Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MsaWSJob	15	98	52	0.00%	Show methods

Class MsaWSJob

Class MsaWSJob	Line # 15	Total Statements 98	Complexity 52	TOTAL Coverage 0.00%
MsaWSJob(MsaWSThread,int,SequenceI[])   MsaWSJob(MsaWSThread,int,SequenceI[])	4848	7.07	2.02	0.0 0.00%
prepareInput(SequenceI[],int) : boolean   prepareInput(SequenceI[],int) : boolean	7676	19.019	10.010	0.0 0.00%
hasResults() : boolean   hasResults() : boolean	134134	3.03	6.06	0.0 0.00%
getAlignment() : Object[]   getAlignment() : Object[]	153153	46.046	18.018	0.0 0.00%
cancel() : void   cancel() : void	264264	3.03	1.01	0.0 0.00%
hasValidInput() : boolean   hasValidInput() : boolean	275275	3.03	3.03	0.0 0.00%
setStatus(String) : void   setStatus(String) : void	290290	2.02	1.01	0.0 0.00%
getStatus() : String   getStatus() : String	297297	1.01	1.01	0.0 0.00%
hasStatus() : boolean   hasStatus() : boolean	303303	1.01	1.01	0.0 0.00%
getLastChunk() : long   getLastChunk() : long	312312	1.01	1.01	0.0 0.00%
setLastChunk(long) : void   setLastChunk(long) : void	321321	1.01	1.01	0.0 0.00%
getAlignmentProgram() : String   getAlignmentProgram() : String	328328	1.01	1.01	0.0 0.00%
hasArguments() : boolean   hasArguments() : boolean	333333	1.01	1.01	0.0 0.00%
addInitialStatus() : void   addInitialStatus() : void	342342	9.09	5.05	0.0 0.00%

 

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1		package jalview.ws.gui;
2
3		import jalview.analysis.AlignSeq;
4		import jalview.datamodel.AlignmentI;
5		import jalview.datamodel.AlignmentOrder;
6		import jalview.datamodel.Sequence;
7		import jalview.datamodel.SequenceI;
8		import jalview.util.MessageManager;
9		import jalview.ws.jws2.dm.JabaWsParamSet;
10		import jalview.ws.params.ArgumentI;
11
12		import java.util.ArrayList;
13		import java.util.Vector;
14
		0% Uncovered Elements: 172 (172) Complexity: 52 Complexity Density: 0.53
15		class MsaWSJob extends WsJob
16		{
17		/**
18		* holds basic MSA analysis configuration - todo - encapsulate
19		*/
20		private final MsaWSThread msaWSThread;
21
22		long lastChunk = 0;
23
24		/**
25		* input
26		*/
27		ArrayList<SequenceI> seqs = new ArrayList<>();
28
29		/**
30		* output
31		*/
32		AlignmentI alignment;
33
34		// set if the job didn't get run - then the input is simply returned to the
35		// user
36		private boolean returnInput = false;
37
38		/**
39		* MsaWSJob
40		*
41		* @param jobNum
42		* int
43		* @param msaWSThread
44		* TODO - abstract the properties provided by the thread
45		* @param jobId
46		* String
47		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
48	0	public MsaWSJob(MsaWSThread msaWSThread, int jobNum, SequenceI[] inSeqs)...
49		{
50	0	this.msaWSThread = msaWSThread;
51	0	this.jobnum = jobNum;
52	0	if (!prepareInput(inSeqs, 2))
53		{
54	0	submitted = true;
55	0	subjobComplete = true;
56	0	returnInput = true;
57		} else
58		{
59	0	validInput = true;
60		}
61
62		}
63
64		Vector<String[]> emptySeqs = new Vector();
65
66		/**
67		* prepare input sequences for MsaWS service
68		*
69		* @param seqs
70		* jalview sequences to be prepared
71		* @param minlen
72		* minimum number of residues required for this MsaWS service
73		* @return true if seqs contains sequences to be submitted to service.
74		*/
75		// TODO: return compbio.seqs list or nothing to indicate validity.
		0% Uncovered Elements: 35 (35) Complexity: 10 Complexity Density: 0.53
76	0	private boolean prepareInput(SequenceI[] seqs, int minlen)...
77		{
78		// TODO: service specific input data is generated in this method - for
79		// JABAWS it is client-side
80		// prepared, but for Slivka it could be uploaded at this stage.
81
82	0	int nseqs = 0;
83	0	if (minlen < 0)
84		{
85	0	throw new Error(MessageManager.getString(
86		"error.implementation_error_minlen_must_be_greater_zero"));
87		}
88	0	for (int i = 0; i < seqs.length; i++)
89		{
90	0	if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
91		{
92	0	nseqs++;
93		}
94		}
95	0	boolean valid = nseqs > 1; // need at least two seqs
96	0	Sequence seq;
97	0	for (int i = 0, n = 0; i < seqs.length; i++)
98		{
99	0	String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
100		// for
101		// any
102		// subjob
103	0	SeqNames.put(newname,
104		jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
105	0	if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
106		{
107		// make new input sequence with or without gaps
108	0	seq = new Sequence(newname,
109	0	(this.msaWSThread.submitGaps) ? seqs[i].getSequenceAsString()
110		: AlignSeq.extractGaps(
111		jalview.util.Comparison.GapChars,
112		seqs[i].getSequenceAsString()));
113	0	this.seqs.add(seq);
114		}
115		else
116		{
117	0	String empty = null;
118	0	if (seqs[i].getEnd() >= seqs[i].getStart())
119		{
120	0	empty = (this.msaWSThread.submitGaps) ? seqs[i].getSequenceAsString()
121		: AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
122		seqs[i].getSequenceAsString());
123		}
124	0	emptySeqs.add(new String[] { newname, empty });
125		}
126		}
127	0	return valid;
128		}
129
130		/**
131		*
132		* @return true if getAlignment will return a valid alignment result.
133		*/
		0% Uncovered Elements: 5 (5) Complexity: 6 Complexity Density: 2
134	0	@Override...
135		public boolean hasResults()
136		{
137	0	if (subjobComplete && isFinished() && (alignment != null
138		|| (emptySeqs != null && emptySeqs.size() > 0)))
139		{
140	0	return true;
141		}
142	0	return false;
143		}
144
145		/**
146		*
147		* get the alignment including any empty sequences in the original order
148		* with original ids. Caller must access the alignment.getMetadata() object
149		* to annotate the final result passsed to the user.
150		*
151		* @return { SequenceI[], AlignmentOrder }
152		*/
		0% Uncovered Elements: 78 (78) Complexity: 18 Complexity Density: 0.39
153	0	public Object[] getAlignment()...
154		{
155		// TODO: make this generic based on MsaResultI
156		// TODO: decide if the data loss for this return signature is avoidable
157		// (ie should we just return AlignmentI instead ?)
158	0	if (hasResults())
159		{
160	0	SequenceI[] alseqs = null;
161	0	char alseq_gapchar = '-';
162	0	int alseq_l = 0;
163	0	alseqs = new SequenceI[alignment.getSequences().size()];
164	0	if (alignment.getSequences().size() > 0)
165		{
166	0	for (SequenceI seq : alignment
167		.getSequences())
168		{
169	0	alseqs[alseq_l++] = new Sequence(seq);
170		}
171	0	alseq_gapchar = alignment.getGapCharacter();
172
173		}
174		// add in the empty seqs.
175	0	if (emptySeqs.size() > 0)
176		{
177	0	SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
178		// get width
179	0	int i, w = 0;
180	0	if (alseq_l > 0)
181		{
182	0	for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
183		{
184	0	if (w < alseqs[i].getLength())
185		{
186	0	w = alseqs[i].getLength();
187		}
188	0	t_alseqs[i] = alseqs[i];
189	0	alseqs[i] = null;
190		}
191		}
192		// check that aligned width is at least as wide as emptySeqs width.
193	0	int ow = w, nw = w;
194	0	for (i = 0, w = emptySeqs.size(); i < w; i++)
195		{
196	0	String[] es = emptySeqs.get(i);
197	0	if (es != null && es[1] != null)
198		{
199	0	int sw = es[1].length();
200	0	if (nw < sw)
201		{
202	0	nw = sw;
203		}
204		}
205		}
206		// make a gapped string.
207	0	StringBuffer insbuff = new StringBuffer(w);
208	0	for (i = 0; i < nw; i++)
209		{
210	0	insbuff.append(alseq_gapchar);
211		}
212	0	if (ow < nw)
213		{
214	0	for (i = 0; i < alseq_l; i++)
215		{
216	0	int sw = t_alseqs[i].getLength();
217	0	if (nw > sw)
218		{
219		// pad at end
220	0	alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()
221		+ insbuff.substring(0, sw - nw));
222		}
223		}
224		}
225	0	for (i = 0, w = emptySeqs.size(); i < w; i++)
226		{
227	0	String[] es = emptySeqs.get(i);
228	0	if (es[1] == null)
229		{
230	0	t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
231		insbuff.toString(), 1, 0);
232		}
233		else
234		{
235	0	if (es[1].length() < nw)
236		{
237	0	t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
238		es[0],
239		es[1] + insbuff.substring(0, nw - es[1].length()),
240		1, 1 + es[1].length());
241		}
242		else
243		{
244	0	t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
245		es[0], es[1]);
246		}
247		}
248		}
249	0	alseqs = t_alseqs;
250		}
251	0	AlignmentOrder msaorder = new AlignmentOrder(alseqs);
252		// always recover the order - makes parseResult()'s life easier.
253	0	jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
254		// account for any missing sequences
255	0	jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
256	0	return new Object[] { alseqs, msaorder };
257		}
258	0	return null;
259		}
260
261		/**
262		* mark subjob as cancelled and set result object appropriatly
263		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
264	0	void cancel()...
265		{
266	0	cancelled = true;
267	0	subjobComplete = true;
268	0	alignment = null;
269		}
270
271		/**
272		*
273		* @return boolean true if job can be submitted.
274		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
275	0	@Override...
276		public boolean hasValidInput()
277		{
278		// TODO: get attributes for this MsaWS instance to check if it can do two
279		// sequence alignment.
280		// TODO: check type of sequences are valid for this service
281	0	if (seqs != null && seqs.size() >= 2) // two or more sequences is valid ?
282		{
283	0	return true;
284		}
285	0	return false;
286		}
287
288		StringBuffer jobProgress = new StringBuffer();
289
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
290	0	@Override...
291		public void setStatus(String string)
292		{
293	0	jobProgress.setLength(0);
294	0	jobProgress.append(string);
295		}
296
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
297	0	@Override...
298		public String getStatus()
299		{
300	0	return jobProgress.toString();
301		}
302
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
303	0	@Override...
304		public boolean hasStatus()
305		{
306	0	return jobProgress != null;
307		}
308
309		/**
310		* @return the lastChunk
311		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
312	0	public long getLastChunk()...
313		{
314	0	return lastChunk;
315		}
316
317		/**
318		* @param lastChunk
319		* the lastChunk to set
320		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
321	0	public void setLastChunk(long lastChunk)...
322		{
323	0	this.lastChunk = lastChunk;
324		}
325
326		String alignmentProgram = null;
327
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
328	0	public String getAlignmentProgram()...
329		{
330	0	return alignmentProgram;
331		}
332
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
333	0	public boolean hasArguments()...
334		{
335	0	return (arguments != null && arguments.size() > 0)
336		|| (preset != null && preset instanceof JabaWsParamSet);
337		}
338
339		/**
340		* add a progess header to status string containing presets/args used
341		*/
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
342	0	public void addInitialStatus()...
343		{
344		// TODO: decide if it is useful to report 'JABAWS format' argument lists
345		// rather than generic Jalview service arguments
346	0	if (preset != null)
347		{
348	0	jobProgress.append(
349	0	"Using " + (preset.isModifiable() ? "Server" : "User")
350		+ "Preset: " + preset.getName());
351	0	for (ArgumentI opt : preset.getArguments())
352		{
353	0	jobProgress.append(opt.getName() + " " + opt.getValue() + "\n");
354		}
355		}
356		else
357		{
358	0	if (arguments != null && arguments.size() > 0)
359		{
360	0	jobProgress.append("With custom parameters : \n");
361		// merge arguments with preset's own arguments.
362	0	for (ArgumentI opt : arguments)
363		{
364	0	jobProgress.append(opt.getName() + " " + opt.getValue() + "\n");
365		}
366		}
367	0	jobProgress.append("\nJob Output:\n");
368		}
369		}
370		}