Ejemplo n.º 1
0
 /// <summary>
 /// Initializes a new instance of the MUMmerAttributes class.
 /// </summary>
 public MUMmerAttributes()
 {
     AlignmentInfo alignmentAttribute = new AlignmentInfo(
             Properties.Resource.LENGTH_OF_MUM_NAME,
             Properties.Resource.LENGTH_OF_MUM_DESCRIPTION,
             true,
             "20",
             AlignmentInfo.IntType,
             null);
     Attributes.Add(LengthOfMUM, alignmentAttribute);
 }
Ejemplo n.º 2
0
        /// <summary>
        /// Initializes a new instance of the NUCmerAttributes class.
        /// </summary>
        public NUCmerAttributes()
        {
            AlignmentInfo alignmentAttribute;

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.FIXED_SEPARATION_NAME,
                Properties.Resource.FIXED_SEPARATION_DESCRIPTION,
                true,
                ClusterBuilder.DefaultFixedSeparation.ToString(CultureInfo.InvariantCulture),
                AlignmentInfo.IntType,
                null);
            Attributes.Add(FixedSeparation, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.MAXIMUM_SEPARATION_NAME,
                Properties.Resource.MAXIMUM_SEPARATION_DESCRIPTION,
                true,
                ClusterBuilder.DefaultMaximumSeparation.ToString(CultureInfo.InvariantCulture),
                AlignmentInfo.IntType,
                null);
            Attributes.Add(MaximumSeparation, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.MINIMUM_SCORE_NAME,
                Properties.Resource.MINIMUM_SCORE_DESCRIPTION,
                true,
                ClusterBuilder.DefaultMinimumScore.ToString(CultureInfo.InvariantCulture),
                AlignmentInfo.IntType,
                null);
            Attributes.Add(MinimumScore, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.SEPARATION_FACTOR_NAME,
                Properties.Resource.SEPARATION_FACTOR_DESCRIPTION,
                true,
                ClusterBuilder.DefaultSeparationFactor.ToString(CultureInfo.InvariantCulture),
                AlignmentInfo.FloatType,
                null);
            Attributes.Add(SeparationFactor, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.BREAK_LENGTH_NAME,
                Properties.Resource.BREAK_LENGTH_DESCRIPTION,
                true,
                ModifiedSmithWaterman.DefaultBreakLength.ToString(CultureInfo.InvariantCulture),
                AlignmentInfo.IntType,
                null);
            Attributes.Add(BreakLength, alignmentAttribute);
        }
Ejemplo n.º 3
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        /// <summary>
        /// Initializes a new instance of the NUCmerAttributes class.
        /// </summary>
        public NUCmerAttributes()
        {
            AlignmentInfo alignmentAttribute;

            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.FIXED_SEPARATION_NAME,
                    Properties.Resource.FIXED_SEPARATION_DESCRIPTION,
                    true,
                    ClusterBuilder.DefaultFixedSeparation.ToString(CultureInfo.InvariantCulture),
                    AlignmentInfo.IntType,
                    null);
            Attributes.Add(FixedSeparation, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.MAXIMUM_SEPARATION_NAME,
                    Properties.Resource.MAXIMUM_SEPARATION_DESCRIPTION,
                    true,
                    ClusterBuilder.DefaultMaximumSeparation.ToString(CultureInfo.InvariantCulture),
                    AlignmentInfo.IntType,
                    null);
            Attributes.Add(MaximumSeparation, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.MINIMUM_SCORE_NAME,
                    Properties.Resource.MINIMUM_SCORE_DESCRIPTION,
                    true,
                    ClusterBuilder.DefaultMinimumScore.ToString(CultureInfo.InvariantCulture),
                    AlignmentInfo.IntType,
                    null);
            Attributes.Add(MinimumScore, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.SEPARATION_FACTOR_NAME,
                    Properties.Resource.SEPARATION_FACTOR_DESCRIPTION,
                    true,
                    ClusterBuilder.DefaultSeparationFactor.ToString(CultureInfo.InvariantCulture),
                    AlignmentInfo.FloatType,
                    null);
            Attributes.Add(SeparationFactor, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.BREAK_LENGTH_NAME,
                    Properties.Resource.BREAK_LENGTH_DESCRIPTION,
                    true,
                    ModifiedSmithWaterman.DefaultBreakLength.ToString(CultureInfo.InvariantCulture),
                    AlignmentInfo.IntType,
                    null);
            Attributes.Add(BreakLength, alignmentAttribute);
        }
Ejemplo n.º 4
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        /// <summary>
        /// Initializes a new instance of the PairwiseAlignmentAttributes class.
        /// </summary>
        public PairwiseAlignmentAttributes()
        {
            attributes = new Dictionary <string, AlignmentInfo>();

            StringListValidator similarityMatrixList = new StringListValidator(
                Properties.Resource.SimilarityMatrix_AutoDetectString, // Autodetect
                Properties.Resource.SimilarityMatrix_DiagonalSM,
                SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
                SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
                SM.StandardSimilarityMatrix.Blosum45.ToString(),
                SM.StandardSimilarityMatrix.Blosum50.ToString(),
                SM.StandardSimilarityMatrix.Blosum62.ToString(),
                SM.StandardSimilarityMatrix.Blosum80.ToString(),
                SM.StandardSimilarityMatrix.Blosum90.ToString(),
                SM.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
                SM.StandardSimilarityMatrix.Pam250.ToString(),
                SM.StandardSimilarityMatrix.Pam30.ToString(),
                SM.StandardSimilarityMatrix.Pam70.ToString());

            AlignmentInfo alignmentAttribute = new AlignmentInfo(
                Properties.Resource.SIMILARITY_MATRIX_NAME,
                Properties.Resource.SIMILARITY_MATRIX_DESCRIPTION,
                true,
                Properties.Resource.SimilarityMatrix_AutoDetectString,
                AlignmentInfo.StringListType,
                similarityMatrixList);

            attributes.Add(SimilarityMatrix, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.GAP_COST_NAME,
                Properties.Resource.GAP_COST_DESCRIPTION,
                true,
                "-8",
                AlignmentInfo.IntType,
                null);
            attributes.Add(GapOpenCost, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                Properties.Resource.GAP_EXTENSION_COST_NAME,
                Properties.Resource.GAP_EXTENSION_COST_DESCRIPTION,
                true,
                "-8",
                AlignmentInfo.IntType,
                null);
            attributes.Add(GapExtensionCost, alignmentAttribute);
        }
Ejemplo n.º 5
0
        /// <summary>
        /// Initializes a new instance of the PairwiseAlignmentAttributes class.
        /// </summary>
        public PairwiseAlignmentAttributes()
        {
            attributes = new Dictionary<string, AlignmentInfo>();

            StringListValidator similarityMatrixList = new StringListValidator(
                Properties.Resource.SimilarityMatrix_DiagonalSM,
                SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
                SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
                SM.StandardSimilarityMatrix.Blosum45.ToString(),
                SM.StandardSimilarityMatrix.Blosum50.ToString(),
                SM.StandardSimilarityMatrix.Blosum62.ToString(),
                SM.StandardSimilarityMatrix.Blosum80.ToString(),
                SM.StandardSimilarityMatrix.Blosum90.ToString(),
                SM.StandardSimilarityMatrix.DiagonalScoreMatrix.ToString(),
                SM.StandardSimilarityMatrix.Pam250.ToString(),
                SM.StandardSimilarityMatrix.Pam30.ToString(),
                SM.StandardSimilarityMatrix.Pam70.ToString());

            AlignmentInfo alignmentAttribute = new AlignmentInfo(
                Properties.Resource.SIMILARITY_MATRIX_NAME,
                Properties.Resource.SIMILARITY_MATRIX_DESCRIPTION,
                true,
                SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
                AlignmentInfo.StringListType,
                similarityMatrixList);
            attributes.Add(SimilarityMatrix, alignmentAttribute);
            
            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.GAP_COST_NAME,
                    Properties.Resource.GAP_COST_DESCRIPTION,
                    true,
                    "-10",
                    AlignmentInfo.IntType,
                    null);
            attributes.Add(GapOpenCost, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                    Properties.Resource.GAP_EXTENSION_COST_NAME,
                    Properties.Resource.GAP_EXTENSION_COST_DESCRIPTION,
                    true,
                    "-8",
                    AlignmentInfo.IntType,
                    null);
            attributes.Add(GapExtensionCost, alignmentAttribute);
        }
Ejemplo n.º 6
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        /// <summary>
        /// This method would create text field.
        /// </summary>
        /// <param name="alignmentAttribute">Alignment parameter</param>
        /// <param name="parentPanel">Stack panel, the field will be added to this stackpanel</param>
        /// <param name="tag">Tag of the control object</param>
        private void CreateTextField(
                AlignmentInfo alignmentAttribute,
                StackPanel parentPanel,
                string tag)
        {
            TextBlock block = new TextBlock {
                Margin = new Thickness(0, 10, 0, 0),
                TextWrapping = TextWrapping.Wrap,
                Text = alignmentAttribute.Name,
                Height = 20
            };

            TextBox box = new TextBox {
                HorizontalAlignment = HorizontalAlignment.Left,
                Margin = new Thickness(0, 0, 0, 0),
                TextWrapping = TextWrapping.Wrap,
                Text = alignmentAttribute.DefaultValue,
                Tag = tag,
                Width = 120,
                Height = 20,
                ToolTip = alignmentAttribute.Description
            };

            parentPanel.Children.Add(block);
            parentPanel.Children.Add(box);
        }
Ejemplo n.º 7
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        /// <summary>
        /// This method would create combo field.
        /// </summary>
        /// <param name="alignmentAttribute">Alignment parameter</param>
        /// <param name="parentPanel">Stack panel, the field will be added to this stackpanel</param>
        /// <param name="tag">Tag of the control object</param>
        private void CreateComboField(
            AlignmentInfo alignmentAttribute,
                StackPanel parentPanel,
                string tag)
        {
            TextBlock block = new TextBlock {
                Margin = new Thickness(0, 10, 0, 0),
                TextWrapping = TextWrapping.Wrap,
                Text = alignmentAttribute.Name,
                Height = 20
            };

            ComboBox combo = new ComboBox {
                HorizontalAlignment = HorizontalAlignment.Left,
                IsSynchronizedWithCurrentItem = true,
                Margin = new Thickness(0, 0, 0, 0),
                Tag = tag,
                Width = 180,
                Height = 22,
                ToolTip = alignmentAttribute.Description
            };

            StringListValidator validator = alignmentAttribute.Validator as StringListValidator;
            combo.ItemsSource = validator.ValidValues;
            combo.SelectedIndex = validator.ValidValues.ToList().IndexOf(alignmentAttribute.DefaultValue);

            if (alignmentAttribute.Name == "Similarity Matrix")
            {
                combo.SelectedIndex = validator.ValidValues.ToList().IndexOf(GetDefaultSM(this.sequenceAlphabet));
            }

            parentPanel.Children.Add(block);
            parentPanel.Children.Add(combo);
        }
Ejemplo n.º 8
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        /// <summary>
        /// Initializes a new instance of the PairwiseAlignmentAttributes class.
        /// </summary>
        public PamsamAlignmentAttributes()
        {
            AlignmentInfo alignmentAttribute;
            attributes = new Dictionary<string, AlignmentInfo>();

            alignmentAttribute = new AlignmentInfo(
                KmerLength,
                "Kmer Length",
                true,
                "3",
                AlignmentInfo.IntType,
                null);
            attributes.Add(KmerLength, alignmentAttribute);

            StringListValidator listValidator = new StringListValidator(
                Enum.GetNames(typeof(DistanceFunctionTypes))
                );
            alignmentAttribute = new AlignmentInfo(
                DistanceFunctionType,
                "Distance Function Type",
                true,
                DistanceFunctionTypes.EuclideanDistance.ToString(),
                AlignmentInfo.StringListType,
                listValidator);
            attributes.Add(DistanceFunctionType, alignmentAttribute);

            listValidator = new StringListValidator(
                Enum.GetNames(typeof(UpdateDistanceMethodsTypes))
                );
            alignmentAttribute = new AlignmentInfo(
                UpdateDistanceMethodsType,
                "Update Distance Methods Type",
                true,
                UpdateDistanceMethodsTypes.Average.ToString(),
                AlignmentInfo.StringListType,
                listValidator);
            attributes.Add(UpdateDistanceMethodsType, alignmentAttribute);

            listValidator = new StringListValidator(
                Enum.GetNames(typeof(ProfileAlignerNames))
                );
            alignmentAttribute = new AlignmentInfo(
                ProfileAlignerName,
                "Profile Aligner Name",
                true,
                ProfileAlignerNames.NeedlemanWunschProfileAligner.ToString(),
                AlignmentInfo.StringListType,
                listValidator);
            attributes.Add(ProfileAlignerName, alignmentAttribute);

            listValidator = new StringListValidator(
                Enum.GetNames(typeof(ProfileScoreFunctionNames))
                );
            alignmentAttribute = new AlignmentInfo(
                ProfileScoreFunctionName,
                "Profile Score Function Name",
                true,
                ProfileScoreFunctionNames.WeightedInnerProduct.ToString(),
                AlignmentInfo.StringListType,
                listValidator);
            attributes.Add(ProfileScoreFunctionName, alignmentAttribute);

            listValidator = new StringListValidator(
                SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
                SM.StandardSimilarityMatrix.AmbiguousRna.ToString(),
                SM.StandardSimilarityMatrix.Blosum45.ToString(),
                SM.StandardSimilarityMatrix.Blosum50.ToString(),
                SM.StandardSimilarityMatrix.Blosum62.ToString(),
                SM.StandardSimilarityMatrix.Blosum80.ToString(),
                SM.StandardSimilarityMatrix.Blosum90.ToString(),
                SM.StandardSimilarityMatrix.Pam250.ToString(),
                SM.StandardSimilarityMatrix.Pam30.ToString(),
                SM.StandardSimilarityMatrix.Pam70.ToString()                
                );

            alignmentAttribute = new AlignmentInfo(
                SimilarityMatrix,
                "Describes matrix that determines the score for any possible pair of symbols",
                true,
                SM.StandardSimilarityMatrix.AmbiguousDna.ToString(),
                AlignmentInfo.StringListType,
                listValidator);
            attributes.Add(SimilarityMatrix, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                GapOpenPenalty,
                "Gap Open Penalty",
                true,
                "-4",
                AlignmentInfo.IntType,
                null);
            attributes.Add(GapOpenPenalty, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                GapExtendPenalty,
                "Gap Extension Penalty",
                true,
                "-1",
                AlignmentInfo.IntType,
                null);
            attributes.Add(GapExtendPenalty, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                NumberOfPartitions,
                "Number Of Partitions",
                true,
                (Environment.ProcessorCount * 2).ToString(),
                AlignmentInfo.IntType,
                null);
            attributes.Add(NumberOfPartitions, alignmentAttribute);

            alignmentAttribute = new AlignmentInfo(
                DegreeOfParallelism,
                "Degree Of Parallelism",
                true,
                Environment.ProcessorCount.ToString(),
                AlignmentInfo.IntType,
                null);
            attributes.Add(DegreeOfParallelism, alignmentAttribute);
        }