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  1. Project Clover database Mon Nov 11 2024 16:01:40 GMT
  2. Package jalview.ws.jabaws

File RNAStructExportImport.java

 

Code metrics

34
97
7
1
349
270
30
0.31
13.86
7
4.29

Classes

Class Line # Actions
RNAStructExportImport 66 97 30
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.ws.jabaws;
22   
23    import java.util.Locale;
24   
25    import static org.testng.AssertJUnit.assertNotNull;
26    import static org.testng.AssertJUnit.assertTrue;
27   
28    import jalview.bin.Cache;
29    import jalview.bin.Console;
30    import jalview.datamodel.AlignmentAnnotation;
31    import jalview.datamodel.AlignmentI;
32    import jalview.gui.JvOptionPane;
33    import jalview.io.AnnotationFile;
34    import jalview.io.DataSourceType;
35    import jalview.io.FileFormat;
36    import jalview.io.FormatAdapter;
37    import jalview.io.StockholmFileTest;
38    import jalview.project.Jalview2XML;
39    import jalview.ws.jws2.Jws2Discoverer;
40    import jalview.ws.jws2.RNAalifoldClient;
41    import jalview.ws.jws2.SequenceAnnotationWSClient;
42    import jalview.ws.jws2.jabaws2.Jws2Instance;
43    import jalview.ws.params.AutoCalcSetting;
44   
45    import java.awt.Component;
46    import java.io.File;
47    import java.util.ArrayList;
48    import java.util.List;
49   
50    import javax.swing.JMenu;
51    import javax.swing.JMenuItem;
52   
53    import org.testng.Assert;
54    import org.testng.annotations.AfterClass;
55    import org.testng.annotations.BeforeClass;
56    import org.testng.annotations.Test;
57   
58    import compbio.metadata.Argument;
59    import compbio.metadata.WrongParameterException;
60   
61    /*
62    * All methods in this class are set to the Network group because setUpBeforeClass will fail
63    * if there is no network.
64    */
65    @Test(singleThreaded = true)
 
66    public class RNAStructExportImport
67    {
68   
 
69  0 toggle @BeforeClass(alwaysRun = true)
70    public void setUpJvOptionPane()
71    {
72  0 JvOptionPane.setInteractiveMode(false);
73  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
74    }
75   
76    private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
77   
78    public static String testseqs = "examples/RF00031_folded.stk";
79   
80    public static Jws2Discoverer disc;
81   
82    public static Jws2Instance rnaalifoldws;
83   
84    jalview.ws.jws2.RNAalifoldClient alifoldClient;
85   
86    public static jalview.gui.AlignFrame af = null;
87   
 
88  0 toggle @BeforeClass(alwaysRun = true)
89    public static void setUpBeforeClass() throws Exception
90    {
91  0 Cache.loadProperties("test/jalview/io/testProps.jvprops");
92  0 Console.initLogger();
93  0 disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
94   
95  0 while (disc.isRunning())
96    {
97    // don't get services until discoverer has finished
98  0 Thread.sleep(100);
99    }
100   
101  0 for (Jws2Instance svc : disc.getServices())
102    {
103   
104  0 if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
105    .contains("rnaalifoldws"))
106    {
107  0 rnaalifoldws = svc;
108    }
109    }
110   
111  0 System.out.println("State of rnaalifoldws: " + rnaalifoldws);
112   
113  0 if (rnaalifoldws == null)
114    {
115  0 Assert.fail("no web service");
116    }
117   
118  0 jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
119   
120  0 af = fl.LoadFileWaitTillLoaded(testseqs,
121    jalview.io.DataSourceType.FILE);
122   
123  0 assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
124   
125    // remove any existing annotation
126  0 List<AlignmentAnnotation> aal = new ArrayList<>();
127  0 for (AlignmentAnnotation rna : af.getViewport().getAlignment()
128    .getAlignmentAnnotation())
129    {
130  0 if (rna.isRNA())
131    {
132  0 aal.add(rna);
133    }
134    }
135  0 for (AlignmentAnnotation rna : aal)
136    {
137  0 af.getViewport().getAlignment().deleteAnnotation(rna);
138    }
139  0 af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel
140    // public?
141    }
142   
 
143  0 toggle @AfterClass(alwaysRun = true)
144    public static void tearDownAfterClass() throws Exception
145    {
146  0 if (af != null)
147    {
148  0 af.setVisible(false);
149  0 af.dispose();
150  0 File f = new File(JAR_FILE_NAME);
151  0 if (f.exists())
152    {
153  0 f.delete();
154    }
155    }
156    }
157   
 
158  0 toggle @Test(groups = { "Network" })
159    public void testRNAAliFoldValidStructure()
160    {
161   
162  0 alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
163   
164  0 af.getViewport().getCalcManager().startWorker(alifoldClient);
165   
166  0 do
167    {
168  0 try
169    {
170  0 Thread.sleep(50);
171    } catch (InterruptedException x)
172    {
173    }
174  0 } while (af.getViewport().getCalcManager().isWorking());
175   
176  0 AlignmentI orig_alig = af.getViewport().getAlignment();
177  0 for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
178    {
179  0 if (alifoldClient.involves(aa))
180    {
181  0 if (aa.isRNA())
182    {
183  0 assertTrue(
184    "Did not create valid structure from RNAALiFold prediction",
185    aa.isValidStruc());
186    }
187    }
188    }
189    }
190   
 
191  0 toggle @Test(groups = { "Network" })
192    public void testRNAStructExport()
193    {
194   
195  0 alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
196   
197  0 af.getViewport().getCalcManager().startWorker(alifoldClient);
198   
199  0 do
200    {
201  0 try
202    {
203  0 Thread.sleep(50);
204    } catch (InterruptedException x)
205    {
206    }
207  0 } while (af.getViewport().getCalcManager().isWorking());
208   
209  0 AlignmentI orig_alig = af.getViewport().getAlignment();
210    // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
211    // annotation is mistakenly recognised as an RNA annotation row when read in
212    // as an annotation file.
213  0 verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
214   
215    }
216   
 
217  0 toggle static void verifyAnnotationFileIO(String testname, AlignmentI al)
218    {
219  0 try
220    {
221    // what format would be appropriate for RNAalifold annotations?
222  0 String aligfileout = FileFormat.Pfam.getWriter(null)
223    .print(al.getSequencesArray(), true);
224   
225  0 String anfileout = new AnnotationFile()
226    .printAnnotationsForAlignment(al);
227  0 assertNotNull("Test " + testname
228    + "\nAlignment annotation file was not regenerated. Null string",
229    anfileout);
230  0 assertTrue("Test " + testname
231    + "\nAlignment annotation file was not regenerated. Empty string",
232    anfileout.length() > "JALVIEW_ANNOTATION".length());
233   
234  0 System.out.println(
235    "Output annotation file:\n" + anfileout + "\n<<EOF\n");
236   
237    // again what format would be appropriate?
238  0 AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
239    DataSourceType.PASTE, FileFormat.Pfam);
240  0 assertTrue("Test " + testname
241    + "\nregenerated annotation file did not annotate alignment.",
242    new AnnotationFile().readAnnotationFile(al_new, anfileout,
243    DataSourceType.PASTE));
244   
245    // test for consistency in io
246  0 StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
247    false);
248  0 return;
249    } catch (Exception e)
250    {
251  0 e.printStackTrace();
252    }
253  0 Assert.fail("Test " + testname
254    + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
255    }
256   
 
257  0 toggle @Test(groups = { "Network" })
258    public void testRnaalifoldSettingsRecovery()
259    {
260  0 List<Argument> opts = new ArrayList<>();
261  0 for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
262    .getArguments())
263    {
264  0 if (rg.getDescription().contains("emperature"))
265    {
266  0 try
267    {
268  0 rg.setValue("292");
269    } catch (WrongParameterException q)
270    {
271  0 Assert.fail("Couldn't set the temperature parameter "
272    + q.getStackTrace());
273    }
274  0 opts.add(rg);
275    }
276  0 if (rg.getDescription().contains("max"))
277    {
278  0 opts.add(rg);
279    }
280    }
281  0 alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
282   
283  0 af.getViewport().getCalcManager().startWorker(alifoldClient);
284   
285  0 do
286    {
287  0 try
288    {
289  0 Thread.sleep(50);
290    } catch (InterruptedException x)
291    {
292    }
293  0 ;
294  0 } while (af.getViewport().getCalcManager().isWorking());
295  0 AutoCalcSetting oldacs = af.getViewport()
296    .getCalcIdSettingsFor(alifoldClient.getCalcId());
297  0 String oldsettings = oldacs.getWsParamFile();
298    // write out parameters
299  0 jalview.gui.AlignFrame nalf = null;
300  0 assertTrue("Couldn't write out the Jar file", new Jalview2XML(false)
301    .saveAlignment(af, JAR_FILE_NAME, "trial parameter writeout"));
302  0 assertTrue("Couldn't read back the Jar file",
303    (nalf = new Jalview2XML(false)
304    .loadJalviewAlign(JAR_FILE_NAME)) != null);
305  0 if (nalf != null)
306    {
307  0 AutoCalcSetting acs = af.getViewport()
308    .getCalcIdSettingsFor(alifoldClient.getCalcId());
309  0 assertTrue("Calc ID settings not recovered from viewport stash",
310    acs.equals(oldacs));
311  0 assertTrue(
312    "Serialised Calc ID settings not identical to those recovered from viewport stash",
313    acs.getWsParamFile().equals(oldsettings));
314  0 JMenu nmenu = new JMenu();
315  0 new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
316    rnaalifoldws, af);
317  0 assertTrue("Couldn't get menu entry for service",
318    nmenu.getItemCount() > 0);
319  0 for (Component itm : nmenu.getMenuComponents())
320    {
321  0 if (itm instanceof JMenuItem)
322    {
323  0 JMenuItem i = (JMenuItem) itm;
324  0 if (i.getText().equals(
325    rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
326    {
327  0 i.doClick();
328  0 break;
329    }
330    }
331    }
332  0 while (af.getViewport().isCalcInProgress())
333    {
334  0 try
335    {
336  0 Thread.sleep(200);
337    } catch (Exception x)
338    {
339    }
340  0 ;
341    }
342  0 AutoCalcSetting acs2 = af.getViewport()
343    .getCalcIdSettingsFor(alifoldClient.getCalcId());
344  0 assertTrue(
345    "Calc ID settings after recalculation has not been recovered.",
346    acs2.getWsParamFile().equals(oldsettings));
347    }
348    }
349    }