X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fmath%2FMatrixI.java;h=e98007e5b084cf243c3d5919599a2a4ff7d13984;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=05fe22ffa887fee646501d628d81d1764fbc7614;hpb=d6a30c6516e8e2f923c8c2f6dce7592cb3b7d974;p=jalview.git
diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index 05fe22f..e98007e 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -1,7 +1,31 @@
+/*
+ * 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
+ * This method simply returns the result of in.preMultiply(this) + * + * @param in + * + * @return + * @throws IllegalArgumentException + * if the number of rows in the post-multiplier is not equal to the + * number of columns in the multiplicand (this) + * @see #preMultiply(Matrix) + */ MatrixI postMultiply(MatrixI m); double[] getD(); double[] getE(); + void setD(double[] v); + + void setE(double[] v); + void print(PrintStream ps, String format); void printD(PrintStream ps, String format); @@ -65,12 +130,44 @@ public interface MatrixI void tred(); - double getMaxValue(); + /** + * Reverses the range of the matrix values, so that the smallest values become + * the largest, and the largest become the smallest. This operation supports + * using a distance measure as a similarity measure, or vice versa. + *
+ * If parameter maxToZero
is true, then the maximum value becomes
+ * zero, i.e. all values are subtracted from the maximum. This is consistent
+ * with converting an identity similarity score to a distance score - the most
+ * similar (identity) corresponds to zero distance. However note that the
+ * operation is not reversible (unless the original minimum value is zero).
+ * For example a range of 10-40 would become 30-0, which would reverse a
+ * second time to 0-30. Also note that a general similarity measure (such as
+ * BLOSUM) may give different 'identity' scores for different sequences, so
+ * they cannot all convert to zero distance.
+ *
+ * If parameter maxToZero
is false, then the values are reflected
+ * about the average of {min, max} (effectively swapping min and max). This
+ * operation is reversible.
+ *
+ * @param maxToZero
+ */
+ void reverseRange(boolean maxToZero);
/**
- * Update each value in the matrix by subtracting it from the given value
+ * Multiply all entries by the given value
*
- * @param val
+ * @param d
+ */
+ void multiply(double d);
+
+ /**
+ * Answers true if the two matrices have the same dimensions, and
+ * corresponding values all differ by no more than delta (which should be a
+ * positive value), else false
+ *
+ * @param m2
+ * @param delta
+ * @return
*/
- void subtractAllFrom(double val);
+ boolean equals(MatrixI m2, double delta);
}