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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.util

File Format.java

 

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176
285
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0.52
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Classes

Class Line # Actions
Format 37 285 149 229
0.525879952.6%
 

Contributing tests

This file is covered by 106 tests. .

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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    /**
22    * A class for formatting numbers that follows printf conventions.
23    * Also implements C-like atoi and atof functions
24    * @version 1.03 25 Oct 1997
25    * @author Cay Horstmann
26    */
27    package jalview.util;
28   
29    import java.util.Arrays;
30   
31    /**
32    * DOCUMENT ME!
33    *
34    * @author $author$
35    * @version $Revision$
36    */
 
37    public class Format
38    {
39    private int width;
40   
41    private int precision;
42   
43    private String pre;
44   
45    private String post;
46   
47    private boolean leading_zeroes;
48   
49    private boolean show_plus;
50   
51    private boolean alternate;
52   
53    private boolean show_space;
54   
55    private boolean left_align;
56   
57    private char fmt; // one of cdeEfgGiosxXos
58   
59    private final String formatString;
60   
61    /**
62    * Creates a new Format object.
63    *
64    * @param s
65    * DOCUMENT ME!
66    */
 
67  20369 toggle public Format(String s)
68    {
69  20369 formatString = s;
70  20369 width = 0;
71  20369 precision = -1;
72  20369 pre = "";
73  20369 post = "";
74  20369 leading_zeroes = false;
75  20369 show_plus = false;
76  20369 alternate = false;
77  20369 show_space = false;
78  20369 left_align = false;
79  20369 fmt = ' ';
80   
81  20369 int length = s.length();
82  20369 int parse_state = 0;
83   
84    // 0 = prefix, 1 = flags, 2 = width, 3 = precision,
85    // 4 = format, 5 = end
86  20369 int i = 0;
87   
88  43010 while (parse_state == 0)
89    {
90  22641 if (i >= length)
91    {
92  0 parse_state = 5;
93    }
94  22641 else if (s.charAt(i) == '%')
95    {
96  20369 if (i < (length - 1))
97    {
98  20369 if (s.charAt(i + 1) == '%')
99    {
100  0 pre = pre + '%';
101  0 i++;
102    }
103    else
104    {
105  20369 parse_state = 1;
106    }
107    }
108    else
109    {
110  0 throw new java.lang.IllegalArgumentException();
111    }
112    }
113    else
114    {
115  2272 pre = pre + s.charAt(i);
116    }
117   
118  22641 i++;
119    }
120   
121  41697 while (parse_state == 1)
122    {
123  21328 if (i >= length)
124    {
125  0 parse_state = 5;
126    }
127  21328 else if (s.charAt(i) == ' ')
128    {
129  0 show_space = true;
130    }
131  21328 else if (s.charAt(i) == '-')
132    {
133  959 left_align = true;
134    }
135  20369 else if (s.charAt(i) == '+')
136    {
137  0 show_plus = true;
138    }
139  20369 else if (s.charAt(i) == '0')
140    {
141  0 leading_zeroes = true;
142    }
143  20369 else if (s.charAt(i) == '#')
144    {
145  0 alternate = true;
146    }
147    else
148    {
149  20369 parse_state = 2;
150  20369 i--;
151    }
152   
153  21328 i++;
154    }
155   
156  62207 while (parse_state == 2)
157    {
158  41838 if (i >= length)
159    {
160  0 parse_state = 5;
161    }
162  41838 else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
163    {
164  21469 width = ((width * 10) + s.charAt(i)) - '0';
165  21469 i++;
166    }
167  20369 else if (s.charAt(i) == '.')
168    {
169  152 parse_state = 3;
170  152 precision = 0;
171  152 i++;
172    }
173    else
174    {
175  20217 parse_state = 4;
176    }
177    }
178   
179  20673 while (parse_state == 3)
180    {
181  304 if (i >= length)
182    {
183  0 parse_state = 5;
184    }
185  304 else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
186    {
187  152 precision = ((precision * 10) + s.charAt(i)) - '0';
188  152 i++;
189    }
190    else
191    {
192  152 parse_state = 4;
193    }
194    }
195   
196  20369 if (parse_state == 4)
197    {
198  20369 if (i >= length)
199    {
200  0 parse_state = 5;
201    }
202    else
203    {
204  20369 fmt = s.charAt(i);
205    }
206   
207  20369 i++;
208    }
209   
210  20369 if (i < length)
211    {
212  142 post = s.substring(i, length);
213    }
214    }
215   
216    /**
217    * Formats the number following printf conventions. Main limitation: Can only
218    * handle one format parameter at a time Use multiple Format objects to format
219    * more than one number
220    *
221    * @param s
222    * the format string following printf conventions The string has a
223    * prefix, a format code and a suffix. The prefix and suffix become
224    * part of the formatted output. The format code directs the
225    * formatting of the (single) parameter to be formatted. The code has
226    * the following structure
227    * <ul>
228    * <li>a % (required)
229    * <li>a modifier (optional)
230    * <dl>
231    * <dt>+
232    * <dd>forces display of + for positive numbers
233    * <dt>0
234    * <dd>show leading zeroes
235    * <dt>-
236    * <dd>align left in the field
237    * <dt>space
238    * <dd>prepend a space in front of positive numbers
239    * <dt>#
240    * <dd>use "alternate" format. Add 0 or 0x for octal or hexadecimal
241    * numbers. Don't suppress trailing zeroes in general floating point
242    * format.
243    * </dl>
244    * <li>an integer denoting field width (optional)
245    * <li>a period followed by an integer denoting precision (optional)
246    * <li>a format descriptor (required)
247    * <dl>
248    * <dt>f
249    * <dd>floating point number in fixed format
250    * <dt>e, E
251    * <dd>floating point number in exponential notation (scientific
252    * format). The E format results in an uppercase E for the exponent
253    * (1.14130E+003), the e format in a lowercase e.
254    * <dt>g, G
255    * <dd>floating point number in general format (fixed format for
256    * small numbers, exponential format for large numbers). Trailing
257    * zeroes are suppressed. The G format results in an uppercase E for
258    * the exponent (if any), the g format in a lowercase e.
259    * <dt>d, i
260    * <dd>integer in decimal
261    * <dt>x
262    * <dd>integer in hexadecimal
263    * <dt>o
264    * <dd>integer in octal
265    * <dt>s
266    * <dd>string
267    * <dt>c
268    * <dd>character
269    * </dl>
270    * </ul>
271    * @exception IllegalArgumentException
272    * if bad format
273    *
274    */
 
275  8982 toggle public static String getHexString(java.awt.Color color)
276    {
277  8982 String r;
278  8982 String g;
279  8982 String b;
280  8982 r = Integer.toHexString(color.getRed());
281   
282  8982 if (r.length() < 2)
283    {
284  59 r = "0" + r;
285    }
286   
287  8982 g = Integer.toHexString(color.getGreen());
288   
289  8982 if (g.length() < 2)
290    {
291  255 g = "0" + g;
292    }
293   
294  8982 b = Integer.toHexString(color.getBlue());
295   
296  8982 if (b.length() < 2)
297    {
298  788 b = "0" + b;
299    }
300   
301  8982 return r + g + b;
302    }
303   
304    /**
305    * prints a formatted number following printf conventions
306    *
307    * @param s
308    * a PrintStream
309    * @param fmt
310    * the format string
311    * @param x
312    * the double to print
313    */
 
314  0 toggle public static void print(java.io.PrintStream s, String fmt, double x)
315    {
316  0 s.print(new Format(fmt).form(x));
317    }
318   
319    /**
320    * prints a formatted number following printf conventions
321    *
322    * @param s
323    * a PrintStream
324    * @param fmt
325    * the format string
326    * @param x
327    * the long to print
328    */
 
329  0 toggle public static void print(java.io.PrintStream s, String fmt, long x)
330    {
331  0 s.print(new Format(fmt).form(x));
332    }
333   
334    /**
335    * prints a formatted number following printf conventions
336    *
337    * @param s
338    * a PrintStream
339    * @param fmt
340    * the format string
341    * @param x
342    * the character to
343    */
 
344  0 toggle public static void print(java.io.PrintStream s, String fmt, char x)
345    {
346  0 s.print(new Format(fmt).form(x));
347    }
348   
349    /**
350    * prints a formatted number following printf conventions
351    *
352    * @param s
353    * a PrintStream, fmt the format string
354    * @param x
355    * a string that represents the digits to print
356    */
 
357  0 toggle public static void print(java.io.PrintStream s, String fmt, String x)
358    {
359  0 s.print(new Format(fmt).form(x));
360    }
361   
362    /**
363    * Converts a string of digits (decimal, octal or hex) to an integer
364    *
365    * @param s
366    * a string
367    * @return the numeric value of the prefix of s representing a base 10 integer
368    */
 
369  0 toggle public static int atoi(String s)
370    {
371  0 return (int) atol(s);
372    }
373   
374    /**
375    * Converts a string of digits (decimal, octal or hex) to a long integer
376    *
377    * @param s
378    * a string
379    * @return the numeric value of the prefix of s representing a base 10 integer
380    */
 
381  0 toggle public static long atol(String s)
382    {
383  0 int i = 0;
384   
385  0 while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
386    {
387  0 i++;
388    }
389   
390  0 if ((i < s.length()) && (s.charAt(i) == '0'))
391    {
392  0 if (((i + 1) < s.length())
393    && ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X')))
394    {
395  0 return parseLong(s.substring(i + 2), 16);
396    }
397    else
398    {
399  0 return parseLong(s, 8);
400    }
401    }
402    else
403    {
404  0 return parseLong(s, 10);
405    }
406    }
407   
408    /**
409    * DOCUMENT ME!
410    *
411    * @param s
412    * DOCUMENT ME!
413    * @param base
414    * DOCUMENT ME!
415    *
416    * @return DOCUMENT ME!
417    */
 
418  0 toggle private static long parseLong(String s, int base)
419    {
420  0 int i = 0;
421  0 int sign = 1;
422  0 long r = 0;
423   
424  0 while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
425    {
426  0 i++;
427    }
428   
429  0 if ((i < s.length()) && (s.charAt(i) == '-'))
430    {
431  0 sign = -1;
432  0 i++;
433    }
434  0 else if ((i < s.length()) && (s.charAt(i) == '+'))
435    {
436  0 i++;
437    }
438   
439  0 while (i < s.length())
440    {
441  0 char ch = s.charAt(i);
442   
443  0 if (('0' <= ch) && (ch < ('0' + base)))
444    {
445  0 r = ((r * base) + ch) - '0';
446    }
447  0 else if (('A' <= ch) && (ch < (('A' + base) - 10)))
448    {
449  0 r = ((r * base) + ch) - 'A' + 10;
450    }
451  0 else if (('a' <= ch) && (ch < (('a' + base) - 10)))
452    {
453  0 r = ((r * base) + ch) - 'a' + 10;
454    }
455    else
456    {
457  0 return r * sign;
458    }
459   
460  0 i++;
461    }
462   
463  0 return r * sign;
464    }
465   
466    /**
467    * Converts a string of digits to an double
468    *
469    * @param s
470    * a string
471    */
 
472  0 toggle public static double atof(String s)
473    {
474  0 int i = 0;
475  0 int sign = 1;
476  0 double r = 0; // integer part
477    // double f = 0; // fractional part
478  0 double p = 1; // exponent of fractional part
479  0 int state = 0; // 0 = int part, 1 = frac part
480   
481  0 while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
482    {
483  0 i++;
484    }
485   
486  0 if ((i < s.length()) && (s.charAt(i) == '-'))
487    {
488  0 sign = -1;
489  0 i++;
490    }
491  0 else if ((i < s.length()) && (s.charAt(i) == '+'))
492    {
493  0 i++;
494    }
495   
496  0 while (i < s.length())
497    {
498  0 char ch = s.charAt(i);
499   
500  0 if (('0' <= ch) && (ch <= '9'))
501    {
502  0 if (state == 0)
503    {
504  0 r = ((r * 10) + ch) - '0';
505    }
506  0 else if (state == 1)
507    {
508  0 p = p / 10;
509  0 r = r + (p * (ch - '0'));
510    }
511    }
512  0 else if (ch == '.')
513    {
514  0 if (state == 0)
515    {
516  0 state = 1;
517    }
518    else
519    {
520  0 return sign * r;
521    }
522    }
523  0 else if ((ch == 'e') || (ch == 'E'))
524    {
525  0 long e = (int) parseLong(s.substring(i + 1), 10);
526   
527  0 return sign * r * Math.pow(10, e);
528    }
529    else
530    {
531  0 return sign * r;
532    }
533   
534  0 i++;
535    }
536   
537  0 return sign * r;
538    }
539   
540    /**
541    * Formats a double into a string (like sprintf in C)
542    *
543    * @param x
544    * the number to format
545    * @return the formatted string
546    * @exception IllegalArgumentException
547    * if bad argument
548    */
 
549  68155 toggle public String form(double x)
550    {
551  68155 String r;
552   
553  68155 if (precision < 0)
554    {
555  0 precision = 6;
556    }
557   
558  68155 int s = 1;
559   
560  68155 if (x < 0)
561    {
562  0 x = -x;
563  0 s = -1;
564    }
565   
566  68155 if (fmt == 'f')
567    {
568  68152 r = fixed_format(x);
569    }
570  3 else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') || (fmt == 'G'))
571    {
572  3 r = exp_format(x);
573    }
574    else
575    {
576  0 throw new java.lang.IllegalArgumentException();
577    }
578   
579  68155 return pad(sign(s, r));
580    }
581   
582    /**
583    * Formats a long integer into a string (like sprintf in C)
584    *
585    * @param x
586    * the number to format
587    * @return the formatted string
588    */
 
589  19144 toggle public String form(long x)
590    {
591  19144 String r;
592  19144 int s = 0;
593   
594  19144 if ((fmt == 'd') || (fmt == 'i'))
595    {
596  19144 if (x < 0)
597    {
598  0 r = ("" + x).substring(1);
599  0 s = -1;
600    }
601    else
602    {
603  19144 r = "" + x;
604  19144 s = 1;
605    }
606    }
607  0 else if (fmt == 'o')
608    {
609  0 r = convert(x, 3, 7, "01234567");
610    }
611  0 else if (fmt == 'x')
612    {
613  0 r = convert(x, 4, 15, "0123456789abcdef");
614    }
615  0 else if (fmt == 'X')
616    {
617  0 r = convert(x, 4, 15, "0123456789ABCDEF");
618    }
619    else
620    {
621  0 throw new java.lang.IllegalArgumentException();
622    }
623   
624  19144 return pad(sign(s, r));
625    }
626   
627    /**
628    * Formats a character into a string (like sprintf in C)
629    *
630    * @param debounceTrap
631    * the value to format
632    * @return the formatted string
633    */
 
634  0 toggle public String form(char c)
635    {
636  0 if (fmt != 'c')
637    {
638  0 throw new java.lang.IllegalArgumentException();
639    }
640   
641  0 String r = "" + c;
642   
643  0 return pad(r);
644    }
645   
646    /**
647    * Formats a string into a larger string (like sprintf in C)
648    *
649    * @param debounceTrap
650    * the value to format
651    * @return the formatted string
652    */
 
653  2133 toggle public String form(String s)
654    {
655  2133 if (fmt != 's')
656    {
657  0 throw new java.lang.IllegalArgumentException();
658    }
659   
660  2133 if (precision >= 0)
661    {
662  0 s = s.substring(0, precision);
663    }
664   
665  2133 return pad(s);
666    }
667   
668    /**
669    * Returns a string consisting of n repeats of character c
670    *
671    * @param c
672    * @param n
673    *
674    * @return
675    */
 
676  176734 toggle static String repeat(char c, int n)
677    {
678  176734 if (n <= 0)
679    {
680  155997 return "";
681    }
682  20737 char[] chars = new char[n];
683  20737 Arrays.fill(chars, c);
684  20737 return new String(chars);
685    }
686   
687    /**
688    * DOCUMENT ME!
689    *
690    * @param x
691    * DOCUMENT ME!
692    * @param n
693    * DOCUMENT ME!
694    * @param m
695    * DOCUMENT ME!
696    * @param d
697    * DOCUMENT ME!
698    *
699    * @return DOCUMENT ME!
700    */
 
701  0 toggle private static String convert(long x, int n, int m, String d)
702    {
703  0 if (x == 0)
704    {
705  0 return "0";
706    }
707   
708  0 String r = "";
709   
710  0 while (x != 0)
711    {
712  0 r = d.charAt((int) (x & m)) + r;
713  0 x = x >>> n;
714    }
715   
716  0 return r;
717    }
718   
719    /**
720    * DOCUMENT ME!
721    *
722    * @param r
723    * DOCUMENT ME!
724    *
725    * @return DOCUMENT ME!
726    */
 
727  89432 toggle private String pad(String r)
728    {
729  89432 String p = repeat(' ', width - r.length());
730   
731  89432 if (left_align)
732    {
733  973 return pre + r + p + post;
734    }
735    else
736    {
737  88459 return pre + p + r + post;
738    }
739    }
740   
741    /**
742    * DOCUMENT ME!
743    *
744    * @param s
745    * DOCUMENT ME!
746    * @param r
747    * DOCUMENT ME!
748    *
749    * @return DOCUMENT ME!
750    */
 
751  87299 toggle private String sign(int s, String r)
752    {
753  87299 String p = "";
754   
755  87299 if (s < 0)
756    {
757  0 p = "-";
758    }
759  87299 else if (s > 0)
760    {
761  87299 if (show_plus)
762    {
763  0 p = "+";
764    }
765  87299 else if (show_space)
766    {
767  0 p = " ";
768    }
769    }
770    else
771    {
772  0 if ((fmt == 'o') && alternate && (r.length() > 0)
773    && (r.charAt(0) != '0'))
774    {
775  0 p = "0";
776    }
777  0 else if ((fmt == 'x') && alternate)
778    {
779  0 p = "0x";
780    }
781  0 else if ((fmt == 'X') && alternate)
782    {
783  0 p = "0X";
784    }
785    }
786   
787  87299 int w = 0;
788   
789  87299 if (leading_zeroes)
790    {
791  0 w = width;
792    }
793  87299 else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X')
794    || (fmt == 'o')) && (precision > 0))
795    {
796  0 w = precision;
797    }
798   
799  87299 return p + repeat('0', w - p.length() - r.length()) + r;
800    }
801   
802    /**
803    * DOCUMENT ME!
804    *
805    * @param d
806    * DOCUMENT ME!
807    *
808    * @return DOCUMENT ME!
809    */
 
810  68155 toggle private String fixed_format(double d)
811    {
812  68155 boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;
813   
814    // remove trailing zeroes and decimal point
815  68155 if (d > 0x7FFFFFFFFFFFFFFFL)
816    {
817  0 return exp_format(d);
818    }
819   
820  68155 if (precision == 0)
821    {
822  6 return (long) (d + 0.5) + (removeTrailing ? "" : ".");
823    }
824   
825  68149 long whole = (long) d;
826  68149 double fr = d - whole; // fractional part
827   
828  68149 if ((fr >= 1) || (fr < 0))
829    {
830  0 return exp_format(d);
831    }
832   
833  68149 double factor = 1;
834  68149 String leading_zeroes = "";
835   
836  406587 for (int i = 1; (i <= precision)
837    && (factor <= 0x7FFFFFFFFFFFFFFFL); i++)
838    {
839  338438 factor *= 10;
840  338438 leading_zeroes = leading_zeroes + "0";
841    }
842   
843  68149 long l = (long) ((factor * fr) + 0.5);
844   
845  68149 if (l >= factor)
846    {
847  10 l = 0;
848  10 whole++;
849    }
850   
851    // CSH 10-25-97
852  68149 String z = leading_zeroes + l;
853  68149 z = "." + z.substring(z.length() - precision, z.length());
854   
855  68149 if (removeTrailing)
856    {
857  0 int t = z.length() - 1;
858   
859  0 while ((t >= 0) && (z.charAt(t) == '0'))
860    {
861  0 t--;
862    }
863   
864  0 if ((t >= 0) && (z.charAt(t) == '.'))
865    {
866  0 t--;
867    }
868   
869  0 z = z.substring(0, t + 1);
870    }
871   
872  68149 return whole + z;
873    }
874   
875    /**
876    * DOCUMENT ME!
877    *
878    * @param d
879    * DOCUMENT ME!
880    *
881    * @return DOCUMENT ME!
882    */
 
883  3 toggle private String exp_format(double d)
884    {
885  3 String f = "";
886  3 int e = 0;
887  3 double dd = d;
888   
889  3 if (d != 0)
890    {
891  10 while (dd > 10)
892    {
893  7 e++;
894  7 dd = dd / 10;
895    }
896   
897  313 while (dd < 1)
898    {
899  310 e--;
900  310 dd = dd * 10;
901    }
902    }
903   
904  3 if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision))
905    {
906  0 return fixed_format(d);
907    }
908   
909  3 f = f + fixed_format(dd);
910   
911  3 if ((fmt == 'e') || (fmt == 'g'))
912    {
913  3 f = f + "e";
914    }
915    else
916    {
917  0 f = f + "E";
918    }
919   
920  3 String p = "000";
921   
922  3 if (e >= 0)
923    {
924  2 f = f + "+";
925  2 p = p + e;
926    }
927    else
928    {
929  1 f = f + "-";
930  1 p = p + (-e);
931    }
932   
933  3 return f + p.substring(p.length() - 3, p.length());
934    }
935   
 
936  0 toggle @Override
937    public String toString()
938    {
939  0 return formatString;
940    }
941   
942    /**
943    * Bespoke method to format percentage float value to the specified number of
944    * decimal places. Avoids use of general-purpose format parsers as a
945    * processing hotspot.
946    *
947    * @param sb
948    * @param value
949    * @param dp
950    */
 
951  135186 toggle public static void appendPercentage(StringBuilder sb, float value, int dp)
952    {
953    /*
954    * rounding first
955    */
956  135186 double d = value;
957  135186 long factor = 1L;
958  135200 for (int i = 0; i < dp; i++)
959    {
960  16 factor *= 10;
961    }
962  135191 d *= factor;
963  135190 d += 0.5;
964   
965    /*
966    * integer part
967    */
968  135188 value = (float) (d / factor);
969  135188 sb.append((long) value);
970   
971    /*
972    * decimal places
973    */
974  135197 if (dp > 0)
975    {
976  10 sb.append(".");
977  26 while (dp > 0)
978    {
979  16 value = value - (int) value;
980  16 value *= 10;
981  16 sb.append((int) value);
982  16 dp--;
983    }
984    }
985    }
986    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.