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  1. Project Clover database Thu Nov 7 2024 17:01:39 GMT
  2. Package jalview.math

File MatrixI.java

 

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MatrixI 29 0 0
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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.math;
22   
23    import java.io.PrintStream;
24   
25    /**
26    * An interface that describes a rectangular matrix of double values and
27    * operations on it
28    */
 
29    public interface MatrixI
30    {
31    /**
32    * Answers the number of columns
33    *
34    * @return
35    */
36    int width();
37   
38    /**
39    * Answers the number of rows
40    *
41    * @return
42    */
43    int height();
44   
45    /**
46    * Answers the value at row i, column j
47    *
48    * @param i
49    * @param j
50    * @return
51    */
52    double getValue(int i, int j);
53   
54    /**
55    * Sets the value at row i, colum j
56    *
57    * @param i
58    * @param j
59    * @param d
60    */
61    void setValue(int i, int j, double d);
62   
63    /**
64    * Returns the matrix as a double[][] array
65    *
66    * @return
67    */
68    double[][] asArray();
69   
70    /**
71    * Answers a copy of the values in the i'th row
72    *
73    * @return
74    */
75    double[] getRow(int i);
76   
77    /**
78    * Answers a copy of the values in the i'th column
79    *
80    * @return
81    */
82    double[] getColumn(int i);
83   
84    /**
85    * Answers a new matrix with a copy of the values in this one
86    *
87    * @return
88    */
89    MatrixI copy();
90   
91    /**
92    * Returns a new matrix which is the transpose of this one
93    *
94    * @return
95    */
96    MatrixI transpose();
97   
98    /**
99    * Returns a new matrix which is the result of premultiplying this matrix by
100    * the supplied argument. If this of size AxB (A rows and B columns), and the
101    * argument is CxA (C rows and A columns), the result is of size CxB.
102    *
103    * @param in
104    *
105    * @return
106    * @throws IllegalArgumentException
107    * if the number of columns in the pre-multiplier is not equal to
108    * the number of rows in the multiplicand (this)
109    */
110    MatrixI preMultiply(MatrixI m);
111   
112    /**
113    * Returns a new matrix which is the result of postmultiplying this matrix by
114    * the supplied argument. If this of size AxB (A rows and B columns), and the
115    * argument is BxC (B rows and C columns), the result is of size AxC.
116    * <p>
117    * This method simply returns the result of in.preMultiply(this)
118    *
119    * @param in
120    *
121    * @return
122    * @throws IllegalArgumentException
123    * if the number of rows in the post-multiplier is not equal to the
124    * number of columns in the multiplicand (this)
125    * @see #preMultiply(Matrix)
126    */
127    MatrixI postMultiply(MatrixI m);
128   
129    double[] getD();
130   
131    double[] getE();
132   
133    void setD(double[] v);
134   
135    void setE(double[] v);
136   
137    void print(PrintStream ps, String format);
138   
139    void printD(PrintStream ps, String format);
140   
141    void printE(PrintStream ps, String format);
142   
143    void tqli() throws Exception;
144   
145    void tred();
146   
147    /**
148    * Reverses the range of the matrix values, so that the smallest values become
149    * the largest, and the largest become the smallest. This operation supports
150    * using a distance measure as a similarity measure, or vice versa.
151    * <p>
152    * If parameter <code>maxToZero</code> is true, then the maximum value becomes
153    * zero, i.e. all values are subtracted from the maximum. This is consistent
154    * with converting an identity similarity score to a distance score - the most
155    * similar (identity) corresponds to zero distance. However note that the
156    * operation is not reversible (unless the original minimum value is zero).
157    * For example a range of 10-40 would become 30-0, which would reverse a
158    * second time to 0-30. Also note that a general similarity measure (such as
159    * BLOSUM) may give different 'identity' scores for different sequences, so
160    * they cannot all convert to zero distance.
161    * <p>
162    * If parameter <code>maxToZero</code> is false, then the values are reflected
163    * about the average of {min, max} (effectively swapping min and max). This
164    * operation <em>is</em> reversible.
165    *
166    * @param maxToZero
167    */
168    void reverseRange(boolean maxToZero);
169   
170    /**
171    * Multiply all entries by the given value
172    *
173    * @param d
174    */
175    void multiply(double d);
176   
177    /**
178    * Add d to all entries of this matrix
179    *
180    * @param d
181    * ~ value to add
182    */
183    void add(double d);
184   
185    /**
186    * Answers true if the two matrices have the same dimensions, and
187    * corresponding values all differ by no more than delta (which should be a
188    * positive value), else false
189    *
190    * @param m2
191    * @param delta
192    * @return
193    */
194    boolean equals(MatrixI m2, double delta);
195   
196    /**
197    * Returns a copy in which every value in the matrix is its absolute
198    */
199    MatrixI absolute();
200   
201    /**
202    * Returns the mean of each row
203    */
204    double[] meanRow();
205   
206    /**
207    * Returns the mean of each column
208    */
209    double[] meanCol();
210   
211    /**
212    * Returns a flattened matrix containing the sum of each column
213    *
214    * @return
215    */
216    double[] sumCol();
217   
218    /**
219    * returns the mean value of the complete matrix
220    */
221    double mean();
222   
223    /**
224    * fills up a diagonal matrix with its transposed copy !other side should be
225    * filled with either 0 or Double.NaN
226    */
227    void fillDiagonal();
228   
229    /**
230    * counts the number of Double.NaN in the matrix
231    *
232    * @return
233    */
234    int countNaN();
235   
236    /**
237    * performs an element-wise addition of this matrix by another matrix
238    * !matrices have to be the same size
239    *
240    * @param m
241    * ~ other matrix
242    *
243    * @return
244    * @throws IllegalArgumentException
245    * if this and m do not have the same dimensions
246    */
247    MatrixI add(MatrixI m);
248   
249    /**
250    * performs an element-wise subtraction of this matrix by another matrix
251    * !matrices have to be the same size
252    *
253    * @param m
254    * ~ other matrix
255    *
256    * @return
257    * @throws IllegalArgumentException
258    * if this and m do not have the same dimensions
259    */
260    MatrixI subtract(MatrixI m);
261   
262    /**
263    * performs an element-wise multiplication of this matrix by another matrix ~
264    * this * m !matrices have to be the same size
265    *
266    * @param m
267    * ~ other matrix
268    *
269    * @return
270    * @throws IllegalArgumentException
271    * if this and m do not have the same dimensions
272    */
273    MatrixI elementwiseMultiply(MatrixI m);
274   
275    /**
276    * performs an element-wise division of this matrix by another matrix ~ this /
277    * m !matrices have to be the same size
278    *
279    * @param m
280    * ~ other matrix
281    *
282    * @return
283    * @throws IllegalArgumentException
284    * if this and m do not have the same dimensions
285    */
286    MatrixI elementwiseDivide(MatrixI m);
287   
288    /**
289    * calculates the root-mean-square for two matrices
290    *
291    * @param m
292    * ~ other matrix
293    *
294    * @return
295    */
296    double rmsd(MatrixI m);
297   
298    /**
299    * calculates the Frobenius norm of this matrix
300    *
301    * @return
302    */
303    double norm();
304   
305    /**
306    * returns the sum of all values in this matrix
307    *
308    * @return
309    */
310    double sum();
311   
312    /**
313    * returns the sum-product of this matrix with vector v
314    *
315    * @param v
316    * ~ vector
317    *
318    * @return
319    * @throws IllegalArgumentException
320    * if this.cols and v do not have the same length
321    */
322    double[] sumProduct(double[] v);
323   
324    /**
325    * mirrors the columns of this matrix
326    *
327    * @return
328    */
329    MatrixI mirrorCol();
330    }