6 -6 -2 1 3 -6 0 11 -5 -4 -3 1 9 -1 -5 -6 -3 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 7 1 1 -6 -6 -1 -1 0 -1 -9
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 2 1 -3 -3 -1 1 0 0 -9
-T 1 -1 1 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 3 -6 -3 0 0 0 0 -9
-W -7 3 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -7 -5 -9
-Y -4 -5 -3 -5 1 -5 -5 -6 0 -1 -1 -5 -2 9 -6 -3 -3 0 13 -3 -4 -5 -2 -9
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -3 2 -1 -1 -1 0 -7 -3 5 -2 -2 -1 -9
-B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 -1 1 0 -6 -4 -2 3 2 0 -9
-Z 0 0 1 3 -6 3 4 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 4 -1 -9
-X 0 -1 0 -1 -3 0 -1 -1 -1 -1 -1 -1 -1 -3 -1 0 0 -5 -2 -1 0 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM30 b/Butterfly/src/src/jaligner/matrix/matrices/PAM30
deleted file mode 100644
index 8a01c88..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM30
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -5.06, Entropy = 2.57 bits
-#
-# Lowest score = -17, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
-R -7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
-N -4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
-D -3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
-C -6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
-Q -4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
-E -2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
-G -2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
-H -7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
-I -5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
-L -6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
-K -7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
-M -5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
-F -8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
-P -2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
-S 0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
-T -1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
-W -13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
-Y -8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
-V -2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
-B -3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
-Z -3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
-X -3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM300 b/Butterfly/src/src/jaligner/matrix/matrices/PAM300
deleted file mode 100644
index 5d1a5a8..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM300
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 300 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.835, Entropy = 0.254 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 0 -2 0 0 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
-R -1 7 0 -1 -4 2 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -5 -3 0 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -2 -2 2 1 0 -9
-D 0 -1 2 4 -6 2 4 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
-C -2 -4 -4 -6 15 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
-E 0 -1 2 4 -6 3 4 0 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 -1 -9
-G 2 -2 1 1 -4 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -3 -2 -2 -3 -2 5 3 -2 3 1 -2 -1 0 -6 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -4 -3 -1 -9
-K -1 4 1 0 -6 1 0 -2 0 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 -1 -9
-F -4 -5 -4 -6 -5 -5 -6 -5 -2 1 3 -6 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 -1 -9
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -6 3 -5 -7 -9 -5 -8 -8 -3 -6 -2 -4 -5 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
-Y -4 -5 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -3 -4 -5 -2 -9
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -3 5 -2 -2 0 -9
-B 0 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
-Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 -1 -9
-X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 -1 0 0 -4 -2 0 0 -1 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM310 b/Butterfly/src/src/jaligner/matrix/matrices/PAM310
deleted file mode 100644
index cd0e5b0..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM310
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 310 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.779, Entropy = 0.238 bits
-#
-# Lowest score = -9, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 0 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -9
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -9
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -9
-D 0 -1 2 4 -5 2 4 1 1 -2 -4 0 -2 -6 -1 0 0 -7 -5 -2 3 3 -1 -9
-C -2 -4 -4 -5 15 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 1 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 0 0 -1 -5 -4 -2 2 3 0 -9
-E 0 -1 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -9
-G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 1 -2 -1 0 -5 -1 4 -2 -2 -1 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -3 -3 -2 -2 0 2 -3 -3 -1 -9
-K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -9
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 4 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 -1 -9
-F -4 -5 -4 -6 -4 -5 -6 -5 -2 1 3 -5 1 11 -5 -4 -3 1 9 -1 -5 -5 -2 -9
-P 1 0 0 -1 -3 0 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -6 3 -4 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 1 -6 -3 -6 22 0 -7 -6 -6 -4 -9
-Y -4 -4 -2 -5 1 -4 -5 -6 0 -1 0 -5 -2 9 -5 -3 -3 0 12 -2 -4 -4 -2 -9
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
-B 0 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -9
-Z 0 0 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -9
-X 0 -1 0 -1 -3 0 -1 -1 0 -1 -1 -1 -1 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM320 b/Butterfly/src/src/jaligner/matrix/matrices/PAM320
deleted file mode 100644
index d7fbbd2..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM320
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 320 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.741, Entropy = 0.224 bits
-#
-# Lowest score = -8, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 0 0 0 -8
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -5 0 0 -1 3 -4 -2 0 0 -1 -8
-N 0 0 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -4 -2 -2 2 1 0 -8
-D 1 -1 2 4 -5 2 3 1 1 -2 -4 0 -2 -6 0 0 0 -7 -5 -2 3 3 -1 -8
-C -2 -4 -4 -5 15 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 0 0 -5 -4 -2 2 3 0 -8
-E 0 -1 2 3 -5 2 4 1 1 -2 -3 0 -2 -5 0 0 0 -7 -5 -2 3 3 0 -8
-G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 0 -7 -5 -1 1 0 -1 -8
-H -1 2 2 1 -4 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 0 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -2 -2 0 2 -3 -3 -1 -8
-K -1 4 1 0 -6 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -5 -2 1 1 -1 -8
-M -1 0 -2 -2 -5 -1 -2 -3 -2 2 4 0 6 1 -2 -1 -1 -4 -2 2 -2 -2 0 -8
-F -4 -5 -4 -6 -4 -5 -5 -5 -2 1 3 -5 1 11 -5 -3 -3 1 9 -1 -5 -5 -2 -8
-P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 -1 0 0 -2 0 0 0 -1 0 -2 0 -1 -3 1 1 2 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -6 -6 -4 -8
-Y -4 -4 -2 -5 1 -4 -5 -5 0 -1 0 -5 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
-B 0 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -3 -2 2 2 0 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -4 -2 2 3 0 -8
-X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM330 b/Butterfly/src/src/jaligner/matrix/matrices/PAM330
deleted file mode 100644
index 77db35e..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM330
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 330 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.693, Entropy = 0.210 bits
-#
-# Lowest score = -8, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
-R -1 6 0 -1 -4 1 -1 -2 2 -2 -3 4 0 -4 0 0 -1 3 -4 -2 0 0 -1 -8
-N 0 0 2 2 -4 1 2 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
-D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
-C -2 -4 -4 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
-E 0 -1 2 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -2 2 3 0 -8
-G 1 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
-H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -8
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 4 -2 -2 0 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -3 -1 -2 0 2 -3 -2 -1 -8
-K -1 4 1 0 -5 1 0 -1 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 1 -1 -8
-M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -5 -3 -3 1 9 -1 -4 -5 -2 -8
-P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -8
-S 1 0 1 0 0 0 0 1 -1 -1 -3 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 -1 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 1 -6 -3 -5 22 1 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
-B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM340 b/Butterfly/src/src/jaligner/matrix/matrices/PAM340
deleted file mode 100644
index 02c8540..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM340
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 340 substitution matrix, scale = ln(2)/4 = 0.173287
-#
-# Expected score = -0.680, Entropy = 0.198 bits
-#
-# Lowest score = -8, Highest score = 22
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 0 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 -8
-R -1 6 0 -1 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 0 -1 -8
-N 0 0 1 2 -3 1 1 1 1 -2 -3 1 -1 -3 0 1 0 -4 -2 -1 2 1 0 -8
-D 1 -1 2 3 -5 2 3 1 1 -2 -4 0 -2 -5 0 0 0 -7 -4 -2 3 3 0 -8
-C -2 -4 -3 -5 15 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 3 2 -1 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -2 1 3 0 -8
-E 0 0 1 3 -5 2 3 1 1 -2 -3 0 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
-G 1 -2 1 1 -3 -1 1 4 -2 -2 -4 -1 -2 -5 0 1 0 -7 -5 -1 1 0 -1 -8
-H -1 2 1 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 0 -1 -2 0 -2 1 2 0 -8
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 2 1 -2 -1 0 -5 0 3 -2 -2 0 -8
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 6 -3 4 3 -2 -2 -1 -2 0 2 -3 -2 -1 -8
-K -1 4 1 0 -5 1 0 -1 0 -2 -3 4 0 -5 -1 0 0 -3 -4 -2 1 1 0 -8
-M -1 0 -1 -2 -5 -1 -2 -2 -2 2 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -8
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 1 3 -5 1 10 -4 -3 -3 1 9 -1 -4 -5 -2 -8
-P 1 0 0 0 -3 0 0 0 0 -2 -2 -1 -2 -4 5 1 1 -5 -5 -1 0 0 0 -8
-S 1 0 1 0 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 0 0 0 -2 0 0 0 -1 0 -1 0 0 -3 1 1 2 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 1 -5 -3 -5 22 1 -6 -5 -6 -4 -8
-Y -3 -4 -2 -4 1 -4 -4 -5 0 0 0 -4 -2 9 -5 -3 -3 1 12 -2 -3 -4 -2 -8
-V 0 -2 -1 -2 -2 -2 -1 -1 -2 3 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 0 -8
-B 0 0 2 3 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -2 2 2 0 -8
-Z 0 0 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -8
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM350 b/Butterfly/src/src/jaligner/matrix/matrices/PAM350
deleted file mode 100644
index 140a6f2..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM350
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 350 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.701, Entropy = 0.186 bits
-#
-# Lowest score = -10, Highest score = 27
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 2 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 7 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 -1 4 -5 -3 0 1 -1 -10
-N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -10
-D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -3 -6 0 1 0 -8 -5 -2 3 3 -1 -10
-C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -5 -3 0 -2 -10 1 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 4 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -5 -2 2 3 0 -10
-E 1 0 2 4 -6 3 4 1 1 -2 -4 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -10
-G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -10
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 -1 -1 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 5 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
-L -2 -3 -3 -4 -7 -2 -4 -4 -2 4 8 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -10
-K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -10
-M -1 0 -2 -3 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -5 -2 2 -2 -2 0 -10
-F -4 -5 -4 -6 -5 -5 -6 -6 -2 2 3 -6 1 13 -5 -4 -3 1 11 -1 -5 -6 -2 -10
-P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -7 -6 -1 0 0 0 -10
-S 1 0 1 1 0 0 0 1 -1 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 -1 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -4 -5 1 -7 -3 -6 27 1 -7 -6 -7 -5 -10
-Y -4 -5 -3 -5 1 -5 -5 -6 0 0 0 -5 -2 11 -6 -3 -3 1 14 -2 -4 -5 -2 -10
-V 0 -3 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 5 -2 -2 0 -10
-B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 3 2 0 -10
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -6 0 0 0 -7 -5 -2 2 3 0 -10
-X 0 -1 0 -1 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -5 -2 0 0 0 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM360 b/Butterfly/src/src/jaligner/matrix/matrices/PAM360
deleted file mode 100644
index 5f6cd46..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM360
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 360 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.697, Entropy = 0.175 bits
-#
-# Lowest score = -9, Highest score = 27
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
-R -1 6 1 -1 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 -1 -9
-N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 1 -5 -3 -2 2 2 0 -9
-D 1 -1 2 4 -6 2 4 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -9
-C -2 -4 -4 -6 18 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 3 3 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
-E 1 0 2 4 -6 3 4 1 1 -2 -3 0 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
-G 2 -2 1 1 -4 -1 1 5 -2 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 7 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -7 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -2 -2 0 3 -4 -3 -1 -9
-K -1 4 1 1 -6 1 0 -1 1 -2 -3 5 0 -6 -1 0 0 -4 -5 -2 1 1 -1 -9
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 6 1 -2 -2 -1 -4 -2 2 -2 -2 0 -9
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 3 -6 1 12 -5 -4 -3 2 11 -1 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -3 0 -2 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 1 0 -2 0 0 1 -1 0 -2 0 -1 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -7 4 -5 -8 -9 -5 -8 -8 -3 -6 -2 -4 -4 2 -6 -3 -6 27 1 -7 -6 -7 -4 -9
-Y -4 -5 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
-V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 3 -2 2 -1 -1 -1 0 -7 -2 4 -2 -2 0 -9
-B 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -9
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 -1 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM370 b/Butterfly/src/src/jaligner/matrix/matrices/PAM370
deleted file mode 100644
index f72261f..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM370
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 370 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.649, Entropy = 0.165 bits
-#
-# Lowest score = -9, Highest score = 27
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 -1 -9
-N 0 1 2 2 -4 1 2 1 2 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 4 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 18 -6 -6 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -9 1 -2 -5 -6 -3 -9
-Q 0 2 1 2 -6 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
-E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 0 0 -8 -5 -2 3 3 0 -9
-G 2 -2 1 1 -3 -1 1 5 -2 -2 -4 -1 -3 -5 0 1 1 -8 -6 -1 1 0 -1 -9
-H -1 2 2 1 -4 3 1 -2 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 5 3 -3 -3 -1 -2 0 3 -3 -3 -1 -9
-K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 -1 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -9
-F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 3 -6 1 12 -5 -4 -3 2 11 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -2 -3 -1 -2 -5 6 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -7 3 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 27 1 -7 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -6 0 0 0 -5 -2 11 -5 -3 -3 1 14 -2 -4 -5 -2 -9
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -9
-B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 1 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -6 -5 -2 2 3 0 -9
-X 0 -1 0 0 -3 0 0 -1 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM380 b/Butterfly/src/src/jaligner/matrix/matrices/PAM380
deleted file mode 100644
index cbcf063..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM380
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 380 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.612, Entropy = 0.156 bits
-#
-# Lowest score = -9, Highest score = 26
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 2 1 2 -5 3 2 -1 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 3 3 0 -9
-G 2 -2 1 1 -3 -1 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -2 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -3 -1 -2 0 3 -3 -3 -1 -9
-K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -2 2 -2 -1 0 -9
-F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 3 -5 1 12 -5 -4 -3 2 10 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -9
-W -6 3 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 26 1 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -2 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -2 0 -9
-B 1 0 2 3 -4 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -4 -2 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM390 b/Butterfly/src/src/jaligner/matrix/matrices/PAM390
deleted file mode 100644
index 8206530..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM390
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 390 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.581, Entropy = 0.147 bits
-#
-# Lowest score = -9, Highest score = 26
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
-R -1 6 1 0 -4 1 0 -2 2 -2 -3 4 0 -5 0 0 0 3 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -4 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -5 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 17 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 3 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -5 -1 2 3 0 -9
-G 1 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 3 7 -3 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -9
-K -1 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -2 3 4 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 3 -5 1 12 -5 -3 -3 2 10 0 -5 -5 -2 -9
-P 1 0 0 0 -3 0 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
-W -6 3 -4 -7 -9 -5 -7 -7 -3 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 0 -5 -1 10 -5 -3 -3 1 13 -2 -4 -4 -2 -9
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -6 -2 4 -2 -1 0 -9
-B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -9
-Z 0 1 1 3 -5 3 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM40 b/Butterfly/src/src/jaligner/matrix/matrices/PAM40
deleted file mode 100644
index e0df4f6..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM40
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -4.27, Entropy = 2.26 bits
-#
-# Lowest score = -15, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2 -3 -2 -3 -15
-R -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7 -6 -3 -5 -15
-N -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7 6 -2 -3 -15
-D -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7 6 2 -5 -15
-C -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5 -11 -12 -8 -15
-Q -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6 -2 6 -4 -15
-E -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6 2 6 -4 -15
-G -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5 -2 -4 -4 -15
-H -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6 -1 0 -4 -15
-I -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2 -5 -5 -4 -15
-L -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2 -8 -6 -5 -15
-K -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8 -2 -3 -4 -15
-M -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1 -8 -4 -4 -15
-F -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7 -9 -12 -7 -15
-P -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5 -6 -3 -4 -15
-S 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5 -1 -4 -2 -15
-T 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2 -2 -5 -3 -15
-W -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14 -9 -13 -9 -15
-Y -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6 -6 -8 -7 -15
-V -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7 -7 -6 -4 -15
-B -3 -6 6 6 -11 -2 2 -2 -1 -5 -8 -2 -8 -9 -6 -1 -2 -9 -6 -7 6 1 -4 -15
-Z -2 -3 -2 2 -12 6 6 -4 0 -5 -6 -3 -4 -12 -3 -4 -5 -13 -8 -6 1 6 -4 -15
-X -3 -5 -3 -5 -8 -4 -4 -4 -4 -4 -5 -4 -4 -7 -4 -2 -3 -9 -7 -4 -4 -4 -4 -15
-* -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM400 b/Butterfly/src/src/jaligner/matrix/matrices/PAM400
deleted file mode 100644
index 4d99c84..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM400
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 400 substitution matrix, scale = ln(2)/5 = 0.138629
-#
-# Expected score = -0.521, Entropy = 0.139 bits
-#
-# Lowest score = -8, Highest score = 26
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 -1 0 -2 -1 -1 -3 1 1 1 -6 -3 0 1 0 0 -8
-R -1 5 1 0 -4 1 0 -2 2 -2 -3 4 0 -4 0 0 0 3 -4 -2 0 1 0 -8
-N 0 1 1 2 -3 1 2 1 1 -1 -3 1 -1 -3 0 1 0 -4 -3 -1 2 1 0 -8
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -2 2 2 0 -8
-C -2 -4 -3 -5 17 -5 -5 -3 -3 -2 -6 -5 -5 -4 -2 0 -2 -8 1 -2 -4 -5 -3 -8
-Q 0 1 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 0 0 0 -5 -4 -1 2 2 0 -8
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 0 0 -7 -4 -1 2 3 0 -8
-G 1 -2 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -7 -5 -1 1 0 0 -8
-H -1 2 1 1 -3 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -8
-I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -8
-L -2 -3 -3 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -2 0 3 -3 -2 -1 -8
-K -1 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -8
-M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 5 1 -1 -1 0 -4 -1 2 -2 -1 0 -8
-F -3 -4 -3 -5 -4 -4 -5 -5 -2 2 3 -5 1 11 -4 -3 -3 2 10 0 -4 -5 -2 -8
-P 1 0 0 0 -2 0 0 0 0 -1 -2 0 -1 -4 5 1 1 -6 -5 -1 0 0 0 -8
-S 1 0 1 1 0 0 0 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -8
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -8
-W -6 3 -4 -7 -8 -5 -7 -7 -2 -5 -2 -3 -4 2 -6 -3 -5 26 1 -6 -5 -6 -4 -8
-Y -3 -4 -3 -4 1 -4 -4 -5 0 0 0 -4 -1 10 -5 -3 -3 1 13 -2 -3 -4 -2 -8
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -8
-B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -5 -3 -1 2 2 0 -8
-Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -8
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -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 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM410 b/Butterfly/src/src/jaligner/matrix/matrices/PAM410
deleted file mode 100644
index b7c9bfd..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM410
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 410 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.617, Entropy = 0.131 bits
-#
-# Lowest score = -10, Highest score = 31
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 -1 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 1 -5 -3 -1 2 2 0 -10
-D 1 0 2 3 -6 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-C -2 -4 -4 -6 20 -6 -6 -4 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
-E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-G 2 -2 1 1 -4 0 1 5 -1 -2 -4 -1 -3 -6 0 1 1 -8 -6 -1 1 0 0 -10
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
-L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 8 -3 5 4 -3 -3 -1 -2 1 3 -3 -3 -1 -10
-K -1 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -2 -2 -6 -1 -2 -3 -2 3 5 0 5 1 -2 -1 0 -4 -2 2 -2 -2 0 -10
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 14 -5 -4 -3 2 12 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 0 0 -2 -3 0 -2 -5 6 1 1 -7 -5 -1 0 0 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 0 1 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 2 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -7 -3 -6 31 2 -7 -6 -7 -4 -10
-Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -2 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
-B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -2 -5 0 0 0 -7 -5 -2 2 3 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM420 b/Butterfly/src/src/jaligner/matrix/matrices/PAM420
deleted file mode 100644
index 53e0caf..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM420
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 420 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.599, Entropy = 0.124 bits
-#
-# Lowest score = -10, Highest score = 31
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 2 0 -10
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-C -2 -4 -4 -5 20 -6 -6 -3 -4 -3 -7 -6 -6 -4 -3 0 -2 -10 1 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -2 2 3 0 -10
-E 1 0 2 3 -6 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 0 1 1 -8 -6 -1 1 0 0 -10
-H -1 2 1 1 -4 3 1 -1 6 -2 -2 1 -2 -2 0 0 -1 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -3 -2 -2 -2 -2 4 4 -2 3 2 -2 -1 0 -6 0 4 -2 -2 0 -10
-L -2 -3 -3 -4 -7 -2 -3 -4 -2 4 7 -3 5 4 -2 -3 -1 -2 1 3 -3 -3 -1 -10
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 5 0 -6 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -1 -2 -6 -1 -2 -2 -2 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -10
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -6 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 0 0 -2 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -3 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -6 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -7 -4 -10
-Y -4 -5 -3 -5 1 -4 -5 -6 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -10
-V 0 -2 -1 -2 -2 -2 -2 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -2 -2 0 -10
-B 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -2 2 2 0 -10
-Z 0 1 2 3 -6 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -7 -5 -2 2 3 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM430 b/Butterfly/src/src/jaligner/matrix/matrices/PAM430
deleted file mode 100644
index 2450215..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM430
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 430 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.543, Entropy = 0.117 bits
-#
-# Lowest score = -9, Highest score = 31
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -9
-R -1 6 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -7 -5 -2 3 3 0 -9
-C -2 -4 -4 -5 20 -6 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 3 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -9
-G 2 -2 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 4 -2 -2 0 -9
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -9
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 5 1 -2 -1 0 -4 -1 2 -2 -1 0 -9
-F -4 -5 -4 -6 -4 -5 -6 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -2 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -7 4 -5 -7 -9 -5 -8 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 31 2 -7 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -5 -2 -9
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 4 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -9
-B 1 0 2 3 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 3 -5 3 3 0 2 -2 -3 1 -1 -5 0 0 0 -6 -5 -1 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM440 b/Butterfly/src/src/jaligner/matrix/matrices/PAM440
deleted file mode 100644
index 0429e87..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM440
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 440 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.529, Entropy = 0.111 bits
-#
-# Lowest score = -9, Highest score = 30
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -6 -4 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -2 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -2 2 2 0 -9
-C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 1 -2 -4 -5 -3 -9
-Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
-G 2 -2 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -3 0 -2 1 2 0 -9
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -4 -5 -4 -6 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -4 -3 2 12 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -2 -3 -4 2 -6 -3 -6 30 2 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 15 -2 -4 -4 -2 -9
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 4 -1 -1 0 -9
-B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 3 0 -9
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 -1 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM450 b/Butterfly/src/src/jaligner/matrix/matrices/PAM450
deleted file mode 100644
index 30cc7a2..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM450
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 450 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.476, Entropy = 0.105 bits
-#
-# Lowest score = -9, Highest score = 30
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 -1 0 -2 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -4 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-C -2 -4 -4 -5 20 -5 -5 -3 -4 -2 -6 -5 -5 -4 -2 0 -2 -9 1 -2 -4 -5 -2 -9
-Q 0 2 1 2 -5 3 2 0 3 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 3 0 -9
-G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 0 1 1 -8 -5 -1 1 0 0 -9
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 -1 -2 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 4 3 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -2 -3 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -4 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 13 -5 -3 -3 2 12 0 -4 -5 -2 -9
-P 1 0 0 0 -2 1 0 0 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 -1 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
-W -6 4 -4 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 1 -4 -5 -5 0 0 1 -5 -1 12 -5 -3 -3 2 14 -2 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
-B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 3 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM460 b/Butterfly/src/src/jaligner/matrix/matrices/PAM460
deleted file mode 100644
index 7491d6c..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM460
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 460 substitution matrix, scale = ln(2)/6 = 0.115525
-#
-# Expected score = -0.429, Entropy = 0.0994 bits
-#
-# Lowest score = -9, Highest score = 30
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
-R -1 5 1 0 -4 1 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -3 0 1 0 -4 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
-C -2 -4 -3 -5 19 -5 -5 -3 -3 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
-Q 0 1 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 1 2 0 -9
-E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -4 -1 2 2 0 -9
-G 1 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -7 -5 -1 1 0 0 -9
-H 0 2 1 1 -3 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 3 -2 2 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -1 -2 -2 -3 -6 -2 -3 -3 -2 3 7 -2 4 3 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -4 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 2 4 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -4 -3 -5 -3 -4 -5 -5 -2 2 3 -5 1 12 -4 -3 -3 2 11 0 -4 -5 -2 -9
-P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 0 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -5 -3 0 0 0 0 -9
-W -6 4 -4 -7 -9 -5 -7 -7 -2 -5 -1 -3 -4 2 -6 -3 -5 30 2 -6 -6 -6 -4 -9
-Y -3 -4 -3 -4 2 -4 -4 -5 0 0 1 -4 -1 11 -5 -3 -3 2 14 -2 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
-B 1 0 1 2 -4 1 2 1 1 -2 -3 1 -2 -4 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 2 0 2 -2 -2 1 -1 -5 0 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM470 b/Butterfly/src/src/jaligner/matrix/matrices/PAM470
deleted file mode 100644
index 9d5e333..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM470
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 470 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.520, Entropy = 0.0942 bits
-#
-# Lowest score = -10, Highest score = 35
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 1 1 -2 0 1 2 -1 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 6 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -5 -2 0 1 0 -10
-N 1 1 1 2 -4 1 2 1 1 -2 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
-D 1 0 2 3 -5 2 3 1 1 -2 -4 1 -2 -6 0 1 0 -8 -5 -2 3 3 0 -10
-C -2 -4 -4 -5 22 -6 -5 -3 -4 -2 -6 -6 -6 -4 -3 0 -2 -10 2 -2 -5 -6 -3 -10
-Q 0 2 1 2 -6 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -8 -5 -1 2 3 0 -10
-G 2 -1 1 1 -3 0 1 5 -1 -2 -4 -1 -2 -6 1 1 1 -8 -6 -1 1 1 0 -10
-H -1 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
-I 0 -2 -2 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
-L -2 -3 -3 -4 -6 -2 -3 -4 -2 4 8 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -1 -2 -6 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
-F -4 -5 -4 -6 -4 -5 -6 -6 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -4 -3 -1 1 0 0 -10
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
-W -7 4 -5 -8 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -4 -6 35 2 -7 -6 -7 -4 -10
-Y -4 -5 -3 -5 2 -4 -5 -6 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
-V 0 -2 -1 -2 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 4 -1 -1 0 -10
-B 1 0 2 3 -5 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
-Z 0 1 1 3 -6 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -7 -5 -1 2 3 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM480 b/Butterfly/src/src/jaligner/matrix/matrices/PAM480
deleted file mode 100644
index c777c62..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM480
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 480 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.494, Entropy = 0.0893 bits
-#
-# Lowest score = -10, Highest score = 35
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 1 1 -2 0 1 2 0 0 -2 0 -1 -4 1 1 1 -7 -4 0 1 0 0 -10
-R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -10
-N 1 1 1 2 -4 1 2 1 1 -1 -3 1 -1 -4 0 1 0 -5 -3 -1 2 1 0 -10
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -6 0 1 0 -7 -5 -1 2 2 0 -10
-C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -6 -5 -4 -3 0 -2 -10 2 -2 -4 -5 -3 -10
-Q 0 2 1 2 -5 3 2 0 3 -2 -2 1 -1 -5 1 0 0 -5 -4 -1 2 2 0 -10
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -8 -5 -1 2 3 0 -10
-G 2 -1 1 1 -3 0 1 4 -1 -2 -4 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -10
-H 0 2 1 1 -4 3 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -10
-I 0 -2 -1 -2 -2 -2 -2 -2 -2 4 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -10
-L -2 -3 -3 -3 -6 -2 -3 -4 -2 4 7 -3 5 4 -2 -2 -1 -2 1 3 -3 -3 -1 -10
-K 0 4 1 1 -6 1 1 -1 1 -2 -3 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -10
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -10
-F -4 -5 -4 -6 -4 -5 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -10
-P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 5 1 1 -6 -5 -1 0 1 0 -10
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -10
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -10
-W -7 4 -5 -7 -10 -5 -8 -8 -3 -5 -2 -3 -4 3 -6 -3 -6 35 2 -7 -6 -6 -4 -10
-Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 16 -2 -4 -5 -2 -10
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -7 -2 3 -1 -1 0 -10
-B 1 0 2 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -10
-Z 0 1 1 2 -5 2 3 1 2 -2 -3 1 -1 -5 1 0 0 -6 -5 -1 2 2 0 -10
-X 0 0 0 0 -3 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM490 b/Butterfly/src/src/jaligner/matrix/matrices/PAM490
deleted file mode 100644
index 107a0c8..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM490
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 490 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.431, Entropy = 0.0847 bits
-#
-# Lowest score = -9, Highest score = 34
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 2 0 0 -1 0 -1 -3 1 1 1 -6 -4 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -1 2 -2 -3 4 0 -5 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -4 1 2 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-C -2 -4 -4 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -4 -3 0 -2 -9 2 -2 -4 -5 -2 -9
-Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-G 2 -1 1 1 -3 0 1 4 -1 -2 -3 -1 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
-H 0 2 1 1 -4 2 1 -1 5 -2 -2 1 -1 -2 0 0 0 -3 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -1 -3 -2 -3 -6 -2 -3 -3 -2 4 7 -2 5 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 -1 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -2 -2 -1 3 5 0 4 1 -1 -1 0 -4 -1 2 -2 -1 0 -9
-F -3 -5 -4 -5 -4 -4 -5 -5 -2 2 4 -5 1 14 -5 -4 -3 3 13 0 -5 -5 -2 -9
-P 1 0 0 0 -3 1 0 1 0 -1 -2 0 -1 -5 4 1 1 -6 -5 -1 0 1 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -4 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -6 4 -5 -7 -9 -5 -7 -8 -3 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
-Y -4 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -2 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -2 3 -1 -1 0 -9
-B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -2 -5 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM50 b/Butterfly/src/src/jaligner/matrix/matrices/PAM50
deleted file mode 100644
index 6d37d4b..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM50
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 50 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -3.70, Entropy = 2.00 bits
-#
-# Lowest score = -13, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -5 -2 -2 -5 -3 -1 -1 -5 -3 -5 -5 -4 -7 0 0 0 -11 -6 -1 -2 -2 -2 -13
-R -5 8 -4 -7 -6 0 -7 -7 0 -4 -7 1 -3 -8 -3 -2 -5 -1 -8 -6 -5 -2 -4 -13
-N -2 -4 7 2 -8 -2 -1 -2 1 -4 -6 0 -6 -7 -4 1 -1 -7 -3 -6 5 -1 -2 -13
-D -2 -7 2 7 -11 -1 3 -2 -2 -6 -10 -3 -8 -12 -6 -2 -3 -12 -9 -6 6 2 -4 -13
-C -5 -6 -8 -11 9 -11 -11 -7 -6 -5 -12 -11 -11 -10 -6 -2 -6 -13 -3 -5 -9 -11 -7 -13
-Q -3 0 -2 -1 -11 8 2 -5 2 -6 -4 -2 -3 -10 -2 -4 -4 -10 -9 -5 -2 6 -3 -13
-E -1 -7 -1 3 -11 2 7 -3 -3 -4 -7 -3 -5 -11 -4 -3 -4 -13 -7 -5 2 6 -3 -13
-G -1 -7 -2 -2 -7 -5 -3 6 -7 -8 -9 -6 -7 -8 -4 -1 -4 -12 -11 -4 -2 -4 -4 -13
-H -5 0 1 -2 -6 2 -3 -7 9 -7 -5 -4 -8 -5 -3 -4 -5 -6 -2 -5 0 0 -4 -13
-I -3 -4 -4 -6 -5 -6 -4 -8 -7 8 0 -5 0 -1 -7 -5 -1 -11 -5 3 -5 -5 -3 -13
-L -5 -7 -6 -10 -12 -4 -7 -9 -5 0 6 -6 2 -1 -6 -7 -5 -5 -5 -1 -7 -5 -5 -13
-K -5 1 0 -3 -11 -2 -3 -6 -4 -5 -6 6 -1 -11 -5 -3 -2 -9 -8 -7 -1 -2 -4 -13
-M -4 -3 -6 -8 -11 -3 -5 -7 -8 0 2 -1 10 -3 -6 -4 -3 -10 -8 0 -7 -4 -4 -13
-F -7 -8 -7 -12 -10 -10 -11 -8 -5 -1 -1 -11 -3 9 -8 -5 -7 -3 3 -6 -9 -11 -6 -13
-P 0 -3 -4 -6 -6 -2 -4 -4 -3 -7 -6 -5 -6 -8 8 -1 -3 -11 -11 -4 -5 -3 -4 -13
-S 0 -2 1 -2 -2 -4 -3 -1 -4 -5 -7 -3 -4 -5 -1 6 1 -4 -5 -4 -1 -3 -2 -13
-T 0 -5 -1 -3 -6 -4 -4 -4 -5 -1 -5 -2 -3 -7 -3 1 6 -10 -5 -2 -2 -4 -2 -13
-W -11 -1 -7 -12 -13 -10 -13 -12 -6 -11 -5 -9 -10 -3 -11 -4 -10 13 -4 -12 -8 -11 -9 -13
-Y -6 -8 -3 -9 -3 -9 -7 -11 -2 -5 -5 -8 -8 3 -11 -5 -5 -4 9 -6 -5 -8 -6 -13
-V -1 -6 -6 -6 -5 -5 -5 -4 -5 3 -1 -7 0 -6 -4 -4 -2 -12 -6 7 -6 -5 -3 -13
-B -2 -5 5 6 -9 -2 2 -2 0 -5 -7 -1 -7 -9 -5 -1 -2 -8 -5 -6 5 1 -3 -13
-Z -2 -2 -1 2 -11 6 6 -4 0 -5 -5 -2 -4 -11 -3 -3 -4 -11 -8 -5 1 6 -3 -13
-X -2 -4 -2 -4 -7 -3 -3 -4 -4 -3 -5 -4 -4 -6 -4 -2 -2 -9 -6 -3 -3 -3 -4 -13
-* -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 -13 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM500 b/Butterfly/src/src/jaligner/matrix/matrices/PAM500
deleted file mode 100644
index 617c3f1..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM500
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 500 substitution matrix, scale = ln(2)/7 = 0.0990210
-#
-# Expected score = -0.401, Entropy = 0.0803 bits
-#
-# Lowest score = -9, Highest score = 34
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 1 -1 0 1 -2 0 1 1 0 0 -1 0 -1 -3 1 1 1 -6 -3 0 1 0 0 -9
-R -1 5 1 0 -4 2 0 -1 2 -2 -2 4 0 -4 0 0 0 4 -4 -2 0 1 0 -9
-N 0 1 1 2 -3 1 1 1 1 -1 -2 1 -1 -4 0 1 0 -5 -3 -1 1 1 0 -9
-D 1 0 2 3 -5 2 3 1 1 -2 -3 1 -2 -5 0 1 0 -7 -5 -1 2 2 0 -9
-C -2 -4 -3 -5 22 -5 -5 -3 -4 -2 -6 -5 -5 -3 -2 0 -2 -9 2 -2 -4 -5 -2 -9
-Q 0 2 1 2 -5 2 2 0 2 -1 -2 1 -1 -4 1 0 0 -5 -4 -1 2 2 0 -9
-E 1 0 1 3 -5 2 3 1 1 -2 -3 1 -1 -5 0 1 0 -7 -5 -1 2 2 0 -9
-G 1 -1 1 1 -3 0 1 4 -1 -2 -3 0 -2 -5 1 1 1 -8 -5 -1 1 1 0 -9
-H 0 2 1 1 -4 2 1 -1 4 -2 -2 1 -1 -2 0 0 0 -2 0 -2 1 2 0 -9
-I 0 -2 -1 -2 -2 -1 -2 -2 -2 3 4 -2 3 2 -1 -1 0 -5 0 3 -2 -2 0 -9
-L -1 -2 -2 -3 -6 -2 -3 -3 -2 4 7 -2 4 4 -2 -2 -1 -1 1 3 -3 -2 -1 -9
-K 0 4 1 1 -5 1 1 0 1 -2 -2 4 0 -5 0 0 0 -3 -5 -2 1 1 0 -9
-M -1 0 -1 -2 -5 -1 -1 -2 -1 3 4 0 4 1 -1 -1 0 -4 -1 2 -1 -1 0 -9
-F -3 -4 -4 -5 -3 -4 -5 -5 -2 2 4 -5 1 13 -4 -3 -3 3 13 0 -4 -5 -2 -9
-P 1 0 0 0 -2 1 0 1 0 -1 -2 0 -1 -4 4 1 1 -6 -5 -1 0 1 0 -9
-S 1 0 1 1 0 0 1 1 0 -1 -2 0 -1 -3 1 1 1 -3 -3 -1 1 0 0 -9
-T 1 0 0 0 -2 0 0 1 0 0 -1 0 0 -3 1 1 1 -6 -3 0 0 0 0 -9
-W -6 4 -5 -7 -9 -5 -7 -8 -2 -5 -1 -3 -4 3 -6 -3 -6 34 2 -6 -6 -6 -4 -9
-Y -3 -4 -3 -5 2 -4 -5 -5 0 0 1 -5 -1 13 -5 -3 -3 2 15 -1 -4 -4 -2 -9
-V 0 -2 -1 -1 -2 -1 -1 -1 -2 3 3 -2 2 0 -1 -1 0 -6 -1 3 -1 -1 0 -9
-B 1 0 1 2 -4 2 2 1 1 -2 -3 1 -1 -4 0 1 0 -6 -4 -1 2 2 0 -9
-Z 0 1 1 2 -5 2 2 1 2 -2 -2 1 -1 -5 1 0 0 -6 -4 -1 2 2 0 -9
-X 0 0 0 0 -2 0 0 0 0 0 -1 0 0 -2 0 0 0 -4 -2 0 0 0 0 -9
-* -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM60 b/Butterfly/src/src/jaligner/matrix/matrices/PAM60
deleted file mode 100644
index fba70b9..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM60
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 60 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -3.21, Entropy = 1.79 bits
-#
-# Lowest score = -12, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -5 -2 -2 -5 -3 -1 0 -5 -3 -4 -5 -3 -6 0 1 1 -10 -6 -1 -2 -2 -2 -12
-R -5 8 -3 -6 -6 0 -6 -7 0 -4 -6 2 -2 -7 -2 -2 -4 0 -8 -5 -5 -2 -4 -12
-N -2 -3 6 2 -7 -2 0 -1 1 -4 -5 0 -6 -6 -4 1 -1 -6 -3 -5 5 -1 -2 -12
-D -2 -6 2 7 -10 -1 3 -2 -2 -5 -9 -2 -7 -11 -5 -2 -3 -11 -8 -6 5 2 -3 -12
-C -5 -6 -7 -10 9 -10 -10 -7 -6 -4 -11 -10 -10 -9 -6 -1 -5 -12 -2 -4 -9 -10 -6 -12
-Q -3 0 -2 -1 -10 7 2 -5 2 -5 -3 -1 -2 -9 -1 -3 -4 -9 -8 -5 -1 6 -3 -12
-E -1 -6 0 3 -10 2 7 -2 -3 -4 -7 -3 -5 -10 -3 -2 -4 -12 -7 -4 2 5 -3 -12
-G 0 -7 -1 -2 -7 -5 -2 6 -6 -7 -8 -5 -6 -7 -4 0 -3 -11 -10 -4 -2 -3 -3 -12
-H -5 0 1 -2 -6 2 -3 -6 8 -6 -4 -4 -7 -4 -2 -4 -5 -5 -2 -5 0 0 -3 -12
-I -3 -4 -4 -5 -4 -5 -4 -7 -6 7 0 -4 1 -1 -6 -4 -1 -10 -4 3 -4 -4 -3 -12
-L -4 -6 -5 -9 -11 -3 -7 -8 -4 0 6 -6 2 -1 -5 -6 -5 -4 -5 -1 -7 -5 -4 -12
-K -5 2 0 -2 -10 -1 -3 -5 -4 -4 -6 6 0 -10 -4 -2 -2 -8 -7 -6 -1 -2 -3 -12
-M -3 -2 -6 -7 -10 -2 -5 -6 -7 1 2 0 10 -2 -6 -4 -2 -9 -7 0 -6 -4 -3 -12
-F -6 -7 -6 -11 -9 -9 -10 -7 -4 -1 -1 -10 -2 8 -7 -5 -6 -3 3 -5 -8 -10 -5 -12
-P 0 -2 -4 -5 -6 -1 -3 -4 -2 -6 -5 -4 -6 -7 7 0 -2 -10 -10 -4 -4 -2 -3 -12
-S 1 -2 1 -2 -1 -3 -2 0 -4 -4 -6 -2 -4 -5 0 5 1 -4 -5 -4 0 -3 -2 -12
-T 1 -4 -1 -3 -5 -4 -4 -3 -5 -1 -5 -2 -2 -6 -2 1 6 -9 -5 -1 -2 -4 -2 -12
-W -10 0 -6 -11 -12 -9 -12 -11 -5 -10 -4 -8 -9 -3 -10 -4 -9 13 -3 -11 -8 -11 -8 -12
-Y -6 -8 -3 -8 -2 -8 -7 -10 -2 -4 -5 -7 -7 3 -10 -5 -5 -3 9 -5 -5 -7 -5 -12
-V -1 -5 -5 -6 -4 -5 -4 -4 -5 3 -1 -6 0 -5 -4 -4 -1 -11 -5 6 -5 -5 -3 -12
-B -2 -5 5 5 -9 -1 2 -2 0 -4 -7 -1 -6 -8 -4 0 -2 -8 -5 -5 5 1 -3 -12
-Z -2 -2 -1 2 -10 6 5 -3 0 -4 -5 -2 -4 -10 -2 -3 -4 -11 -7 -5 1 5 -3 -12
-X -2 -4 -2 -3 -6 -3 -3 -3 -3 -3 -4 -3 -3 -5 -3 -2 -2 -8 -5 -3 -3 -3 -3 -12
-* -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 -12 1
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM70 b/Butterfly/src/src/jaligner/matrix/matrices/PAM70
deleted file mode 100644
index b20cdf0..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM70
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -2.77, Entropy = 1.60 bits
-#
-# Lowest score = -11, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 5 -4 -2 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -6 0 1 1 -9 -5 -1 -1 -1 -2 -11
-R -4 8 -3 -6 -5 0 -5 -6 0 -3 -6 2 -2 -7 -2 -1 -4 0 -7 -5 -4 -2 -3 -11
-N -2 -3 6 3 -7 -1 0 -1 1 -3 -5 0 -5 -6 -3 1 0 -6 -3 -5 5 -1 -2 -11
-D -1 -6 3 6 -9 0 3 -1 -1 -5 -8 -2 -7 -10 -4 -1 -2 -10 -7 -5 5 2 -3 -11
-C -4 -5 -7 -9 9 -9 -9 -6 -5 -4 -10 -9 -9 -8 -5 -1 -5 -11 -2 -4 -8 -9 -6 -11
-Q -2 0 -1 0 -9 7 2 -4 2 -5 -3 -1 -2 -9 -1 -3 -3 -8 -8 -4 -1 5 -2 -11
-E -1 -5 0 3 -9 2 6 -2 -2 -4 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -3 -11
-G 0 -6 -1 -1 -6 -4 -2 6 -6 -6 -7 -5 -6 -7 -3 0 -3 -10 -9 -3 -1 -3 -3 -11
-H -4 0 1 -1 -5 2 -2 -6 8 -6 -4 -3 -6 -4 -2 -3 -4 -5 -1 -4 0 1 -3 -11
-I -2 -3 -3 -5 -4 -5 -4 -6 -6 7 1 -4 1 0 -5 -4 -1 -9 -4 3 -4 -4 -3 -11
-L -4 -6 -5 -8 -10 -3 -6 -7 -4 1 6 -5 2 -1 -5 -6 -4 -4 -4 0 -6 -4 -4 -11
-K -4 2 0 -2 -9 -1 -2 -5 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -7 -6 -1 -2 -3 -11
-M -3 -2 -5 -7 -9 -2 -4 -6 -6 1 2 0 10 -2 -5 -3 -2 -8 -7 0 -6 -3 -3 -11
-F -6 -7 -6 -10 -8 -9 -9 -7 -4 0 -1 -9 -2 8 -7 -4 -6 -2 4 -5 -7 -9 -5 -11
-P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -5 -4 -5 -7 7 0 -2 -9 -9 -3 -4 -2 -3 -11
-S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -6 -2 -3 -4 0 5 2 -3 -5 -3 0 -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 -2 -11
-W -9 0 -6 -10 -11 -8 -11 -10 -5 -9 -4 -7 -8 -2 -9 -3 -8 13 -3 -10 -7 -10 -7 -11
-Y -5 -7 -3 -7 -2 -8 -6 -9 -1 -4 -4 -7 -7 4 -9 -5 -4 -3 9 -5 -4 -7 -5 -11
-V -1 -5 -5 -5 -4 -4 -4 -3 -4 3 0 -6 0 -5 -3 -3 -1 -10 -5 6 -5 -4 -2 -11
-B -1 -4 5 5 -8 -1 2 -1 0 -4 -6 -1 -6 -7 -4 0 -1 -7 -4 -5 5 1 -2 -11
-Z -1 -2 -1 2 -9 5 5 -3 1 -4 -4 -2 -3 -9 -2 -2 -3 -10 -7 -4 1 5 -3 -11
-X -2 -3 -2 -3 -6 -2 -3 -3 -3 -3 -4 -3 -3 -5 -3 -1 -2 -7 -5 -2 -2 -3 -3 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM80 b/Butterfly/src/src/jaligner/matrix/matrices/PAM80
deleted file mode 100644
index 55aa043..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM80
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 80 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -2.55, Entropy = 1.44 bits
-#
-# Lowest score = -11, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -4 -1 -1 -4 -2 -1 0 -4 -2 -4 -4 -3 -5 0 1 1 -8 -5 0 -1 -1 -1 -11
-R -4 7 -2 -5 -5 0 -4 -6 0 -3 -5 2 -2 -6 -2 -1 -3 0 -7 -5 -3 -1 -3 -11
-N -1 -2 5 3 -6 -1 0 -1 2 -3 -5 0 -4 -5 -3 1 0 -5 -3 -4 4 0 -1 -11
-D -1 -5 3 6 -9 0 4 -1 -1 -4 -7 -2 -6 -9 -4 -1 -2 -10 -7 -5 5 2 -3 -11
-C -4 -5 -6 -9 9 -9 -9 -6 -5 -4 -9 -9 -8 -8 -5 -1 -4 -10 -2 -3 -7 -9 -5 -11
-Q -2 0 -1 0 -9 7 2 -4 2 -4 -3 -1 -2 -8 -1 -3 -3 -8 -7 -4 0 5 -2 -11
-E -1 -4 0 4 -9 2 6 -2 -2 -3 -6 -2 -4 -9 -3 -2 -3 -11 -6 -4 2 5 -2 -11
-G 0 -6 -1 -1 -6 -4 -2 6 -5 -6 -7 -4 -5 -6 -3 0 -2 -10 -8 -3 -1 -2 -3 -11
-H -4 0 2 -1 -5 2 -2 -5 8 -5 -4 -3 -5 -3 -2 -3 -4 -4 -1 -4 0 1 -2 -11
-I -2 -3 -3 -4 -4 -4 -3 -6 -5 7 1 -4 1 0 -5 -4 -1 -8 -3 3 -4 -4 -2 -11
-L -4 -5 -5 -7 -9 -3 -6 -7 -4 1 6 -5 2 0 -4 -5 -4 -3 -4 0 -6 -4 -3 -11
-K -4 2 0 -2 -9 -1 -2 -4 -3 -4 -5 6 0 -9 -4 -2 -1 -7 -6 -5 -1 -1 -3 -11
-M -3 -2 -4 -6 -8 -2 -4 -5 -5 1 2 0 9 -2 -5 -3 -2 -7 -6 1 -5 -3 -2 -11
-F -5 -6 -5 -9 -8 -8 -9 -6 -3 0 0 -9 -2 8 -7 -4 -5 -2 4 -4 -7 -8 -5 -11
-P 0 -2 -3 -4 -5 -1 -3 -3 -2 -5 -4 -4 -5 -7 7 0 -2 -9 -8 -3 -3 -2 -2 -11
-S 1 -1 1 -1 -1 -3 -2 0 -3 -4 -5 -2 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -11
-T 1 -3 0 -2 -4 -3 -3 -2 -4 -1 -4 -1 -2 -5 -2 2 5 -8 -4 -1 -1 -3 -1 -11
-W -8 0 -5 -10 -10 -8 -11 -10 -4 -8 -3 -7 -7 -2 -9 -3 -8 13 -2 -10 -7 -9 -7 -11
-Y -5 -7 -3 -7 -2 -7 -6 -8 -1 -3 -4 -6 -6 4 -8 -4 -4 -2 9 -5 -4 -6 -4 -11
-V 0 -5 -4 -5 -3 -4 -4 -3 -4 3 0 -5 1 -4 -3 -3 -1 -10 -5 6 -4 -4 -2 -11
-B -1 -3 4 5 -7 0 2 -1 0 -4 -6 -1 -5 -7 -3 0 -1 -7 -4 -4 5 2 -2 -11
-Z -1 -1 0 2 -9 5 5 -2 1 -4 -4 -1 -3 -8 -2 -2 -3 -9 -6 -4 2 5 -2 -11
-X -1 -3 -1 -3 -5 -2 -2 -3 -2 -2 -3 -3 -2 -5 -2 -1 -1 -7 -4 -2 -2 -2 -3 -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
diff --git a/Butterfly/src/src/jaligner/matrix/matrices/PAM90 b/Butterfly/src/src/jaligner/matrix/matrices/PAM90
deleted file mode 100644
index fa2d5b3..0000000
--- a/Butterfly/src/src/jaligner/matrix/matrices/PAM90
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
-#
-# PAM 90 substitution matrix, scale = ln(2)/2 = 0.346574
-#
-# Expected score = -2.26, Entropy = 1.30 bits
-#
-# Lowest score = -10, Highest score = 13
-#
- A R N D C Q E G H I L K M F P S T W Y V B Z X *
-A 4 -4 -1 -1 -3 -2 0 0 -4 -2 -3 -3 -2 -5 0 1 1 -8 -5 0 -1 -1 -1 -10
-R -4 7 -2 -5 -5 0 -4 -5 1 -3 -5 2 -2 -6 -1 -1 -3 0 -6 -4 -3 -1 -2 -10
-N -1 -2 5 3 -6 -1 0 -1 2 -3 -4 1 -4 -5 -2 1 0 -5 -2 -4 4 0 -1 -10
-D -1 -5 3 6 -8 0 4 -1 -1 -4 -7 -2 -5 -8 -4 -1 -2 -9 -6 -4 5 3 -2 -10
-C -3 -5 -6 -8 9 -8 -8 -5 -5 -3 -9 -8 -8 -7 -5 -1 -4 -10 -1 -3 -7 -8 -5 -10
-Q -2 0 -1 0 -8 6 2 -3 2 -4 -3 -1 -2 -7 -1 -2 -3 -7 -6 -4 0 5 -2 -10
-E 0 -4 0 4 -8 2 6 -1 -1 -3 -5 -2 -4 -8 -2 -2 -2 -10 -6 -3 2 5 -2 -10
-G 0 -5 -1 -1 -5 -3 -1 5 -5 -5 -6 -4 -5 -6 -3 0 -2 -9 -8 -3 -1 -2 -2 -10
-H -4 1 2 -1 -5 2 -1 -5 8 -5 -3 -2 -5 -3 -2 -3 -3 -4 -1 -4 1 1 -2 -10
-I -2 -3 -3 -4 -3 -4 -3 -5 -5 6 1 -3 1 0 -4 -3 0 -8 -3 3 -3 -3 -2 -10
-L -3 -5 -4 -7 -9 -3 -5 -6 -3 1 6 -5 2 0 -4 -5 -3 -3 -3 0 -5 -4 -3 -10
-K -3 2 1 -2 -8 -1 -2 -4 -2 -3 -5 5 0 -8 -3 -1 -1 -6 -6 -5 0 -1 -2 -10
-M -2 -2 -4 -5 -8 -2 -4 -5 -5 1 2 0 9 -1 -4 -3 -2 -7 -6 1 -5 -3 -2 -10
-F -5 -6 -5 -8 -7 -7 -8 -6 -3 0 0 -8 -1 8 -6 -4 -5 -2 4 -4 -6 -8 -4 -10
-P 0 -1 -2 -4 -5 -1 -2 -3 -2 -4 -4 -3 -4 -6 7 0 -1 -8 -8 -3 -3 -2 -2 -10
-S 1 -1 1 -1 -1 -2 -2 0 -3 -3 -5 -1 -3 -4 0 4 2 -3 -4 -3 0 -2 -1 -10
-T 1 -3 0 -2 -4 -3 -2 -2 -3 0 -3 -1 -2 -5 -1 2 5 -7 -4 -1 -1 -2 -1 -10
-W -8 0 -5 -9 -10 -7 -10 -9 -4 -8 -3 -6 -7 -2 -8 -3 -7 13 -2 -9 -7 -8 -6 -10
-Y -5 -6 -2 -6 -1 -6 -6 -8 -1 -3 -3 -6 -6 4 -8 -4 -4 -2 9 -4 -4 -6 -4 -10
-V 0 -4 -4 -4 -3 -4 -3 -3 -4 3 0 -5 1 -4 -3 -3 -1 -9 -4 6 -4 -3 -2 -10
-B -1 -3 4 5 -7 0 2 -1 1 -3 -5 0 -5 -6 -3 0 -1 -7 -4 -4 4 2 -2 -10
-Z -1 -1 0 3 -8 5 5 -2 1 -3 -4 -1 -3 -8 -2 -2 -2 -8 -6 -3 2 5 -2 -10
-X -1 -2 -1 -2 -5 -2 -2 -2 -2 -2 -3 -2 -2 -4 -2 -1 -1 -6 -4 -2 -2 -2 -2 -10
-* -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1
diff --git a/Butterfly/src/src/jaligner/matrix/package.html b/Butterfly/src/src/jaligner/matrix/package.html
deleted file mode 100644
index 4024755..0000000
--- a/Butterfly/src/src/jaligner/matrix/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head><!--$Id: package.html,v 1.1 2005/05/25 19:56:30 ahmed Exp $--></head>
-<body bgcolor="white">
-Scoring matrices package.
- at author Ahmed Moustafa (ahmed at users.sf.net)
-</body>
-</html>
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/package.html b/Butterfly/src/src/jaligner/package.html
deleted file mode 100644
index c71d65c..0000000
--- a/Butterfly/src/src/jaligner/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head><!--$Id: package.html,v 1.1 2005/05/25 19:56:30 ahmed Exp $--></head>
-<body bgcolor="white">
-Core classes for the implementation of Smith-Waterman-Gotoh algorithm
- at author Ahmed Moustafa (ahmed at users.sf.net)
-</body>
-</html>
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/test/NeedlemanWunschGotohTester.java b/Butterfly/src/src/jaligner/test/NeedlemanWunschGotohTester.java
deleted file mode 100644
index 7ee3516..0000000
--- a/Butterfly/src/src/jaligner/test/NeedlemanWunschGotohTester.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * $Id: NeedlemanWunschGotohTester.java,v 1.1 2006/02/03 05:00:22 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.test;
-
-import jaligner.Alignment;
-import jaligner.NeedlemanWunschGotoh;
-import jaligner.Sequence;
-import jaligner.formats.Format;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixLoader;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Random;
-
-/**
- * Testing the scores of the alignments of {@link jaligner.NeedlemanWunschGotoh}.
- *
- * @author Bram Minnaert
- */
-
-public class NeedlemanWunschGotohTester {
-
- public static void main(String[] args) {
-
- int numberOfTests = Integer.parseInt(args[0]);
- int sequencesSize = Integer.parseInt(args[1]);
- Random random = new Random();
- Format format = new Pair();
-
- try {
- ArrayList matrices = new ArrayList();
- for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) {
- matrices.add(i.next());
- }
- int countOfMatrices = matrices.size();
-
- int i = 1;
- while (i <= numberOfTests) {
-
- System.gc();
-
- String s1 = RandomSequenceGenerator.generate(sequencesSize);
- String s2 = RandomSequenceGenerator.generate(sequencesSize);
-
- int o = random.nextInt(50);
- int e = random.nextInt(10);
-
- if (s1.length() > 0 && s2.length() > 0 && o >= e) {
-
- Matrix matrix = (Matrix) MatrixLoader
- .load((String) matrices.get(random
- .nextInt(countOfMatrices)));
- Sequence seq1 = new Sequence(s1);
- Sequence seq2 = new Sequence(s2);
-
- Alignment alignment1 = NeedlemanWunschGotoh.align(seq1,
- seq2, matrix, o, e);
-
- if (!alignment1.checkScore()) {
- System.err.println("Invalid alignment found:");
- System.err.println("Sequence 1 = " + s1);
- System.err.println("Sequence 2 = " + s2);
- System.err.println(format.format(alignment1));
- System.err.println(alignment1.getSummary());
- System.err
- .println("The score of the alignment above is: "
- + alignment1.calculateScore());
- System.exit(1);
- }
-
- Alignment alignment2 = NeedlemanWunschGotoh.align(seq2,
- seq1, matrix, o, e);
- if (!alignment1.checkScore()) {
- System.err.println("Invalid alignment found:");
- System.err.println("Sequence 1 = " + s2);
- System.err.println("Sequence 2 = " + s1);
- System.err.println(format.format(alignment2));
- System.err.println(alignment2.getSummary());
- System.err
- .println("The score of the alignment above is: "
- + alignment2.calculateScore());
- System.exit(1);
- }
-
- if (alignment1.getScore() != alignment2.getScore()) {
- System.err.println("Not symmetric alignment:");
-
- System.err.println("Alignment #1: ");
- System.err.println("Sequence 1 = " + s1);
- System.err.println("Sequence 2 = " + s2);
- System.err.println(format.format(alignment1));
- System.err.println(alignment1.getSummary());
-
- System.err.println();
-
- System.err.println("Alignment #2: ");
- System.err.println("Sequence 1 = " + s2);
- System.err.println("Sequence 2 = " + s1);
- System.err.println(format.format(alignment2));
- System.err.println(alignment2.getSummary());
-
- System.exit(1);
- }
- }
- System.out.println("Processed " + i + "/" + numberOfTests);
- i++;
- }
- } catch (Exception e) {
- e.printStackTrace();
- System.exit(1);
- }
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/test/NeedlemanWunschTester.java b/Butterfly/src/src/jaligner/test/NeedlemanWunschTester.java
deleted file mode 100644
index d2ca49a..0000000
--- a/Butterfly/src/src/jaligner/test/NeedlemanWunschTester.java
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- * $Id: NeedlemanWunschTester.java,v 1.4 2006/02/03 05:00:22 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.test;
-
-import jaligner.Alignment;
-import jaligner.NeedlemanWunsch;
-import jaligner.Sequence;
-import jaligner.formats.Format;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixLoader;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Random;
-
-/**
- * Testing the scores of the alignments of {@link jaligner.NeedlemanWunsch}.
- *
- * @author Ahmed Moustafa
- */
-
-public class NeedlemanWunschTester {
-
- public static void main(String[] args) {
-
- int numberOfTests = Integer.parseInt(args[0]);
- int sequencesSize = Integer.parseInt(args[1]);
- Random random = new Random();
- Format format = new Pair();
-
- try {
- ArrayList matrices = new ArrayList();
- for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) {
- matrices.add(i.next());
- }
- int countOfMatrices = matrices.size();
-
- int i = 1;
- while (i <= numberOfTests) {
- System.gc();
-
- String s1 = RandomSequenceGenerator.generate(sequencesSize);
- String s2 = RandomSequenceGenerator.generate(sequencesSize);
-
- float gap = random.nextInt(1000);
-
- if (s1.length() > 0 && s2.length() > 0) {
-
- Matrix matrix = (Matrix) MatrixLoader
- .load((String) matrices.get(random
- .nextInt(countOfMatrices)));
- Sequence seq1 = new Sequence(s1);
- Sequence seq2 = new Sequence(s2);
-
- Alignment alignment1 = NeedlemanWunsch.align(seq1, seq2,
- matrix, gap);
-
- if (!alignment1.checkScore()) {
- System.out.println("Invalid alignment found:");
- System.out.println("Sequence 1 = " + s1);
- System.out.println("Sequence 2 = " + s2);
- System.out.println(format.format(alignment1));
- System.out.println(alignment1.getSummary());
- System.out
- .println("The score of the alignment above is: "
- + alignment1.calculateScore());
- System.exit(1);
- }
-
- Alignment alignment2 = NeedlemanWunsch.align(seq2, seq1,
- matrix, gap);
- if (!alignment1.checkScore()) {
- System.out.println("Invalid alignment found:");
- System.out.println("Sequence 1 = " + s2);
- System.out.println("Sequence 2 = " + s1);
- System.out.println(format.format(alignment2));
- System.out.println(alignment2.getSummary());
- System.out
- .println("The score of the alignment above is: "
- + alignment2.calculateScore());
- System.exit(1);
- }
-
- if (alignment1.getScore() != alignment2.getScore()) {
- System.out.println("Not symmetric alignment:");
-
- System.out.println("Alignment #1: ");
- System.out.println("Sequence 1 = " + s1);
- System.out.println("Sequence 2 = " + s2);
- System.out.println(format.format(alignment1));
- System.out.println(alignment1.getSummary());
-
- System.out.println();
-
- System.out.println("Alignment #2: ");
- System.out.println("Sequence 1 = " + s2);
- System.out.println("Sequence 2 = " + s1);
- System.out.println(format.format(alignment2));
- System.out.println(alignment2.getSummary());
-
- System.exit(1);
- }
- }
- System.out.println("Processed " + i + "/" + numberOfTests);
- i++;
- }
- } catch (Exception e) {
- e.printStackTrace();
- System.exit(1);
- }
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/test/RandomSequenceGenerator.java b/Butterfly/src/src/jaligner/test/RandomSequenceGenerator.java
deleted file mode 100644
index fb531d8..0000000
--- a/Butterfly/src/src/jaligner/test/RandomSequenceGenerator.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * $Id: RandomSequenceGenerator.java,v 1.3 2006/02/03 05:00:22 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.test;
-
-import java.util.Random;
-
-/**
- * This class contains a random generator for protein sequences.
- *
- * @author Bram Minnaert
- */
-
-public class RandomSequenceGenerator {
-
- /**
- * All possible characters
- */
- private static final char[] CHARS = { 'A', 'R', 'N', 'D', 'C', 'Q', 'E',
- 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V' };
-
- /**
- * Number of possible characters
- */
- private static final int NUMBER_OF_CHARS = CHARS.length;
-
- /**
- * Random generator
- */
- private static Random random = new Random();
-
- /**
- * Returns random sequence
- *
- * @param length
- * Size of the sequence
- * @return Random sequence
- */
- public static String generate(int length) {
- StringBuffer buffer = new StringBuffer();
- char randomChar;
- int randomInt;
- for (int i = 0; i < length; i++) {
- randomInt = random.nextInt(NUMBER_OF_CHARS);
- randomChar = CHARS[randomInt];
- buffer.append(randomChar);
- }
- return buffer.toString();
- }
-
- /**
- * Displays 10 random protein sequences with length 50.
- *
- * @param args
- * no args
- */
- public static void main(String[] args) {
- for (int i = 0; i < 10; i++) {
- System.out.println("S" + i + " = " + generate(50));
- }
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/test/SmithWatermanGotohTester.java b/Butterfly/src/src/jaligner/test/SmithWatermanGotohTester.java
deleted file mode 100644
index 50c9995..0000000
--- a/Butterfly/src/src/jaligner/test/SmithWatermanGotohTester.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * $Id: SmithWatermanGotohTester.java,v 1.1 2006/02/03 05:00:22 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.test;
-
-import jaligner.Alignment;
-import jaligner.Sequence;
-import jaligner.SmithWatermanGotoh;
-import jaligner.formats.Format;
-import jaligner.formats.Pair;
-import jaligner.matrix.Matrix;
-import jaligner.matrix.MatrixLoader;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Random;
-
-/**
- * Testing the scores of the alignments of {@link jaligner.SmithWatermanGotoh}.
- *
- * @author Bram Minnaert
- */
-
-public class SmithWatermanGotohTester {
-
- public static void main(String[] args) {
-
- int numberOfTests = Integer.parseInt(args[0]);
- int sequencesSize = Integer.parseInt(args[1]);
- Random random = new Random();
- Format format = new Pair();
-
- try {
- ArrayList matrices = new ArrayList();
- for (Iterator i = MatrixLoader.list().iterator(); i.hasNext();) {
- matrices.add(i.next());
- }
- int countOfMatrices = matrices.size();
-
- int i = 1;
- while (i <= numberOfTests) {
-
- System.gc();
-
- String s1 = RandomSequenceGenerator.generate(sequencesSize);
- String s2 = RandomSequenceGenerator.generate(sequencesSize);
-
- int o = random.nextInt(50);
- int e = random.nextInt(10);
-
- if (s1.length() > 0 && s2.length() > 0 && o >= e) {
-
- Matrix matrix = (Matrix) MatrixLoader
- .load((String) matrices.get(random
- .nextInt(countOfMatrices)));
- Sequence seq1 = new Sequence(s1);
- Sequence seq2 = new Sequence(s2);
-
- Alignment alignment1 = SmithWatermanGotoh.align(seq1, seq2,
- matrix, o, e);
-
- if (!alignment1.checkScore()) {
- System.err.println("Invalid alignment found:");
- System.err.println("Sequence 1 = " + s1);
- System.err.println("Sequence 2 = " + s2);
- System.err.println(format.format(alignment1));
- System.err.println(alignment1.getSummary());
- System.err
- .println("The score of the alignment above is: "
- + alignment1.calculateScore());
- System.exit(1);
- }
-
- Alignment alignment2 = SmithWatermanGotoh.align(seq2, seq1,
- matrix, o, e);
- if (!alignment1.checkScore()) {
- System.err.println("Invalid alignment found:");
- System.err.println("Sequence 1 = " + s2);
- System.err.println("Sequence 2 = " + s1);
- System.err.println(format.format(alignment2));
- System.err.println(alignment2.getSummary());
- System.err
- .println("The score of the alignment above is: "
- + alignment2.calculateScore());
- System.exit(1);
- }
-
- if (alignment1.getScore() != alignment2.getScore()) {
- System.err.println("Not symmetric alignment:");
-
- System.err.println("Alignment #1: ");
- System.err.println("Sequence 1 = " + s1);
- System.err.println("Sequence 2 = " + s2);
- System.err.println(format.format(alignment1));
- System.err.println(alignment1.getSummary());
-
- System.err.println();
-
- System.err.println("Alignment #2: ");
- System.err.println("Sequence 1 = " + s2);
- System.err.println("Sequence 2 = " + s1);
- System.err.println(format.format(alignment2));
- System.err.println(alignment2.getSummary());
-
- System.exit(1);
- }
- }
- System.out.println("Processed " + i + "/" + numberOfTests);
- i++;
- }
- } catch (Exception e) {
- e.printStackTrace();
- System.exit(1);
- }
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/test/package.html b/Butterfly/src/src/jaligner/test/package.html
deleted file mode 100644
index 01d9547..0000000
--- a/Butterfly/src/src/jaligner/test/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head><!--$Id: package.html,v 1.1 2005/05/25 19:56:30 ahmed Exp $--></head>
-<body bgcolor="white">
-Testing package.
- at author Bram Minnaert
-</body>
-</html>
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/ui/filechooser/NamedInputStream.java b/Butterfly/src/src/jaligner/ui/filechooser/NamedInputStream.java
deleted file mode 100644
index c03752f..0000000
--- a/Butterfly/src/src/jaligner/ui/filechooser/NamedInputStream.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * $Id: NamedInputStream.java,v 1.1 2005/05/25 19:56:22 ahmed Exp $
- *
- * This program inputStream free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program inputStream distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.ui.filechooser;
-
-import java.io.InputStream;
-import java.io.Serializable;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class NamedInputStream extends Object implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 3256441404384686387L;
-
- /**
- * Name.
- */
- private String name = null;
-
- /**
- * Input stream.
- */
- private InputStream inputStream = null;
-
- /**
- *
- */
- public NamedInputStream(String name, InputStream inputStream) {
- this.name = name;
- this.inputStream = inputStream;
- }
-
- /**
- * @return Returns the inputStream.
- */
- public InputStream getInputStream() {
- return this.inputStream;
- }
-
- /**
- * @return Returns the name.
- */
- public String getName() {
- return this.name;
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/util/Commons.java b/Butterfly/src/src/jaligner/util/Commons.java
deleted file mode 100644
index 1132e99..0000000
--- a/Butterfly/src/src/jaligner/util/Commons.java
+++ /dev/null
@@ -1,222 +0,0 @@
-/*
- * $Id: Commons.java,v 1.3 2006/07/27 16:28:24 ahmed Exp $
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.util;
-
-import java.net.JarURLConnection;
-import java.net.URL;
-import java.util.jar.Attributes;
-import java.util.jar.JarFile;
-import java.util.jar.Manifest;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * Global constants/variables/settings
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public abstract class Commons {
- /**
- * Tab
- */
- public static final String TAB = "\t";
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(Commons.class
- .getName());
-
- /**
- * Build timestamp attribute in the manifest in the jar
- */
- private static final String BUILD_TIMESTAMP = "Created-At";
-
- /**
- *
- */
- private static final String currentRelease = "TrinityVersion"; // getManifestBuildTimestamp();
-
- /**
- * Default home directory
- */
- private static final String DEFAULT_USER_DIRECTORY = ".";
-
- /**
- * Default file separator
- */
- private static final String DEFAULT_FILE_SEPARATOR = "/";
-
- /**
- * Default line separator
- */
- private static final String DEFAULT_LINE_SEPARATOR = "\r\n";
-
- /**
- * User home directory
- */
- private static String userDirectory = DEFAULT_USER_DIRECTORY;
- static {
- try {
- userDirectory = System.getProperty("user.dir");
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting user current directory: "
- + e.getMessage(), e);
- }
- }
-
- /**
- * Line separator
- */
- private static String fileSeparator = DEFAULT_FILE_SEPARATOR;
- static {
- try {
- fileSeparator = System.getProperty("file.separator");
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting system file separator: "
- + e.getMessage(), e);
- }
- }
-
- /**
- * Line separator
- */
- private static String lineSeparator = DEFAULT_LINE_SEPARATOR;
-
- static {
- try {
- lineSeparator = System.getProperty("line.separator");
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting system line separator: "
- + e.getMessage(), e);
- }
- }
-
- /**
- * JNLP enabled
- */
- private static boolean jnlp = false;
- static {
- try {
- jnlp = "true".equalsIgnoreCase(System.getProperty("jnlp.enabled"));
- } catch (Exception e) {
- logger.log(Level.WARNING, "Failed getting jnlp enabled property: "
- + e.getMessage(), e);
- }
- setJnlp(jnlp);
- }
-
- /**
- * Returns system file separator.
- *
- * @return file separator
- */
- public static String getFileSeparator() {
- return fileSeparator;
- }
-
- /**
- * Returns system line separator.
- *
- * @return line separator
- */
- public static String getLineSeparator() {
- return lineSeparator;
- }
-
- /**
- * Returns user's current directory.
- *
- * @return user's current directory
- */
- public static String getUserDirectory() {
- return userDirectory;
- }
-
- /**
- * Sets the JNLP flag to true of false
- *
- * @param jnlp
- * true or false
- */
- public static void setJnlp(boolean jnlp) {
- Commons.jnlp = jnlp;
- }
-
- /**
- * Returns true if jnlp is enabled
- *
- * @return true if jnlp is enabled, otherwise returns false
- */
- public static boolean isJnlp() {
- return jnlp;
- }
-
- /**
- * Gets the build teimstamp from the jar manifest
- *
- * @return build timestamp
- */
- private static String getManifestBuildTimestamp() {
- JarURLConnection connection = null;
- JarFile jarFile = null;
- URL url = Commons.class.getClassLoader().getResource("jaligner");
- try {
- // Get jar connection
- connection = (JarURLConnection) url.openConnection();
-
- // Get the jar file
- jarFile = connection.getJarFile();
-
- // Get the manifest
- Manifest manifest = jarFile.getManifest();
-
- // Get the manifest entries
- Attributes attributes = manifest.getMainAttributes();
-
- Attributes.Name name = new Attributes.Name(BUILD_TIMESTAMP);
- return attributes.getValue(name);
- } catch (Exception e) {
- String message = "Failed getting the current release info: "
- + e.getMessage();
- logger.log(Level.WARNING, message);
- }
- return null;
- }
-
- /**
- * Returns the current release version of JAligner
- *
- * @return current release
- */
- public static String getCurrentRelease() {
- return currentRelease;
- }
-
- /**
- * Returns information about JAligner
- *
- * @return information about JAligner
- */
- public static String getJAlignerInfo() {
- return "JAligner - Build: " + getCurrentRelease()
- + " - By: Ahmed Moustafa (ahmed at users.sf.net)";
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/util/SequenceParser.java b/Butterfly/src/src/jaligner/util/SequenceParser.java
deleted file mode 100644
index 27ee681..0000000
--- a/Butterfly/src/src/jaligner/util/SequenceParser.java
+++ /dev/null
@@ -1,215 +0,0 @@
-/*
- * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.util;
-
-
-import jaligner.Sequence;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-/**
- * SequenceParser to sequences from different formats.
- * <br>
- * Currently the supported formats are:
- * <ul>
- * <li>Plain sequence</li>
- * <li><a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">Sequence</a></li>
- * </ul>
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class SequenceParser {
-
- /**
- * Logger
- */
- private static final Logger logger = Logger.getLogger(SequenceParser.class.getName());
-
- /**
- * Returns a parsed Sequence from a string.
- * @param sequence string to parse
- * @return parsed sequence
- * @throws SequenceParserException
- * @see Sequence
- */
- public static Sequence parse (String sequence) throws SequenceParserException {
- if (sequence == null) {
- throw new SequenceParserException ( "Null sequence" );
- }
-
- if (sequence.trim().length() == 0) {
- throw new SequenceParserException ( "Empty sequence" );
- }
-
- sequence = sequence.replaceAll("\r\n", "\n");
-
- String sequenceName = null;
- String sequenceDescription = null;
-
- if (sequence.startsWith(">")) {
- // FASTA format
- int index = sequence.indexOf("\n");
-
- if (index == -1) {
- throw new SequenceParserException ( "Invalid sequence format" );
- }
-
- String first = sequence.substring(1, index);
- sequence = sequence.substring(index);
-
- index = 0;
- for (int i = 0; i < first.length() && first.charAt(i) != ' ' && first.charAt(i) != '\t'; i++, index++) {
- // Skip white spaces
- }
- sequenceName = first.substring(0, index);
- StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|");
- while (stringTokenizer.hasMoreTokens()) {
- sequenceName = stringTokenizer.nextToken();
- }
- sequenceDescription = index + 1 > first.length() ? "" : first.substring(index + 1);
- } else {
- // Plain format ... nothing to do here
- }
-
- Sequence s = new Sequence(prepare(sequence), sequenceName, sequenceDescription, Sequence.PROTEIN);
-
- return s;
- }
-
- /**
- * Returns a Sequence parsed and loaded from a file
- * @param file to parse
- * @return parsed sequence
- * @throws SequenceParserException
- * @see Sequence
- */
- public static Sequence parse (File file) throws SequenceParserException {
- String sequenceName = null;
- String sequenceDescription = null;
- BufferedReader reader = null;
- try {
- reader = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
- StringBuffer buffer = new StringBuffer();
-
- // Read & parse the first line
- String line = reader.readLine();
-
- if (line.startsWith(">")) {
- // FASTA sequence
-
- line = line.substring(1).trim();
- int index = 0;
- for (int i = 0; i < line.length() && line.charAt(i) != ' ' && line.charAt(i) != '\t'; i++, index++) {
- // Skip white spaces
- }
-
- sequenceName = line.substring(0, index);
- StringTokenizer stringTokenizer = new StringTokenizer(sequenceName, "|");
- while (stringTokenizer.hasMoreTokens()) {
- sequenceName = stringTokenizer.nextToken();
- }
- sequenceDescription = index + 1 > line.length() ? "" : line.substring(index + 1);
- } else {
- // Plain sequence
- buffer.append(prepare(line));
- }
-
- // Read the remaining the file (the actual sequence)
- while ((line = reader.readLine()) != null) {
- buffer.append(prepare(line));
- }
- reader.close();
-
- Sequence s = new Sequence(buffer.toString(), sequenceName, sequenceDescription, Sequence.PROTEIN);
- return s;
- } catch (Exception e) {
- throw new SequenceParserException(e.getMessage());
- } finally {
- if (reader != null) {
- try {
- reader.close();
- } catch (Exception silent) {
- logger.log(Level.WARNING, "Failed closing reader: " + silent.getMessage(), silent);
- }
- }
- }
-
- }
-
- /**
- * Removes whitespaces from a sequence and validates other characters.
- * @param sequence sequence to be prepared
- * @return prepared array of characters
- * @throws SequenceParserException
- */
- private static String prepare (String sequence) throws SequenceParserException {
- StringBuffer buffer = new StringBuffer();
- String copy = sequence.trim().toUpperCase();
-
- for (int i = 0, n = copy.length(); i < n; i++) {
- switch ( copy.charAt(i) ) {
- // skip whitespaces
- case 9:
- case 10:
- case 13:
- case 32: break;
-
- // add a valid character
- case 'A':
- case 'B':
- case 'C':
- case 'D':
- case 'E':
- case 'F':
- case 'G':
- case 'H':
- case 'I':
- case 'K':
- case 'L':
- case 'M':
- case 'N':
- case 'P':
- case 'Q':
- case 'R':
- case 'S':
- case 'T':
- case 'U':
- case 'V':
- case 'W':
- case 'Y':
- case 'Z':
- case 'X':
-
- case '-':
- case '*': buffer.append(copy.charAt(i)); break;
-
- // throw an exception for anything else
- default: throw new SequenceParserException( "Invalid sequence character: '" + copy.charAt(i) + "'");
- }
- }
- return buffer.toString();
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/util/SequenceParserException.java b/Butterfly/src/src/jaligner/util/SequenceParserException.java
deleted file mode 100644
index 450169f..0000000
--- a/Butterfly/src/src/jaligner/util/SequenceParserException.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * @author Ahmed Moustafa (ahmed at users.sourceforge.net)
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- */
-
-package jaligner.util;
-
-/**
- *
- * @author Ahmed Moustafa (ahmed at users.sf.net)
- */
-
-public class SequenceParserException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 3258417248288191543L;
-
- /**
- * @param message
- */
- public SequenceParserException(String message) {
- super(message);
- }
-}
\ No newline at end of file
diff --git a/Butterfly/src/src/jaligner/util/package.html b/Butterfly/src/src/jaligner/util/package.html
deleted file mode 100644
index d89358e..0000000
--- a/Butterfly/src/src/jaligner/util/package.html
+++ /dev/null
@@ -1,8 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head><!--$Id: package.html,v 1.1 2005/05/25 19:56:30 ahmed Exp $--></head>
-<body bgcolor="white">
-Utility classes for helping core and GUI classes.
- at author Ahmed Moustafa (ahmed at users.sf.net)
-</body>
-</html>
\ No newline at end of file
diff --git a/Makefile b/Makefile
index 3ec8304..169e99d 100644
--- a/Makefile
+++ b/Makefile
@@ -50,7 +50,9 @@ clean:
test_trinity:
- cd sample_data/test_Trinity_Assembly && make test
+ cd sample_data/test_Trinity_Assembly && make test_trinity
+
+test_gg_trinity:
cd sample_data/test_GenomeGuidedTrinity && make test
test_all:
diff --git a/Release.Notes b/Release.Notes
index 92ace01..c952654 100644
--- a/Release.Notes
+++ b/Release.Notes
@@ -1,5 +1,13 @@
-## pre-release v2.0.3
+# Release v2.0.4
+
+ -Trimmomatic symlink set w/ capital T
+ -additional testing built in
+ -use parallel samtools always (not just w/ v1.1, silly!)
+
+
+
+## Release v2.0.3
-Trinity is by default less verbose. For a more verbose run, use the new --verbose flag.
diff --git a/Trinity b/Trinity
index 2d76cfe..c27d31f 100755
--- a/Trinity
+++ b/Trinity
@@ -13,11 +13,13 @@ use Cwd;
use Carp;
use COMMON;
use Getopt::Long qw(:config posix_default no_ignore_case pass_through);
-use LWP::Simple;
use Pipeliner;
use Fasta_reader;
+my $VERSION = "v2.0.4";
+
+
BEGIN {
$ENV{TRINITY_HOME} = "$FindBin::Bin";
@@ -44,8 +46,6 @@ my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
-#&version_check();
-
# Site specific setup
@@ -138,7 +138,6 @@ my $help_flag;
my $advanced_help_flag;
my $SHOW_CITATION_FLAG = 0;
-my $VERSION = "Trinity_v2.0.2";
my $show_version_flag = 0;
## Kmer methods
@@ -294,6 +293,8 @@ my $full_usage = qq^
#
# --no_cleanup :retain all intermediate input files.
#
+# --no_version_check :dont run a network check to determine if software updates are available.
+#
####################################################
# Inchworm and K-mer counting-related options: #####
#
@@ -550,6 +551,8 @@ my $SEE = 0;
my $ANANAS_DIR = "";
+my $NO_VERSION_CHECK = 0;
+
&GetOptions(
@@ -559,6 +562,8 @@ my $ANANAS_DIR = "";
'verbose' => \$SEE,
+ 'no_version_check' => \$NO_VERSION_CHECK,
+
## general opts
"seqType=s" => \$seqType,
"left=s{,}" => \@left_files,
@@ -705,7 +710,8 @@ if ($help_flag) {
}
if ($show_version_flag) {
- print "Trinity version: $VERSION\n";
+ &version_check();
+
exit(1);
}
@@ -823,6 +829,11 @@ unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_
}
}
+
+unless ($NO_VERSION_CHECK || $TRINITY_COMPLETE_FLAG) {
+ &version_check();
+}
+
# Give the variable with memory size and a user-oriented name
sub bfly_check {
@@ -916,13 +927,7 @@ elsif ($CUFFFLY_MODE) {
-my $PARALLEL_SAMTOOLS_SORT_TOKEN = "";
-{
- my $samtools_version_info = `samtools 2>&1`;
- if ($samtools_version_info =~ /Version: 1.1/) {
- $PARALLEL_SAMTOOLS_SORT_TOKEN = "-\@ $CPU";
- }
-}
+my $PARALLEL_SAMTOOLS_SORT_TOKEN = "-\@ $CPU";
unless (basename($output_directory) =~ /trinity/i) {
@@ -939,7 +944,6 @@ if ($grid_conf_file) {
main: {
$ENV{OMP_NUM_THREADS} = $CPU;
-
unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG) {
print STDERR "-since butterfly will eventually be run, lets test for proper execution of java\n" if $SEE;
@@ -1437,7 +1441,7 @@ sub run_chrysalis {
$pipeliner->add_commands( new Command($cmd, "$iworm_min100_fa_file.bowtie_build.ok"));
my $bowtie_sam_file = "$chrysalis_output_dir/iworm.bowtie.nameSorted.bam";
- $cmd = "bash -c \" set -o pipefail; bowtie -a -m 20 --best --strata --threads $CPU --chunkmbs 512 -q -S -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view -F4 -Sb - | samtools sort $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
+ $cmd = "bash -c \" set -o pipefail; bowtie -a -m 20 --best --strata --threads $CPU --chunkmbs 512 -q -S -f $iworm_min100_fa_file $bowtie_reads_fa | samtools view $PARALLEL_SAMTOOLS_SORT_TOKEN -F4 -Sb - | samtools sort $PARALLEL_SAMTOOLS_SORT_TOKEN -no - - > $bowtie_sam_file\" ";
unless ($SEE) {
$cmd .= " 2>/dev/null";
@@ -2845,15 +2849,43 @@ sub add_fifo_for_gzip {
}
sub version_check {
- my $content = get("http://rt-trinity.uits.indiana.edu/flask/version/" . $VERSION . "?timestamp=" . time);
- if (defined $content) {
- if ($content ne 'yes') {
- print "Trinity version " . $content . " is available";
- }
+
+ print "Trinity version: $VERSION\n";
+
+ my $url = "http://rt-trinity.uits.indiana.edu/flask/version/" . $VERSION . "?timestamp=" . time;
+ my $content = `curl --connect-timeout 10 -s "$url"`;
+
+ ## get release info from here:
+ ## https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases
+
+ $url = "https://api.github.com/repos/trinityrnaseq/trinityrnaseq/releases";
+ $content = `curl --connect-timeout 10 -s "$url"`;
+
+ if ($?) {
+
+ print STDERR "-ERROR: couldn't run the network check to confirm latest Trinity software version.\n\n";
}
else {
- print "Version check failed";
+
+ if ($content =~ /\"tag_name\": \"([^\"]+)\"/) {
+ my $latest_version_tag = $1;
+ if ($VERSION eq '__TRINITY_VERSION_TAG__') {
+ print STDERR "-using Trinity devel version. Note, latest production release is: $latest_version_tag\n\n";
+ }
+ elsif ($latest_version_tag ne $VERSION) {
+ print "** NOTE: Latest version of Trinity is $latest_version_tag, and can be obtained at:\n"
+ . "\thttps://github.com/trinityrnaseq/trinityrnaseq/releases\n\n";
+ }
+ else {
+ print STDERR "-currently using the latest production release of Trinity.\n\n";
+ }
+ }
+ else {
+ print STDERR "-ERROR: couldn't parse latest version tag info from github: $content\n\n";
+ }
}
+
+ return;
}
diff --git a/sample_data/test_Trinity_Assembly/Makefile b/sample_data/test_Trinity_Assembly/Makefile
index 86f59c5..5658a5e 100644
--- a/sample_data/test_Trinity_Assembly/Makefile
+++ b/sample_data/test_Trinity_Assembly/Makefile
@@ -1,8 +1,14 @@
+test_trinity:
+ ./runMe.sh
+
+
test:
./runMe.sh
- ./misc_run_tests/runMe_no_qualTrim.sh
- ./__test_runMe_with_jaccard_clip.sh
+ ./misc_run_tests/__test_runMe_include_normalization.sh
+ ./misc_run_tests/__runMe_with_qual_trimming.sh
+ ./misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
+ ./misc_run_tests/__test_runMe_with_jaccard_clip.sh
test_full:
./runMe.sh 1
diff --git a/sample_data/test_Trinity_Assembly/__test_runMe_with_jaccard_clip.sh b/sample_data/test_Trinity_Assembly/__test_runMe_with_jaccard_clip.sh
deleted file mode 100755
index 639b22d..0000000
--- a/sample_data/test_Trinity_Assembly/__test_runMe_with_jaccard_clip.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash -ve
-
-../../Trinity --seqType fq --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 --jaccard_clip --max_memory 1G --output trinity_w_jaccard
-
-
-
diff --git a/sample_data/test_Trinity_Assembly/cleanme.pl b/sample_data/test_Trinity_Assembly/cleanme.pl
index f1ade13..22d1b29 100755
--- a/sample_data/test_Trinity_Assembly/cleanme.pl
+++ b/sample_data/test_Trinity_Assembly/cleanme.pl
@@ -52,6 +52,8 @@ my %keep = map { + $_ => 1 } @files_to_keep;
`rm -rf ./trinity_test_no_qtrim` if (-d "trinity_test_no_qtrim");
`rm -rf ./trinity_w_jaccard` if (-d "trinity_w_jaccard");
+`rm -rf ./__test_trinity*`;
+
foreach my $file (<*>) {
diff --git a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
index 633427c..baf4560 100755
--- a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
+++ b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
@@ -16,7 +16,7 @@ fi
#######################################################
## use jellyfish
-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --trimmomatic
+../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --output __test_trinity_with_trimmomatic
##### Done Running Trinity #####
diff --git a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
index b57a688..32b2092 100755
--- a/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
+++ b/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
@@ -16,7 +16,7 @@ fi
#######################################################
## use jellyfish
-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads
+../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm
##### Done Running Trinity #####
diff --git a/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh b/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh
index 66df7cf..2711e77 100755
--- a/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh
+++ b/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh
@@ -16,7 +16,7 @@ fi
#######################################################
## use jellyfish
-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --normalize_reads
+../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --normalize_reads --output __test_trinity_w_normalization
##### Done Running Trinity #####
diff --git a/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh b/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh
index b2729cd..a8dedb8 100755
--- a/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh
+++ b/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh
@@ -1,6 +1,6 @@
#!/bin/bash -ve
-../../Trinity.pl --seqType fq --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 --jaccard_clip --JM 1G
+../../Trinity --seqType fq --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 --jaccard_clip --max_memory 1G --output __test_trinity_w_jaccard
diff --git a/trinity-plugins/GAL_0.2.1/README b/trinity-plugins/GAL_0.2.1/README
deleted file mode 100644
index e1eee06..0000000
--- a/trinity-plugins/GAL_0.2.1/README
+++ /dev/null
@@ -1,6 +0,0 @@
-fasta_tool comes from:
-
-http://www.sequenceontology.org/software/GAL.html
-
-The Genome Annotation Library
-
diff --git a/trinity-plugins/GAL_0.2.1/fasta_tool b/trinity-plugins/GAL_0.2.1/fasta_tool
deleted file mode 100755
index b30727c..0000000
--- a/trinity-plugins/GAL_0.2.1/fasta_tool
+++ /dev/null
@@ -1,1053 +0,0 @@
-#!/usr/bin/env perl
-
-eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-use strict;
-use warnings;
-use FindBin;
-use lib "$FindBin::Bin/../lib";
-use lib "$FindBin::Bin/../perl/lib";
-use Getopt::Long;
-use Bio::SeqIO;
-use IO::All;
-
-
-
-#-----------------------------------------------------------------------------
-#----------------------------------- MAIN ------------------------------------
-#-----------------------------------------------------------------------------
-my $usage = "
-
-Synopsis:
-
-fasta_tool [-options] fasta_file
-
-Description:
-The script takes a fasta file and can search it, reformat it, and manipulate it
-in a large variety of ways that can prove very very usful. For options that
-provide the ability to evaluate code, use Perl.
-
-Options:
- --summary
- For functions that can report data for every sequence (nt_count),
- use this flag to report only summary data for all sequences combined.
-
- --chunks <integer>
- Break up a single fasta file into the given number of chunks
-
- --split
- Split a multi-fasta into individual files. One for each fasta.
-
- --eval_code <code>
- Run the given code on (\$seq_obj, \$sequence or \$header). If the code
- block returns a positive value then the sequence is printed. This can be
- used to build complex and custom filters.
-
- --eval_all <code>
- Run the given code on (\$seq_obj, \$sequence or \$header). Prints all
- sequences regardless of the return value of the evaled code. This can
- but used to perform operations (e.g. soft to hard masking with
- s/[a-z]/N/g, but still print every sequence even if it's unaltered.
-
- --extract_ids <id_file.txt>
- Extract all of the sequences who's IDs are found in the given file.
-
- --grep_header <pattern>
- Grep through a multi fasta file and print out only the fasta
- sequences that have a match in the header. Use grepv_header for
- negation.
-
- --grep_seq <pattern>
- Grep throught a multi fasta file and print out only the fasta
- sequences that have a match in the sequence. Use grepv_seq for
- negation.
-
- --wrap <integer>
- Wrap the sequence output to a given number of columns.
-
- --translate <string>
- Translate a given nucleotide sequence to protein sequence.
- Accepts 0,1,2 (for the phase) or 'maker' if you want to use the
- frame from MAKER produced headers
-
- --trim_maker_utr
- Prints MAKER produced transcipts without the leading and trailing
- UTR sequence
-
- --seq_only
- Print only the sequence (without the header) to STDOUT. This
- can also be accomplished with grep -v '>' fasta_file.
-
- --nt_count
- Print the number and percentage of every nt/aa found in the
- sequence.
-
- --length
- Print the length of each sequence.
-
- --total_length
- Print the total length of all sequences.
-
- --n50
- Calculate the N-50 (http://en.wikipedia.org/wiki/N50_statistic)
- of the sequences in the file.
-
- --tab
- Print the header and sequence on the same line separated by a tab.
-
- --table
- Print in table format rather than fasta format.
-
- --print
- Print the sequence. Use in conjuction with 'wrap' or other formatting
- commands to reformat the sequence.
-
- --reverse
- Reverse the order of the sequences in a fasta file.
-
- --rev_seq
- Reverse the order of the nt/aa in each sequence.
-
- --comp_seq
- Complement the nucleotide sequence.
-
- --rev_comp
- Reverse compliment a sequence. Same as --rev_seq && --comp_seq together.
-
- --uniq
-
- Print only uniq sequences. This method only compares complete
- sequences.
-
- --uniq_sub
-
- Print only uniq sequences, but also check that shorter sequences
- are not perfect substrings of longer sequences.
-
- --shuffle_order
- Randomize the order of sequences in a multi-fasta file.
-
- --shuffle_seq
- Randomize the order of the nt/aa in each sequence.
-
- --shuffle_codon
- Randomize the order of the codons in a nucleotide sequence.
-
- --shuffle_pick
- Pick a given number of sequences from a multi-fasta file.
-
- --select
- Pass in a file with IDs and return sequences with these IDs.
-
- --remove
- Pass in a file with IDs and remove sequences with these IDs.
-
- --swap_ids
- Pass in a file with two columns of IDs and map the IDs in the
- fasta headers from the first column of the ID file to the second
- column of the ID file. If an ID in the fasta header is not found
- in the first column of the ID file then issue a warning, but leave
- the ID unmapped.
-
- --fix_prot
- Fix protein fasta files for use as blast database. Removes spaces
- and '*' and replaces any non amino acid codes with C.
-
- --subseq
- Grab a sub-sequence from a fasta file based on coordinates. The
- requested coordinates are in the form seqid:start-end;
-
-
-";
-
-my ($summary, $chunks, $split, $eval_code, $eval_all, $extract_ids,
- $grep_header, $grepv_header, $grep_seq, $grepv_seq, $wrap, $count,
- $translate, $seq_only, $nt_count, $length, $total_length, $n50,
- $tab, $reverse, $rev_seq, $comp_seq, $rev_comp, $uniq, $uniq_sub,
- $shuffle_order, $shuffle_seq, $shuffle_codon, $shuffle_pick,
- $select_file, $remove_file, $print, $mRNAseq, $EST,
- $trim_maker_utr, $table, $swap_ids, $fix_prot, $subseq, $tile);
-
-GetOptions('summary' => \$summary,
- 'chunks=i' => \$chunks,
- 'split' => \$split,
- 'eval_code=s' => \$eval_code,
- 'eval_all=s' => \$eval_all,
- 'extract_ids=s' => \$extract_ids,
- 'grep_header=s' => \$grep_header,
- 'grep_seq=s' => \$grep_seq,
- 'grepv_header=s' => \$grepv_header,
- 'grepv_seq=s' => \$grepv_seq,
- 'wrap=i' => \$wrap,
- 'count' => \$count,
- 'translate=s' => \$translate,
- 'trim_maker_utr' => \$trim_maker_utr,
- 'seq_only' => \$seq_only,
- 'nt_count' => \$nt_count,
- 'length' => \$length,
- 'total_length' => \$total_length,
- 'n50' => \$n50,
- 'tab' => \$tab,
- 'table' => \$table,
- 'print' => \$print,
- 'reverse' => \$reverse,
- 'rev_seq' => \$rev_seq,
- 'comp_seq' => \$comp_seq,
- 'rev_comp' => \$rev_comp,
- 'uniq' => \$uniq,
- 'uniq_sub' => \$uniq_sub,
- 'shuffle_order' => \$shuffle_order,
- 'shuffle_seq' => \$shuffle_seq,
- 'shuffle_codon' => \$shuffle_codon,
- 'shuffle_pick=i' => \$shuffle_pick,
- 'remove=s' => \$remove_file,
- 'select=s' => \$select_file,
- 'fix_prot' => \$fix_prot,
- 'mRNAseq' => \$mRNAseq,
- 'EST' => \$EST,
- 'swap_ids=s' => \$swap_ids,
- 'subseq=s' => \$subseq,
- 'tile=s' => \$tile,
- );
-
-my $file = shift;
-unless (($file && -r $file) || ! -t STDIN){
- print $usage;
- exit;
-}
-
-if ($rev_comp) {$rev_seq++; $comp_seq++}
-
-my $warning = "\n\n" . ('#' x 40) . "\nThis function is not yet thouroughly tested!!\n" . ('#' x 40) . "\n\n";
-
-warn $warning if grep {$_} ($extract_ids,
- $reverse,
- $rev_seq,
- $comp_seq,
- $shuffle_order,
- $shuffle_seq,
- $shuffle_codon,
- $shuffle_pick,
- );
-
-# These functions handle their own printing;
-$print++ unless grep {$_} ($chunks,
- $split,
- $eval_code,
- $eval_all,
- $extract_ids,
- $grep_header,
- $grep_seq,
- $grepv_header,
- $grepv_seq,
- $count,
- $translate,
- $seq_only,
- $nt_count,
- $length,
- $total_length,
- $n50,
- $reverse,
- $rev_seq,
- $comp_seq,
- $uniq,
- $uniq_sub,
- $shuffle_order,
- $shuffle_seq,
- $shuffle_codon,
- $shuffle_pick,
- $remove_file,
- $select_file,
- $mRNAseq,
- $EST,
- $swap_ids,
- $subseq,
- $tile,
- );
-
-$nt_count++ if $summary;
-
-if(defined $translate && $translate !~ /^\d+$/ && $translate ne 'maker'){
- $translate = 0;
-}
-
-my $IN;
-if (! $file && ! -t STDIN) {
- open ($IN, "<&=STDIN") or die "Can't open STDIN\n";
-}
-else {
- open ($IN, $file) or die "Can't open $file for reading: $!\n";
-}
-
-#Bioperl object for main fasta input file.
-my $seq_io = Bio::SeqIO->new(-fh => $IN,
- -format => 'Fasta');
-
-chunks($file, $chunks) if $chunks;
-split_fasta() if $split;
-eval_code($eval_code) if $eval_code;
-eval_all($eval_all) if $eval_all;
-extract_ids($extract_ids) if $extract_ids;
-grep_header($grep_header) if $grep_header;
-grep_seq($grep_seq) if $grep_seq;
-grepv_header($grepv_header) if $grepv_header;
-grepv_seq($grepv_seq) if $grepv_seq;
-translate() if defined($translate);
-trim_maker_utr() if $trim_maker_utr;
-seq_only() if $seq_only;
-nt_count() if $nt_count;
-seq_length() if $length;
-total_length() if $total_length;
-n50() if $n50;
-tab() if $tab;
-reverse_order() if $reverse;
-rev_comp() if $rev_seq;
-rev_comp() if $comp_seq;
-uniq() if $uniq;
-uniq_sub() if $uniq_sub;
-shuffle_order() if $shuffle_order;
-shuffle_seq() if $shuffle_seq;
-shuffle_codon() if $shuffle_codon;
-shuffle_pick($shuffle_pick) if $shuffle_pick;
-remove_ids($remove_file) if $remove_file;
-select_ids($select_file) if $select_file;
-swap_ids($swap_ids) if $swap_ids;
-subseq($file, $subseq) if $subseq;
-fix_prot() if $fix_prot;
-print_seq() if $print;
-mRNAseq() if $mRNAseq;
-EST() if $EST;
-
-#-----------------------------------------------------------------------------
-#-------------------------------- SUBROUTINES --------------------------------
-#-----------------------------------------------------------------------------
-sub chunks {
- my($file, $chunks) = @_;
-
- my $outfile_base; #Create a base name for the output file.
- ($outfile_base = $file) =~ s/\.[^\.]*$//; #Input file name minus it's extension.
-
- my $file_size = io($file)->size; #What's the size of our input file.
-
- #How many chunks should the input file be split into?
- my $chunk_size = int($file_size/$chunks) + ($file_size % $chunks);
-
- #How many digits should the output file interations be sprintf'ed to=?
- my $digits = int(log($chunks)/log(10)) + 1;
-
- #I felt like using a closure today.
- my $file_counter = make_file_counter();
-
- my $out;
- my $file_name;
- #Loop over each sequence
- while ( my $seq = $seq_io->next_seq() ) {
- #Get an Bio::SeqIO fh if we don't have one, or if the current output file
- #has grown too large.
- if (! $out || (io($file_name)->size > $chunk_size)) {
- ($out, $file_name) = get_output_stream($outfile_base, $digits, $file_counter);
- }
- #Write it to the file.
- $out->write_seq($seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub get_output_stream{
- my ($outfile_base, $digits, $file_counter) = @_;
- my $file_count = $file_counter->();
- #Build/format the file_name.
- $file_count = sprintf "%0${digits}s", $file_count;
- my $file_name = $outfile_base . "_$file_count" . '.fasta';
- #Get Bio::SeqIO object
- my $out = Bio::SeqIO->new(-file => ">$file_name",
- -format => 'fasta');
- return ($out, $file_name);
-}
-#-----------------------------------------------------------------------------
-sub make_file_counter {
- #Initialize the counter.
- my $file_counter = 0;
-
- #Increment the counter.
- return sub{$file_counter++}
-}
-#-----------------------------------------------------------------------------
-sub split_fasta {
- while ( my $seq = $seq_io->next_seq() ) {
- my $file_out = $seq->display_id . ".fasta";
-
- #Get Bio::SeqIO object
- my $out = Bio::SeqIO->new(-file => ">$file_out",
- -format => 'fasta');
- #Write it to the file.
- $out->write_seq($seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub eval_code {
- my ($code) = @_;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
-
- my $return_value = eval $code;
- die "Fatal Error in code ref:\n$@\n" if $@;
- next unless $return_value;
- print_this_seq($header, $seq);
- }
-
-}
-#-----------------------------------------------------------------------------s
-sub eval_all {
- my ($code) = @_;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
-
- eval $code;
- die "Fatal Error in code ref:\n$@\n" if $@;
- print_this_seq($header, $seq);
- }
-
-}
-#-----------------------------------------------------------------------------
-sub extract_ids {
-
- my $id_file = shift;
-
- open(my $IN, '<', $id_file) or die "Can't open $id_file for reading\n$!\n";
-
- my %ids = map {$_ => 1 unless (/^\#/ || ! $_)} (<$IN>);
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $id = $seq_obj->display_id;
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
-
- if (exists $ids{$id}) {
- print_this_seq($header, $seq);
- }
- }
-}
-#-----------------------------------------------------------------------------
-sub grep_header {
- my ($pattern) = @_;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- $header .= " " . $seq_obj->description;
- my $seq = $seq_obj->seq;
-
- if ($header =~ /$pattern/) {
- print_this_seq($header, $seq);
- }
- }
-}
-#-----------------------------------------------------------------------------
-sub grepv_header {
- my ($pattern) = @_;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
-
- if ($header !~ /$pattern/) {
- print_this_seq($header, $seq);
- }
- }
-}
-#-----------------------------------------------------------------------------
-{my $i = 0;
-sub mRNAseq {
- my $size = 50;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $seq = $seq_obj->seq;
-
- my $len = length($seq);
-
- for (my $j = 0; $j < $len/5; $j++){
- my $range = $len - $size;
-
- my $start; my $end;
- if($range < 0){
- $start = 0 ;
- $end = $len - 1;
- }
- else{
- $start = int(rand($range));
- $end = $start + $size - 1;
- }
-
- my $l = $end - $start + 1;
-
- my $header = "sequence_".$i++;
- print_this_seq($header, substr($seq, $start, $l));
- }
- }
-}
-#-----------------------------------------------------------------------------
-sub EST {
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $seq = $seq_obj->seq;
-
- my $len = length($seq);
-
-
- my $range = $len - 500;
- my $min = 250;
-
- if($range < 0 || $min < 0){
- my $header = "sequence_".$i++;
- print_this_seq($header, $seq);
- next;
- }
-
- my $A = int(rand($range) + $min);
- my $start = int(rand($range) + $min);
- my $end = int(rand($range));
- my $B = int(rand($range) + $min);
-
- my $l = abs($end - $start + 1);
- if($l > 250){
- my $header = "sequence_".$i++;
- print_this_seq($header, substr($seq, $start, $l));
- }
-
- $l = abs($A - 0 + 1);
- if($l > 250){
- my $header = "sequence_".$i++;
- print_this_seq($header, substr($seq, 0, $l));
- }
-
- $l = abs($len - $B + 1);
- if($l > 250){
- my $header = "sequence_".$i++;
- print_this_seq($header, substr($seq, $B, $l));
- }
-
- }
-}
-}
-#-----------------------------------------------------------------------------
-sub grep_seq {
- my ($pattern) = @_;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- $seq =~ s/\s//g;
-
- if ($seq =~ /$pattern/) {
- print_this_seq($header, $seq);
- }
- }
-}
-#-----------------------------------------------------------------------------
-sub grepv_seq {
- my ($pattern) = @_;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- $seq =~ s/\s//g;
-
- if ($seq !~ /$pattern/) {
- print_this_seq($header, $seq);
- }
- }
-}
-#-----------------------------------------------------------------------------
-sub fix_prot {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- $seq =~ s/[\s\*]//g;
- $seq =~ s/[^abcdefghiklmnpqrstvwyzxABCDEFGHIKLMNPQRSTVWYZX\-\n]/C/g;
- next if($seq eq ''); #skip empty fasta entries
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub translate {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $frame;
- my $offset;
- if($translate eq 'maker'){
- $header =~ /offset:(\d+)/;
- $frame = ($1 % 3);
- $offset = ($1 - $frame)/3;
- }
- else{
- $frame = $translate % 3;
- $offset = ($translate - $frame)/3;
- }
- my $pep_seq = $seq_obj->translate(-frame => $frame)->seq;
- $pep_seq = substr($pep_seq, $offset);
- $pep_seq =~ s/^([^\*]+).*/$1/;
- print_this_seq($header, $pep_seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub trim_maker_utr {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $frame;
- my $offset;
-
- $header =~ /offset:(\d+)/;
-
- die "ERROR: These do not appear to be MAKER produced transcripts\n"
- if(! defined $1 || $1 eq '');
- $frame = ($1 % 3);
- $offset = ($1 - $frame)/3; #peptide offet without frame
-
- my $tra_seq = $seq_obj->seq;
- my $pep_seq = $seq_obj->translate(-frame => $frame)->seq;
-
- $pep_seq = substr($pep_seq, $offset);
- $pep_seq =~ s/^([^\*]+\*?).*/$1/;
- $offset = 3 * $offset + $frame; #make transcript offset
- my $length = 3 * length($pep_seq); #length of substring to get
- my $fix = $offset + $length - length($tra_seq);
- $length -= $fix if($fix > 0);
- $tra_seq = substr($tra_seq, $offset, $length);
-
- print_this_seq($header, $tra_seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub seq_only {
- while (my $seq_obj = $seq_io->next_seq) {
- my $seq = $seq_obj->seq;
- $seq = wrap_seq($seq, $wrap) if $wrap;
- print $seq . "\n";
- }
-}
-#-----------------------------------------------------------------------------
-sub nt_count {
- my %all_seq_count;
- my $total_count;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my %this_seq_count;
- my $this_count;
- my $id = $seq_obj->display_id;
- my $seq = $seq_obj->seq;
- $seq =~ s/\s//g;
- my @nts = split //, $seq;
- for my $nt (@nts) {
- $all_seq_count{$nt}++;
- $this_seq_count{$nt}++;
- $this_count++;
- $total_count++;
- }
-
- next if $summary;
- print "$id:\n";
- print '-' x 80;
- print "\n";
- for my $nt (sort keys %this_seq_count) {
- my $round = sprintf ("%.4f", $this_seq_count{$nt} / $this_count * 100);
- print join "\t", ($nt,
- $this_seq_count{$nt},
- $round,
- );
- print '%' . "\n";
- }
-
- my %this_report;
- map {$this_report{aA} += $this_seq_count{$_} if $this_seq_count{$_}} qw(a A);
- map {$this_report{tT} += $this_seq_count{$_} if $this_seq_count{$_}} qw(t T);
- map {$this_report{gG} += $this_seq_count{$_} if $this_seq_count{$_}} qw(g G);
- map {$this_report{cC} += $this_seq_count{$_} if $this_seq_count{$_}} qw(c C);
-
- map {$this_report{aAtT} += $this_report{$_} if $this_report{$_}} qw(aA tT);
- map {$this_report{gGcC} += $this_report{$_} if $this_report{$_}} qw(gG cC);
- map {$this_report{aAtTgGcC} += $this_report{$_} if $this_report{$_}} qw(aAtT gGcC);
-
- map {$this_report{atgc} += $this_seq_count{$_} if $this_seq_count{$_}} qw(a t g c);
- map {$this_report{nN} += $this_seq_count{$_} if $this_seq_count{$_}} qw(n N);
- map {$this_report{atgcnN} += $this_seq_count{$_} if $this_seq_count{$_}} qw(atgc nN);
-
- for my $key (sort keys %this_report) {
-
- print join "\t", ($key,
- $this_report{$key},
- sprintf ("%.4f", $this_report{$key} / $this_count * 100),
- );
- print '%' . "\n";
- }
- print "\n\n";
- }
-
- print "All sequences combined:\n";
- print '-' x 80;
- print "\n";
-
- for my $nt (sort keys %all_seq_count) {
- print join "\t", ($nt,
- $all_seq_count{$nt},
- sprintf ("%.4f", $all_seq_count{$nt} / $total_count * 100),
- );
- print '%' . "\n";
- }
-
- my %all_report;
- map {$all_report{aA} += $all_seq_count{$_} if $all_seq_count{$_}} qw(a A);
- map {$all_report{tT} += $all_seq_count{$_} if $all_seq_count{$_}} qw(t T);
- map {$all_report{gG} += $all_seq_count{$_} if $all_seq_count{$_}} qw(g G);
- map {$all_report{cC} += $all_seq_count{$_} if $all_seq_count{$_}} qw(c C);
-
- map {$all_report{aAtT} += $all_report{$_} if $all_report{$_}} qw(aA tT);
- map {$all_report{gGcC} += $all_report{$_} if $all_report{$_}} qw(gG cC);
- map {$all_report{aAtTgGcC} += $all_report{$_} if $all_report{$_}} qw(aAtT gGcC);
-
- map {$all_report{atgc} += $all_seq_count{$_} if $all_seq_count{$_}} qw(a t g c);
- map {$all_report{nN} += $all_seq_count{$_} if $all_seq_count{$_}} qw(n N);
- map {$all_report{atgcnN} += $all_seq_count{$_} if $all_seq_count{$_}} qw(atgc nN);
-
- for my $key (sort keys %all_report) {
-
- print join "\t", ($key,
- $all_report{$key},
- sprintf ("%.4f", $all_report{$key} / $total_count * 100),
- );
- print '%' . "\n";
- }
- print "\n";
- print "Total nts\t$total_count\n";
-}
-#-----------------------------------------------------------------------------
-sub seq_length {
- my $count = 0;
- my $total;
- while (my $seq_obj = $seq_io->next_seq) {
- my $id = $seq_obj->display_id;
- my $length = $seq_obj->length;
- $total += $length;
- $count++;
- print "$id\t$length\n";
- }
- print "Total\t$total\n" if $count > 1;
-}
-#-----------------------------------------------------------------------------
-sub total_length {
- my $total_length;
- while (my $seq_obj = $seq_io->next_seq) {
- $total_length += $seq_obj->length;
- }
- print $total_length . "\n";
-}
-#-----------------------------------------------------------------------------
-sub n50 {
- my $total_length;
- my @lengths;
- while (my $seq_obj = $seq_io->next_seq) {
- my $length = $seq_obj->length;
- $total_length += $length;
- push @lengths, $length;
- }
- my $cumulative_length;
- my $last_length;
- my $n50;
- for my $length (sort {$b <=> $a} @lengths) {
- $cumulative_length += $length;
- if ($cumulative_length > $total_length / 2) {
- $n50 = $length;
- last;
- }
- elsif ($cumulative_length == $total_length / 2) {
- $n50 = $length;
- $last_length = $length;
- last;
- }
- $last_length = $length;
- }
- $n50 = int((($n50 + $last_length) / 2) + 0.5);
- print $n50 . "\n";
-}
-#-----------------------------------------------------------------------------
-sub tab {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- $seq =~ s/[\s\n\t]//g;
- print "$header\t$seq\n";
- }
-}
-#-----------------------------------------------------------------------------
-sub print_seq {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- print_this_seq($header, $seq);
-
- }
-}
-#-----------------------------------------------------------------------------
-sub reverse_order {
- my @seqs;
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- push @seqs, {seq => $seq,
- header => $header,
- };
- }
-
- @seqs = reverse @seqs;
-
- for my $seq (@seqs) {
- print_this_seq($seq->{header}, $seq->{seq});
- }
-}
-#-----------------------------------------------------------------------------
-sub rev_comp{
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- $seq = reverse $seq if $rev_seq;
- if ($comp_seq) {
- $seq =~ tr/acgtrymkswhdbvACGTRYMKSWHDBV
- /tgcayrkmswdhvbTGCAYRKMSWDHVB/;
- }
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub uniq{
- my %seen;
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- print_this_seq($header, $seq) unless exists $seen{$seq};
- $seen{$seq}++;
- }
-}
-#-----------------------------------------------------------------------------
-sub uniq_sub {
- my @seqs;
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- push @seqs, [$header, $seq];
- }
-
- @seqs = sort {length $a->[1] <=> length $b->[1]} @seqs;
-
- OUTER:
- for my $outer_idx (0 .. $#seqs) {
- my $start_idx = $outer_idx + 1;
- for my $inner_idx ($start_idx .. $#seqs) {
- if ($seqs[$inner_idx][1] =~ /$seqs[$outer_idx][1]/) {
- print STDERR "WARN : skipping_sequence : ($seqs[$outer_idx][0]) " .
- "$seqs[$outer_idx][1]\n";
- next OUTER;
- }
- }
- print_this_seq($seqs[$outer_idx][0], $seqs[$outer_idx][1]);
- }
-}
-#-----------------------------------------------------------------------------
-sub shuffle_order {
- my @seqs;
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- push @seqs, {seq => $seq,
- header => $header,
- };
- }
-
- shuffle(\@seqs);
-
- for my $seq (@seqs) {
- print_this_seq($seq->{header}, $seq->{seq});
- }
-}
-#-----------------------------------------------------------------------------
-sub shuffle_seq {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my @seq = split //, $seq_obj->seq;
- shuffle(\@seq);
- my $seq = join '', @seq;
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub shuffle_codon {
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- my @codons = $seq =~ /(.{3})/g;
- shuffle(\@codons);
- $seq = join '', @codons;
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub shuffle_pick {
- my $shuffle_pick = shift;
-
- my @seqs;
- while (my $seq_obj = $seq_io->next_seq) {
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- push @seqs, {seq => $seq,
- header => $header,
- };
- }
-
- my @picks;
- for (1 .. $shuffle_pick) {
- push @picks, splice @seqs, int(rand(scalar @seqs)), 1;
- }
-
- for my $pick (@picks) {
- print_this_seq($pick->{header}, $pick->{seq});
- }
-}
-#-----------------------------------------------------------------------------
-sub remove_ids {
-
- my $remove_file = shift;
- open (my $IN, '<', $remove_file) or die "Can't open $remove_file for reading\n";
- my %ids = map {chomp;$_, 1} (<$IN>);
- while (my $seq_obj = $seq_io->next_seq) {
- my $id = $seq_obj->display_id;
- next if $ids{$id};
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub select_ids {
-
- my $select_file = shift;
- open (my $IN, '<', $select_file) or die "Can't open $select_file for reading\n";
- my %ids = map {chomp;$_, 1} (<$IN>);
- while (my $seq_obj = $seq_io->next_seq) {
- my $id = $seq_obj->display_id;
- next unless $ids{$id};
- my $header = get_header($seq_obj);
- my $seq = $seq_obj->seq;
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub print_this_seq {
- my ($header, $seq) = @_;
-
- if($table){
- chomp $seq;
- ($header) = $header =~ /^([^\s+]+)/;
- print join("\t", $header, uc($seq))."\n";
- }
- else{
- $seq = wrap_seq($seq, $wrap) if $wrap;
- chomp $seq;
- my $join = $tab ? "\t" : "\n";
- print join $join, (">$header", "$seq\n");
- }
-}
-#-----------------------------------------------------------------------------
-sub wrap_seq {
- my ($seq, $wrap) = @_;
-
- if ($wrap > 0) {
- $seq =~ s/\s//g;
- $seq =~ s/(.{$wrap})/$1\n/g;
- }
- chomp $seq;
- return $seq;
-}
-#-----------------------------------------------------------------------------
-sub get_header {
- my $seq_obj = shift;
- return $seq_obj->display_id . " " . $seq_obj->description;
-
-}
-#-----------------------------------------------------------------------------
-sub shuffle {
- #Fisher-Yates Shuffle
- my $array = shift;
-
- my $n = scalar @{$array};
- while ($n > 1) {
- my $k = int rand($n--);
- ($array->[$n], $array->[$k]) = ($array->[$k], $array->[$n]);
- }
-}
-#-----------------------------------------------------------------------------
-sub swap_ids {
-
- my $id_file = shift;
- open (my $IN, '<', $id_file) or die "Can't open $id_file for reading\n";
- my %ids;
- while (<$IN>) {
- chomp;
- my($id1, $id2) = split /\t/, $_;
- # $id1 =~ s/\.\d+$//;
- $ids{$id1} = $id2;
- }
- while (my $seq_obj = $seq_io->next_seq) {
- my $id = $seq_obj->display_id;
- # gi|71999842|ref|NM_073020.2|
- # my ($x, $y, $z, $id) = split /\|/, $id_text;
- # $id =~ s/\.\d+//;
- my $header = get_header($seq_obj);
- if (exists $ids{$id}) {
- $header = $ids{$id};
- }
- my $seq = $seq_obj->seq;
- print_this_seq($header, $seq);
- }
-}
-#-----------------------------------------------------------------------------
-sub subseq {
-
- my ($file, $coordinates) = @_;
-
- require Bio::DB::Fasta;
- my $fasta = Bio::DB::Fasta->new($file);
-
- my ($seqid, $start, $end) = split /[:-]/, $coordinates;
-
- print $fasta->seq($seqid, $start, $end);
- print "\n";
-}
-#-----------------------------------------------------------------------------
-
-sub tile_seq {
-
- my $tile = shift;
-
- my ($tile_length, $step) = split /,/, $tile;
- $tile_length ||= 50;
- $step ||= 1;
-
- while (my $seq_obj = $seq_io->next_seq) {
- my $id = $seq_obj->display_id;
- my $seq = $seq_obj->seq;
- my $seq_length = length($seq);
- my $start;
- for ($start = 1;$start <= ($seq_length - $tile_length); $start += $step) {
- my $header = "$id:$start-" . ($start + $tile_length - 1);
- my $subseq = substr($seq, $start, $tile_length);
- print ">$header\n$subseq\n";
- }
- }
-}
-
-#-----------------------------------------------------------------------------
diff --git a/trinity-plugins/Makefile b/trinity-plugins/Makefile
index 040defe..9988036 100644
--- a/trinity-plugins/Makefile
+++ b/trinity-plugins/Makefile
@@ -24,7 +24,7 @@ TRIMMOMATIC_CODE=Trimmomatic-0.32
trinity_essentials: jellyfish fastool_target parafly_target trimmomatic_target
trimmomatic_target:
- ln -sf ${TRIMMOMATIC_CODE} trimmomatic
+ ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
jellyfish:
@@ -74,7 +74,7 @@ clean:
rm -f ./fastool # rm symlink
cd parafly && $(MAKE) clean
rm -f ./parafly # rm symlink
- rm -f ./trimmomatic # rm symlink
+ rm -f ./Trimmomatic # rm symlink
cd slclust && $(MAKE) clean
cd collectl && rm -rf bin doc man
@echo "\n\n** Done cleaning plugins area **"
diff --git a/trinity-plugins/TransDecoder_r20140704.tar.gz b/trinity-plugins/TransDecoder_r20140704.tar.gz
deleted file mode 100644
index ec5e294..0000000
Binary files a/trinity-plugins/TransDecoder_r20140704.tar.gz and /dev/null differ
diff --git a/trinity-plugins/Trimmomatic-0.32/LICENSE b/trinity-plugins/Trimmomatic-0.32/LICENSE
deleted file mode 100644
index 94a9ed0..0000000
--- a/trinity-plugins/Trimmomatic-0.32/LICENSE
+++ /dev/null
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
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- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- <program> Copyright (C) <year> <name of author>
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/trinity-plugins/Trimmomatic-0.32/adapters/NexteraPE-PE.fa b/trinity-plugins/Trimmomatic-0.32/adapters/NexteraPE-PE.fa
deleted file mode 100644
index a986757..0000000
--- a/trinity-plugins/Trimmomatic-0.32/adapters/NexteraPE-PE.fa
+++ /dev/null
@@ -1,12 +0,0 @@
->PrefixNX/1
-AGATGTGTATAAGAGACAG
->PrefixNX/2
-AGATGTGTATAAGAGACAG
->Trans1
-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
->Trans1_rc
-CTGTCTCTTATACACATCTGACGCTGCCGACGA
->Trans2
-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
->Trans2_rc
-CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
\ No newline at end of file
diff --git a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq2-PE.fa b/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq2-PE.fa
deleted file mode 100644
index cef17cc..0000000
--- a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq2-PE.fa
+++ /dev/null
@@ -1,16 +0,0 @@
->PrefixPE/1
-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
->PrefixPE/2
-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
->PCR_Primer1
-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
->PCR_Primer1_rc
-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
->PCR_Primer2
-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
->PCR_Primer2_rc
-AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG
->FlowCell1
-TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC
->FlowCell2
-TTTTTTTTTTCAAGCAGAAGACGGCATACGA
diff --git a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq2-SE.fa b/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq2-SE.fa
deleted file mode 100644
index 30eaeae..0000000
--- a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq2-SE.fa
+++ /dev/null
@@ -1,6 +0,0 @@
->TruSeq2_SE
-AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
->TruSeq2_PE_f
-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
->TruSeq2_PE_r
-AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
diff --git a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa b/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa
deleted file mode 100644
index b205511..0000000
--- a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa
+++ /dev/null
@@ -1,12 +0,0 @@
->PrefixPE/1
-TACACTCTTTCCCTACACGACGCTCTTCCGATCT
->PrefixPE/2
-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
->PE1
-TACACTCTTTCCCTACACGACGCTCTTCCGATCT
->PE1_rc
-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
->PE2
-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
->PE2_rc
-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
\ No newline at end of file
diff --git a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-PE.fa b/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-PE.fa
deleted file mode 100644
index e370ca1..0000000
--- a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-PE.fa
+++ /dev/null
@@ -1,4 +0,0 @@
->PrefixPE/1
-TACACTCTTTCCCTACACGACGCTCTTCCGATCT
->PrefixPE/2
-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
\ No newline at end of file
diff --git a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-SE.fa b/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-SE.fa
deleted file mode 100644
index 3fbad17..0000000
--- a/trinity-plugins/Trimmomatic-0.32/adapters/TruSeq3-SE.fa
+++ /dev/null
@@ -1,4 +0,0 @@
->TruSeq3_IndexedAdapter
-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
->TruSeq3_UniversalAdapter
-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
diff --git a/trinity-plugins/Trimmomatic-0.32/trimmomatic-0.32.jar b/trinity-plugins/Trimmomatic-0.32/trimmomatic-0.32.jar
deleted file mode 100644
index c32e6c1..0000000
Binary files a/trinity-plugins/Trimmomatic-0.32/trimmomatic-0.32.jar and /dev/null differ
diff --git a/trinity-plugins/Trimmomatic-0.32/trimmomatic.jar b/trinity-plugins/Trimmomatic-0.32/trimmomatic.jar
deleted file mode 120000
index 7df34ff..0000000
--- a/trinity-plugins/Trimmomatic-0.32/trimmomatic.jar
+++ /dev/null
@@ -1 +0,0 @@
-trimmomatic-0.32.jar
\ No newline at end of file
diff --git a/trinity-plugins/collectl/Tests.py b/trinity-plugins/collectl/Tests.py
deleted file mode 100755
index 7297760..0000000
--- a/trinity-plugins/collectl/Tests.py
+++ /dev/null
@@ -1,117 +0,0 @@
-__author__ = 'befulton'
-
-import unittest
-import make_data_files
-
-def generate(lines):
- for line in lines:
- yield line
-
-class CollectlTests(unittest.TestCase):
-
- def test_build_datasets_returns_last_line_time_as_end_time(self):
- lines = ["20140919 13:10:49\n",
- "20140919 11:10:49\n",
- "20140919 11:27:49\n"]
- _, _, _, _, end_time = make_data_files.build_datasets(generate(lines))
- self.assertEquals(['20140919', '11:27:49'], end_time)
-
- def test_build_datasets_adds_inchworm_to_line_dict(self):
- lines = ["20140919 11:08:49 44009 user 20 44008 0 R 10975748 0 10837764 10957692 92 128 3416 9 0.00 4.99 99 "
- "01:33:35 0 0 0 0 0 0 0 0 1 /N/test/Inchworm/bin/inchworm --kmers jellyfish.kmers.fa --run_inchworm "
- "-K 25 -L 25 --monitor 1"]
- _, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
- self.assertEquals(lines, line_dict['inchworm'])
-
- def test_build_datasets_adds_bowtie_build_to_line_dict_if_no_path(self):
- lines = ["20140919 11:11:24 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 "
- "02:27.86 0 960 0 960 0 124 0 0 0 bowtie-build /N/test/trinity_out/jaccard_clip_workdir/iworm.fa "
- "/N/trinity_out/jaccard_clip_workdir/iworm.fa",
- "20140919 11:11:29 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 02:27.86"
- " 0 960 0 960 0 124 0 0 0 bowtie-build /N/trinity_out/jaccard_clip_workdir/iworm.fa "
- "/N/trinity_out/jaccard_clip_workdir/iworm.fa",
- "20140919 11:11:34 44143 user 20 44131 0 R 547552 0 502040 535608 164 260 3244 9 0.01 4.98 99 02:27.86"
- " 0 960 0 960 0 124 0 0 0 some_app /N/trinity_out/bowtie-build/jaccard_clip_workdir/iworm.fa "
- "/N/trinity_out/jaccard_clip_workdir/iworm.fa"]
- _, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
- self.assertEquals(lines[0:2], line_dict['bowtie-build'])
-
- def test_Chrysalis_is_identified_correctly(self):
- lines = ["20140920 11:29:54 49383 befulton 20 43684 0 S 18468 0 1464 300 92 236 3416 8 0.00 0.00 0 00:02.44 "
- "0 0 0 0 0 0 0 0 0 /trinity/Chrysalis/Chrysalis "
- "-i both.fa -iworm /jobdir/trinity_out/inchworm.K25.L25.fa.clipped.fa -o "
- "/jobdir/trinity_out/chrysalis -cpu 16 -min_glue 2 "
- "-min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 "
- "-sort_buffer_size 20G -max_mem_reads 1000000 -strand 1 -paired -reads_for_pairs both.fa "
- "-butterfly /trinity/Butterfly/Butterfly.jar"]
- _, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
- self.assertEquals(lines, line_dict['Chrysalis'])
-
- def test_Butterfly_is_identified_correctly(self):
- lines = ["20140920 17:28:14 30084 befulton 20 62435 0 S 24215176 0 37768 24080384 92 4 14420 30 0.03 0.17 "
- "4 00:00.20 0 6 519 0 203 1 0 0 1056 java -Xmx20G -Xms1G -jar /trinity/Butterfly/Butterfly.jar "
- "-N 100000 -L 200 -F 500 -C /jobdir/trinity_out/chrysalis/Component_bins/Cbin5/c6058.graph "
- "--max_number_of_paths_per_node=10 --path_reinforcement_distance=75 --triplet-lock"]
- _, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
- self.assertEquals(lines, line_dict['Butterfly'])
-
- def test_shell_c_commands_are_dropped(self):
- lines = ["20140919 10:06:14 43812 befulton 20 43684 0 S 108160 0 1228 196 92 848 1832 1 0.00 0.00 0 00:00.00 " \
- "0 0 0 0 0 0 0 0 0 sh -c /trinity/trinity-plugins/fastool/fastool --rev --illumina-trinity " \
- "--to-fasta /jobdir/reads.left.fq >> left.fa"]
- _, line_dict, _, _, _ = make_data_files.build_datasets(generate(lines))
- self.assertEquals(0, len(line_dict))
-
- def test_prettyprocess_combines_sort_and_binsort(self):
- line = "20140919 11:08:49 44009 user 20 44008 0 R 10975748 0 10837764 10957692 92 128 3416 9 0.00 4.99 99 " \
- "01:33:35 0 0 0 0 0 0 0 0 1 /bin/sort"
- self.assertEquals("sort", make_data_files.prettyprocess(line))
- line = "20140919 11:08:49 44009 user 20 44008 0 R 10975748 0 10837764 10957692 92 128 3416 9 0.00 4.99 99 " \
- "01:33:35 0 0 0 0 0 0 0 0 1 sort"
- self.assertEquals("sort", make_data_files.prettyprocess(line))
-
- def test_sort(self):
- line = "20140919 16:06:24 45210 befulton 20 45209 0 R 973936 0 966268 965740 92 88 1824 10 1.96 0.94 58 " \
- "04:26.85 0 188211 178646 188416 82 92 0 0 0 sort -T . -S 2G -k 1,1 -k 3,3 right_fa.sam"
- self.assertEquals("sort", make_data_files.prettyprocess(line))
-
- def test_GraphFromFasta_identified(self):
- line = "20141008 04:38:10 15672 befulton 20 15671 0 R 91636 0 11216 73412 92 292 3416 1 0.01 5.18 103" \
- " 00:05.19 0 0 1342 0 337 3 0 0 579 " \
- "/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/Chrysalis/GraphFromFasta " \
- "-i /dev/shm/trinity72/trinity_out/inchworm.K25.L25.fa -r both.fa -min_contig_length 200 -min_glue 2 " \
- "-glue_factor 0.05 -min_iso_ratio 0.05 -t 32 -k 24 -kk 48 -strand -scaffolding iworm_scaffolds.txt"
-
- self.assertEquals("GraphFromFasta", make_data_files.prettyprocess(line))
-
- def test_Samtools_identified_with_verb(self):
- line = "20141008 01:51:30 14984 befulton 20 14982 0 S 17752 0 820 200 92 384 2664 2 0.00 0.00 0 00:00.00 99" \
- " 0 1 0 2 0 0 0 61 samtools view -F4 -Sb -"
- self.assertEquals("samtools_view", make_data_files.prettyprocess(line))
- line = "20141008 01:51:30 14985 befulton 20 14982 0 S 17748 0 740 196 92 384 2664 16 0.00 0.00 0 00:00.00 26" \
- " 0 1 0 2 0 0 0 59 samtools sort -no - -"
- self.assertEquals("samtools_sort", make_data_files.prettyprocess(line))
-
- def test_Jellyfish_identified(self):
- line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
- " 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
- "/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/trinity-plugins/jellyfish/bin/jellyfish " \
- "count -t 32 -m 25 -s 1380200998 both.fa"
- self.assertEquals("jellyfish", make_data_files.prettyprocess(line))
-
- def test_Unrecognized_gives_binary_and_unknown(self):
- line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
- " 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
- "/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/trinity-plugins/new_app/bin/new_app " \
- "count -t 32 -m 25 -s 1380200998 both.fa"
- self.assertEquals("new_app_unknown", make_data_files.prettyprocess(line))
-
- def test_Unknown_apps_in_Chrysalis_directory_are_not_Chrysalis(self):
- line = "20141008 00:03:55 14423 befulton 20 14226 0 S 11316512 0 9153040 11314672 92 1732 0 17 3.14 19.75" \
- " 457 00:22.89 0 0 26047 0 3257 0 0 10 1129 " \
- "/N/dc2/scratch/befulton/TrinityMason/trinityrnaseq_r20140717/Chrysalis/new_app " \
- "count -t 32 -m 25 -s 1380200998 both.fa"
- self.assertEquals("new_app_unknown", make_data_files.prettyprocess(line))
-
-
-
diff --git a/trinity-plugins/collectl/build_collectl.sh b/trinity-plugins/collectl/build_collectl.sh
deleted file mode 100755
index 71cadbd..0000000
--- a/trinity-plugins/collectl/build_collectl.sh
+++ /dev/null
@@ -1,53 +0,0 @@
-#!/bin/bash
-# this is a manual selection derived from the INSTALL script of collectl
-
-#switch to the folder of this script
-DESTDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-cd $DESTDIR
-BINDIR=$DESTDIR/bin
-DOCDIR=$DESTDIR/doc
-MANDIR=$DESTDIR/man
-rm -rf $BINDIR
-rm -rf $DOCDIR
-rm -rf $MANDIR
-
-FILE=`ls -1 -d collectl*| tail -1`
-tar xzf ${FILE}
-INSTALLDIR=`find . -maxdepth 1 -type d -iname "*collect*" | tail -1`
-
-echo "DESTDIR=$DESTDIR"
-echo "FILE=$FILE"
-echo "INSTALLDIR=$INSTALLDIR"
-
-mkdir -p $BINDIR
-mkdir -p $DOCDIR
-mkdir -p $MANDIR
-
-cp make_data_files.py $BINDIR
-cp plot.py $BINDIR
-cp timetable.py $BINDIR
-cd ${INSTALLDIR}
-cp collectl.pl $BINDIR/collectl
-cp collectl.conf $BINDIR
-cp -r man1 $MANDIR
-
-cp docs/* $DOCDIR
-cp GPL ARTISTIC COPYING $DOCDIR
-cp RELEASE-collectl $DOCDIR
-
-cp UNINSTALL $BINDIR
-cp *.ph $BINDIR
-cp envrules.std $BINDIR
-cp client.pl $BINDIR
-cp col2tlviz.pl $BINDIR
-
-chmod 444 $BINDIR/collectl.conf
-chmod 755 $BINDIR/collectl
-chmod 444 $DOCDIR/ARTISTIC $DOCDIR/COPYING $DOCDIR/GPL
-chmod 755 $BINDIR/*.pl
-chmod 444 $BINDIR/*.ph
-
-cd ${DESTDIR}
-rm -rf ${INSTALLDIR}
-
-
diff --git a/trinity-plugins/collectl/collectl-3.6.9.src.tar.gz b/trinity-plugins/collectl/collectl-3.6.9.src.tar.gz
deleted file mode 100644
index 08a716d..0000000
Binary files a/trinity-plugins/collectl/collectl-3.6.9.src.tar.gz and /dev/null differ
diff --git a/trinity-plugins/collectl/collectl-3.7.4.src.tar.gz b/trinity-plugins/collectl/collectl-3.7.4.src.tar.gz
deleted file mode 100644
index 2389dc3..0000000
Binary files a/trinity-plugins/collectl/collectl-3.7.4.src.tar.gz and /dev/null differ
diff --git a/trinity-plugins/collectl/make_data_files.py b/trinity-plugins/collectl/make_data_files.py
deleted file mode 100644
index a6d9f7c..0000000
--- a/trinity-plugins/collectl/make_data_files.py
+++ /dev/null
@@ -1,181 +0,0 @@
-__author__ = 'befulton'
-from subprocess import call, Popen, PIPE
-from collections import defaultdict
-import os
-import time
-import re
-import datetime
-import sys
-
-def total_seconds(td):
- # Since this function is not available in Python 2.6
- return (td.microseconds + (td.seconds + td.days * 24 * 3600) * 10**6) / 10**6
-
-def open_collectl(filename, start_time=None):
- bindir = os.path.dirname(sys.argv[0])
- args = [bindir+os.sep+"collectl", "-P", "-p", filename, "-sZ"]
- if start_time:
- midnight = datetime.datetime.combine(start_time, datetime.datetime.min.time())
- offsettime = total_seconds(midnight - start_time + datetime.timedelta(minutes=1))
- print "offsettime: %s s" % offsettime
- args += ["--offsettime", str(offsettime)]
- p = Popen(args, stdout=PIPE)
- return p
-
-def wait_for_collectl(filename):
- finished = call(["gzip", "-tf", filename])
- count = 0
- while finished != 0 and count < 300:
- print "collectl has not yet finished"
- time.sleep(1)
- finished = call(["gzip", "-tf", filename])
- count += 1
-
-def get_start_time(filename):
- p = open_collectl(filename)
- print p.stdout.readline()
- print p.stdout.readline()
- s = p.stdout.readline().split()
-
- p.stdout.close()
- return s[0:2]
- #return datetime.datetime.strptime(s[0] + ' ' + s[1], "%Y%m%d %H:%M:%S")
-
-def replay(filename, start_time):
- if filename.endswith('gz'):
- p = open_collectl(filename, start_time)
- print p.stdout.readline()
- print p.stdout.readline()
- while True:
- retcode = p.poll() #returns None while subprocess is running
- line = p.stdout.readline()
- yield line
- if(retcode is not None):
- break
- else:
- with open(filename) as f:
- for line in f:
- yield line
-
-def timedelta(filename):
- print filename
- p = Popen(["zcat", filename], stdout=PIPE)
- p.stdout.readline()
- params = p.stdout.readline().split()
- i = next(param for param in params if param.startswith('-i'))
- p.stdout.close()
- return i[2:]
-
-
-def prettyprocess(line):
- s = line.split()[29:]
- if not s:
- return None
- if s[0] in ("-bash", 'sh', '/bin/bash', 'bash', 'ln', '/bin/pwd', 'mkdir', 'date', 'touch', '/usr/bin/env'):
- return None
-
- exes = ['fastool', 'ParaFly','Butterfly','ReadsToTranscripts', 'jellyfish',
- 'inchworm', 'FastaToDeBruijn', 'QuantifyGraph', 'GraphFromFasta', 'CreateIwormFastaBundle',
- 'bowtie-build', 'bowtie', 'Chrysalis', 'cat', 'sort', 'cp', 'wc', 'rm', 'find']
- perl_scripts = ['scaffold_iworm_contigs', 'Trinity', 'collectl', 'print_butterfly_assemblies',
- 'partition_chrysalis_graphs_n_reads', 'fasta_filter_by_min_length', 'partitioned_trinity_aggregator']
-
- for k in exes:
- if s[0].endswith(k):
- return k
-
- if s[0] == 'samtools':
- return ('samtools_' + s[1]) if len(s) > 1 else 'samtools'
-
- if s[0] == '/bin/sort':
- return 'sort'
-
- if s[0] == 'java':
- if 'Butterfly.jar' in " ".join(s):
- return 'Butterfly'
- if 'ExitTester.jar' in " ".join(s):
- return 'ExitTester'
- if '-version' in " ".join(s):
- return 'java_version'
-
- return 'java'
-
- if s[0] == 'perl':
- for k in perl_scripts:
- if k in s[1]:
- return k
- return 'perl'
-
- if s[0] == '/usr/bin/perl' and 'collectl' in s[2]:
- return 'collectl'
-
- return os.path.basename(s[0])+'_unknown'
-
-
-def build_datasets(line_generator):
- line_dict = defaultdict(list)
- sum_dict = defaultdict(lambda: [0]*27)
- grand_sum_dict = defaultdict(lambda: [0]*27)
-
- last_line = ''
- ordered_keys = []
- for line in line_generator:
- if line: last_line = line
- key = prettyprocess(line)
- if key:
- if key not in ordered_keys:
- ordered_keys.append(key)
- line_dict[key].append(line)
- s = line.split()
- data = sum_dict[key, s[0], s[1]]
- total = grand_sum_dict[tuple(s[0:2])]
- for i in range(27):
- try:
- data[i] += float(s[i + 2])
- total[i] += float(s[i + 2])
- except ValueError:
- pass
-
- return ordered_keys, line_dict, sum_dict, grand_sum_dict, last_line.split()[0:2]
-
-def write_times(start_time, end_time, colpar):
- ref = start_time[0] + " 00:00:00"
- e = datetime.datetime.strptime(" ".join(end_time), "%Y%m%d %H:%M:%S")
- r = datetime.datetime.strptime(ref, "%Y%m%d %H:%M:%S")
-
- with open("global.time", "w") as f:
- f.write("date %s\n" % " ".join(start_time))
- f.write("start %s\n" % ref)
- f.write("end %s\n" % " ".join(end_time))
- f.write("runtime %s\n" % total_seconds(e-r))
- f.write("interval %s\n" % colpar)
-
-
-def write_files(keys, line_dict, sum_dict, grand_sum_dict):
- for id, tool in enumerate(keys):
- if line_dict[tool]:
- with open("%s.%s.data" % (id + 1, tool), "w") as f:
- f.writelines(line_dict[tool])
- with open("%s.%s.sum" % (id + 1, tool), "w") as f:
- lines = (key for key in sum_dict.keys() if key[0] == tool)
- for line in sorted(lines):
- f.write(" ".join(list(line[1:]) + [('%f' % val).rstrip('0').rstrip('.')
- for val in sum_dict[line]]) + "\n")
- with open("collectZ.proc", "w") as f:
- for k in sorted(grand_sum_dict.keys()):
- f.write(" ".join(list(k) + ['{0:g}'.format(val) for val in grand_sum_dict[k]]) + "\n")
-
-if __name__ == '__main__':
- filename = next(file for file in os.listdir(".") if file.endswith(".gz"))
- wait_for_collectl(filename)
- colpar = timedelta(filename)
- start_time = get_start_time(filename)
-
- start = datetime.datetime.strptime(" ".join(start_time), "%Y%m%d %H:%M:%S")
- ordered_keys, line_dict, sum_dict, grand_sum_dict, end_time = build_datasets(replay(filename, start))
- write_files(ordered_keys, line_dict, sum_dict, grand_sum_dict)
- write_times(start_time, end_time, colpar)
-
- sum_files = sorted((file for file in os.listdir(".") if file.endswith(".sum")), key=lambda f: int(f.split('.')[0]))
- for id, sf in enumerate(sum_files):
- os.rename(sf, "%s.%s" % (id+1, sf))
diff --git a/trinity-plugins/collectl/plot.py b/trinity-plugins/collectl/plot.py
deleted file mode 100644
index b1ac081..0000000
--- a/trinity-plugins/collectl/plot.py
+++ /dev/null
@@ -1,176 +0,0 @@
-__author__ = 'befulton'
-
-import os
-import sys
-import subprocess
-
-def get_times():
- d = dict()
- with open("global.time") as f:
- for line in f:
- s = line.split()
- d[s[0]] = s[1:]
- return d
-
-times = get_times()
-date = times['start'][0]
-start = times['start'][1]
-end = times['end'][1]
-tics = int(end.split(':')[0]) + 1
-
-prettycolors = False
-if len(sys.argv) > 1:
- name = sys.argv[1]
-else:
- name = os.path.split(os.getcwd())[1]
-
-if len(sys.argv) > 2:
- cpu_count = int(sys.argv[2])
-else:
- cpu_count = 64
-
-
-def build_plot(files, stat):
- d = []
- for i, file in enumerate(sorted(files, key=lambda fn: int(fn.split('.')[0]))):
- title = file.split('.')[2]
- d.append("'%s' using 1:(%s) title \"%s\" ls %s" % (file, stat, title, i+1))
- return d
-
-
-def write_files(name):
- files = [file for file in os.listdir(".") if file.endswith(".sum")]
-
- with open("defs.gnu", 'w') as f:
- f.write("#generated gnuplot file\n")
- f.write("set xrange ['%s %s':'%s %s']\n" % (date, start, date, end))
- f.write("set xtics (")
- f.write(", ".join(["\"{0}\" '{1} {0:02d}:00:00'".format(i, date) for i in range(tics)]))
- f.write(" )\n")
- f.write("ncpu=%s" % cpu_count)
- f.write("\n")
-
- with open("common.gnu", 'w') as f:
- f.write(common_text.format(name))
- if prettycolors:
- colorset = color_sets[len(files)-1]
- for i, c in enumerate(colorset.split()):
- f.write("set style line %s lt 1 lc rgb \"%s\" lw mylw1 pt mypt1 ps myps1\n" % i, c)
- else:
- for i in range(len(files)):
- f.write("set style line %s lw mylw1 pt mypt1 ps myps1\n" % (i+1))
-
- with open('ram.gnu', 'w') as f:
- f.write(gnu_head % ('ram', end, "RAM usage GiB", ""))
- d = build_plot(files, "fg*$11")
- f.write(",\\\n ".join(d))
-
- with open('cpu.gnu', 'w') as f:
- f.write(gnu_head % ('cpu', end, "Core Utilization", "ncpu"))
- d = build_plot(files, "$19/100")
- f.write(",\\\n ".join(d))
-
- with open('io.gnu', 'w') as f:
- f.write(gnu_io_head % end)
- d = build_plot(files, "fm*($23+$24)")
- f.write(",\\\n ".join(d))
-
- for gnu in ['ram.gnu', 'cpu.gnu', 'io.gnu']:
- subprocess.Popen(['gnuplot', gnu]).wait()
-
-common_text = """
-set terminal postscript color eps "Times" 14
-#set termoption enhanced
-
-set style data points
-
-# ram and cpu
-mypt1=7
-mylw1=0
-#myps1=0.3
-myps1=0.6
-
-set key below
-set timefmt "%Y%m%d %H:%M:%S"
-set xdata time
-set format x "%k"
-set xrange [*:*]
-unset grid
-set grid x
-unset title
-#set title "{0}" noenhanced
-set title "{0}"
-
-fm=1./(1024.0)
-fg=1./(1024.0)/(1024.0)
-
-#set multiplot layout 3,1
-#set tmargin 0
-#set tmargin 0.8
-#set bmargin 0.8
-
-#set tics nomirror scale 0.66
-#set xtics scale 0
-
-#myvertoffset=0.02
-
-"""
-
-gnu_head = """load 'common.gnu'
-load 'defs.gnu'
-
-set out '%s.eps'
-
-set xlabel "Runtime [h] %s"
-set ylabel "%s"
-set yrange [0:%s]
-
-plot """
-
-gnu_io_head = """load 'common.gnu'
-load 'defs.gnu'
-
-set out 'io.eps'
-
-set xlabel "Runtime [h] %s"
-set ylabel "I/O MiB/s"
-set yrange [0.005:2000]
-set logscale y
-set ytics ("10^{-3}" 0.001, "10^{-2}" 0.01, "10^{-1}" 0.1, "10^{0}" 1, "10^{1}" 10, "10^{2}" 100, "10^{3}" 1000)
-
-plot """
-
-color_sets = [
- '#f800ff',
- '#ff00e3 #f100ff',
- "#ffa900 #00ffdc #0096ff",
- "#ff005d #19ff00 #00ffc8 #c200ff",
- "#ff00c7 #9cff00 #00ff61 #0042ff #5700ff",
- "#ff00cb #ff1500 #59ff00 #00ffb5 #00b4ff #4f00ff",
- "#ff00f2 #ff000f #c0ff00 #0bff00 #00ffdd #0007ff #7800ff",
- "#ff004d #ff0100 #ffe800 #64ff00 #00ff94 #00daff #0070ff #c800ff",
- "#ff0081 #ff0031 #ffa500 #6aff00 #23ff00 #00ffb5 #0058ff #1300ff #ab00ff",
- "#ff00af #ff003b #ff4b00 #fff900 #6aff00 #00ff98 #00feff #00b6ff #3c00ff #8700ff",
- "#ff00de #ff1100 #ff7d00 #fff600 #59ff00 #1bff00 #00ff64 #00e7ff #009cff #7100ff #bc00ff",
- "#ff00b7 #ff0062 #ff5200 #ffdb00 #baff00 #54ff00 #00ff5e #00ff87 #0087ff #0083ff #7800ff #cc00ff",
- "#ff00b9 #ff0037 #ff2600 #ffa500 #bbff00 #84ff00 #00ff03 #00ff64 #00ffb5 #00cfff #0048ff #2b00ff #ba00ff",
- '#ff00d8 #ff0047 #ff0007 #ff7f00 #ffee00 #88ff00 #32ff00 #00ff67 #00ff75 #00c9ff #0070ff #0005ff #6c00ff #8f00ff',
- "#ff00db #ff0066 #ff2d00 #ff3400 #fff600 #adff00 #7eff00 #00ff03 #00ff72 #00ffc5 #00c6ff #0052ff #002fff #9500ff #bb00ff",
- "#ff00c8 #ff009b #ff0004 #ff7600 #ffbe00 #ffef00 #98ff00 #54ff00 #00ff2c #00ff6a #00ffbf #0088ff #004fff #0010ff #8900ff #b300ff",
- "#ff00ed #ff0053 #ff0005 #ff4200 #ffc200 #f9ff00 #aaff00 #52ff00 #14ff00 #00ff74 #00ffb5 #00ffe6 #00b4ff #0025ff #0003ff #6300ff #be00ff",
- "#ff00a9 #ff006c #ff004a #ff4000 #ff5a00 #ffae00 #e8ff00 #9bff00 #36ff00 #00ff3a #00ff7a #00fff4 #00bdff #007cff #0017ff #2a00ff #5d00ff #be00ff",
- "#ff00cb #ff007f #ff0054 #ff0b00 #ff7d00 #ffa700 #ffe400 #aaff00 #7cff00 #18ff00 #00ff41 #00ffb1 #00ffe1 #009cff #0071ff #001eff #1900ff #8a00ff #b400ff",
- "#ff00e1 #ff0086 #ff0037 #ff0400 #ff6f00 #ff8400 #fff100 #aeff00 #71ff00 #05ff00 #00ff22 #00ff56 #00ffd2 #00ecff #00c4ff #003eff #001cff #3300ff #8000ff #c700ff",
- "#ff00f0 #ff009c #ff004e #ff0004 #ff3300 #ff7400 #ffcc00 #f4ff00 #9fff00 #53ff00 #13ff00 #00ff3a #00ff9c #00ffb5 #00f1ff #00b4ff #0078ff #0007ff #3700ff #8a00ff #eb00ff",
- "#ff00d4 #ff00a1 #ff0064 #ff001f #ff3100 #ff9d00 #ffa200 #ffeb00 #a5ff00 #80ff00 #43ff00 #02ff00 #00ff49 #00ff88 #00ffe4 #00e6ff #008fff #004fff #001dff #4300ff #7900ff #b000ff",
- "#ff00f6 #ff00af #ff0047 #ff0012 #ff2e00 #ff6300 #ffc700 #fffc00 #bcff00 #6bff00 #63ff00 #0fff00 #00ff29 #00ff8b #00ffc5 #00fff1 #00c5ff #0072ff #0053ff #0200ff #3600ff #7700ff #bd00ff",
- "#ff00d7 #ff009e #ff0061 #ff0037 #ff3000 #ff7200 #ffaa00 #ffec00 #cfff00 #94ff00 #4eff00 #10ff00 #08ff00 #00ff59 #00ff86 #00ffc1 #00dcff #00b5ff #006cff #0041ff #1d00ff #5100ff #9800ff #d100ff",
- "#ff00e4 #ff0094 #ff007e #ff003b #ff0000 #ff4e00 #ff9100 #ffb000 #ffec00 #ccff00 #76ff00 #28ff00 #00ff17 #00ff50 #00ff5c #00ffa9 #00fff1 #00e6ff #008bff #005bff #0005ff #1b00ff #7000ff #8a00ff #c500ff",
- "#ff00ed #ff00a9 #ff0059 #ff0034 #ff0009 #ff4d00 #ff6200 #ffab00 #fffe00 #e3ff00 #8bff00 #7aff00 #41ff00 #00ff06 #00ff45 #00ff7c #00ffb5 #00fff7 #00b2ff #00a4ff #0067ff #0033ff #2e00ff #5a00ff #9d00ff #d500ff",
- "#ff00e2 #ff00af #ff0059 #ff0033 #ff1000 #ff2c00 #ff7500 #ffb100 #ffe600 #faff00 #c9ff00 #94ff00 #50ff00 #17ff00 #00ff39 #00ff74 #00ffad #00ffe6 #00fff9 #00c8ff #0089ff #004cff #0019ff #1700ff #6e00ff #9400ff #d600ff",
- "#ff00cd #ff00af #ff008a #ff003a #ff0020 #ff2f00 #ff6c00 #ff8300 #ffc200 #ffea00 #b5ff00 #82ff00 #71ff00 #12ff00 #00ff16 #00ff58 #00ff69 #00ffb6 #00ffd5 #00d0ff #00bcff #0077ff #002cff #0020ff #3c00ff #5900ff #9e00ff #be00ff",
- "#ff00d6 #ff00b4 #ff007e #ff005d #ff0013 #ff0f00 #ff4400 #ff8a00 #ffb300 #fff100 #e1ff00 #beff00 #6eff00 #31ff00 #03ff00 #00ff28 #00ff68 #00ff83 #00ffad #00ffe7 #00deff #0099ff #0053ff #0038ff #0011ff #4100ff #6d00ff #8800ff #e800ff",
- "#ff00d8 #ff00ae #ff0078 #ff0036 #ff0003 #ff0400 #ff5500 #ff8600 #ffb100 #ffd100 #cfff00 #b4ff00 #7dff00 #65ff00 #1cff00 #00ff0c #00ff4b #00ff86 #00ffb9 #00ffe5 #00f5ff #00a2ff #0086ff #0064ff #0014ff #2d00ff #4a00ff #8200ff #b100ff #de00ff",
-]
-if __name__ == '__main__':
- write_files(name)
\ No newline at end of file
diff --git a/trinity-plugins/collectl/timetable.py b/trinity-plugins/collectl/timetable.py
deleted file mode 100644
index 7f5ff07..0000000
--- a/trinity-plugins/collectl/timetable.py
+++ /dev/null
@@ -1,33 +0,0 @@
-__author__ = 'befulton'
-import os
-import datetime
-
-def to_date(s):
- return datetime.datetime.strptime(s[0] + ' ' + s[1], "%Y%m%d %H:%M:%S")
-
-files = [file for file in os.listdir(".") if file.endswith(".sum")]
-
-files = [file for file in os.listdir(".") if file.endswith(".sum")]
-
-interval = 5
-runtimes = dict()
-for file in files:
- app_name = file.split('.')[2]
- linecount = 0
- with open(file) as f:
- line = f.readline().split()
- if line:
- linecount = 1
- app_start = to_date(line)
- for line in f:
- linecount += 1
- if linecount > 1:
- line = line.split()
- app_end = to_date(line)
- runtimes[app_name] = linecount * interval
-
-with open('runtime.csv', 'w') as f:
- f.write("application runtime[s]\n")
- for k, v in runtimes.iteritems():
- f.write("%s %s\n" % (k, v))
-
diff --git a/trinity-plugins/parafly-code/LICENSE b/trinity-plugins/parafly-code/LICENSE
deleted file mode 100644
index 6a9679e..0000000
--- a/trinity-plugins/parafly-code/LICENSE
+++ /dev/null
@@ -1,17 +0,0 @@
-Copyright (c) 2011, The Broad Institute, Inc. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-
-· Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-
-· Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-
-· Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.**
-
-THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE
-BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO,
-PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
-EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
diff --git a/trinity-plugins/parafly-code/Makefile.am b/trinity-plugins/parafly-code/Makefile.am
deleted file mode 100644
index af437a6..0000000
--- a/trinity-plugins/parafly-code/Makefile.am
+++ /dev/null
@@ -1 +0,0 @@
-SUBDIRS = src
diff --git a/trinity-plugins/parafly-code/Makefile.in b/trinity-plugins/parafly-code/Makefile.in
deleted file mode 100644
index 99b30b8..0000000
--- a/trinity-plugins/parafly-code/Makefile.in
+++ /dev/null
@@ -1,671 +0,0 @@
-# Makefile.in generated by automake 1.11.1 from Makefile.am.
-# @configure_input@
-
-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
-# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
-# Inc.
-# This Makefile.in is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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-
- at SET_MAKE@
-VPATH = @srcdir@
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-NORMAL_INSTALL = :
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-am__aclocal_m4_deps = $(top_srcdir)/configure.ac
-am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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-am__CONFIG_DISTCLEAN_FILES = config.status config.cache config.log \
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-all: config.h
- $(MAKE) $(AM_MAKEFLAGS) all-recursive
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diff --git a/trinity-plugins/parafly-code/config.h b/trinity-plugins/parafly-code/config.h
deleted file mode 100644
index 31b7679..0000000
--- a/trinity-plugins/parafly-code/config.h
+++ /dev/null
@@ -1,23 +0,0 @@
-/* config.h. Generated from config.h.in by configure. */
-/* config.h.in. Generated from configure.ac by autoheader. */
-
-/* Name of package */
-#define PACKAGE "parafly"
-
-/* Define to the address where bug reports for this package should be sent. */
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-
-/* Define to the full name of this package. */
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-
-/* Define to the full name and version of this package. */
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-
-/* Define to the one symbol short name of this package. */
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-
-/* Define to the version of this package. */
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-
-/* Version number of package */
-#define VERSION "0.1"
diff --git a/trinity-plugins/parafly-code/config.h.in b/trinity-plugins/parafly-code/config.h.in
deleted file mode 100644
index c364eda..0000000
--- a/trinity-plugins/parafly-code/config.h.in
+++ /dev/null
@@ -1,22 +0,0 @@
-/* config.h.in. Generated from configure.ac by autoheader. */
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-/* Name of package */
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-/* Define to the full name and version of this package. */
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-/* Define to the one symbol short name of this package. */
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-
-/* Define to the version of this package. */
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-
-/* Version number of package */
-#undef VERSION
diff --git a/trinity-plugins/parafly-code/configure b/trinity-plugins/parafly-code/configure
deleted file mode 100755
index 740f187..0000000
--- a/trinity-plugins/parafly-code/configure
+++ /dev/null
@@ -1,4685 +0,0 @@
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-# Guess values for system-dependent variables and create Makefiles.
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-# output is simply discarded. So we exec the FD to /dev/null,
-# effectively closing config.log, so it can be properly (re)opened and
-# appended to by config.status. When coming back to configure, we
-# need to make the FD available again.
-if test "$no_create" != yes; then
- ac_cs_success=:
- ac_config_status_args=
- test "$silent" = yes &&
- ac_config_status_args="$ac_config_status_args --quiet"
- exec 5>/dev/null
- $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
- exec 5>>config.log
- # Use ||, not &&, to avoid exiting from the if with $? = 1, which
- # would make configure fail if this is the last instruction.
- $ac_cs_success || { (exit 1); exit 1; }
-fi
-if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
- { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
-$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
-fi
-
diff --git a/trinity-plugins/parafly-code/configure.ac b/trinity-plugins/parafly-code/configure.ac
deleted file mode 100644
index aa22549..0000000
--- a/trinity-plugins/parafly-code/configure.ac
+++ /dev/null
@@ -1,15 +0,0 @@
-AC_INIT([Parafly], [0.1], [bug-report at address])
-AM_INIT_AUTOMAKE([foreign -Wall -Werror])
-AC_LANG([C++])
-AC_PROG_CXX
-#AC_OPENMP # requires autoconf >= 2.62
-AC_SUBST([AM_CXXFLAGS], [-m64])
-case $CXX in
- g++*) AC_SUBST([AM_CXXFLAGS],["-pedantic -fopenmp -Wall -Wextra -Wno-long-long -Wno-deprecated $AM_CXXFLAGS"]);;
- sunCC*) AC_SUBST([AM_CXXFLAGS], ["-library=stlport4 -xopenmp -xvpara -fast $AM_CXXFLAGS"]) ;;
- icpc*) AC_SUBST([AM_CXXFLAGS], ["-Wall -openmp $AM_CXXFLAGS"]) ;;
-esac
-AC_SEARCH_LIBS([cos], [m])
-AC_CONFIG_HEADERS([config.h])
-AC_CONFIG_FILES([Makefile src/Makefile])
-AC_OUTPUT
diff --git a/trinity-plugins/parafly-code/depcomp b/trinity-plugins/parafly-code/depcomp
deleted file mode 100755
index bd0ac08..0000000
--- a/trinity-plugins/parafly-code/depcomp
+++ /dev/null
@@ -1,688 +0,0 @@
-#! /bin/sh
-# depcomp - compile a program generating dependencies as side-effects
-
-scriptversion=2011-12-04.11; # UTC
-
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009, 2010,
-# 2011 Free Software Foundation, Inc.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
-
-case $1 in
- '')
- echo "$0: No command. Try \`$0 --help' for more information." 1>&2
- exit 1;
- ;;
- -h | --h*)
- cat <<\EOF
-Usage: depcomp [--help] [--version] PROGRAM [ARGS]
-
-Run PROGRAMS ARGS to compile a file, generating dependencies
-as side-effects.
-
-Environment variables:
- depmode Dependency tracking mode.
- source Source file read by `PROGRAMS ARGS'.
- object Object file output by `PROGRAMS ARGS'.
- DEPDIR directory where to store dependencies.
- depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputting dependencies.
- libtool Whether libtool is used (yes/no).
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "depcomp $scriptversion"
- exit $?
- ;;
-esac
-
-if test -z "$depmode" || test -z "$source" || test -z "$object"; then
- echo "depcomp: Variables source, object and depmode must be set" 1>&2
- exit 1
-fi
-
-# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
-depfile=${depfile-`echo "$object" |
- sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
-tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
-
-rm -f "$tmpdepfile"
-
-# Some modes work just like other modes, but use different flags. We
-# parameterize here, but still list the modes in the big case below,
-# to make depend.m4 easier to write. Note that we *cannot* use a case
-# here, because this file can only contain one case statement.
-if test "$depmode" = hp; then
- # HP compiler uses -M and no extra arg.
- gccflag=-M
- depmode=gcc
-fi
-
-if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
-fi
-
-cygpath_u="cygpath -u -f -"
-if test "$depmode" = msvcmsys; then
- # This is just like msvisualcpp but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvisualcpp
-fi
-
-if test "$depmode" = msvc7msys; then
- # This is just like msvc7 but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvc7
-fi
-
-case "$depmode" in
-gcc3)
-## gcc 3 implements dependency tracking that does exactly what
-## we want. Yay! Note: for some reason libtool 1.4 doesn't like
-## it if -MD -MP comes after the -MF stuff. Hmm.
-## Unfortunately, FreeBSD c89 acceptance of flags depends upon
-## the command line argument order; so add the flags where they
-## appear in depend2.am. Note that the slowdown incurred here
-## affects only configure: in makefiles, %FASTDEP% shortcuts this.
- for arg
- do
- case $arg in
- -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
- *) set fnord "$@" "$arg" ;;
- esac
- shift # fnord
- shift # $arg
- done
- "$@"
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- mv "$tmpdepfile" "$depfile"
- ;;
-
-gcc)
-## There are various ways to get dependency output from gcc. Here's
-## why we pick this rather obscure method:
-## - Don't want to use -MD because we'd like the dependencies to end
-## up in a subdir. Having to rename by hand is ugly.
-## (We might end up doing this anyway to support other compilers.)
-## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say).
-## - Using -M directly means running the compiler twice (even worse
-## than renaming).
- if test -z "$gccflag"; then
- gccflag=-MD,
- fi
- "$@" -Wp,"$gccflag$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
- sed -e 's/^[^:]*: / /' \
- -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the `deleted header file' problem.
-## The problem is that when a header file which appears in a .P file
-## is deleted, the dependency causes make to die (because there is
-## typically no way to rebuild the header). We avoid this by adding
-## dummy dependencies for each header file. Too bad gcc doesn't do
-## this for us directly.
- tr ' ' '
-' < "$tmpdepfile" |
-## Some versions of gcc put a space before the `:'. On the theory
-## that the space means something, we add a space to the output as
-## well. hp depmode also adds that space, but also prefixes the VPATH
-## to the object. Take care to not repeat it in the output.
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-sgi)
- if test "$libtool" = yes; then
- "$@" "-Wp,-MDupdate,$tmpdepfile"
- else
- "$@" -MDupdate "$tmpdepfile"
- fi
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
-
- if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
- echo "$object : \\" > "$depfile"
-
- # Clip off the initial element (the dependent). Don't try to be
- # clever and replace this with sed code, as IRIX sed won't handle
- # lines with more than a fixed number of characters (4096 in
- # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
- # the IRIX cc adds comments like `#:fec' to the end of the
- # dependency line.
- tr ' ' '
-' < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
- tr '
-' ' ' >> "$depfile"
- echo >> "$depfile"
-
- # The second pass generates a dummy entry for each header file.
- tr ' ' '
-' < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> "$depfile"
- else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
-
-aix)
- # The C for AIX Compiler uses -M and outputs the dependencies
- # in a .u file. In older versions, this file always lives in the
- # current directory. Also, the AIX compiler puts `$object:' at the
- # start of each line; $object doesn't have directory information.
- # Version 6 uses the directory in both cases.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
- if test "$libtool" = yes; then
- tmpdepfile1=$dir$base.u
- tmpdepfile2=$base.u
- tmpdepfile3=$dir.libs/$base.u
- "$@" -Wc,-M
- else
- tmpdepfile1=$dir$base.u
- tmpdepfile2=$dir$base.u
- tmpdepfile3=$dir$base.u
- "$@" -M
- fi
- stat=$?
-
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- # Each line is of the form `foo.o: dependent.h'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- # That's a tab and a space in the [].
- sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- # The sourcefile does not contain any dependencies, so just
- # store a dummy comment line, to avoid errors with the Makefile
- # "include basename.Plo" scheme.
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
-
-icc)
- # Intel's C compiler understands `-MD -MF file'. However on
- # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
- # ICC 7.0 will fill foo.d with something like
- # foo.o: sub/foo.c
- # foo.o: sub/foo.h
- # which is wrong. We want:
- # sub/foo.o: sub/foo.c
- # sub/foo.o: sub/foo.h
- # sub/foo.c:
- # sub/foo.h:
- # ICC 7.1 will output
- # foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using \ :
- # foo.o: sub/foo.c ... \
- # sub/foo.h ... \
- # ...
-
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- # Each line is of the form `foo.o: dependent.h',
- # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
- sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp2)
- # The "hp" stanza above does not work with aCC (C++) and HP's ia64
- # compilers, which have integrated preprocessors. The correct option
- # to use with these is +Maked; it writes dependencies to a file named
- # 'foo.d', which lands next to the object file, wherever that
- # happens to be.
- # Much of this is similar to the tru64 case; see comments there.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
- if test "$libtool" = yes; then
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir.libs/$base.d
- "$@" -Wc,+Maked
- else
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir$base.d
- "$@" +Maked
- fi
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile1" "$tmpdepfile2"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
- # Add `dependent.h:' lines.
- sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
- else
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile" "$tmpdepfile2"
- ;;
-
-tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in `foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
- test "x$dir" = "x$object" && dir=
- base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
-
- if test "$libtool" = yes; then
- # With Tru64 cc, shared objects can also be used to make a
- # static library. This mechanism is used in libtool 1.4 series to
- # handle both shared and static libraries in a single compilation.
- # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
- #
- # With libtool 1.5 this exception was removed, and libtool now
- # generates 2 separate objects for the 2 libraries. These two
- # compilations output dependencies in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
- tmpdepfile2=$dir$base.o.d # libtool 1.5
- tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
- tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.o.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- tmpdepfile4=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
- if test $stat -eq 0; then :
- else
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
- # That's a tab and a space in the [].
- sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
- else
- echo "#dummy" > "$depfile"
- fi
- rm -f "$tmpdepfile"
- ;;
-
-msvc7)
- if test "$libtool" = yes; then
- showIncludes=-Wc,-showIncludes
- else
- showIncludes=-showIncludes
- fi
- "$@" $showIncludes > "$tmpdepfile"
- stat=$?
- grep -v '^Note: including file: ' "$tmpdepfile"
- if test "$stat" = 0; then :
- else
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- # The first sed program below extracts the file names and escapes
- # backslashes for cygpath. The second sed program outputs the file
- # name when reading, but also accumulates all include files in the
- # hold buffer in order to output them again at the end. This only
- # works with sed implementations that can handle large buffers.
- sed < "$tmpdepfile" -n '
-/^Note: including file: *\(.*\)/ {
- s//\1/
- s/\\/\\\\/g
- p
-}' | $cygpath_u | sort -u | sed -n '
-s/ /\\ /g
-s/\(.*\)/ \1 \\/p
-s/.\(.*\) \\/\1:/
-H
-$ {
- s/.*/ /
- G
- p
-}' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvc7msys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-#nosideeffect)
- # This comment above is used by automake to tell side-effect
- # dependency tracking mechanisms from slower ones.
-
-dashmstdout)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove `-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for `:'
- # in the target name. This is to cope with DOS-style filenames:
- # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
- "$@" $dashmflag |
- sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
- rm -f "$depfile"
- cat < "$tmpdepfile" > "$depfile"
- tr ' ' '
-' < "$tmpdepfile" | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-dashXmstdout)
- # This case only exists to satisfy depend.m4. It is never actually
- # run, as this mode is specially recognized in the preamble.
- exit 1
- ;;
-
-makedepend)
- "$@" || exit $?
- # Remove any Libtool call
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
- # X makedepend
- shift
- cleared=no eat=no
- for arg
- do
- case $cleared in
- no)
- set ""; shift
- cleared=yes ;;
- esac
- if test $eat = yes; then
- eat=no
- continue
- fi
- case "$arg" in
- -D*|-I*)
- set fnord "$@" "$arg"; shift ;;
- # Strip any option that makedepend may not understand. Remove
- # the object too, otherwise makedepend will parse it as a source file.
- -arch)
- eat=yes ;;
- -*|$object)
- ;;
- *)
- set fnord "$@" "$arg"; shift ;;
- esac
- done
- obj_suffix=`echo "$object" | sed 's/^.*\././'`
- touch "$tmpdepfile"
- ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
- rm -f "$depfile"
- # makedepend may prepend the VPATH from the source file name to the object.
- # No need to regex-escape $object, excess matching of '.' is harmless.
- sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
- sed '1,2d' "$tmpdepfile" | tr ' ' '
-' | \
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile" "$tmpdepfile".bak
- ;;
-
-cpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove `-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- "$@" -E |
- sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
- sed '$ s: \\$::' > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- cat < "$tmpdepfile" >> "$depfile"
- sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvisualcpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- IFS=" "
- for arg
- do
- case "$arg" in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift
- shift
- ;;
- esac
- done
- "$@" -E 2>/dev/null |
- sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
- echo " " >> "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvcmsys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-none)
- exec "$@"
- ;;
-
-*)
- echo "Unknown depmode $depmode" 1>&2
- exit 1
- ;;
-esac
-
-exit 0
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
diff --git a/trinity-plugins/parafly-code/install-sh b/trinity-plugins/parafly-code/install-sh
deleted file mode 100755
index a9244eb..0000000
--- a/trinity-plugins/parafly-code/install-sh
+++ /dev/null
@@ -1,527 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2011-01-19.21; # UTC
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
-# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
-# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-#
-# Except as contained in this notice, the name of the X Consortium shall not
-# be used in advertising or otherwise to promote the sale, use or other deal-
-# ings in this Software without prior written authorization from the X Consor-
-# tium.
-#
-#
-# FSF changes to this file are in the public domain.
-#
-# Calling this script install-sh is preferred over install.sh, to prevent
-# `make' implicit rules from creating a file called install from it
-# when there is no Makefile.
-#
-# This script is compatible with the BSD install script, but was written
-# from scratch.
-
-nl='
-'
-IFS=" "" $nl"
-
-# set DOITPROG to echo to test this script
-
-# Don't use :- since 4.3BSD and earlier shells don't like it.
-doit=${DOITPROG-}
-if test -z "$doit"; then
- doit_exec=exec
-else
- doit_exec=$doit
-fi
-
-# Put in absolute file names if you don't have them in your path;
-# or use environment vars.
-
-chgrpprog=${CHGRPPROG-chgrp}
-chmodprog=${CHMODPROG-chmod}
-chownprog=${CHOWNPROG-chown}
-cmpprog=${CMPPROG-cmp}
-cpprog=${CPPROG-cp}
-mkdirprog=${MKDIRPROG-mkdir}
-mvprog=${MVPROG-mv}
-rmprog=${RMPROG-rm}
-stripprog=${STRIPPROG-strip}
-
-posix_glob='?'
-initialize_posix_glob='
- test "$posix_glob" != "?" || {
- if (set -f) 2>/dev/null; then
- posix_glob=
- else
- posix_glob=:
- fi
- }
-'
-
-posix_mkdir=
-
-# Desired mode of installed file.
-mode=0755
-
-chgrpcmd=
-chmodcmd=$chmodprog
-chowncmd=
-mvcmd=$mvprog
-rmcmd="$rmprog -f"
-stripcmd=
-
-src=
-dst=
-dir_arg=
-dst_arg=
-
-copy_on_change=false
-no_target_directory=
-
-usage="\
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- or: $0 [OPTION]... SRCFILES... DIRECTORY
- or: $0 [OPTION]... -t DIRECTORY SRCFILES...
- or: $0 [OPTION]... -d DIRECTORIES...
-
-In the 1st form, copy SRCFILE to DSTFILE.
-In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
-In the 4th, create DIRECTORIES.
-
-Options:
- --help display this help and exit.
- --version display version info and exit.
-
- -c (ignored)
- -C install only if different (preserve the last data modification time)
- -d create directories instead of installing files.
- -g GROUP $chgrpprog installed files to GROUP.
- -m MODE $chmodprog installed files to MODE.
- -o USER $chownprog installed files to USER.
- -s $stripprog installed files.
- -t DIRECTORY install into DIRECTORY.
- -T report an error if DSTFILE is a directory.
-
-Environment variables override the default commands:
- CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
- RMPROG STRIPPROG
-"
-
-while test $# -ne 0; do
- case $1 in
- -c) ;;
-
- -C) copy_on_change=true;;
-
- -d) dir_arg=true;;
-
- -g) chgrpcmd="$chgrpprog $2"
- shift;;
-
- --help) echo "$usage"; exit $?;;
-
- -m) mode=$2
- case $mode in
- *' '* | *' '* | *'
-'* | *'*'* | *'?'* | *'['*)
- echo "$0: invalid mode: $mode" >&2
- exit 1;;
- esac
- shift;;
-
- -o) chowncmd="$chownprog $2"
- shift;;
-
- -s) stripcmd=$stripprog;;
-
- -t) dst_arg=$2
- # Protect names problematic for `test' and other utilities.
- case $dst_arg in
- -* | [=\(\)!]) dst_arg=./$dst_arg;;
- esac
- shift;;
-
- -T) no_target_directory=true;;
-
- --version) echo "$0 $scriptversion"; exit $?;;
-
- --) shift
- break;;
-
- -*) echo "$0: invalid option: $1" >&2
- exit 1;;
-
- *) break;;
- esac
- shift
-done
-
-if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
- # When -d is used, all remaining arguments are directories to create.
- # When -t is used, the destination is already specified.
- # Otherwise, the last argument is the destination. Remove it from $@.
- for arg
- do
- if test -n "$dst_arg"; then
- # $@ is not empty: it contains at least $arg.
- set fnord "$@" "$dst_arg"
- shift # fnord
- fi
- shift # arg
- dst_arg=$arg
- # Protect names problematic for `test' and other utilities.
- case $dst_arg in
- -* | [=\(\)!]) dst_arg=./$dst_arg;;
- esac
- done
-fi
-
-if test $# -eq 0; then
- if test -z "$dir_arg"; then
- echo "$0: no input file specified." >&2
- exit 1
- fi
- # It's OK to call `install-sh -d' without argument.
- # This can happen when creating conditional directories.
- exit 0
-fi
-
-if test -z "$dir_arg"; then
- do_exit='(exit $ret); exit $ret'
- trap "ret=129; $do_exit" 1
- trap "ret=130; $do_exit" 2
- trap "ret=141; $do_exit" 13
- trap "ret=143; $do_exit" 15
-
- # Set umask so as not to create temps with too-generous modes.
- # However, 'strip' requires both read and write access to temps.
- case $mode in
- # Optimize common cases.
- *644) cp_umask=133;;
- *755) cp_umask=22;;
-
- *[0-7])
- if test -z "$stripcmd"; then
- u_plus_rw=
- else
- u_plus_rw='% 200'
- fi
- cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
- *)
- if test -z "$stripcmd"; then
- u_plus_rw=
- else
- u_plus_rw=,u+rw
- fi
- cp_umask=$mode$u_plus_rw;;
- esac
-fi
-
-for src
-do
- # Protect names problematic for `test' and other utilities.
- case $src in
- -* | [=\(\)!]) src=./$src;;
- esac
-
- if test -n "$dir_arg"; then
- dst=$src
- dstdir=$dst
- test -d "$dstdir"
- dstdir_status=$?
- else
-
- # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
- # might cause directories to be created, which would be especially bad
- # if $src (and thus $dsttmp) contains '*'.
- if test ! -f "$src" && test ! -d "$src"; then
- echo "$0: $src does not exist." >&2
- exit 1
- fi
-
- if test -z "$dst_arg"; then
- echo "$0: no destination specified." >&2
- exit 1
- fi
- dst=$dst_arg
-
- # If destination is a directory, append the input filename; won't work
- # if double slashes aren't ignored.
- if test -d "$dst"; then
- if test -n "$no_target_directory"; then
- echo "$0: $dst_arg: Is a directory" >&2
- exit 1
- fi
- dstdir=$dst
- dst=$dstdir/`basename "$src"`
- dstdir_status=0
- else
- # Prefer dirname, but fall back on a substitute if dirname fails.
- dstdir=`
- (dirname "$dst") 2>/dev/null ||
- expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$dst" : 'X\(//\)[^/]' \| \
- X"$dst" : 'X\(//\)$' \| \
- X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
- echo X"$dst" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'
- `
-
- test -d "$dstdir"
- dstdir_status=$?
- fi
- fi
-
- obsolete_mkdir_used=false
-
- if test $dstdir_status != 0; then
- case $posix_mkdir in
- '')
- # Create intermediate dirs using mode 755 as modified by the umask.
- # This is like FreeBSD 'install' as of 1997-10-28.
- umask=`umask`
- case $stripcmd.$umask in
- # Optimize common cases.
- *[2367][2367]) mkdir_umask=$umask;;
- .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
-
- *[0-7])
- mkdir_umask=`expr $umask + 22 \
- - $umask % 100 % 40 + $umask % 20 \
- - $umask % 10 % 4 + $umask % 2
- `;;
- *) mkdir_umask=$umask,go-w;;
- esac
-
- # With -d, create the new directory with the user-specified mode.
- # Otherwise, rely on $mkdir_umask.
- if test -n "$dir_arg"; then
- mkdir_mode=-m$mode
- else
- mkdir_mode=
- fi
-
- posix_mkdir=false
- case $umask in
- *[123567][0-7][0-7])
- # POSIX mkdir -p sets u+wx bits regardless of umask, which
- # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
- ;;
- *)
- tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
- if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
- then
- if test -z "$dir_arg" || {
- # Check for POSIX incompatibilities with -m.
- # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
- # other-writeable bit of parent directory when it shouldn't.
- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
- case $ls_ld_tmpdir in
- d????-?r-*) different_mode=700;;
- d????-?--*) different_mode=755;;
- *) false;;
- esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
- }
- }
- then posix_mkdir=:
- fi
- rmdir "$tmpdir/d" "$tmpdir"
- else
- # Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
- fi
- trap '' 0;;
- esac;;
- esac
-
- if
- $posix_mkdir && (
- umask $mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
- )
- then :
- else
-
- # The umask is ridiculous, or mkdir does not conform to POSIX,
- # or it failed possibly due to a race condition. Create the
- # directory the slow way, step by step, checking for races as we go.
-
- case $dstdir in
- /*) prefix='/';;
- [-=\(\)!]*) prefix='./';;
- *) prefix='';;
- esac
-
- eval "$initialize_posix_glob"
-
- oIFS=$IFS
- IFS=/
- $posix_glob set -f
- set fnord $dstdir
- shift
- $posix_glob set +f
- IFS=$oIFS
-
- prefixes=
-
- for d
- do
- test X"$d" = X && continue
-
- prefix=$prefix$d
- if test -d "$prefix"; then
- prefixes=
- else
- if $posix_mkdir; then
- (umask=$mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
- # Don't fail if two instances are running concurrently.
- test -d "$prefix" || exit 1
- else
- case $prefix in
- *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
- *) qprefix=$prefix;;
- esac
- prefixes="$prefixes '$qprefix'"
- fi
- fi
- prefix=$prefix/
- done
-
- if test -n "$prefixes"; then
- # Don't fail if two instances are running concurrently.
- (umask $mkdir_umask &&
- eval "\$doit_exec \$mkdirprog $prefixes") ||
- test -d "$dstdir" || exit 1
- obsolete_mkdir_used=true
- fi
- fi
- fi
-
- if test -n "$dir_arg"; then
- { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
- { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
- test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
- else
-
- # Make a couple of temp file names in the proper directory.
- dsttmp=$dstdir/_inst.$$_
- rmtmp=$dstdir/_rm.$$_
-
- # Trap to clean up those temp files at exit.
- trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
-
- # Copy the file name to the temp name.
- (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
-
- # and set any options; do chmod last to preserve setuid bits.
- #
- # If any of these fail, we abort the whole thing. If we want to
- # ignore errors from any of these, just make sure not to ignore
- # errors from the above "$doit $cpprog $src $dsttmp" command.
- #
- { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
- { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
- { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
- { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
-
- # If -C, don't bother to copy if it wouldn't change the file.
- if $copy_on_change &&
- old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
- new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
-
- eval "$initialize_posix_glob" &&
- $posix_glob set -f &&
- set X $old && old=:$2:$4:$5:$6 &&
- set X $new && new=:$2:$4:$5:$6 &&
- $posix_glob set +f &&
-
- test "$old" = "$new" &&
- $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
- then
- rm -f "$dsttmp"
- else
- # Rename the file to the real destination.
- $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
-
- # The rename failed, perhaps because mv can't rename something else
- # to itself, or perhaps because mv is so ancient that it does not
- # support -f.
- {
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
- test ! -f "$dst" ||
- $doit $rmcmd -f "$dst" 2>/dev/null ||
- { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
- { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
- } ||
- { echo "$0: cannot unlink or rename $dst" >&2
- (exit 1); exit 1
- }
- } &&
-
- # Now rename the file to the real destination.
- $doit $mvcmd "$dsttmp" "$dst"
- }
- fi || exit 1
-
- trap '' 0
- fi
-done
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
diff --git a/trinity-plugins/parafly-code/missing b/trinity-plugins/parafly-code/missing
deleted file mode 100755
index 86a8fc3..0000000
--- a/trinity-plugins/parafly-code/missing
+++ /dev/null
@@ -1,331 +0,0 @@
-#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
-
-scriptversion=2012-01-06.13; # UTC
-
-# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
-# 2008, 2009, 2010, 2011, 2012 Free Software Foundation, Inc.
-# Originally by Fran,cois Pinard <pinard at iro.umontreal.ca>, 1996.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-if test $# -eq 0; then
- echo 1>&2 "Try \`$0 --help' for more information"
- exit 1
-fi
-
-run=:
-sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
-sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
-
-# In the cases where this matters, `missing' is being run in the
-# srcdir already.
-if test -f configure.ac; then
- configure_ac=configure.ac
-else
- configure_ac=configure.in
-fi
-
-msg="missing on your system"
-
-case $1 in
---run)
- # Try to run requested program, and just exit if it succeeds.
- run=
- shift
- "$@" && exit 0
- # Exit code 63 means version mismatch. This often happens
- # when the user try to use an ancient version of a tool on
- # a file that requires a minimum version. In this case we
- # we should proceed has if the program had been absent, or
- # if --run hadn't been passed.
- if test $? = 63; then
- run=:
- msg="probably too old"
- fi
- ;;
-
- -h|--h|--he|--hel|--help)
- echo "\
-$0 [OPTION]... PROGRAM [ARGUMENT]...
-
-Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
-error status if there is no known handling for PROGRAM.
-
-Options:
- -h, --help display this help and exit
- -v, --version output version information and exit
- --run try to run the given command, and emulate it if it fails
-
-Supported PROGRAM values:
- aclocal touch file \`aclocal.m4'
- autoconf touch file \`configure'
- autoheader touch file \`config.h.in'
- autom4te touch the output file, or create a stub one
- automake touch all \`Makefile.in' files
- bison create \`y.tab.[ch]', if possible, from existing .[ch]
- flex create \`lex.yy.c', if possible, from existing .c
- help2man touch the output file
- lex create \`lex.yy.c', if possible, from existing .c
- makeinfo touch the output file
- yacc create \`y.tab.[ch]', if possible, from existing .[ch]
-
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
-
-Send bug reports to <bug-automake at gnu.org>."
- exit $?
- ;;
-
- -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
- echo "missing $scriptversion (GNU Automake)"
- exit $?
- ;;
-
- -*)
- echo 1>&2 "$0: Unknown \`$1' option"
- echo 1>&2 "Try \`$0 --help' for more information"
- exit 1
- ;;
-
-esac
-
-# normalize program name to check for.
-program=`echo "$1" | sed '
- s/^gnu-//; t
- s/^gnu//; t
- s/^g//; t'`
-
-# Now exit if we have it, but it failed. Also exit now if we
-# don't have it and --version was passed (most likely to detect
-# the program). This is about non-GNU programs, so use $1 not
-# $program.
-case $1 in
- lex*|yacc*)
- # Not GNU programs, they don't have --version.
- ;;
-
- *)
- if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
- # We have it, but it failed.
- exit 1
- elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
- # Could not run --version or --help. This is probably someone
- # running `$TOOL --version' or `$TOOL --help' to check whether
- # $TOOL exists and not knowing $TOOL uses missing.
- exit 1
- fi
- ;;
-esac
-
-# If it does not exist, or fails to run (possibly an outdated version),
-# try to emulate it.
-case $program in
- aclocal*)
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-clean: clean-am
-
-clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
-
-distclean: distclean-am
- -rm -rf ./$(DEPDIR)
- -rm -f Makefile
-distclean-am: clean-am distclean-compile distclean-generic \
- distclean-tags
-
-dvi: dvi-am
-
-dvi-am:
-
-html: html-am
-
-html-am:
-
-info: info-am
-
-info-am:
-
-install-data-am:
-
-install-dvi: install-dvi-am
-
-install-dvi-am:
-
-install-exec-am: install-binPROGRAMS
-
-install-html: install-html-am
-
-install-html-am:
-
-install-info: install-info-am
-
-install-info-am:
-
-install-man:
-
-install-pdf: install-pdf-am
-
-install-pdf-am:
-
-install-ps: install-ps-am
-
-install-ps-am:
-
-installcheck-am:
-
-maintainer-clean: maintainer-clean-am
- -rm -rf ./$(DEPDIR)
- -rm -f Makefile
-maintainer-clean-am: distclean-am maintainer-clean-generic
-
-mostlyclean: mostlyclean-am
-
-mostlyclean-am: mostlyclean-compile mostlyclean-generic
-
-pdf: pdf-am
-
-pdf-am:
-
-ps: ps-am
-
-ps-am:
-
-uninstall-am: uninstall-binPROGRAMS
-
-.MAKE: install-am install-strip
-
-.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
- clean-generic ctags distclean distclean-compile \
- distclean-generic distclean-tags distdir dvi dvi-am html \
- html-am info info-am install install-am install-binPROGRAMS \
- install-data install-data-am install-dvi install-dvi-am \
- install-exec install-exec-am install-html install-html-am \
- install-info install-info-am install-man install-pdf \
- install-pdf-am install-ps install-ps-am install-strip \
- installcheck installcheck-am installdirs maintainer-clean \
- maintainer-clean-generic mostlyclean mostlyclean-compile \
- mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
- uninstall-am uninstall-binPROGRAMS
-
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:
diff --git a/trinity-plugins/parafly-code/src/ParaFly.cpp b/trinity-plugins/parafly-code/src/ParaFly.cpp
deleted file mode 100644
index fdf1437..0000000
--- a/trinity-plugins/parafly-code/src/ParaFly.cpp
+++ /dev/null
@@ -1,268 +0,0 @@
-#include <iostream>
-#include <string>
-#include <fstream>
-#include <cstdlib>
-#include <sstream>
-#include <omp.h>
-#include <vector>
-#include <map>
-#include <algorithm>
-#include <signal.h>
-#include <sys/wait.h>
-
-#include "argProcessor.hpp"
-
-
-string usage();
-
-
-using namespace std;
-
-
-static int VERBOSE_LEVEL = 0;
-
-int main(int argc, char* argv[]) {
-
- /* This program executes commands in Parallel using C++, the program is a wrapper designed for the orignal Trinity Program
- for seemless parallel OPENMP execution, Authors of this wrapper are MB Couger (mbcouger(AT Symbol)gmail.com, Matt Stowe mstowe(AT Symbol)okstate.edu*/
- // code modified by bhaas for general cmd-line processing
-
-
- ArgProcessor args(argc, argv);
-
- bool shuffle_flag = false;
-
-
- if (args.isArgSet("-help")
- || ! (args.isArgSet("-c") )
- || ! (args.isArgSet("-CPU") )
- ) {
- cerr << usage() << endl << endl;
- return(1);
- }
-
- if (args.isArgSet("-v")) {
- VERBOSE_LEVEL = 1;
- }
- else if (args.isArgSet("-vv")) {
- VERBOSE_LEVEL = 2;
- }
-
- if (args.isArgSet("-shuffle")) {
- shuffle_flag = true;
- }
-
-
- string commands_file = args.getStringVal("-c");
-
- int num_cpus = args.getIntVal("-CPU");
-
-
- string failed_commands_filename = "FailedCommands";
- if (args.isArgSet("-failed_cmds")) {
- failed_commands_filename = args.getStringVal("-failed_cmds");
- }
-
- //declare variables start input stream
- ifstream in; // Create an input file stream.
- in.open(commands_file.c_str()); // Use it to read from a file named data.txt.
- if ( ! in ) {
- stringstream errstr;
- errstr << "Error, cannot open file : " << commands_file << endl;
- cerr << errstr.str();
- exit(1);
- }
-
-
- // check to see if any commands had completed
- map<string,bool> previously_completed_commands;
- bool have_previously_completed_commands = false;
-
- ofstream successfully_completed_fh;
-
- {
- ifstream prev_completed_fh;
- stringstream completed_commands_filename_ss;
- completed_commands_filename_ss << commands_file << ".completed";
- string completed_commands_filename = completed_commands_filename_ss.str();
- prev_completed_fh.open(completed_commands_filename.c_str());
-
- if (prev_completed_fh) {
- have_previously_completed_commands = true;
-
- string command_line;
- getline(prev_completed_fh, command_line);
- while(! prev_completed_fh.eof()) {
- previously_completed_commands[command_line] = true;
- getline(prev_completed_fh, command_line);
- }
- prev_completed_fh.close();
- }
-
- successfully_completed_fh.open(completed_commands_filename.c_str(), ios_base::app); // open for append
- }
-
- long int NumberofCommands;
- NumberofCommands=0;
-
- vector<string> commandsArray;
-
- string line;
- getline(in,line);
-
- while (! in.eof()) {
-
- if (have_previously_completed_commands
- &&
- previously_completed_commands.find(line) != previously_completed_commands.end()) {
-
- // this command has been run before successfully, not running it again.
- if (VERBOSE_LEVEL) {
- cerr << "warning, command: " << line << " has successfully completed from a previous run. Skipping it here." << endl;
- }
-
-
- }
- else {
- NumberofCommands++;
- commandsArray.push_back(line);
- }
- getline(in,line);
- }
-
- if (VERBOSE_LEVEL) {
- cerr << "Number of Commands: " << NumberofCommands << endl;
- }
-
- //Parrell Execution of Individual Commands
- vector<string> failedCommands;
- int num_failed_commands = 0;
- int num_succeeded_commands = 0;
-
- if (shuffle_flag) {
- random_shuffle(commandsArray.begin(), commandsArray.end());
- }
-
- omp_set_dynamic(0);
- omp_set_num_threads(num_cpus);
-
- #pragma omp parallel for schedule (dynamic)
- for (long int i=0;i<NumberofCommands;i++) {
- string command = commandsArray[i];
-
- if (VERBOSE_LEVEL == 2) {
-
- int thread_no = omp_get_thread_num();
-
- #pragma omp critical (standard_error)
- {
- cerr << "CMD[" << i << "], thread[" << thread_no << "]: " << command << endl;
- }
- }
-
- int ret = system(command.c_str());
-
- // exit if child received SIGINT or SIGQUIT
- if (WIFSIGNALED(ret) &&
- (WTERMSIG(ret) == SIGINT || WTERMSIG(ret) == SIGQUIT)) {
- #pragma omp critical (exit_critical)
- exit(ret); // behavior undefined if exit() called more than once
- }
- else if (ret != 0) {
-
- #pragma omp critical (capture_failed_command)
- {
- num_failed_commands++;
- failedCommands.push_back(command);
- }
-
-
- if (VERBOSE_LEVEL == 2) {
- #pragma omp critical (standard_error)
- {
- cerr << "FAILURE:[" << i << "] " << command << endl;
- }
- }
-
- }
- else {
- #pragma omp critical (report_success)
- {
- num_succeeded_commands++;
-
- successfully_completed_fh << command << endl;
- }
-
- if (VERBOSE_LEVEL == 2) {
- #pragma omp critical (standard_error)
- cerr << "SUCCESS:[" << i << "] " << command << endl;
- }
- }
-
- if (VERBOSE_LEVEL == 1) {
-
- stringstream ss;
- ss << "\rsucceeded(" << num_succeeded_commands << ")";
- if (num_failed_commands > 0) {
- ss << ", failed(" << num_failed_commands << ")";
- }
- int total_executed = num_succeeded_commands + num_failed_commands;
- float percent_done = (float)total_executed/NumberofCommands * 100;
-
- ss << " " << percent_done << "% completed. ";
-
- #pragma omp critical (standard_error)
- cerr << ss.str();
- }
- }
-
- successfully_completed_fh.close();
-
-
- //ErrorCheckingOut
- if (num_failed_commands != 0) {
- ofstream outdata(failed_commands_filename.c_str());
- for (int t=0;t<num_failed_commands; ++t) {
- outdata << failedCommands[t] << endl;
- }
- outdata.close();
- cout << endl << endl << "We are sorry, commands in file: [" << failed_commands_filename << "] failed. :-( " << endl << endl;
-
- exit(1);
- }
- else {
- if (VERBOSE_LEVEL) {
- cout << endl << endl << "All commands completed successfully. :-)" << endl << endl;
- }
- exit(0); // used to be return(0), but sometimes in OMP land this would not exit 0....?!?!
- }
-
-}
-
-string usage () {
-
- stringstream ss;
-
- ss << endl
- << "##########################################################" << endl
- << "#" << endl
- << "# Usage: ParaFly (opts)" << endl
- << "#" << endl
- << "# Required: " << endl
- << "# -c <str> :filename containing list of bash-style commands to execute." << endl
- << "# -CPU <int> :number_of_threads" << endl
- << "#" << endl
- << "# Optional:" << endl
- << "# -shuffle :randomly shuffles the command order. " << endl
- << "# -failed_cmds <str> :filename to capture failed commands. default(\"FailedCommands\")" << endl
- << "# -v :simple progress monitoring." << endl
- << "# -vv :increased verbosity in progress monitoring." << endl
- << "#" << endl
- << "##########################################################" << endl << endl;
-
- ss << "Note: This process creates a file named based on your commands filename with a .completed extension." << endl
- << "This enables a resume functionality, where if rerun, only those commands not completed successfully will be reprocessed." << endl << endl;
-
- return(ss.str());
-}
-
diff --git a/trinity-plugins/parafly-code/src/argProcessor.cpp b/trinity-plugins/parafly-code/src/argProcessor.cpp
deleted file mode 100755
index 4842ac3..0000000
--- a/trinity-plugins/parafly-code/src/argProcessor.cpp
+++ /dev/null
@@ -1,61 +0,0 @@
-#include "argProcessor.hpp"
-#include <stdlib.h>
-// #include <cstdlib>
-
-ArgProcessor::ArgProcessor(int argc, char* argv[]) {
-
- for (int i=1; i < argc; i++) {
- char* arg = argv[i];
- string myArg (arg);
- if (arg[0] == '-') {
-
- argSet[myArg] = true;
-
- // see if next argument is another arg or value:
- if (i != argc-1) {
- // value:
- string nextArg (argv[i+1]);
- argVal[myArg] = nextArg;
- }
- }
- }
-
-}
-
-
-bool ArgProcessor::isArgSet(string arg) {
-
- map<string,bool>::const_iterator it;
-
- it = argSet.find(arg);
- if (it != argSet.end()) {
- return(true);
- }
- else {
- return(false);
- }
-}
-
-int ArgProcessor::getIntVal(string arg) {
-
- return(atoi(argVal[arg].c_str()));
-
-}
-
-long ArgProcessor::getLongVal(string arg) {
- return(atol(argVal[arg].c_str()));
-}
-
-
-float ArgProcessor::getFloatVal(string arg) {
-
- return(atof(argVal[arg].c_str()));
-}
-
-
-string ArgProcessor::getStringVal(string arg) {
-
- return(argVal[arg]);
-}
-
-
diff --git a/trinity-plugins/parafly-code/src/argProcessor.hpp b/trinity-plugins/parafly-code/src/argProcessor.hpp
deleted file mode 100755
index ac1ed45..0000000
--- a/trinity-plugins/parafly-code/src/argProcessor.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#ifndef __argProcessor__
-#define __argProcessor__
-
-#include <map>
-#include <string>
-using namespace std;
-
-class ArgProcessor {
-
-public:
- ArgProcessor(int argc, char* argv[]);
-
- bool isArgSet(string arg);
-
- int getIntVal(string arg);
-
- long getLongVal(string arg);
-
- float getFloatVal(string arg);
-
- string getStringVal(string arg);
-
-private:
- map<string,bool> argSet;
- map<string,string> argVal;
-
-};
-
-
-#endif
-
diff --git a/trinity-plugins/parafly-code/stamp-h1 b/trinity-plugins/parafly-code/stamp-h1
deleted file mode 100644
index 4547fe1..0000000
--- a/trinity-plugins/parafly-code/stamp-h1
+++ /dev/null
@@ -1 +0,0 @@
-timestamp for config.h
diff --git a/trinity-plugins/rsem-1.2.19.tar.gz b/trinity-plugins/rsem-1.2.19.tar.gz
deleted file mode 100644
index c591033..0000000
Binary files a/trinity-plugins/rsem-1.2.19.tar.gz and /dev/null differ
diff --git a/util/align_and_estimate_abundance.pl b/util/align_and_estimate_abundance.pl
index b11e243..c4ad94b 100755
--- a/util/align_and_estimate_abundance.pl
+++ b/util/align_and_estimate_abundance.pl
@@ -461,22 +461,22 @@ main: {
if ($aln_method eq 'bowtie') {
if ($left && $right) {
- $bowtie_cmd = "bowtie $read_type " . $aligner_params{"${aln_method}_${est_method}"} . " -X $max_ins_size -S -p $thread_count $db_index_name -1 $left -2 $right | samtools view -F 4 -S -b -o $bam_file -";
+ $bowtie_cmd = "set -o pipefail && bowtie $read_type " . $aligner_params{"${aln_method}_${est_method}"} . " -X $max_ins_size -S -p $thread_count $db_index_name -1 $left -2 $right | samtools view -F 4 -S -b -o $bam_file -";
}
else {
- $bowtie_cmd = "bowtie $read_type " . $aligner_params{"${aln_method}_${est_method}"} . " -S -p $thread_count $db_index_name $single | samtools view -F 4 -S -b -o $bam_file -";
+ $bowtie_cmd = "set -o pipefail && bowtie $read_type " . $aligner_params{"${aln_method}_${est_method}"} . " -S -p $thread_count $db_index_name $single | samtools view -F 4 -S -b -o $bam_file -";
}
}
elsif ($aln_method eq 'bowtie2') {
if ($left && $right) {
- $bowtie_cmd = "bowtie2 " . $aligner_params{"${aln_method}_${est_method}"} . " $read_type -X $max_ins_size -x $db_index_name -1 $left -2 $right -p $thread_count | samtools view -F 4 -S -b -o $bam_file -";
+ $bowtie_cmd = "set -o pipefail && bowtie2 " . $aligner_params{"${aln_method}_${est_method}"} . " $read_type -X $max_ins_size -x $db_index_name -1 $left -2 $right -p $thread_count | samtools view -F 4 -S -b -o $bam_file -";
}
else {
- $bowtie_cmd = "bowtie2 " . $aligner_params{"${aln_method}_${est_method}"} . " $read_type -x $db_index_name -U $single -p $thread_count | samtools view -F 4 -S -b -o $bam_file -";
+ $bowtie_cmd = "set -o pipefail && bowtie2 " . $aligner_params{"${aln_method}_${est_method}"} . " $read_type -x $db_index_name -U $single -p $thread_count | samtools view -F 4 -S -b -o $bam_file -";
}
}
diff --git a/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl b/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
index b062823..c396a28 100755
--- a/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
+++ b/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
@@ -71,7 +71,8 @@ main: {
unless (-d "$genomeBaseDir/$genomeDir") {
- my $cmd = "gmap_build -D $genomeBaseDir -d $genomeBaseDir/$genomeDir -k 13 $genome >&2";
+ #my $cmd = "gmap_build -D $genomeBaseDir -d $genomeBaseDir/$genomeDir -k 13 $genome >&2";
+ my $cmd = "gmap_build -D $genomeBaseDir -T $genomeBaseDir -d $genomeDir -k 13 $genome >&2";
&process_cmd($cmd);
}
diff --git a/util/misc/run_GSNAP.pl b/util/misc/run_GSNAP.pl
index f27b4b8..0681b7d 100755
--- a/util/misc/run_GSNAP.pl
+++ b/util/misc/run_GSNAP.pl
@@ -25,6 +25,7 @@ my $usage = <<__EOUSAGE__;
# -G <string> GTF file for incorporating reference splice site info.
# --CPU <int> number of threads (default: 2)
# --out_prefix <string> output prefix (default: gsnap)
+# --no_sarray skip the sarray in the gmap-build
#
#######################################################################
@@ -44,7 +45,7 @@ my $help_flag;
my $num_top_hits = 1;
my $out_prefix = "gsnap";
my $gtf_file;
-
+my $no_sarray = "";
&GetOptions( 'h' => \$help_flag,
'genome=s' => \$genome,
@@ -54,13 +55,17 @@ my $gtf_file;
'N=i' => \$num_top_hits,
'out_prefix=s' => \$out_prefix,
'G=s' => \$gtf_file,
- );
+ 'no_sarray' => \$no_sarray,
+ );
unless ($genome && $reads) {
die $usage;
}
+if ($no_sarray) {
+ $no_sarray = "--no-sarray";
+}
main: {
@@ -73,7 +78,9 @@ main: {
unless (-d "$genomeBaseDir/$genomeDir") {
- my $cmd = "gmap_build -D $genomeBaseDir -d $genomeDir -k 13 $genome >&2";
+
+
+ my $cmd = "gmap_build -D $genomeBaseDir -d $genomeDir -T $genomeBaseDir -k 13 $no_sarray $genome >&2";
&process_cmd($cmd);
}
@@ -88,21 +95,53 @@ main: {
&process_cmd($cmd);
$cmd = "iit_store -o $splice_file.iit < $splice_file";
+ &process_cmd($cmd);
}
$splice_param = "--use-splicing=$splice_file.iit";
}
-
+
## run GMAP
- my $cmd = "gsnap -D $genomeBaseDir -d $genomeDir -A sam -N 1 -w $max_intron -n $num_top_hits -t $CPU $reads $splice_param | samtools view -bS - | samtools sort -@ $CPU - $out_prefix.cSorted";
+ my $gsnap_use_sarray = ($no_sarray) ? "--use-sarray=0" : "";
+
+ $reads = &add_zcat_fifo($reads);
+
+ my $cmd = "bash -c \"set -o pipefail && gsnap -D $genomeBaseDir -d $genomeDir -A sam -N 1 -w $max_intron $gsnap_use_sarray -n $num_top_hits -t $CPU $reads $splice_param | samtools view -bS -F 4 - | samtools sort -@ $CPU - $out_prefix.cSorted \"";
&process_cmd($cmd);
-
+
+ if (-s "$out_prefix.cSorted.bam") {
+ $cmd = "samtools index $out_prefix.cSorted.bam";
+ &process_cmd($cmd);
+ }
exit(0);
}
+
+####
+sub add_zcat_fifo {
+ my ($reads) = @_;
+
+ my @adj_reads_list;
+
+ foreach my $reads_file (split(/\s+/, $reads) ) {
+ if ($reads_file =~ /\.gz$/) {
+ $reads_file = "<(zcat $reads_file)";
+ }
+ push (@adj_reads_list, $reads_file);
+ }
+
+ my $adj_reads = join(" ", @adj_reads_list);
+
+ return($adj_reads);
+}
+
+
+
+
+
####
sub process_cmd {
my ($cmd) = @_;
diff --git a/util/support_scripts/tests.py b/util/support_scripts/tests.py
index 0f24adc..8bb17d3 100644
--- a/util/support_scripts/tests.py
+++ b/util/support_scripts/tests.py
@@ -13,8 +13,7 @@ import time
# Copy the .gz files in sample_data/test_Trinity_Assembly to current directory
# Run using nosetests
MEM_FLAG = "--max_memory 2G"
-TEMP_FILES = ['both.fa', 'bowtie.nameSorted.bam', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa',
- 'scaffolding_entries.sam', 'target.fa', 'target.1.ebwt']
+TEMP_FILES = ['both.fa', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa', 'scaffolding_entries.sam']
class TestTrinity(unittest.TestCase):
@@ -35,7 +34,7 @@ class TestTrinity(unittest.TestCase):
handle = open("trinity_out_dir/Trinity.fasta", "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
- self.assertTrue(75 <= seq_count <= 85, msg='Found %s sequences' % seq_count)
+ self.assertTrue(75 <= seq_count <= 90, msg='Found %s sequences' % seq_count)
def test_sample_data_trimmed_and_normalized(self):
self.trinity(
@@ -72,13 +71,6 @@ class TestTrinity(unittest.TestCase):
self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_run_chrysalis" % MEM_FLAG)
self.assertEquals(0, len(os.listdir('trinity_out_dir/chrysalis')))
- def test_no_run_butterfly(self):
- self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_run_butterfly" % MEM_FLAG)
- self.assertTrue(os.path.isfile("trinity_out_dir/chrysalis/butterfly_commands"),
- msg="butterfly_commands file does not exist")
- self.assertFalse(os.path.isfile("trinity_out_dir/butterfly_commands.completed"),
- msg="Butterfly appears to have run although no_run_butterfly was specified")
-
def test_no_run_inchworm(self):
self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_run_inchworm" % MEM_FLAG)
self.assertFalse(os.path.isfile("trinity_out_dir/inchworm.K25.L25.fa.finished"),
@@ -91,14 +83,14 @@ class TestTrinity(unittest.TestCase):
self.assertFalse(os.path.isfile("trinity_out_dir/bowtie.nameSorted.bam"),
msg="Bowtie appears to have run although no_bowtie was specified")
- def test_no_run_quantifygraph(self):
- self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_run_quantifygraph" % MEM_FLAG)
- self.assertTrue(os.path.isfile("trinity_out_dir/chrysalis/file_partitioning.ok"),
- msg="file_partitioning.ok flag file does not exist")
- self.assertTrue(os.path.isfile("trinity_out_dir/chrysalis/quantifyGraph_commands"),
- msg="quantifyGraph_commands file does not exist")
+ def test_no_distributed_trinity_exec(self):
+ self.trinity("Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --no_distributed_trinity_exec" % MEM_FLAG)
+ self.assertTrue(os.path.isfile("trinity_out_dir/inchworm.K25.L25.fa.finished"),
+ msg="Inchworm did not appear to run with no_distributed_trinity_exec flag")
+ self.assertTrue(os.path.isfile("trinity_out_dir/jellyfish.1.finished"),
+ msg="Jellyfish did not appear to run with no_distributed_trinity_exec flag")
self.assertFalse(os.path.isfile("trinity_out_dir/Trinity.fasta"),
- msg="Trinity.fasta created with no_run_quantifygraph")
+ msg="Trinity.fasta created with no_distributed_trinity_exec")
def test_single_end_with_fa_and_reverse(self):
self.fq2fa()
@@ -110,12 +102,6 @@ class TestTrinity(unittest.TestCase):
self.assertTrue(os.path.exists("trinity_test"), msg="Changed output directory but it was not created")
shutil.rmtree('trinity_test', True)
- def test_chrysalis_output_correctly_changes_dir(self):
- self.trinity(
- "Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --chrysalis_output chrysalis_test" % MEM_FLAG)
- self.assertTrue(os.path.exists("trinity_out_dir/chrysalis_test"),
- msg="Changed chrysalis output directory but it was not created")
-
### information tests
def test_cite(self):
expected = '\n\n* Trinity:\nFull-length transcriptome assembly from RNA-Seq data without a reference genome.\nGrabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L,\nRaychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F,\nBirren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.\nNature Biotechnology 29, 644\xe2\x80\x93652 (2011)\nPaper: http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html\nCode: http://trinityrna [...]
@@ -127,8 +113,9 @@ class TestTrinity(unittest.TestCase):
subprocess.check_output(["Trinity", "--version"])
self.fail("Version returned 0 errorcode!")
except subprocess.CalledProcessError as e:
- self.assertEqual('Trinity version: BLEEDING_EDGE\n', e.output)
+ #self.assertEqual('Trinity version: BLEEDING_EDGE\n', e.output)
#self.assertEqual('Trinity version: trinityrnaseq_r20140717\n', e.output)
+ self.assertEqual('Trinity version: Trinity_v2.0.2\n', e.output)
def test_show_full_usage_info(self):
@@ -146,11 +133,6 @@ class TestTrinity(unittest.TestCase):
error = self.get_error("Trinity --seqType fq --single reads.left.fq --SS_lib_type F")
self.assertTrue("Error, must specify max memory for jellyfish to use, eg. --max_memory 10G" in error)
- def test_chrysalis_output_must_include_chrysalis(self):
- error = self.get_error(
- "Trinity %s --seqType fq --single reads.left.fq --SS_lib_type F --chrysalis_output invalid_name" % MEM_FLAG)
- self.assertTrue("Error, chrysalis output directory name must include 'chrysalis' in the name" in error)
-
def test_invalid_option_error(self):
error = self.get_error("Trinity --squidward")
self.assertTrue("Error, do not understand options: --squidward" in error)
--
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