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@cctsou
cctsou committed Nov 13, 2015
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4 changes: 3 additions & 1 deletion .gitignore
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/Umpire-SpectrumParser/nbproject/private/
/Umpire-UmpireSearch/nbproject/private/
/Umpire-Utility/nbproject/private/
/DIA-Umpire/nbproject/private/
/DIA-Umpire/nbproject/private/
/DIA_Umpire_To_Skyline/nbproject/private/
/MS1Quant/nbproject/private/
6 changes: 3 additions & 3 deletions ...e/src/ExtPackages/JAligner/Alignment.java → .../ExternalPackages/JAligner/Alignment.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

import ExtPackages.JAligner.matrix.Matrix;
import ExtPackages.JAligner.util.Commons;
import ExternalPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.util.Commons;

import java.text.DecimalFormat;

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2 changes: 1 addition & 1 deletion ...Umpire/src/ExtPackages/JAligner/Cell.java → ...e/src/ExternalPackages/JAligner/Cell.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

/**
* A cell in a similarity matrix, to hold row, column and score.
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

/**
* Traceback directions.
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2 changes: 1 addition & 1 deletion ...ire/src/ExtPackages/JAligner/Markups.java → ...rc/ExternalPackages/JAligner/Markups.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

/**
* Markups line characters.
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4 changes: 2 additions & 2 deletions ...ExtPackages/JAligner/NeedlemanWunsch.java → ...nalPackages/JAligner/NeedlemanWunsch.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

import ExtPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.Matrix;

/**
* An implementation of the Needleman-Wunsch algorithm for biological global
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4 changes: 2 additions & 2 deletions ...ckages/JAligner/NeedlemanWunschGotoh.java → ...ckages/JAligner/NeedlemanWunschGotoh.java
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* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
package ExtPackages.JAligner;
package ExternalPackages.JAligner;

import ExtPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.Matrix;

import java.util.logging.Logger;

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4 changes: 2 additions & 2 deletions ...re/src/ExtPackages/JAligner/Sequence.java → ...c/ExternalPackages/JAligner/Sequence.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

import ExtPackages.JAligner.util.Commons;
import ExternalPackages.JAligner.util.Commons;

import java.io.Serializable;

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4 changes: 2 additions & 2 deletions ...Packages/JAligner/SmithWatermanGotoh.java → ...Packages/JAligner/SmithWatermanGotoh.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

import ExtPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.Matrix;

import java.util.logging.Logger;

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2 changes: 1 addition & 1 deletion ...c/ExtPackages/JAligner/TracebackNode.java → ...ernalPackages/JAligner/TracebackNode.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner;
package ExternalPackages.JAligner;

/**
* Traceback node
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18 changes: 9 additions & 9 deletions ...igner/example/NeedlemanWunschExample.java → ...igner/example/NeedlemanWunschExample.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.example;
package ExternalPackages.JAligner.example;

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.NeedlemanWunsch;
import ExtPackages.JAligner.Sequence;
import ExtPackages.JAligner.formats.Pair;
import ExtPackages.JAligner.matrix.Matrix;
import ExtPackages.JAligner.matrix.MatrixGenerator;
import ExtPackages.JAligner.util.SequenceParser;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.NeedlemanWunsch;
import ExternalPackages.JAligner.Sequence;
import ExternalPackages.JAligner.formats.Pair;
import ExternalPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.MatrixGenerator;
import ExternalPackages.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 ExtPackages.JAligner.NeedlemanWunsch}.
* with Needleman-Wunsch algorithm {@link ExternalPackages.JAligner.NeedlemanWunsch}.
*
* @author Ahmed Moustafa
*/
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18 changes: 9 additions & 9 deletions .../example/NeedlemanWunschGotohExample.java → .../example/NeedlemanWunschGotohExample.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.example;
package ExternalPackages.JAligner.example;
/*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.NeedlemanWunschGotoh;
import ExtPackages.JAligner.Sequence;
import ExtPackages.JAligner.formats.Pair;
import ExtPackages.JAligner.matrix.Matrix;
import ExtPackages.JAligner.matrix.MatrixGenerator;
import ExtPackages.JAligner.util.SequenceParser;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.NeedlemanWunschGotoh;
import ExternalPackages.JAligner.Sequence;
import ExternalPackages.JAligner.formats.Pair;
import ExternalPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.MatrixGenerator;
import ExternalPackages.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 ExtPackages.JAligner.NeedlemanWunschGotoh}.
* with {@link ExternalPackages.JAligner.NeedlemanWunschGotoh}.
*
* @author Ahmed Moustafa
*/
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14 changes: 7 additions & 7 deletions ...er/example/SmithWatermanGotohExample.java → ...er/example/SmithWatermanGotohExample.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.example;
package ExternalPackages.JAligner.example;

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.Sequence;
import ExtPackages.JAligner.SmithWatermanGotoh;
import ExtPackages.JAligner.formats.Pair;
import ExtPackages.JAligner.matrix.MatrixLoader;
import ExtPackages.JAligner.util.SequenceParser;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.Sequence;
import ExternalPackages.JAligner.SmithWatermanGotoh;
import ExternalPackages.JAligner.formats.Pair;
import ExternalPackages.JAligner.matrix.MatrixLoader;
import ExternalPackages.JAligner.util.SequenceParser;

import java.io.IOException;
import java.io.InputStream;
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4 changes: 2 additions & 2 deletions ...ExtPackages/JAligner/formats/CLUSTAL.java → ...nalPackages/JAligner/formats/CLUSTAL.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.formats;
package ExternalPackages.JAligner.formats;

import ExtPackages.JAligner.Alignment;
import ExternalPackages.JAligner.Alignment;

/**
* CLUSTAL format.
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6 changes: 3 additions & 3 deletions ...c/ExtPackages/JAligner/formats/FASTA.java → ...ernalPackages/JAligner/formats/FASTA.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.formats;
package ExternalPackages.JAligner.formats;

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.Sequence;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.Sequence;

/**
* <a href="http://www.ncbi.nlm.nih.gov/BLAST/fasta.html">FASTA</a> format.
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.formats;
package ExternalPackages.JAligner.formats;

import ExtPackages.JAligner.Alignment;
import ExternalPackages.JAligner.Alignment;

/**
* Abstract format
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2 changes: 1 addition & 1 deletion ...kages/JAligner/formats/FormatFactory.java → ...kages/JAligner/formats/FormatFactory.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.formats;
package ExternalPackages.JAligner.formats;

import java.util.Collection;
import java.util.HashMap;
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.formats;
package ExternalPackages.JAligner.formats;

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.util.Commons;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.util.Commons;

/**
* <a href="http://emboss.sourceforge.net/docs/themes/AlignFormats.html">Alignment Formats</a>.
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.matrix;
package ExternalPackages.JAligner.matrix;

import java.util.Comparator;

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* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
package ExtPackages.JAligner.matrix;
package ExternalPackages.JAligner.matrix;

import java.io.Serializable;

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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.matrix;
package ExternalPackages.JAligner.matrix;

/**
* A utility class to generate a scoring matrix from a fixed match and mismatch
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6 changes: 3 additions & 3 deletions ...ackages/JAligner/matrix/MatrixLoader.java → ...ackages/JAligner/matrix/MatrixLoader.java
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* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
package ExtPackages.JAligner.matrix;
package ExternalPackages.JAligner.matrix;

import ExtPackages.JAligner.ui.filechooser.NamedInputStream;
import ExtPackages.JAligner.util.Commons;
import ExternalPackages.JAligner.ui.filechooser.NamedInputStream;
import ExternalPackages.JAligner.util.Commons;

import java.io.BufferedReader;
import java.io.File;
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.matrix;
package ExternalPackages.JAligner.matrix;

/**
*
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18 changes: 9 additions & 9 deletions ...gner/test/NeedlemanWunschGotohTester.java → ...gner/test/NeedlemanWunschGotohTester.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.test;
package ExternalPackages.JAligner.test;

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.NeedlemanWunschGotoh;
import ExtPackages.JAligner.Sequence;
import ExtPackages.JAligner.formats.Format;
import ExtPackages.JAligner.formats.Pair;
import ExtPackages.JAligner.matrix.Matrix;
import ExtPackages.JAligner.matrix.MatrixLoader;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.NeedlemanWunschGotoh;
import ExternalPackages.JAligner.Sequence;
import ExternalPackages.JAligner.formats.Format;
import ExternalPackages.JAligner.formats.Pair;
import ExternalPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.MatrixLoader;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Random;

/**
* Testing the scores of the alignments of {@link ExtPackages.JAligner.NeedlemanWunschGotoh}.
* Testing the scores of the alignments of {@link ExternalPackages.JAligner.NeedlemanWunschGotoh}.
*
* @author Bram Minnaert
*/
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18 changes: 9 additions & 9 deletions .../JAligner/test/NeedlemanWunschTester.java → .../JAligner/test/NeedlemanWunschTester.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.test;
package ExternalPackages.JAligner.test;

import ExtPackages.JAligner.Alignment;
import ExtPackages.JAligner.NeedlemanWunsch;
import ExtPackages.JAligner.Sequence;
import ExtPackages.JAligner.formats.Format;
import ExtPackages.JAligner.formats.Pair;
import ExtPackages.JAligner.matrix.Matrix;
import ExtPackages.JAligner.matrix.MatrixLoader;
import ExternalPackages.JAligner.Alignment;
import ExternalPackages.JAligner.NeedlemanWunsch;
import ExternalPackages.JAligner.Sequence;
import ExternalPackages.JAligner.formats.Format;
import ExternalPackages.JAligner.formats.Pair;
import ExternalPackages.JAligner.matrix.Matrix;
import ExternalPackages.JAligner.matrix.MatrixLoader;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Random;

/**
* Testing the scores of the alignments of {@link ExtPackages.JAligner.NeedlemanWunsch}.
* Testing the scores of the alignments of {@link ExternalPackages.JAligner.NeedlemanWunsch}.
*
* @author Ahmed Moustafa
*/
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2 changes: 1 addition & 1 deletion ...Aligner/test/RandomSequenceGenerator.java → ...Aligner/test/RandomSequenceGenerator.java
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/

package ExtPackages.JAligner.test;
package ExternalPackages.JAligner.test;

import java.util.Random;

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