Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParsePackedSet	39	105	36	0.00%	Show methods

Class ParsePackedSet

Class ParsePackedSet	Line # 39	Total Statements 105	Complexity 36	TOTAL Coverage 0.00%
getAlignment(JalviewDataset,Iterable<DataProvider>) : Object[]   getAlignment(JalviewDataset,Iterable<DataProvider>) : Object[]	5353	71.071	27.027	0.0 0.00%
main(String[]) : void   main(String[]) : void	229229	34.034	9.09	0.0 0.00%

 

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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.io.packed;
22
23		import java.io.BufferedReader;
24		import java.io.IOException;
25		import java.util.ArrayList;
26		import java.util.HashMap;
27		import java.util.List;
28		import java.util.Locale;
29
30		import jalview.datamodel.AlignmentI;
31		import jalview.io.AppletFormatAdapter;
32		import jalview.io.FileFormatI;
33		import jalview.io.FileParse;
34		import jalview.io.FormatAdapter;
35		import jalview.io.IdentifyFile;
36		import jalview.io.packed.DataProvider.JvDataType;
37
38
		0% Uncovered Elements: 157 (157) Complexity: 36 Complexity Density: 0.34
39		public class ParsePackedSet
40		{
41
42		/**
43		* return results as a series of jalview.datamodel objects suitable for
44		* display
45		*
46		* @param context
47		* - context which is updated with new data
48		* @param files
49		* - source data
50		* @return list of data objects added to context
51		* @throws Exception
52		*/
		0% Uncovered Elements: 109 (109) Complexity: 27 Complexity Density: 0.38
53	0	public Object[] getAlignment(JalviewDataset context,...
54		Iterable<DataProvider> files) throws Exception
55		{
56	0	List<Object> rslt = new ArrayList<>();
57	0	if (context == null)
58		{
59	0	context = new JalviewDataset();
60		}
61	0	boolean deuniquify = false;
62	0	for (DataProvider dta : files)
63		{
64	0	Exception exerror = null;
65	0	String errmsg = null;
66	0	FileParse src = dta.getDataSource();
67	0	if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
68		{
69	0	FileFormatI fmt = null;
70	0	try
71		{
72	0	fmt = new IdentifyFile().identify(src, false, false);
73		} catch (Exception ex)
74		{
75	0	exerror = ex;
76	0	errmsg = "Couldn't identify alignment format.";
77		}
78
79	0	if (fmt != null)
80		{
81		// parse the alignment
82	0	AlignmentI al = null;
83	0	try
84		{
85	0	al = new FormatAdapter().readFromFile(src, fmt);
86		} catch (Exception e)
87		{
88	0	errmsg = "Failed to parse alignment from result set";
89	0	exerror = e;
90		}
91	0	if (al != null)
92		{
93		// deuniquify and construct/merge additional dataset entries if
94		// necessary.
95	0	context.addAlignment(al);
96	0	context.updateSetModified(true);
97	0	rslt.add(al);
98	0	deuniquify = true;
99		}
100		}
101		}
102	0	if (dta.getType().equals(JvDataType.ANNOTATION))
103		{
104	0	if (!context.hasAlignments())
105		{
106	0	errmsg = "No alignment or sequence dataset to associate annotation with.";
107		// could duplicate the dataset reference here as default behaviour for
108		// sequence associated annotation ?
109		}
110	0	try
111		{
112	0	BufferedReader br;
113	0	if (src.getReader() instanceof BufferedReader)
114		{
115	0	br = (BufferedReader) src.getReader();
116		}
117		else
118		{
119	0	br = new BufferedReader(src.getReader());
120		}
121		// TODO: add columnSelection to context
122	0	if (new jalview.io.AnnotationFile().parseAnnotationFrom(
123		context.getLastAlignment(), null, br))
124		{
125	0	context.updateSetModified(true);
126		}
127		else
128		{
129	0	errmsg = "Annotation file contained no data.";
130		}
131
132		} catch (Exception e)
133		{
134	0	errmsg = ((errmsg == null) ? "" : errmsg)
135		+ "Failed to parse the annotation file associated with the alignment.";
136	0	exerror = e;
137		}
138		}
139	0	if (dta.getType().equals(JvDataType.SEQASSOCATED))
140		{
141	0	if (!context.hasSequenceAssoc())
142		{
143	0	errmsg = "No sequence to associate data with.";
144
145		}
146	0	errmsg = "parsing of sequence associated data is not implemented";
147	0	exerror = new Exception(errmsg);
148		}
149	0	if (dta.getType().equals(JvDataType.FEATURES))
150		{
151		// check the context has a place to store feature rendering definitions,
152		// if not, create one.
153	0	if (context.featureColours == null)
154		{
155	0	context.featureColours = new HashMap<>();
156		}
157	0	try
158		{
159	0	jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
160	0	context.updateSetModified(ff.parse(context.getLastAlignment(),
161		context.featureColours, false,
162		context.relaxedIdMatching));
163		} catch (Exception e)
164		{
165	0	errmsg = ("Failed to parse the Features file associated with the alignment.");
166	0	exerror = e;
167		}
168		}
169	0	if (dta.getType().equals(JvDataType.TREE))
170		{
171	0	try
172		{
173	0	jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
174	0	if (!nf.isValid())
175		{
176	0	nf.close();
177	0	nf = null;
178		}
179		else
180		{
181		// do association to current alignment.
182
183	0	context.addTreeFromFile(nf);
184	0	rslt.add(nf);
185	0	context.updateSetModified(true);
186		}
187		} catch (Exception e)
188		{
189	0	errmsg = ("Failed to parse the treeFile associated with the result.");
190	0	exerror = e;
191		}
192
193		}
194	0	if (exerror != null)
195		{
196	0	if (errmsg != null && errmsg.length() > 0)
197		{
198	0	throw new IOException(errmsg, exerror);
199		}
200		else
201		{
202	0	throw new IOException(errmsg, exerror);
203		}
204		}
205		else
206		{
207	0	if (errmsg != null && errmsg.length() > 0)
208		{
209	0	throw new IOException(errmsg);
210		}
211		}
212		}
213	0	if (deuniquify)
214		{
215	0	context.getLastAlignmentSet().deuniquifyAlignment();
216		}
217	0	return rslt.toArray();
218		}
219
220		/**
221		* simple command line test. Arguments should be one or more pairs of
222		* <DataProvider.JvDataType> <Filename> arguments. The routine will attempt to
223		* read each source in turn, and report what kind of Jalview datamodel objects
224		* would be created.
225		*
226		* @param args
227		* @j2sIgnore
228		*/
		0% Uncovered Elements: 46 (46) Complexity: 9 Complexity Density: 0.26
229	0	public static void main(String args[])...
230		{
231		// make data providers from the set of keys/files
232	0	int i = 0;
233	0	List<DataProvider> dp = new ArrayList<>();
234	0	while ((i + 1) < args.length)
235		{
236	0	String type = args[i++];
237	0	final String file = args[i++];
238	0	final JvDataType jtype = DataProvider.JvDataType
239		.valueOf(type.toUpperCase(Locale.ROOT));
240	0	if (jtype != null)
241		{
242	0	final FileParse fp;
243	0	try
244		{
245	0	fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
246		} catch (Exception e)
247		{
248	0	jalview.bin.Console
249		.errPrintln("Couldn't handle datasource of type " + jtype
250		+ " using URI " + file);
251	0	e.printStackTrace();
252	0	return;
253		}
254	0	dp.add(new SimpleDataProvider(jtype, fp, null));
255		}
256		else
257		{
258	0	jalview.bin.Console.outPrintln("Couldn't parse source type token '"
259		+ type.toUpperCase(Locale.ROOT) + "'");
260		}
261		}
262	0	if (i < args.length)
263		{
264	0	System.out.print("** WARNING\nIgnoring unused arguments:\n");
265	0	while (i < args.length)
266		{
267	0	System.out.print(" " + args[i]);
268		}
269	0	System.out.print("\n");
270
271		}
272	0	jalview.bin.Console.outPrintln("Now trying to parse set:");
273	0	JalviewDataset context;
274	0	Object[] newdm;
275	0	ParsePackedSet pps;
276	0	try
277		{
278	0	newdm = (pps = new ParsePackedSet())
279		.getAlignment(context = new JalviewDataset(), dp);
280		} catch (Exception e)
281		{
282	0	jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
283	0	e.printStackTrace(System.out);
284	0	return;
285		}
286	0	if (newdm != null)
287		{
288	0	for (Object o : newdm)
289		{
290	0	jalview.bin.Console
291		.outPrintln("Will need to create an " + o.getClass());
292		}
293
294		// now test uniquify/deuniquify stuff
295		// uniquify alignment and write alignment, annotation, features, and trees
296		// to buffers.
297		// import with deuniquify info, and compare results to input.
298
299		}
300		else
301		{
302	0	if (context.getLastAlignmentSet().isModified())
303		{
304	0	jalview.bin.Console.errPrintln(
305		"Initial alignment set was modified and any associated views should be updated.");
306		}
307		}
308		}
309		}