Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParsePackedSet	40	105	36	0.00%	Show methods

Class ParsePackedSet

Class ParsePackedSet	Line # 40	Total Statements 105	Complexity 36	TOTAL Coverage 0.00%
getAlignment(JalviewDataset,Iterable<DataProvider>) : Object[]   getAlignment(JalviewDataset,Iterable<DataProvider>) : Object[]	5454	71.071	27.027	0.0 0.00%
main(String[]) : void   main(String[]) : void	230230	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.util.Locale;
24
25		import jalview.api.FeatureColourI;
26		import jalview.datamodel.AlignmentI;
27		import jalview.io.AppletFormatAdapter;
28		import jalview.io.FileFormatI;
29		import jalview.io.FileParse;
30		import jalview.io.FormatAdapter;
31		import jalview.io.IdentifyFile;
32		import jalview.io.packed.DataProvider.JvDataType;
33
34		import java.io.BufferedReader;
35		import java.io.IOException;
36		import java.util.ArrayList;
37		import java.util.HashMap;
38		import java.util.List;
39
		0% Uncovered Elements: 157 (157) Complexity: 36 Complexity Density: 0.34
40		public class ParsePackedSet
41		{
42
43		/**
44		* return results as a series of jalview.datamodel objects suitable for
45		* display
46		*
47		* @param context
48		* - context which is updated with new data
49		* @param files
50		* - source data
51		* @return list of data objects added to context
52		* @throws Exception
53		*/
		0% Uncovered Elements: 109 (109) Complexity: 27 Complexity Density: 0.38
54	0	public Object[] getAlignment(JalviewDataset context,...
55		Iterable<DataProvider> files) throws Exception
56		{
57	0	List<Object> rslt = new ArrayList<>();
58	0	if (context == null)
59		{
60	0	context = new JalviewDataset();
61		}
62	0	boolean deuniquify = false;
63	0	for (DataProvider dta : files)
64		{
65	0	Exception exerror = null;
66	0	String errmsg = null;
67	0	FileParse src = dta.getDataSource();
68	0	if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
69		{
70	0	FileFormatI fmt = null;
71	0	try
72		{
73	0	fmt = new IdentifyFile().identify(src, false);
74		} catch (Exception ex)
75		{
76	0	exerror = ex;
77	0	errmsg = "Couldn't identify alignment format.";
78		}
79
80	0	if (fmt != null)
81		{
82		// parse the alignment
83	0	AlignmentI al = null;
84	0	try
85		{
86	0	al = new FormatAdapter().readFromFile(src, fmt);
87		} catch (Exception e)
88		{
89	0	errmsg = "Failed to parse alignment from result set";
90	0	exerror = e;
91		}
92	0	if (al != null)
93		{
94		// deuniquify and construct/merge additional dataset entries if
95		// necessary.
96	0	context.addAlignment(al);
97	0	context.updateSetModified(true);
98	0	rslt.add(al);
99	0	deuniquify = true;
100		}
101		}
102		}
103	0	if (dta.getType().equals(JvDataType.ANNOTATION))
104		{
105	0	if (!context.hasAlignments())
106		{
107	0	errmsg = "No alignment or sequence dataset to associate annotation with.";
108		// could duplicate the dataset reference here as default behaviour for
109		// sequence associated annotation ?
110		}
111	0	try
112		{
113	0	BufferedReader br;
114	0	if (src.getReader() instanceof BufferedReader)
115		{
116	0	br = (BufferedReader) src.getReader();
117		}
118		else
119		{
120	0	br = new BufferedReader(src.getReader());
121		}
122		// TODO: add columnSelection to context
123	0	if (new jalview.io.AnnotationFile().parseAnnotationFrom(
124		context.getLastAlignment(), null, br))
125		{
126	0	context.updateSetModified(true);
127		}
128		else
129		{
130	0	errmsg = "Annotation file contained no data.";
131		}
132
133		} catch (Exception e)
134		{
135	0	errmsg = ((errmsg == null) ? "" : errmsg)
136		+ "Failed to parse the annotation file associated with the alignment.";
137	0	exerror = e;
138		}
139		}
140	0	if (dta.getType().equals(JvDataType.SEQASSOCATED))
141		{
142	0	if (!context.hasSequenceAssoc())
143		{
144	0	errmsg = "No sequence to associate data with.";
145
146		}
147	0	errmsg = "parsing of sequence associated data is not implemented";
148	0	exerror = new Exception(errmsg);
149		}
150	0	if (dta.getType().equals(JvDataType.FEATURES))
151		{
152		// check the context has a place to store feature rendering definitions,
153		// if not, create one.
154	0	if (context.featureColours == null)
155		{
156	0	context.featureColours = new HashMap<>();
157		}
158	0	try
159		{
160	0	jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
161	0	context.updateSetModified(ff.parse(context.getLastAlignment(),
162		context.featureColours, false,
163		context.relaxedIdMatching));
164		} catch (Exception e)
165		{
166	0	errmsg = ("Failed to parse the Features file associated with the alignment.");
167	0	exerror = e;
168		}
169		}
170	0	if (dta.getType().equals(JvDataType.TREE))
171		{
172	0	try
173		{
174	0	jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
175	0	if (!nf.isValid())
176		{
177	0	nf.close();
178	0	nf = null;
179		}
180		else
181		{
182		// do association to current alignment.
183
184	0	context.addTreeFromFile(nf);
185	0	rslt.add(nf);
186	0	context.updateSetModified(true);
187		}
188		} catch (Exception e)
189		{
190	0	errmsg = ("Failed to parse the treeFile associated with the result.");
191	0	exerror = e;
192		}
193
194		}
195	0	if (exerror != null)
196		{
197	0	if (errmsg != null && errmsg.length() > 0)
198		{
199	0	throw new IOException(errmsg, exerror);
200		}
201		else
202		{
203	0	throw new IOException(errmsg, exerror);
204		}
205		}
206		else
207		{
208	0	if (errmsg != null && errmsg.length() > 0)
209		{
210	0	throw new IOException(errmsg);
211		}
212		}
213		}
214	0	if (deuniquify)
215		{
216	0	context.getLastAlignmentSet().deuniquifyAlignment();
217		}
218	0	return rslt.toArray();
219		}
220
221		/**
222		* simple command line test. Arguments should be one or more pairs of
223		* <DataProvider.JvDataType> <Filename> arguments. The routine will attempt to
224		* read each source in turn, and report what kind of Jalview datamodel objects
225		* would be created.
226		*
227		* @param args
228		* @j2sIgnore
229		*/
		0% Uncovered Elements: 46 (46) Complexity: 9 Complexity Density: 0.26
230	0	public static void main(String args[])...
231		{
232		// make data providers from the set of keys/files
233	0	int i = 0;
234	0	List<DataProvider> dp = new ArrayList<>();
235	0	while ((i + 1) < args.length)
236		{
237	0	String type = args[i++];
238	0	final String file = args[i++];
239	0	final JvDataType jtype = DataProvider.JvDataType
240		.valueOf(type.toUpperCase(Locale.ROOT));
241	0	if (jtype != null)
242		{
243	0	final FileParse fp;
244	0	try
245		{
246	0	fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
247		} catch (Exception e)
248		{
249	0	jalview.bin.Console
250		.errPrintln("Couldn't handle datasource of type " + jtype
251		+ " using URI " + file);
252	0	e.printStackTrace();
253	0	return;
254		}
255	0	dp.add(new SimpleDataProvider(jtype, fp, null));
256		}
257		else
258		{
259	0	jalview.bin.Console.outPrintln("Couldn't parse source type token '"
260		+ type.toUpperCase(Locale.ROOT) + "'");
261		}
262		}
263	0	if (i < args.length)
264		{
265	0	System.out.print("** WARNING\nIgnoring unused arguments:\n");
266	0	while (i < args.length)
267		{
268	0	System.out.print(" " + args[i]);
269		}
270	0	System.out.print("\n");
271
272		}
273	0	jalview.bin.Console.outPrintln("Now trying to parse set:");
274	0	JalviewDataset context;
275	0	Object[] newdm;
276	0	ParsePackedSet pps;
277	0	try
278		{
279	0	newdm = (pps = new ParsePackedSet())
280		.getAlignment(context = new JalviewDataset(), dp);
281		} catch (Exception e)
282		{
283	0	jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
284	0	e.printStackTrace(System.out);
285	0	return;
286		}
287	0	if (newdm != null)
288		{
289	0	for (Object o : newdm)
290		{
291	0	jalview.bin.Console
292		.outPrintln("Will need to create an " + o.getClass());
293		}
294
295		// now test uniquify/deuniquify stuff
296		// uniquify alignment and write alignment, annotation, features, and trees
297		// to buffers.
298		// import with deuniquify info, and compare results to input.
299
300		}
301		else
302		{
303	0	if (context.getLastAlignmentSet().isModified())
304		{
305	0	jalview.bin.Console.errPrintln(
306		"Initial alignment set was modified and any associated views should be updated.");
307		}
308		}
309		}
310		}