Package org.broad.igv.util

Examples of org.broad.igv.util.ResourceLocator

75
76
77
78
79
80
81
82
83
84
85
    private void loadHeader() {

        InputStream is = null;
        SAMFileReader reader = null;
        try {
            is = ParsingUtils.openInputStreamGZ(new ResourceLocator(samFile));
            BufferedInputStream bis = new BufferedInputStream(is);
            SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
            reader = new SAMFileReader(bis);
            header = reader.getFileHeader();
        } catch (IOException e) {
View Full Code Here
208
209
210
211
212
213
214
215
216
217
218
        }

        knownSnps = new HashMap();
        AsciiLineReader reader = null;
        try {
            reader = ParsingUtils.openAsciiReader(new ResourceLocator(snpFile));
            String nextLine = "";
            while ((nextLine = reader.readLine()) != null) {
                String[] tokens = nextLine.split("\t");
                String chr = tokens[0];
                Set<Integer> snps = knownSnps.get(chr);
View Full Code Here
118
119
120
121
122
123
124
125
126
127
128
            if (files.length > 0) {

                // Create DataResouceLocators for the selected files
                final List<ResourceLocator> locators = new ArrayList(files.length);
                for (File f : files) {
                    locators.add(new ResourceLocator(f.getAbsolutePath()));
                }

                igv.loadTracks(locators);
            }
        }
View Full Code Here
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
            java.util.List<EncodeFileRecord> records = browser.getSelectedRecords();
            if (records.size() > 0) {
                List<ResourceLocator> locators = new ArrayList<ResourceLocator>(records.size());
                for (EncodeFileRecord record : records) {
                    ResourceLocator rl = new ResourceLocator(record.getPath());
                    rl.setName(record.getTrackName());

                    final String antibody = record.getAttributeValue("antibody");
                    if (antibody != null) {
                        rl.setColor(colors.get(antibody.toUpperCase()));
                    }

                    for(String name : visibleAttributes) {
                        String value = record.getAttributeValue(name);
                        if(value != null) {
                            AttributeManager.getInstance().addAttribute(rl.getName(), name, value);
                        }
                    }

                    locators.add(rl);
                }
View Full Code Here
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
            try {
                List<File> files = (List<File>) transferable.getTransferData(DataFlavor.javaFileListFlavor);

                for (File file : files) {
                    try {
                        ResourceLocator locator = new ResourceLocator(file.getAbsolutePath());
                        IGV.getInstance().load(locator, panel);
                    } catch (DataLoadException de) {
                        messages.append(de.getMessage());
                    }
                }
                String obj = transferable.getTransferData(DataFlavor.stringFlavor).toString();
                if (HttpUtils.isRemoteURL(obj)) {
                    IGV.getInstance().load(new ResourceLocator(obj), panel);
                }
                if (messages != null && !messages.isEmpty()) {
                    log.error(messages.getFormattedMessage());
                    MessageUtils.showMessage(messages.getFormattedMessage());
                }
            } catch (Exception e) {
                String obj = null;
                try {
                    obj = transferable.getTransferData(DataFlavor.stringFlavor).toString();
                    if (HttpUtils.isRemoteURL(obj)) {
                        IGV.getInstance().load(new ResourceLocator(obj), panel);
                    }
                } catch (Exception e1) {
                    log.error(e1);
                    if (messages != null && !messages.isEmpty()) {
                        MessageUtils.showMessage(messages.getFormattedMessage());
View Full Code Here
91
92
93
94
95
96
97
98
99
100
101
    public static LinkedHashSet<String> getNodeURLs(String genomeURL) {

        InputStream is = null;
        LinkedHashSet<String> nodeURLs = null;
        try {
            is = ParsingUtils.openInputStreamGZ(new ResourceLocator(genomeURL));
            BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(is));
            nodeURLs = getResourceUrls(bufferedReader);
        } catch (IOException e) {
            //This is pretty common, if there is no data registry file for the genome the file won't exist
            log.error("Error loading genome registry file", e);
View Full Code Here
200
201
202
203
204
205
206
207
208
209
210
    private static Document readXMLDocument(String url, StringBuffer errors) {
        InputStream is = null;
        Document xmlDocument = null;
        try {
            is = ParsingUtils.openInputStreamGZ(new ResourceLocator(url));
            xmlDocument = Utilities.createDOMDocumentFromXmlStream(is);

            xmlDocument = resolveIncludes(xmlDocument, errors);

        } catch (SAXException e) {
View Full Code Here
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
    public static void buildLocatorTree(DefaultMutableTreeNode treeNode, Element xmlNode,
                                        Set<ResourceLocator> alreadyLoaded, ResourceTree resourceTree) {

        String name = getAttribute(xmlNode, NAME.getText());

        ResourceLocator locator = new ResourceLocator(
                getAttribute(xmlNode, PATH.getText())
        );
        locator.setName(name);

        String infoLink = getAttribute(xmlNode, HYPERLINK.getText());
        if (infoLink == null) {
            infoLink = getAttribute(xmlNode, INFOLINK.getText());
        }
        locator.setTrackInforURL(infoLink);

        if (xmlNode.getTagName().equalsIgnoreCase("Resource")) {

            String resourceType = getAttribute(xmlNode, RESOURCE_TYPE.getText());
            locator.setType(resourceType);


            String sampleId = getAttribute(xmlNode, SAMPLE_ID.getText());
            if (sampleId == null) {
                // legacy option
                sampleId = getAttribute(xmlNode, ID.getText());
            }
            locator.setSampleId(sampleId);
            locator.setFeatureInfoURL(getAttribute(xmlNode, URL.getText()));
            locator.setDescription(getAttribute(xmlNode, DESCRIPTION.getText()));
            locator.setTrackLine(getAttribute(xmlNode, TRACK_LINE.getText()));
            locator.setName(name);
            // Special element for alignment tracks
            locator.setCoverage(getAttribute(xmlNode, COVERAGE.getText()));

            String colorString = getAttribute(xmlNode, COLOR.getText());
            if (colorString != null) {
                try {
                    Color c = ColorUtilities.stringToColor(colorString);
                    locator.setColor(c);
                } catch (Exception e) {
                    log.error("Error setting color: ", e);
                }
            }
        }
View Full Code Here
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
                    url += ":" + port;
                }
                url += "/" + db;

                String table2 = "SAMPLE_INFO";
                ResourceLocator loc2 = new ResourceLocator(url, table2);
                loc2.setDescription("SELECT * FROM " + table2);
//

                String table1 = "CNV";
                ResourceLocator loc1 = new ResourceLocator(url, table1);
                // TODO -- get these mappings from a config table
                String query = "SELECT  Sample Sample, `Probe Median` Value, " +
                        "Chromosome chr,  Start start, Stop end, " +
                        "CONCAT('<br>Event: ', Event,'<br>% CNV Overlap = ', `% of CNV Overlap`) description " +
                        " FROM CNV " +
                        " WHERE Event = 'CN Gain' OR Event = 'CN Loss' OR Event = 'High Copy Gain'";
//                         + "INNER JOIN SAMPLE_INFO ON SAMPLE_INFO.SAMPLE = CNV.SAMPLE " +
//                        "WHERE SAMPLE_INFO.SUBTYPE like 'Classical'";

//                String query = "select * from cnv";
                loc1.setDescription(query);
                loc1.setType(".seg");


                mainFrame.loadTracks(Arrays.asList(loc1, loc2));

                return null;
View Full Code Here
66
67
68
69
70
71
72
73
74
75
76
        TribbleFeatureSource src = featureSourceMap.get(chr);
        if (src == null) {
            String path = pathMap.get(chr);
            if (path != null) {
                try {
                    src = TribbleFeatureSource.getFeatureSource(new ResourceLocator(path), genome);
                } catch (IOException e) {
                    log.error("Error loading tribble source: " + path);
                }
                featureSourceMap.put(chr, src);
            }
View Full Code Here
TOP

Related Classes of org.broad.igv.util.ResourceLocator

  • org.broad.igv.batch.CommandExecutorTest
  • org.broad.igv.cli_plugin.awkPluginTest
  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.cli_plugin.PluginFeatureSourceTest
  • org.broad.igv.cli_plugin.PluginSourceTest
  • org.broad.igv.cli_plugin.VCFEncoderTest
  • org.broad.igv.cursor.CursorUtils
  • org.broad.igv.data.AbstractDataSourceTest
  • org.broad.igv.data.CombinedDataSourceTest
    • 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.