Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParsePackedSet	38	105	36	0.00%	Show methods

Class ParsePackedSet

Class ParsePackedSet	Line # 38	Total Statements 105	Complexity 36	TOTAL Coverage 0.00%
getAlignment(JalviewDataset,Iterable<DataProvider>) : Object[]   getAlignment(JalviewDataset,Iterable<DataProvider>) : Object[]	5252	71.071	27.027	0.0 0.00%
main(String[]) : void   main(String[]) : void	228228	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
		0% Uncovered Elements: 157 (157) Complexity: 36 Complexity Density: 0.34
38		public class ParsePackedSet
39		{
40
41		/**
42		* return results as a series of jalview.datamodel objects suitable for
43		* display
44		*
45		* @param context
46		* - context which is updated with new data
47		* @param files
48		* - source data
49		* @return list of data objects added to context
50		* @throws Exception
51		*/
		0% Uncovered Elements: 109 (109) Complexity: 27 Complexity Density: 0.38
52	0	public Object[] getAlignment(JalviewDataset context,...
53		Iterable<DataProvider> files) throws Exception
54		{
55	0	List<Object> rslt = new ArrayList<>();
56	0	if (context == null)
57		{
58	0	context = new JalviewDataset();
59		}
60	0	boolean deuniquify = false;
61	0	for (DataProvider dta : files)
62		{
63	0	Exception exerror = null;
64	0	String errmsg = null;
65	0	FileParse src = dta.getDataSource();
66	0	if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
67		{
68	0	FileFormatI fmt = null;
69	0	try
70		{
71	0	fmt = new IdentifyFile().identify(src, false, false);
72		} catch (Exception ex)
73		{
74	0	exerror = ex;
75	0	errmsg = "Couldn't identify alignment format.";
76		}
77
78	0	if (fmt != null)
79		{
80		// parse the alignment
81	0	AlignmentI al = null;
82	0	try
83		{
84	0	al = new FormatAdapter().readFromFile(src, fmt);
85		} catch (Exception e)
86		{
87	0	errmsg = "Failed to parse alignment from result set";
88	0	exerror = e;
89		}
90	0	if (al != null)
91		{
92		// deuniquify and construct/merge additional dataset entries if
93		// necessary.
94	0	context.addAlignment(al);
95	0	context.updateSetModified(true);
96	0	rslt.add(al);
97	0	deuniquify = true;
98		}
99		}
100		}
101	0	if (dta.getType().equals(JvDataType.ANNOTATION))
102		{
103	0	if (!context.hasAlignments())
104		{
105	0	errmsg = "No alignment or sequence dataset to associate annotation with.";
106		// could duplicate the dataset reference here as default behaviour for
107		// sequence associated annotation ?
108		}
109	0	try
110		{
111	0	BufferedReader br;
112	0	if (src.getReader() instanceof BufferedReader)
113		{
114	0	br = (BufferedReader) src.getReader();
115		}
116		else
117		{
118	0	br = new BufferedReader(src.getReader());
119		}
120		// TODO: add columnSelection to context
121	0	if (new jalview.io.AnnotationFile().parseAnnotationFrom(
122		context.getLastAlignment(), null, br))
123		{
124	0	context.updateSetModified(true);
125		}
126		else
127		{
128	0	errmsg = "Annotation file contained no data.";
129		}
130
131		} catch (Exception e)
132		{
133	0	errmsg = ((errmsg == null) ? "" : errmsg)
134		+ "Failed to parse the annotation file associated with the alignment.";
135	0	exerror = e;
136		}
137		}
138	0	if (dta.getType().equals(JvDataType.SEQASSOCATED))
139		{
140	0	if (!context.hasSequenceAssoc())
141		{
142	0	errmsg = "No sequence to associate data with.";
143
144		}
145	0	errmsg = "parsing of sequence associated data is not implemented";
146	0	exerror = new Exception(errmsg);
147		}
148	0	if (dta.getType().equals(JvDataType.FEATURES))
149		{
150		// check the context has a place to store feature rendering definitions,
151		// if not, create one.
152	0	if (context.featureColours == null)
153		{
154	0	context.featureColours = new HashMap<>();
155		}
156	0	try
157		{
158	0	jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
159	0	context.updateSetModified(ff.parse(context.getLastAlignment(),
160		context.featureColours, false,
161		context.relaxedIdMatching));
162		} catch (Exception e)
163		{
164	0	errmsg = ("Failed to parse the Features file associated with the alignment.");
165	0	exerror = e;
166		}
167		}
168	0	if (dta.getType().equals(JvDataType.TREE))
169		{
170	0	try
171		{
172	0	jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
173	0	if (!nf.isValid())
174		{
175	0	nf.close();
176	0	nf = null;
177		}
178		else
179		{
180		// do association to current alignment.
181
182	0	context.addTreeFromFile(nf);
183	0	rslt.add(nf);
184	0	context.updateSetModified(true);
185		}
186		} catch (Exception e)
187		{
188	0	errmsg = ("Failed to parse the treeFile associated with the result.");
189	0	exerror = e;
190		}
191
192		}
193	0	if (exerror != null)
194		{
195	0	if (errmsg != null && errmsg.length() > 0)
196		{
197	0	throw new IOException(errmsg, exerror);
198		}
199		else
200		{
201	0	throw new IOException(errmsg, exerror);
202		}
203		}
204		else
205		{
206	0	if (errmsg != null && errmsg.length() > 0)
207		{
208	0	throw new IOException(errmsg);
209		}
210		}
211		}
212	0	if (deuniquify)
213		{
214	0	context.getLastAlignmentSet().deuniquifyAlignment();
215		}
216	0	return rslt.toArray();
217		}
218
219		/**
220		* simple command line test. Arguments should be one or more pairs of
221		* <DataProvider.JvDataType> <Filename> arguments. The routine will attempt to
222		* read each source in turn, and report what kind of Jalview datamodel objects
223		* would be created.
224		*
225		* @param args
226		* @j2sIgnore
227		*/
		0% Uncovered Elements: 46 (46) Complexity: 9 Complexity Density: 0.26
228	0	public static void main(String args[])...
229		{
230		// make data providers from the set of keys/files
231	0	int i = 0;
232	0	List<DataProvider> dp = new ArrayList<>();
233	0	while ((i + 1) < args.length)
234		{
235	0	String type = args[i++];
236	0	final String file = args[i++];
237	0	final JvDataType jtype = DataProvider.JvDataType
238		.valueOf(type.toUpperCase(Locale.ROOT));
239	0	if (jtype != null)
240		{
241	0	final FileParse fp;
242	0	try
243		{
244	0	fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
245		} catch (Exception e)
246		{
247	0	jalview.bin.Console
248		.errPrintln("Couldn't handle datasource of type " + jtype
249		+ " using URI " + file);
250	0	e.printStackTrace();
251	0	return;
252		}
253	0	dp.add(new SimpleDataProvider(jtype, fp, null));
254		}
255		else
256		{
257	0	jalview.bin.Console.outPrintln("Couldn't parse source type token '"
258		+ type.toUpperCase(Locale.ROOT) + "'");
259		}
260		}
261	0	if (i < args.length)
262		{
263	0	System.out.print("** WARNING\nIgnoring unused arguments:\n");
264	0	while (i < args.length)
265		{
266	0	System.out.print(" " + args[i]);
267		}
268	0	System.out.print("\n");
269
270		}
271	0	jalview.bin.Console.outPrintln("Now trying to parse set:");
272	0	JalviewDataset context;
273	0	Object[] newdm;
274	0	ParsePackedSet pps;
275	0	try
276		{
277	0	newdm = (pps = new ParsePackedSet())
278		.getAlignment(context = new JalviewDataset(), dp);
279		} catch (Exception e)
280		{
281	0	jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
282	0	e.printStackTrace(System.out);
283	0	return;
284		}
285	0	if (newdm != null)
286		{
287	0	for (Object o : newdm)
288		{
289	0	jalview.bin.Console
290		.outPrintln("Will need to create an " + o.getClass());
291		}
292
293		// now test uniquify/deuniquify stuff
294		// uniquify alignment and write alignment, annotation, features, and trees
295		// to buffers.
296		// import with deuniquify info, and compare results to input.
297
298		}
299		else
300		{
301	0	if (context.getLastAlignmentSet().isModified())
302		{
303	0	jalview.bin.Console.errPrintln(
304		"Initial alignment set was modified and any associated views should be updated.");
305		}
306		}
307		}
308		}