Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HMMSearch	33	99	28	0.00%	Show methods

Class HMMSearch

Class HMMSearch	Line # 33	Total Statements 99	Complexity 28	TOTAL Coverage 0.00%
HMMSearch(AlignFrame,List<ArgumentI>)   HMMSearch(AlignFrame,List<ArgumentI>)	5050	1.01	1.01	0.0 0.00%
run() : void   run() : void	6161	19.019	4.04	0.0 0.00%
runCommand(File,File,File) : boolean   runCommand(File,File,File) : boolean	120120	7.07	2.02	0.0 0.00%
importData(SequenceI,File,File,File) : void   importData(SequenceI,File,File,File) : void	143143	51.051	16.016	0.0 0.00%
checkForNewSequences() : int   checkForNewSequences() : int	262262	7.07	2.02	0.0 0.00%
realignResults(SequenceI[]) : void   realignResults(SequenceI[]) : void	288288	14.014	3.03	0.0 0.00%

 

Contributing tests

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1		package jalview.hmmer;
2
3		import jalview.bin.Cache;
4		import jalview.bin.Console;
5		import jalview.datamodel.Alignment;
6		import jalview.datamodel.AlignmentAnnotation;
7		import jalview.datamodel.AlignmentI;
8		import jalview.datamodel.Annotation;
9		import jalview.datamodel.HiddenMarkovModel;
10		import jalview.datamodel.SequenceI;
11		import jalview.gui.AlignFrame;
12		import jalview.gui.Desktop;
13		import jalview.gui.JvOptionPane;
14		import jalview.io.DataSourceType;
15		import jalview.io.FileParse;
16		import jalview.io.StockholmFile;
17		import jalview.util.FileUtils;
18		import jalview.util.MessageManager;
19		import jalview.ws.params.ArgumentI;
20		import jalview.ws.params.simple.BooleanOption;
21		import jalview.ws.params.simple.Option;
22
23		import java.io.BufferedReader;
24		import java.io.File;
25		import java.io.FileReader;
26		import java.io.IOException;
27		import java.util.ArrayList;
28		import java.util.Collections;
29		import java.util.List;
30
31		import javax.swing.JOptionPane;
32
		0% Uncovered Elements: 145 (145) Complexity: 28 Complexity Density: 0.28
33		public class HMMSearch extends Search
34		{
35
36		boolean realign = false;
37
38		boolean trim = false;
39
40		boolean returnNoOfNewSeqs = false;
41
42		int seqsToReturn = Integer.MAX_VALUE;
43
44
45		/**
46		* Constructor for the HMMSearchThread
47		*
48		* @param af
49		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	public HMMSearch(AlignFrame af, List<ArgumentI> args)...
51		{
52	0	super(af, args);
53		}
54
55		/**
56		* Runs the HMMSearchThread: the data on the alignment or group is exported,
57		* then the command is executed in the command line and then the data is
58		* imported and displayed in a new frame. Call this method directly to execute
59		* synchronously, or via start() in a new Thread for asynchronously.
60		*/
		0% Uncovered Elements: 23 (23) Complexity: 4 Complexity Density: 0.21
61	0	@Override...
62		public void run()
63		{
64	0	HiddenMarkovModel hmm = getHmmProfile();
65	0	if (hmm == null)
66		{
67		// shouldn't happen if we got this far
68	0	Console.error("Error: no hmm for hmmsearch");
69	0	return;
70		}
71
72	0	SequenceI hmmSeq = hmm.getConsensusSequence();
73	0	long msgId = System.currentTimeMillis();
74	0	af.setProgressBar(MessageManager.getString("status.running_search"),
75		msgId);
76
77	0	try
78		{
79	0	File hmmFile = FileUtils.createTempFile("hmm", ".hmm");
80	0	File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
81		".sto");
82	0	File searchOutputFile = FileUtils.createTempFile("searchOutput",
83		".sto");
84
85	0	exportHmm(hmm, hmmFile.getAbsoluteFile());
86
87	0	boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
88	0	if (!ran)
89		{
90	0	JvOptionPane.showInternalMessageDialog(af, MessageManager
91		.formatMessage("warn.command_failed", "hmmsearch"));
92	0	return;
93		}
94
95	0	importData(hmmSeq, hitsAlignmentFile, hmmFile, searchOutputFile);
96		// TODO make realignment of search results a step at this level
97		// and make it conditional on this.realign
98		} catch (IOException | InterruptedException e)
99		{
100	0	e.printStackTrace();
101		}
102		finally
103		{
104	0	af.setProgressBar("", msgId);
105		}
106		}
107
108		/**
109		* Executes an hmmsearch with the given hmm as input. The database to be
110		* searched is a local file as specified by the 'Database' parameter, or the
111		* current alignment (written to file) if none is specified.
112		*
113		* @param searchOutputFile
114		* @param hitsAlignmentFile
115		* @param hmmFile
116		*
117		* @return
118		* @throws IOException
119		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
120	0	private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,...
121		File hmmFile) throws IOException
122		{
123	0	String command = getCommandPath(HMMSEARCH);
124	0	if (command == null)
125		{
126	0	return false;
127		}
128
129	0	List<String> args = new ArrayList<>();
130	0	args.add(command);
131	0	buildArguments(args, searchOutputFile, hitsAlignmentFile, hmmFile);
132
133	0	return runCommand(args);
134		}
135
136
137		/**
138		* Imports the data from the temporary file to which the output of hmmsearch
139		* was directed. The results are optionally realigned using hmmalign.
140		*
141		* @param hmmSeq
142		*/
		0% Uncovered Elements: 79 (79) Complexity: 16 Complexity Density: 0.31
143	0	private void importData(SequenceI hmmSeq, File inputAlignmentTemp,...
144		File hmmTemp, File searchOutputFile)
145		throws IOException, InterruptedException
146		{
147	0	BufferedReader br = new BufferedReader(
148		new FileReader(inputAlignmentTemp));
149	0	try
150		{
151	0	if (br.readLine() == null)
152		{
153	0	JOptionPane.showMessageDialog(af,
154		MessageManager.getString("label.no_sequences_found"));
155	0	return;
156		}
157	0	StockholmFile file = new StockholmFile(new FileParse(
158		inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
159	0	seqs = file.getSeqsAsArray();
160
161	0	readDomainTable(searchOutputFile, false);
162
163	0	if (searchAlignment)
164		{
165	0	recoverSequences(sequencesHash, seqs);
166		}
167
168		// look for PP cons and ref seq in alignment only annotation
169	0	AlignmentAnnotation modelpos = null, ppcons = null;
170	0	for (AlignmentAnnotation aa : file.getAnnotations())
171		{
172	0	if (aa.sequenceRef == null)
173		{
174	0	if (aa.label.equals("Reference Positions")) // RF feature type in
175		// stockholm parser
176		{
177	0	modelpos = aa;
178		}
179	0	if (aa.label.equals("Posterior Probability"))
180		{
181	0	ppcons = aa;
182		}
183		}
184		}
185
186
187	0	int seqCount = Math.min(seqs.length, seqsToReturn);
188	0	SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
189	0	hmmSeq = hmmSeq.deriveSequence(); // otherwise all bad things happen
190	0	hmmAndSeqs[0] = hmmSeq;
191	0	System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
192	0	if (modelpos != null)
193		{
194		// TODO need - get ungapped sequence method
195	0	hmmSeq.setSequence(
196		hmmSeq.getDatasetSequence().getSequenceAsString());
197	0	Annotation[] refpos = modelpos.annotations;
198		// insert gaps to match with refseq positions
199	0	int gc = 0, lcol = 0;
200	0	for (int c = 0; c < refpos.length; c++)
201		{
202	0	if (refpos[c] != null && ("x".equals(refpos[c].displayCharacter)))
203		{
204	0	if (gc > 0)
205		{
206	0	hmmSeq.insertCharAt(lcol + 1, gc, '-');
207		}
208	0	gc = 0;
209	0	lcol = c;
210		}
211		else
212		{
213	0	gc++;
214		}
215		}
216		}
217
218	0	if (realign)
219		{
220	0	realignResults(hmmAndSeqs);
221		}
222		else
223		{
224	0	AlignmentI al = new Alignment(hmmAndSeqs);
225	0	if (ppcons != null)
226		{
227	0	al.addAnnotation(ppcons);
228		}
229	0	if (modelpos != null)
230		{
231	0	al.addAnnotation(modelpos);
232		}
233	0	AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
234		AlignFrame.DEFAULT_HEIGHT);
235	0	String ttl = "hmmSearch of " + databaseName + " using "
236		+ hmmSeq.getName();
237	0	Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
238		AlignFrame.DEFAULT_HEIGHT);
239
240	0	if (returnNoOfNewSeqs)
241		{
242	0	int nNew = checkForNewSequences();
243	0	JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
244		+ MessageManager.getString("label.new_returned"));
245		}
246
247		}
248
249
250	0	hmmTemp.delete();
251	0	inputAlignmentTemp.delete();
252	0	searchOutputFile.delete();
253		} finally
254		{
255	0	if (br != null)
256		{
257	0	br.close();
258		}
259		}
260		}
261
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
262	0	private int checkForNewSequences()...
263		{
264	0	int nNew = seqs.length;
265
266	0	for (SequenceI resultSeq : seqs)
267		{
268	0	for (SequenceI aliSeq : alignment.getSequencesArray())
269		{
270	0	if (resultSeq.getName().equals(aliSeq.getName()))
271		{
272	0	nNew--;
273	0	break;
274		}
275		}
276		}
277
278	0	return nNew;
279
280		}
281
282		/**
283		* Realigns the given sequences using hmmalign, to the HMM profile sequence
284		* which is the first in the array, and opens the results in a new frame
285		*
286		* @param hmmAndSeqs
287		*/
		0% Uncovered Elements: 18 (18) Complexity: 3 Complexity Density: 0.21
288	0	protected void realignResults(SequenceI[] hmmAndSeqs)...
289		{
290		/*
291		* and align the search results to the HMM profile
292		*/
293	0	AlignmentI al = new Alignment(hmmAndSeqs);
294	0	AlignFrame frame = new AlignFrame(al, 1, 1);
295	0	List<ArgumentI> alignArgs = new ArrayList<>();
296	0	String alignTo = hmmAndSeqs[0].getName();
297	0	List<String> options = Collections.singletonList(alignTo);
298	0	Option option = new Option(MessageManager.getString("label.use_hmm"),
299		"", true, alignTo, alignTo, options, null);
300	0	alignArgs.add(option);
301	0	if (trim)
302		{
303	0	alignArgs.add(new BooleanOption(
304		MessageManager.getString(TRIM_TERMINI_KEY),
305		MessageManager.getString("label.trim_termini_desc"), true,
306		true, true, null));
307		}
308	0	HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
309	0	hmmalign.run();
310
311	0	if (returnNoOfNewSeqs)
312		{
313	0	int nNew = checkForNewSequences();
314	0	JvOptionPane.showMessageDialog(frame.alignPanel,
315		nNew + " " + MessageManager.getString("label.new_returned"));
316		}
317		}
318
319		}