Package org.broad.igv.feature

Examples of org.broad.igv.feature.BasicFeature

101
102
103
104
105
106
107
108
109
110
111
                int l2 = track.getLongestFeatureLength(chr);
                Iterator<BasicFeature> regionFeatures = frame.getFeatureIterator(features, l2, model.getFrameBPWidth());

                while (regionFeatures.hasNext()) {
                    BasicFeature f = regionFeatures.next();

                    Color c = track.getColor();

                    float score = track.getSignal(f);
                    double alpha = Float.isNaN(score) ? 1 : getAlpha(min, max, score);
View Full Code Here
67
68
69
70
71
72
73
74
75
76
77
        String name = editing ? "Edit " + featDispName : "Add annotation to " + MongoFeatureTrack.this.getName();
        JMenuItem item = new JMenuItem(name);
        item.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                Feature feat = editing ? selFeat.getDBFeature() : new BasicFeature(chr, start, end);
                FeatureAnnotDialog dialog = new FeatureAnnotDialog(IGV.getMainFrame(), getCollection(), feat);
                dialog.setVisible(true);
            }
        });
        return item;
View Full Code Here
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
                Feature feature = featureList != null && featureList.size() > 0 ? featureList.get(0) : null;

                if (feature == null)
                    return;
                if (feature instanceof BasicFeature) {
                    BasicFeature bf = (BasicFeature) feature;
                    java.util.List<Exon> exons = bf.getExons();
                    if (exons == null || exons.isEmpty()) {
                        MessageUtils.showMessage("At least one centered feature does not have exon structure");
                        return;
                    }

                    if (forward) {
                        for (Exon exon : bf.getExons()) {
                            //the "+ 1" here is necessary because the rounding in the recentering method
                            //sometimes places the center one base off.  This should be perfectly safe,
                            //but it does assume no one's abusing the exon datastructure and creating
                            //exons that are right next to each other.
                            if (exon.getStart() > vc.getCenter() + 1) {
View Full Code Here
148
149
150
151
152
153
154
155
156
157
158
159
        String hasPhaseId = "LOC_Os01g01010.1:exon_1";
        int expPhaseNum = 1;
        boolean checkedHasPhase = false;

        BasicFeature bf = (BasicFeature) sourceFeats.get(0);
        for (Exon exon : bf.getExons()) {
            if (exon.getName().equals(hasPhaseId)) {
                checkedHasPhase = true;
                assertEquals(expPhaseNum, exon.getReadingFrame());
            } else {
                assertEquals(-1, exon.getReadingFrame());
View Full Code Here
45
46
47
48
49
50
51
52
53
54
55
        final IGVBEDCodec codec = new IGVBEDCodec();

        Function<String, Void> decodeFunc = new Function<String, Void>(){
            @Override
            public Void apply(String input) {
                BasicFeature feat = codec.decode(input);
                return null;
            }
        };

        supplier.reset();
View Full Code Here
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
chr1  .  CDS  7000  7600  .  +  1  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
         */
        Set<Integer> mRNA3CdStarts = new HashSet<Integer>(Arrays.asList(3300, 3390));

        for (Feature feature : features) {
            BasicFeature bf = (BasicFeature) feature;

            String ident = bf.getIdentifier();
            List<Exon> exons = bf.getExons();
            String type = bf.getType();
            if (type.equals("mRNA")) {
                actmRNAFeats++;
                mRNAIds.add(bf.getIdentifier());
            } else if (type.equals("gene")) {
                assertEquals(bf.getIdentifier(), "gene00001");
                continue;
            } else {
                continue;
            }

            Exon lastExon = exons.get(exons.size() - 1);
            assertEquals(7600, lastExon.getCdEnd());
            assertEquals(lastExon.getCdStart(), lastExon.getStart());
            assertEquals(9000, lastExon.getEnd());

            int midCDSInd = 2;

            if (ident.equals("mRNA00001")) {
                assertEquals(4, bf.getExonCount());
                assertEquals(1201 - 1, exons.get(0).getCdStart());

                Exon secExon = exons.get(1);
                assertWholeExonCoding(secExon);
                assertEquals(3000 - 1, secExon.getStart());
                assertEquals(3902, secExon.getEnd());

            }
            if (ident.equals("mRNA00002")) {
                assertEquals(3, bf.getExonCount());
                assertEquals(1201 - 1, exons.get(0).getCdStart());
                midCDSInd = 1;
            }
            if (ident.equals("mRNA00003")) {
                assertEquals(4, bf.getExonCount());
                boolean passedCdStart = false;
                for (Exon exon : exons) {
                    if (exon.isNonCoding()) {
                        assertEquals("Entire exon is UTR but has coding region: " + exon.getName(), 0, exon.getCodingLength());
                        assertEquals("Entire exon is UTR but has coding region: " + exon.getName(), 0, exon.getCdEnd() - exon.getCdEnd());
View Full Code Here
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
        List<Feature> features = getGeneFeatures(filepath, chr, start, end);
        assertEquals(6, features.size());

        for (Feature feat : features) {
            BasicFeature basicFeature = (BasicFeature) feat;
            if (basicFeature.getType().equals("region")) {
                assertEquals("id0", basicFeature.getIdentifier());
            } else if (basicFeature.getType().equals("gene")) {
                assertEquals(1, basicFeature.getExonCount());
                assertTrue(basicFeature.getIdentifier().contains("gene"));
                assertTrue(basicFeature.getName().contains("A1S_"));

                Exon exon = basicFeature.getExons().get(0);
                assertTrue("Exon name incorrect: " + exon.getName(), exon.getName().contains("YP_00"));

                assertWholeExonCoding(exon);
                assertEquals(0, exon.getReadingFrame());
            } else {
                throw new AssertionError("Unknown feature type: " + basicFeature.getType());
            }

        }
    }
View Full Code Here
44
45
46
47
48
49
50
51
52
53
        GFFFeatureSource src = new GFFFeatureSource(TribbleFeatureSource.getFeatureSource(new ResourceLocator(path), null));

        Iterator<Feature> iter = src.getFeatures("I", 0, Integer.MAX_VALUE);
        while (iter.hasNext()) {
            BasicFeature bf = (BasicFeature) iter.next();
            assertEquals(expName, bf.getName());
        }

    }
View Full Code Here
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
        int end = 26848;

        List<Feature> features = getGeneFeatures(filepath, chr, start, end);
        assertEquals(2, features.size());

        BasicFeature gene = null, tRNA = null;
        for (Feature feat : features) {
            if (((BasicFeature) feat).getType().equals("gene")) {
                gene = (BasicFeature) feat;
            } else if (((BasicFeature) feat).getType().equals("tRNA")) {
                tRNA = (BasicFeature) feat;
            }
        }

        assertEquals(gene.getIdentifier(), tRNA.getAttributes().get("Parent"));

        assertEquals(1, tRNA.getExonCount());
        Exon exon = tRNA.getExons().get(0);
        assertEquals(tRNA.getIdentifier(), exon.getAttributes().get("Parent"));
        assertWholeExonNonCoding(exon);
View Full Code Here
67
68
69
70
71
72
73
74
75
76
77
        FeatureSource source = new GFFFeatureSource(tribbleFeatureSource);

        int featureCount = 0;
        Iterator<Feature> iter = source.getFeatures("chr7", 0, Integer.MAX_VALUE);
        while (iter.hasNext()) {
            BasicFeature bf = (BasicFeature) iter.next();
            featureCount++;
        }
        assertEquals(2, featureCount);

    }
View Full Code Here
TOP

Related Classes of org.broad.igv.feature.BasicFeature

  • org.broad.igv.cli_plugin.BEDToolsDecoder
  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.cursor.CursorIdeogramPanel
  • org.broad.igv.cursor.CursorRegion
  • org.broad.igv.cursor.CursorRegion$FeatureIterator
  • org.broad.igv.cursor.CursorUtils
  • org.broad.igv.dev.db.UCSC_SQL_Test
  • org.broad.igv.feature.genome.GenbankParserTest
  • org.broad.igv.feature.tribble.EMBLTableCodec
  • org.broad.igv.feature.tribble.GFFCodec
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.