Annotation of /trunk/gadget/likelihoodprinter.cc

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1 :	agomez	1	#include "areatime.h"
2 :			#include "errorhandler.h"
3 :			#include "likelihoodprinter.h"
4 :			#include "charptrvector.h"
5 :			#include "readword.h"
6 :			#include "gadget.h"
7 :			#include "runid.h"
8 :			#include "global.h"
9 :
10 :
11 :			LikelihoodPrinter::LikelihoodPrinter(CommentStream& infile, const TimeClass* const TimeInfo)
12 :			: Printer(LIKELIHOODPRINTER) {
13 :
14 :			int i = 0;
15 :			char text[MaxStrLength];
16 :			strncpy(text, "", MaxStrLength);
17 :			printtimeid = 0;
18 :
19 :			//read in the names of the likelihood components
20 :			infile >> text >> ws;
21 :			if (strcasecmp(text, "likelihood") != 0)
22 :			handle.logFileUnexpected(LOGFAIL, "likelihood", text);
23 :			infile >> text >> ws;
24 :			while (!infile.eof() && (strcasecmp(text, "printfile") != 0)) {
25 :			likenames.resize(new char[strlen(text) + 1]);
26 :			strcpy(likenames[i++], text);
27 :			infile >> text >> ws;
28 :			}
29 :			if (likenames.Size() == 0)
30 :			handle.logFileMessage(LOGFAIL, "\nError in likelihoodprinter - failed to read component");
31 :
32 :			//read the name of the printfile, and then open the printfile
33 :			filename = new char[MaxStrLength];
34 :			strncpy(filename, "", MaxStrLength);
35 :
36 :			if (strcasecmp(text, "printfile") != 0)
37 :			handle.logFileUnexpected(LOGFAIL, "printfile", text);
38 :			infile >> filename >> ws;
39 :			outfile.open(filename, ios::out);
40 :			handle.checkIfFailure(outfile, filename);
41 :
42 :			//JMB - removed the need to read in the yearsandsteps data
43 :			infile >> ws;
44 :			if (!infile.eof()) {
45 :			char c = infile.peek();
46 :			if ((c == 'y') || (c == 'Y')) {
47 :			infile >> text >> ws;
48 :			if (strcasecmp(text, "yearsandsteps") == 0) {
49 :			handle.logMessage(LOGWARN, "Warning in likelihoodprinter - yearsandsteps data ignored");
50 :			AAT.readFromFile(infile, TimeInfo);
51 :			}
52 :			}
53 :			}
54 :
55 :			//prepare for next printfile component
56 :			infile >> ws;
57 :			if (!infile.eof()) {
58 :			infile >> text >> ws;
59 :			if (strcasecmp(text, "[component]") != 0)
60 :			handle.logFileUnexpected(LOGFAIL, "[component]", text);
61 :			}
62 :			}
63 :
64 :			LikelihoodPrinter::~LikelihoodPrinter() {
65 :			outfile.close();
66 :			outfile.clear();
67 :			int i;
68 :			for (i = 0; i < likenames.Size(); i++)
69 :			delete[] likenames[i];
70 :			}
71 :
72 :			void LikelihoodPrinter::setLikelihood(LikelihoodPtrVector& likevec) {
73 :			int i, j;
74 :
75 :			for (i = 0; i < likevec.Size(); i++)
76 :			for (j = 0; j < likenames.Size(); j++)
77 :			if (strcasecmp(likevec[i]->getName(), likenames[j]) == 0)
78 :			like.resize(likevec[i]);
79 :
80 :			if (like.Size() != likenames.Size()) {
81 :			handle.logMessage(LOGWARN, "Error in likelihoodprinter - failed to match likelihood components");
82 :			for (i = 0; i < like.Size(); i++)
83 :			handle.logMessage(LOGWARN, "Error in likelihoodprinter - found component", like[i]->getName());
84 :			for (i = 0; i < likenames.Size(); i++)
85 :			handle.logMessage(LOGWARN, "Error in likelihoodprinter - looking for component", likenames[i]);
86 :			handle.logMessage(LOGFAIL, ""); //JMB this will exit gadget
87 :			}
88 :
89 :			outfile << "; ";
90 :			RUNID.Print(outfile);
91 :
92 :			for (i = 0; i < like.Size(); i++) {
93 :			outfile << "; Likelihood output file for the likelihood component " << like[i]->getName();
94 :			switch (like[i]->getType()) {
95 :			case CATCHDISTRIBUTIONLIKELIHOOD:
96 :			outfile << "\n; year-step-area-age-length-number\n";
97 :			break;
98 :			case CATCHSTATISTICSLIKELIHOOD:
99 :			outfile << "\n; year-step-area-age-number-mean[-stddev]\n";
100 :			break;
101 :			case CATCHINKILOSLIKELIHOOD:
102 :			outfile << "\n; year-step-area-fleet-biomass\n";
103 :			break;
104 :			case SURVEYDISTRIBUTIONLIKELIHOOD:
105 :			outfile << "\n; year-step-area-age-length-number\n";
106 :			break;
107 :			case STOCKDISTRIBUTIONLIKELIHOOD:
108 :			outfile << "\n; year-step-area-stock-age-length-number\n";
109 :			break;
110 :			case STOMACHCONTENTLIKELIHOOD:
111 :			outfile << "\n; year-step-area-predator-prey-number\n";
112 :			break;
113 :			case SURVEYINDICESLIKELIHOOD:
114 :			outfile << "\n; year-step-area-label-number\n";
115 :			break;
116 :			case TAGLIKELIHOOD:
117 :			outfile << "\n; tagid-year-step-area-length-number\n";
118 :			break;
119 :			case RECSTATISTICSLIKELIHOOD:
120 :			outfile << "\n; tagid-year-step-area-number-mean[-stddev]\n";
121 :			break;
122 :			case MIGRATIONPROPORTIONLIKELIHOOD:
123 :			outfile << "\n; year-step-area-ratio\n";
124 :			break;
125 :			case BOUNDLIKELIHOOD:
126 :			case UNDERSTOCKINGLIKELIHOOD:
127 :			case MIGRATIONPENALTYLIKELIHOOD:
128 :			handle.logMessage(LOGWARN, "Warning in likelihoodprinter - printing not implemented for", like[i]->getName());
129 :			break;
130 :			default:
131 :			handle.logMessage(LOGFAIL, "Error in likelihoodprinter - unrecognised likelihood type", like[i]->getType());
132 :			break;
133 :			}
134 :			}
135 :			outfile.flush();
136 :			}
137 :
138 :			void LikelihoodPrinter::Print(const TimeClass* const TimeInfo, int printtime) {
139 :			if (printtime != printtimeid)
140 :			return;
141 :
142 :			int i;
143 :			for (i = 0; i < like.Size(); i++)
144 :			like[i]->printLikelihood(outfile, TimeInfo);
145 :			outfile.flush();
146 :			}

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