*/
package jalview.analysis;
+import jalview.analysis.scoremodels.PairwiseDistanceModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
- import jalview.datamodel.BinarySequence;
- import jalview.datamodel.BinarySequence.InvalidSequenceTypeException;
- import jalview.math.Matrix;
+ import jalview.math.MatrixI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
import java.io.PrintStream;
String sm = s_m;
if (sm != null)
{
- smtrx = (ScoreMatrix) ((PairwiseDistanceModel) ScoreModels
- scoreMatrix = ResidueProperties.getScoreMatrix(sm);
++ scoreMatrix = (ScoreMatrix) ((PairwiseDistanceModel) ScoreModels
+ .getInstance()
+ .forName(sm)).getScoreModel();
}
- if (smtrx == null)
+ if (scoreMatrix == null)
{
// either we were given a non-existent score matrix or a scoremodel that
// isn't based on a pairwise symbol score matrix
- smtrx = ScoreModels.getInstance().getDefaultModel(!nucleotides);
- scoreMatrix = ResidueProperties
- .getScoreMatrix(sm = (nucleotides ? "DNA" : "BLOSUM62"));
++ scoreMatrix = ScoreModels.getInstance().getDefaultModel(!nucleotides);
}
details.append("PCA calculation using " + sm
+ " sequence similarity matrix\n========\n\n");
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis.scoremodels;
+
++import jalview.math.Matrix;
++import jalview.math.MatrixI;
++
+import java.util.Arrays;
+
+public class ScoreMatrix implements PairwiseScoreModelI
+{
+ public static final short UNMAPPED = (short) -1;
+
+ private static final String BAD_ASCII_ERROR = "Unexpected character %s in getPairwiseScore";
+
+ private static final int MAX_ASCII = 127;
+
+ /*
+ * the name of the model as shown in menus
+ */
+ private String name;
+
+ /*
+ * the characters that the model provides scores for
+ */
+ private char[] symbols;
+
+ /*
+ * the score matrix; both dimensions must equal the number of symbols
+ * matrix[i][j] is the substitution score for replacing symbols[i] with symbols[j]
+ */
+ private float[][] matrix;
+
+ /*
+ * quick lookup to convert from an ascii character value to the index
+ * of the corresponding symbol in the score matrix
+ */
+ private short[] symbolIndex;
+
+ /*
+ * true for Protein Score matrix, false for dna score matrix
+ */
+ private boolean peptide;
+
+ /**
+ * Constructor given a name, symbol alphabet, and matrix of scores for pairs
+ * of symbols. The matrix should be square and of the same size as the
+ * alphabet, for example 20x20 for a 20 symbol alphabet.
+ *
+ * @param name
+ * Unique, human readable name for the matrix
+ * @param alphabet
+ * the symbols to which scores apply
+ * @param matrix
+ * Pairwise scores indexed according to the symbol alphabet
+ */
+ public ScoreMatrix(String name, char[] alphabet, float[][] matrix)
+ {
+ if (alphabet.length != matrix.length)
+ {
+ throw new IllegalArgumentException(
+ "score matrix size must match alphabet size");
+ }
+ for (float[] row : matrix)
+ {
+ if (row.length != alphabet.length)
+ {
+ throw new IllegalArgumentException(
+ "score matrix size must be square");
+ }
+ }
+
+ this.matrix = matrix;
+ this.name = name;
+ this.symbols = alphabet;
+
+ symbolIndex = buildSymbolIndex(alphabet);
+
+ /*
+ * crude heuristic for now...
+ */
+ peptide = alphabet.length >= 20;
+ }
+
+ /**
+ * Returns an array A where A[i] is the position in the alphabet array of the
+ * character whose value is i. For example if the alphabet is { 'A', 'D', 'X'
+ * } then A['D'] = A[68] = 1.
+ * <p>
+ * Unmapped characters (not in the alphabet) get an index of -1.
+ * <p>
+ * Mappings are added automatically for lower case symbols (for non case
+ * sensitive scoring), unless they are explicitly present in the alphabet (are
+ * scored separately in the score matrix).
+ *
+ * @param alphabet
+ * @return
+ */
+ static short[] buildSymbolIndex(char[] alphabet)
+ {
+ short[] index = new short[MAX_ASCII + 1];
+ Arrays.fill(index, UNMAPPED);
+ short pos = 0;
+ for (char c : alphabet)
+ {
+ if (c <= MAX_ASCII)
+ {
+ index[c] = pos;
+ }
+
+ /*
+ * also map lower-case character (unless separately mapped)
+ */
+ if (c >= 'A' && c <= 'Z')
+ {
+ short lowerCase = (short) (c + ('a' - 'A'));
+ if (index[lowerCase] == UNMAPPED)
+ {
+ index[lowerCase] = pos;
+ }
+ }
+ pos++;
+ }
+ return index;
+ }
+
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+
+ @Override
+ public boolean isDNA()
+ {
+ return !peptide;
+ }
+
+ @Override
+ public boolean isProtein()
+ {
+ return peptide;
+ }
+
+ /**
+ * Returns the score matrix as used in getPairwiseScore. If using this matrix
+ * directly, callers <em>must</em> also call <code>getMatrixIndex</code> in
+ * order to get the matrix index for each character (symbol).
+ *
+ * @return
+ * @see #getMatrixIndex(char)
+ */
+ public float[][] getMatrix()
+ {
+ return matrix;
+ }
+
+ /**
+ * Answers the matrix index for a given character, or -1 if unmapped in the
+ * matrix. Use this method only if using <code>getMatrix</code> in order to
+ * compute scores directly (without symbol lookup) for efficiency.
+ *
+ * @param c
+ * @return
+ * @see #getMatrix()
+ */
+ public int getMatrixIndex(char c)
+ {
+ if (c < symbolIndex.length)
+ {
+ return symbolIndex[c];
+ }
+ else
+ {
+ return UNMAPPED;
+ }
+ }
+
+ /**
+ * Returns the pairwise score for substituting c with d, or zero if c or d is
+ * an unscored or unexpected character
+ */
+ @Override
+ public float getPairwiseScore(char c, char d)
+ {
+ if (c >= symbolIndex.length)
+ {
+ System.err.println(String.format(BAD_ASCII_ERROR, c));
+ return 0;
+ }
+ if (d >= symbolIndex.length)
+ {
+ System.err.println(String.format(BAD_ASCII_ERROR, d));
+ return 0;
+ }
+
+ int cIndex = symbolIndex[c];
+ int dIndex = symbolIndex[d];
+ if (cIndex != UNMAPPED && dIndex != UNMAPPED)
+ {
+ return matrix[cIndex][dIndex];
+ }
+ return 0;
+ }
+
+ /**
+ * pretty print the matrix
+ */
+ @Override
+ public String toString()
+ {
+ return outputMatrix(false);
+ }
+
+ /**
+ * Print the score matrix, optionally formatted as html, with the alphabet symbols as column headings and at the start of each row
+ * @param html
+ * @return
+ */
+ public String outputMatrix(boolean html)
+ {
+ StringBuilder sb = new StringBuilder(512);
+
+ /*
+ * heading row with alphabet
+ */
+ if (html)
+ {
+ sb.append("<table border=\"1\">");
+ sb.append(html ? "<tr><th></th>" : "");
+ }
+ for (char sym : symbols)
+ {
+ if (html)
+ {
+ sb.append("<th> ").append(sym).append(" </th>");
+ }
+ else
+ {
+ sb.append("\t").append(sym);
+ }
+ }
+ sb.append(html ? "</tr>\n" : "\n");
+
+ /*
+ * table of scores
+ */
+ for (char c1 : symbols)
+ {
+ if (html)
+ {
+ sb.append("<tr><td>");
+ }
+ sb.append(c1).append(html ? "</td>" : "");
+ for (char c2 : symbols)
+ {
+ sb.append(html ? "<td>" : "\t")
+ .append(matrix[symbolIndex[c1]][symbolIndex[c2]])
+ .append(html ? "</td>" : "");
+ }
+ sb.append(html ? "</tr>\n" : "\n");
+ }
+ if (html)
+ {
+ sb.append("</table>");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Answers the number of symbols coded for (also equal to the number of rows
+ * and columns of the score matrix)
+ *
+ * @return
+ */
+ public int getSize()
+ {
+ return symbols.length;
+ }
++
++ /**
++ * Computes an NxN matrix where N is the number of sequences, and entry [i, j]
++ * is sequence[i] pairwise multiplied with sequence[j], as a sum of scores
++ * computed using the current score matrix. For example
++ * <ul>
++ * <li>Sequences:</li>
++ * <li>FKL</li>
++ * <li>R-D</li>
++ * <li>QIA</li>
++ * <li>GWC</li>
++ * <li>Score matrix is BLOSUM62</li>
++ * <li>Gaps treated same as X (unknown)</li>
++ * <li>product [0, 0] = F.F + K.K + L.L = 6 + 5 + 4 = 15</li>
++ * <li>product [1, 1] = R.R + -.- + D.D = 5 + -1 + 6 = 10</li>
++ * <li>product [2, 2] = Q.Q + I.I + A.A = 5 + 4 + 4 = 13</li>
++ * <li>product [3, 3] = G.G + W.W + C.C = 6 + 11 + 9 = 26</li>
++ * <li>product[0, 1] = F.R + K.- + L.D = -3 + -1 + -3 = -8
++ * <li>and so on</li>
++ * </ul>
++ */
++ public MatrixI computePairwiseScores(String[] seqs)
++ {
++ double[][] values = new double[seqs.length][];
++ for (int row = 0; row < seqs.length; row++)
++ {
++ values[row] = new double[seqs.length];
++ for (int col = 0; col < seqs.length; col++)
++ {
++ int total = 0;
++ int width = Math.min(seqs[row].length(), seqs[col].length());
++ for (int i = 0; i < width; i++)
++ {
++ char c1 = seqs[row].charAt(i);
++ char c2 = seqs[col].charAt(i);
++ float score = getPairwiseScore(c1, c2);
++ total += score;
++ }
++ values[row][col] = total;
++ }
++ }
++ return new Matrix(values);
++ }
+}
+ " is not a valid matrix for "
+ (isNa ? "nucleotide" : "protein") + "sequences");
}
- matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
- : ResidueProperties.aaIndex, matrix.getMatrix());
+ matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex, smtrx.getMatrix());
}
- private void matrixEncode(final int[] aaIndex, final int[][] matrix)
+ private void matrixEncode(final int[] aaIndex, final float[][] matrix)
{
- // Set all matrix to 0
- // dbinary = new double[getSequence().length * 21];
-
int nores = initMatrixGetNoRes();
- // for (int i = 0; i < dbinary.length; i++) {
- // dbinary[i] = 0.0;
- // }
for (int i = 0, iSize = getSequence().length; i < iSize; i++)
{
int aanum = nores - 1;
--- /dev/null
+package jalview.analysis.scoremodels;
+import static org.testng.Assert.assertEquals;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+
++import jalview.math.MatrixI;
++
+import org.testng.annotations.Test;
+
+public class ScoreMatrixTest
+{
+ @Test(groups = "Functional")
+ public void testConstructor()
+ {
+ // note score matrix does not have to be symmetric (though it should be!)
+ float[][] scores = new float[3][];
+ scores[0] = new float[] { 1f, 2f, 3f };
+ scores[1] = new float[] { 4f, 5f, 6f };
+ scores[2] = new float[] { 7f, 8f, 9f };
+ ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+ assertEquals(sm.getSize(), 3);
+ assertArrayEquals(scores, sm.getMatrix());
+ assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
+ assertEquals(sm.getPairwiseScore('b', 'c'), 6f);
+ assertEquals(sm.getPairwiseScore('c', 'b'), 8f);
+ assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
+ assertEquals(sm.getMatrixIndex('c'), 2);
+ assertEquals(sm.getMatrixIndex(' '), -1);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testConstructor_matrixTooSmall()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f, 4f };
+ new ScoreMatrix("Test", "ABC".toCharArray(), scores);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testConstructor_matrixTooBig()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f, 4f };
+ new ScoreMatrix("Test", "A".toCharArray(), scores);
+ }
+
+ @Test(
+ groups = "Functional",
+ expectedExceptions = { IllegalArgumentException.class })
+ public void testConstructor_matrixNotSquare()
+ {
+ float[][] scores = new float[2][];
+ scores[0] = new float[] { 1f, 2f };
+ scores[1] = new float[] { 3f };
+ new ScoreMatrix("Test", "AB".toCharArray(), scores);
+ }
+
+ @Test(groups = "Functional")
+ public void testBuildSymbolIndex()
+ {
+ short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());
+
+ assertEquals(index.length, 128); // ASCII character set size
+
+ assertEquals(index['A'], 0);
+ assertEquals(index['a'], 0); // lower-case mapping added
+ assertEquals(index['X'], 1);
+ assertEquals(index['-'], 2);
+ assertEquals(index['.'], 3);
+ assertEquals(index[' '], 4);
+ assertEquals(index['y'], 5); // lower-case override
+ assertEquals(index['x'], 6); // lower-case override
+ assertEquals(index['Y'], 7);
+ assertEquals(index['p'], 8);
+ assertEquals(index['P'], -1); // lower-case doesn't map upper-case
+
+ /*
+ * check all unmapped symbols have index for unmapped
+ */
+ for (int c = 0; c < index.length; c++)
+ {
+ if (!"AaXx-. Yyp".contains(String.valueOf((char) c)))
+ {
+ assertEquals(index[c], -1);
+ }
+ }
+ }
+
+ /**
+ * check that characters not in the basic ASCII set are simply ignored
+ */
+ @Test(groups = "Functional")
+ public void testBuildSymbolIndex_nonAscii()
+ {
+ char[] weird = new char[] { 128, 245, 'P' };
+ short[] index = ScoreMatrix.buildSymbolIndex(weird);
+ assertEquals(index.length, 128);
+ assertEquals(index['P'], 2);
+ assertEquals(index['p'], 2);
+ for (int c = 0; c < index.length; c++)
+ {
+ if (c != 'P' && c != 'p')
+ {
+ assertEquals(index[c], -1);
+ }
+ }
+ }
+
+ @Test(groups = "Functional")
+ public void testGetMatrixIndex()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMatrixIndex('A'), 0);
+ assertEquals(sm.getMatrixIndex('R'), 1);
+ assertEquals(sm.getMatrixIndex('r'), 1);
+ assertEquals(sm.getMatrixIndex('N'), 2);
+ assertEquals(sm.getMatrixIndex('D'), 3);
+ assertEquals(sm.getMatrixIndex('X'), 22);
+ assertEquals(sm.getMatrixIndex('x'), 22);
+ assertEquals(sm.getMatrixIndex(' '), 23);
+ assertEquals(sm.getMatrixIndex('*'), 24);
+ assertEquals(sm.getMatrixIndex('.'), -1);
+ assertEquals(sm.getMatrixIndex('-'), -1);
+ assertEquals(sm.getMatrixIndex('?'), -1);
+ assertEquals(sm.getMatrixIndex((char) 128), -1);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSize()
+ {
+ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+ assertEquals(sm.getMatrix().length, sm.getSize());
+ }
++
++ @Test(groups = "Functional")
++ public void testComputePairwiseScores()
++ {
++ /*
++ * NB score matrix assumes space for gap - Jalview converts
++ * space to gap before computing PCA or Tree
++ */
++ String[] seqs = new String[] { "FKL", "R D", "QIA", "GWC" };
++ ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
++
++ MatrixI pairwise = sm.computePairwiseScores(seqs);
++
++ /*
++ * should be NxN where N = number of sequences
++ */
++ assertEquals(pairwise.height(), 4);
++ assertEquals(pairwise.width(), 4);
++
++ /*
++ * should be symmetrical (because BLOSUM62 is)
++ */
++ for (int i = 0; i < pairwise.height(); i++)
++ {
++ for (int j = i + 1; j < pairwise.width(); j++)
++ {
++ assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
++ String.format("Not symmetric at [%d, %d]", i, j));
++ }
++ }
++ /*
++ * verify expected BLOSUM dot product scores
++ */
++ // F.F + K.K + L.L = 6 + 5 + 4 = 15
++ assertEquals(pairwise.getValue(0, 0), 15d);
++ // R.R + -.- + D.D = 5 + 1 + 6 = 12
++ assertEquals(pairwise.getValue(1, 1), 12d);
++ // Q.Q + I.I + A.A = 5 + 4 + 4 = 13
++ assertEquals(pairwise.getValue(2, 2), 13d);
++ // G.G + W.W + C.C = 6 + 11 + 9 = 26
++ assertEquals(pairwise.getValue(3, 3), 26d);
++ // F.R + K.- + L.D = -3 + -4 + -4 = -11
++ assertEquals(pairwise.getValue(0, 1), -11d);
++ // F.Q + K.I + L.A = -3 + -3 + -1 = -7
++ assertEquals(pairwise.getValue(0, 2), -7d);
++ // F.G + K.W + L.C = -3 + -3 + -1 = -7
++ assertEquals(pairwise.getValue(0, 3), -7d);
++ // R.Q + -.I + D.A = 1 + -4 + -2 = -5
++ assertEquals(pairwise.getValue(1, 2), -5d);
++ // R.G + -.W + D.C = -2 + -4 + -3 = -9
++ assertEquals(pairwise.getValue(1, 3), -9d);
++ // Q.G + I.W + A.C = -2 + -3 + 0 = -5
++ assertEquals(pairwise.getValue(2, 3), -5d);
++ }
+}
--- /dev/null
+package jalview.analysis.scoremodels;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.analysis.DistanceModelI;
+
+import java.util.Iterator;
+
+import org.testng.annotations.Test;
+
+public class ScoreModelsTest
+{
+ /**
+ * Verify that the singleton constructor successfully loads Jalview's built-in
+ * score models
+ */
+ @Test
+ public void testConstructor()
+ {
+ Iterator<DistanceModelI> models = ScoreModels.getInstance().getModels()
+ .iterator();
+ assertTrue(models.hasNext());
+
+ /*
+ * models are served in order of addition
+ */
+ DistanceModelI sm = models.next();
+ assertTrue(sm instanceof PairwiseDistanceModel);
+ assertEquals(sm.getName(), "BLOSUM62");
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('I', 'R'), -3f);
+
+ sm = models.next();
+ assertTrue(sm instanceof PairwiseDistanceModel);
+ assertEquals(sm.getName(), "PAM250");
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('R', 'C'), -4f);
+
+ sm = models.next();
+ assertTrue(sm instanceof PairwiseDistanceModel);
+ assertEquals(sm.getName(), "Identity (SeqSpace)");
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('R', 'C'), 0f);
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('R', 'r'), 1f);
+
+ sm = models.next();
+ assertTrue(sm instanceof PairwiseDistanceModel);
+ assertEquals(sm.getName(), "DNA");
+ assertEquals(((PairwiseDistanceModel) sm).getScoreModel()
+ .getPairwiseScore('c', 'x'), 1f);
+
+ sm = models.next();
+ assertFalse(sm instanceof PairwiseDistanceModel);
+ assertEquals(sm.getName(), "Sequence Feature Similarity");
+
+ sm = models.next();
+ assertFalse(sm instanceof PairwiseDistanceModel);
+ assertEquals(sm.getName(), "PID");
+ }
++
++ /**
++ * 'Test' that prints out score matrices in tab-delimited format. This test is
++ * intentionally not assigned to any group so would not be run as part of a
++ * suite. It makes no assertions and is just provided as a utility method for
++ * printing out matrices. Relocated here from ScoreMatrixPrinter.
++ */
++ @Test
++ public void printAllMatrices_tabDelimited()
++ {
++ printAllMatrices(false);
++ }
++
++ /**
++ * 'Test' that prints out score matrices in html format. This test is
++ * intentionally not assigned to any group so would not be run as part of a
++ * suite. It makes no assertions and is just provided as a utility method for
++ * printing out matrices. Relocated here from ScoreMatrixPrinter.
++ */
++ @Test
++ public void printAllMatrices_asHtml()
++ {
++ printAllMatrices(true);
++ }
++
++ /**
++ * Print all registered ScoreMatrix as plain or html tables
++ *
++ * @param asHtml
++ */
++ protected void printAllMatrices(boolean asHtml)
++ {
++ for (DistanceModelI dm : ScoreModels.getInstance().getModels())
++ {
++ if (dm instanceof PairwiseDistanceModel)
++ {
++ PairwiseScoreModelI psm = ((PairwiseDistanceModel) dm)
++ .getScoreModel();
++ if (psm instanceof ScoreMatrix)
++ {
++ ScoreMatrix sm = (ScoreMatrix) psm;
++ System.out.println("ScoreMatrix " + sm.getName());
++ System.out.println(sm.outputMatrix(asHtml));
++ }
++ }
++ }
++ }
+}
+++ /dev/null
--/*
-- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
-- * Copyright (C) $$Year-Rel$$ The Jalview Authors
-- *
-- * This file is part of Jalview.
-- *
-- * Jalview 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.
-- *
-- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
-- * The Jalview Authors are detailed in the 'AUTHORS' file.
-- */
--package jalview.schemes;
--
- import jalview.analysis.scoremodels.ScoreMatrix;
- import jalview.analysis.scoremodels.ScoreModels;
- import jalview.api.analysis.DistanceModelI;
- import jalview.gui.JvOptionPane;
-
- import org.testng.annotations.BeforeClass;
- import org.testng.annotations.Test;
-
- public class ScoreMatrixPrinter
- {
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void printAllMatrices()
- {
- for (DistanceModelI sm : ScoreModels.getInstance().getModels())
- {
- System.out.println("Matrix " + sm.getName());
- System.out.println(sm.toString());
- }
- }
-
- @Test(groups = { "Functional" })
- public void printHTMLMatrices()
- {
- for (DistanceModelI sm : ScoreModels.getInstance().getModels())
- {
- if (sm instanceof ScoreMatrix)
- {
- System.out.println("Matrix " + sm.getName());
- System.out.println(((ScoreMatrix) sm).outputMatrix(true));
- }
- }
- }
-
- }
-import jalview.api.analysis.ScoreModelI;
-import jalview.gui.JvOptionPane;
-
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-
-public class ScoreMatrixPrinter
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- public void printAllMatrices()
- {
- for (Map.Entry<String, ScoreModelI> sm : ResidueProperties.scoreMatrices
- .entrySet())
- {
- System.out.println("Matrix " + sm.getKey());
- System.out.println(sm.getValue().toString());
- }
- }
-
- public void printHTMLMatrices()
- {
- for (Map.Entry<String, ScoreModelI> _sm : ResidueProperties.scoreMatrices
- .entrySet())
- {
- if (_sm.getValue() instanceof ScoreMatrix)
- {
- ScoreMatrix sm = (ScoreMatrix) _sm.getValue();
- System.out.println("Matrix " + _sm.getKey());
- System.out.println(sm.outputMatrix(true));
- }
- }
- }
-
-}
git://source.jalview.org / jalview.git / commitdiff