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Coverage Report

  1. Project Clover database Tue Mar 10 2026 14:58:44 GMT
  2. Package jalview.bin

File Console.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
0% of files have more coverage

Code metrics

50
122
40
1
480
381
73
0.6
3.05
40
1.83

Classes

Class Line # Actions
Console 36 122 73
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

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.bin;
22   
23    import java.io.BufferedOutputStream;
24    import java.io.File;
25    import java.io.FileNotFoundException;
26    import java.io.FileOutputStream;
27    import java.io.PrintStream;
28    import java.util.Locale;
29   
30    import jalview.log.JLogger;
31    import jalview.log.JLoggerI.LogLevel;
32    import jalview.log.JLoggerLog4j;
33    import jalview.util.ChannelProperties;
34    import jalview.util.LaunchUtils;
35   
 
36    public class Console
37    {
38   
39    public static JLoggerLog4j log = null;
40   
41    private static PrintStream out = System.out;
42   
43    private static PrintStream err = System.err;
44   
45    private static File logfile = null;
46   
 
47  0 toggle public static PrintStream getOut()
48    {
49  0 return out;
50    }
51   
 
52  0 toggle public static PrintStream getErr()
53    {
54  0 return err;
55    }
56   
 
57  0 toggle public static void setOut(PrintStream p)
58    {
59  0 out = p;
60    }
61   
 
62  0 toggle public static void setErr(PrintStream p)
63    {
64  0 err = p;
65    }
66   
 
67  0 toggle public static boolean setLogFile(String filename, boolean append)
68    {
69  0 boolean usingLogfile = false;
70  0 if (filename != null)
71    {
72  0 if (filename.startsWith("~/"))
73    {
74  0 filename = System.getProperty("user.home") + File.separator
75    + filename.substring(2);
76    }
77  0 logfile = new File(filename);
78   
79  0 try
80    {
81  0 PrintStream logFilePrintStream = new PrintStream(
82    new BufferedOutputStream(
83    new FileOutputStream(logfile, append)),
84    true);
85   
86  0 Console.setOut(logFilePrintStream);
87  0 Console.setErr(logFilePrintStream);
88   
89  0 Console.info(LaunchUtils.LOGFILE_HANDOVER);
90   
91  0 Console.info(ChannelProperties.getProperty("app_name")
92    .toUpperCase(Locale.ROOT) + " start of logging");
93  0 Console.debug(ChannelProperties.getProperty("app_name")
94    + " logging to " + filename);
95   
96  0 usingLogfile = true;
97    } catch (FileNotFoundException e)
98    {
99  0 Console.errPrintln("Error opening logfile: " + e.getMessage());
100    }
101    }
102  0 return usingLogfile;
103    }
104   
 
105  0 toggle public static void debug(String message, Throwable t)
106    {
107  0 if (Console.initLogger())
108    {
109  0 log.debug(message, t);
110    }
111    else
112    {
113  0 outPrintln(message);
114  0 Console.printStackTrace(t);
115    }
116    }
117   
 
118  0 toggle public static void info(String message)
119    {
120  0 if (Console.initLogger())
121    {
122  0 log.info(message, null);
123    }
124    else
125    {
126  0 outPrintln(message);
127    }
128   
129    }
130   
 
131  0 toggle public static void trace(String message, Throwable t)
132    {
133  0 if (Console.initLogger())
134    {
135  0 log.trace(message, t);
136    }
137    else
138    {
139  0 outPrintln(message);
140  0 Console.printStackTrace(t);
141    }
142    }
143   
 
144  0 toggle public static void debug(String message)
145    {
146  0 if (Console.initLogger())
147    {
148  0 log.debug(message, null);
149    }
150    else
151    {
152  0 outPrintln(message);
153    }
154   
155    }
156   
 
157  0 toggle public static void info(String message, Throwable t)
158    {
159  0 if (Console.initLogger())
160    {
161  0 log.info(message, t);
162    }
163    else
164    {
165  0 outPrintln(message);
166  0 Console.printStackTrace(t);
167    }
168   
169    }
170   
 
171  0 toggle public static void warn(String message)
172    {
173  0 if (Console.initLogger())
174    {
175  0 log.warn(message, null);
176    }
177    else
178    {
179  0 outPrintln(message);
180    }
181   
182    }
183   
 
184  0 toggle public static void trace(String message)
185    {
186  0 if (Console.initLogger())
187    {
188  0 log.trace(message, null);
189    }
190    else
191    {
192  0 outPrintln(message);
193    }
194    }
195   
 
196  0 toggle public static void warn(String message, Throwable t)
197    {
198  0 if (Console.initLogger())
199    {
200  0 log.warn(message, t);
201    }
202    else
203    {
204  0 outPrintln(message);
205  0 Console.printStackTrace(t);
206    }
207   
208    }
209   
 
210  0 toggle public static void error(String message)
211    {
212  0 if (Console.initLogger())
213    {
214  0 log.error(message, null);
215    }
216    else
217    {
218  0 jalview.bin.Console.errPrintln(message);
219    }
220   
221    }
222   
 
223  0 toggle public static void error(String message, Throwable t)
224    {
225  0 if (Console.initLogger())
226    {
227  0 log.error(message, t);
228    }
229    else
230    {
231  0 jalview.bin.Console.errPrintln(message);
232  0 Console.printStackTrace(t);
233    }
234   
235    }
236   
 
237  0 toggle public static void fatal(String message)
238    {
239  0 if (Console.initLogger())
240    {
241  0 log.fatal(message, null);
242    }
243    else
244    {
245  0 jalview.bin.Console.errPrintln(message);
246    }
247   
248    }
249   
 
250  0 toggle public static void fatal(String message, Throwable t)
251    {
252  0 if (Console.initLogger())
253    {
254  0 log.fatal(message, t);
255    }
256    else
257    {
258  0 jalview.bin.Console.errPrintln(message);
259  0 Console.printStackTrace(t);
260    }
261   
262    }
263   
 
264  0 toggle public static boolean isDebugEnabled()
265    {
266  0 return log == null ? false : log.isDebugEnabled();
267    }
268   
 
269  0 toggle public static boolean isTraceEnabled()
270    {
271  0 return log == null ? false : log.isTraceEnabled();
272    }
273   
 
274  0 toggle public static JLogger.LogLevel getCachedLogLevel()
275    {
276  0 return Console.getCachedLogLevel(Cache.JALVIEWLOGLEVEL);
277    }
278   
 
279  0 toggle public static JLogger.LogLevel getCachedLogLevel(String key)
280    {
281  0 return getLogLevel(Cache.getDefault(key, "INFO"));
282    }
283   
 
284  0 toggle public static JLogger.LogLevel getLogLevel(String level)
285    {
286  0 return JLogger.toLevel(level);
287    }
288   
 
289  0 toggle public static JLogger getLogger()
290    {
291  0 return log;
292    }
293   
 
294  0 toggle public static boolean initLogger()
295    {
296  0 String level = null;
297  0 try
298    {
299  0 level = System.getProperty("jalview.loglevel");
300  0 if (level != null)
301    {
302  0 level = JLogger.LogLevel.valueOf(level).toString();
303    }
304    } catch (Exception x)
305    {
306  0 Console.errPrintln(
307    "Ignoring value of jalview.loglevel '" + level + "'");
308    }
309  0 return initLogger(level);
310    }
311   
 
312  0 toggle public static boolean initLogger(String providedLogLevel)
313    {
314  0 if (log != null)
315    {
316  0 return true;
317    }
318  0 try
319    {
320  0 JLogger.LogLevel logLevel = JLogger.LogLevel.INFO;
321   
322  0 if (providedLogLevel != null && JLogger.isLevel(providedLogLevel))
323    {
324  0 logLevel = Console.getLogLevel(providedLogLevel);
325    }
326    else
327    {
328  0 logLevel = getCachedLogLevel();
329    }
330   
331  0 JLoggerLog4j.setLogfile(logfile);
332   
333    // log output
334    // is laxis used? Does getLogger do anything without a Logger object?
335    // Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
336  0 JLoggerLog4j.getLogger("org.apache.axis", logLevel);
337   
338    // The main application logger
339  0 log = JLoggerLog4j.getLogger(Cache.JALVIEW_LOGGER_NAME, logLevel);
340  0 log.info("Logging initialised at level: " + logLevel);
341    } catch (NoClassDefFoundError e)
342    {
343  0 jalview.bin.Console
344    .errPrintln("Could not initialise the logger framework");
345  0 Console.printStackTrace(e);
346    }
347   
348    // Test message
349  0 if (log != null)
350    {
351    // Logging test message should go through the logger object
352  0 if (log.loggerExists())
353  0 log.debug(Console.LOGGING_TEST_MESSAGE);
354    // Tell the user that debug is enabled
355  0 debug(ChannelProperties.getProperty("app_name")
356    + " Debugging Output Follows.");
357  0 return true;
358    }
359    else
360    {
361  0 return false;
362    }
363    }
364   
 
365  0 toggle public static void setLogLevel(String logLevelString)
366    {
367  0 LogLevel l = null;
368  0 try
369    {
370  0 l = LogLevel.valueOf(logLevelString);
371    } catch (IllegalArgumentException | NullPointerException e1)
372    {
373  0 Console.debug("Invalid log level '" + logLevelString + "'");
374  0 return;
375    }
376  0 setLogLevel(l);
377    }
378   
 
379  0 toggle public static void setLogLevel(LogLevel l)
380    {
381  0 if (l != null)
382    {
383  0 log.setLevel(l);
384  0 JLoggerLog4j.getLogger("org.apache.axis", l);
385    }
386    }
387   
 
388  0 toggle public static void outPrint()
389    {
390  0 outPrint("");
391    }
392   
 
393  0 toggle public static void outPrintln()
394    {
395  0 outPrintln("");
396    }
397   
 
398  0 toggle public static void outPrint(Object message)
399    {
400  0 outPrintMessage(message, false, false);
401    }
402   
 
403  0 toggle public static void outPrint(Object message, boolean forceStdout)
404    {
405  0 outPrintMessage(message, false, forceStdout);
406    }
407   
 
408  0 toggle public static void outPrintln(Object message)
409    {
410  0 outPrintMessage(message, true, false);
411    }
412   
 
413  0 toggle public static PrintStream outputStream(boolean forceStdout)
414    {
415    // send message to stderr if an output file to stdout is expected
416  0 if (!forceStdout && Jalview.instanceExists()
417    && Jalview.getInstance().getBootstrapArgs() != null
418    && Jalview.getInstance().getBootstrapArgs().outputToStdout())
419    {
420  0 return err;
421    }
422    else
423    {
424  0 return out;
425    }
426    }
427   
 
428  0 toggle public static void outPrintMessage(Object message, boolean newline,
429    boolean forceStdout)
430    {
431  0 PrintStream ps = outputStream(forceStdout);
432  0 if (newline)
433    {
434  0 ps.println(message);
435    }
436    else
437    {
438  0 ps.print(message);
439    }
440    }
441   
 
442  0 toggle public static void errPrint()
443    {
444  0 errPrint("");
445    }
446   
 
447  0 toggle public static void errPrintln()
448    {
449  0 errPrintln("");
450    }
451   
 
452  0 toggle public static void errPrint(Object message)
453    {
454  0 err.print(message);
455    }
456   
 
457  0 toggle public static void errPrintln(Object message)
458    {
459  0 err.println(message);
460    }
461   
 
462  0 toggle public static void debugPrintStackTrace(Throwable t)
463    {
464  0 if (!isDebugEnabled())
465    {
466  0 return;
467    }
468    // send message to stderr if output to stdout is expected
469  0 printStackTrace(t);
470    }
471   
 
472  0 toggle public static void printStackTrace(Throwable t)
473    {
474    // send message to stderr if output to stdout is expected
475  0 t.printStackTrace(err);
476    }
477   
478    public final static String LOGGING_TEST_MESSAGE = "Logging to STDERR";
479   
480    }
  • Report generated by OpenClover v 4.4.1 on Tue Mar 10 2026 14:59:17 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.