Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JackHMMER	27	46	11	0.00%	Show methods

Class JackHMMER

Class JackHMMER	Line # 27	Total Statements 46	Complexity 11	TOTAL Coverage 0.00%
JackHMMER(AlignFrame,List<ArgumentI>)   JackHMMER(AlignFrame,List<ArgumentI>)	3737	1.01	1.01	0.0 0.00%
run() : void   run() : void	4848	18.018	4.04	0.0 0.00%
runCommand(File,File,File) : boolean   runCommand(File,File,File) : boolean	107107	7.07	2.02	0.0 0.00%
importData(File,File,File) : void   importData(File,File,File) : void	127127	20.020	4.04	0.0 0.00%

 

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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.AlignmentI;
7		import jalview.datamodel.SequenceI;
8		import jalview.gui.AlignFrame;
9		import jalview.gui.Desktop;
10		import jalview.gui.JvOptionPane;
11		import jalview.io.DataSourceType;
12		import jalview.io.FileParse;
13		import jalview.io.StockholmFile;
14		import jalview.util.FileUtils;
15		import jalview.util.MessageManager;
16		import jalview.ws.params.ArgumentI;
17
18		import java.io.BufferedReader;
19		import java.io.File;
20		import java.io.FileReader;
21		import java.io.IOException;
22		import java.util.ArrayList;
23		import java.util.List;
24
25		import javax.swing.JOptionPane;
26
		0% Uncovered Elements: 62 (62) Complexity: 11 Complexity Density: 0.24
27		public class JackHMMER extends Search
28		{
29
30		SequenceI seq = null;
31
32		/**
33		* Constructor for the JackhmmerThread
34		*
35		* @param af
36		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
37	0	public JackHMMER(AlignFrame af, List<ArgumentI> args)...
38		{
39	0	super(af, args);
40		}
41
42		/**
43		* Runs the JackhmmerThread: the data on the alignment or group is exported,
44		* then the command is executed in the command line and then the data is
45		* imported and displayed in a new frame. Call this method directly to execute
46		* synchronously, or via start() in a new Thread for asynchronously.
47		*/
		0% Uncovered Elements: 22 (22) Complexity: 4 Complexity Density: 0.22
48	0	@Override...
49		public void run()
50		{
51	0	seq = getSequence();
52	0	if (seq == null)
53		{
54		// shouldn't happen if we got this far
55	0	Console.error("Error: no sequence for jackhmmer");
56	0	return;
57		}
58
59	0	long msgId = System.currentTimeMillis();
60	0	af.setProgressBar(MessageManager.getString("status.running_search"),
61		msgId);
62
63	0	try
64		{
65	0	File seqFile = FileUtils.createTempFile("seq", ".sto");
66	0	File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
67		".sto");
68	0	File searchOutputFile = FileUtils.createTempFile("searchOutput",
69		".txt");
70
71	0	exportStockholm(new SequenceI[] { seq }, seqFile.getAbsoluteFile(),
72		null);
73
74	0	boolean ran = runCommand(searchOutputFile, hitsAlignmentFile,
75		seqFile);
76	0	if (!ran)
77		{
78	0	JvOptionPane.showInternalMessageDialog(af, MessageManager
79		.formatMessage("warn.command_failed", "jackhmmer"));
80	0	return;
81		}
82
83	0	importData(hitsAlignmentFile, seqFile, searchOutputFile);
84		// TODO make realignment of search results a step at this level
85		// and make it conditional on this.realign
86		} catch (IOException | InterruptedException e)
87		{
88	0	e.printStackTrace();
89		} finally
90		{
91	0	af.setProgressBar("", msgId);
92		}
93		}
94
95		/**
96		* Executes an jackhmmer search with the given sequence as input. The database
97		* to be searched is a local file as specified by the 'Database' parameter, or
98		* the current alignment (written to file) if none is specified.
99		*
100		* @param searchOutputFile
101		* @param hitsAlignmentFile
102		* @param seqFile
103		*
104		* @return
105		* @throws IOException
106		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
107	0	private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,...
108		File seqFile) throws IOException
109		{
110	0	String command = getCommandPath(JACKHMMER);
111	0	if (command == null)
112		{
113	0	return false;
114		}
115
116	0	List<String> args = new ArrayList<>();
117	0	args.add(command);
118	0	buildArguments(args, searchOutputFile, hitsAlignmentFile, seqFile);
119
120	0	return runCommand(args);
121		}
122
123		/**
124		* Imports the data from the temporary file to which the output of jackhmmer was
125		* directed.
126		*/
		0% Uncovered Elements: 26 (26) Complexity: 4 Complexity Density: 0.2
127	0	private void importData(File inputAlignmentTemp, File seqTemp,...
128		File searchOutputFile) throws IOException, InterruptedException
129		{
130	0	BufferedReader br = new BufferedReader(
131		new FileReader(inputAlignmentTemp));
132	0	try
133		{
134	0	if (br.readLine() == null)
135		{
136	0	JOptionPane.showMessageDialog(af,
137		MessageManager.getString("label.no_sequences_found"));
138	0	return;
139		}
140	0	StockholmFile file = new StockholmFile(new FileParse(
141		inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
142	0	seqs = file.getSeqsAsArray();
143
144	0	readDomainTable(searchOutputFile, true);
145
146	0	if (searchAlignment)
147		{
148	0	recoverSequences(sequencesHash, seqs);
149		}
150
151
152
153	0	int seqCount = seqs.length;
154
155
156	0	AlignmentI al = new Alignment(seqs);
157
158	0	AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
159		AlignFrame.DEFAULT_HEIGHT);
160	0	String ttl = "jackhmmer search of " + databaseName + " using "
161		+ seqs[0].getName();
162	0	Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
163		AlignFrame.DEFAULT_HEIGHT);
164
165	0	seqTemp.delete();
166	0	inputAlignmentTemp.delete();
167	0	searchOutputFile.delete();
168		} finally
169		{
170	0	if (br != null)
171		{
172	0	br.close();
173		}
174		}
175		}
176
177
178
179
180		}