Package org.broad.igv.exceptions

Examples of org.broad.igv.exceptions.DataLoadException

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            headerLine = reader.next();
            String[] tokens = ParsingUtils.TAB_PATTERN.split(headerLine);
            return readHeader(tokens);
        } catch (Exception e) {
            log.error(e.getMessage(), e);
            throw new DataLoadException("Error reading header: " + e.getMessage(), this.path);
        }
    }
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                }
            }
        }

        if (locator.getPath().contains("genome.ucsc.edu") && type == null) {
            throw new DataLoadException("<html>Feature type is required for UCSC DAS tracks. <br>" +
                    "See http://www.broadinstitute.org/igv/LoadData for more details.",
                    locator.getPath());
        }

        //reader = new DasReader();
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            TDFGroup rootGroup = new TDFGroup("/");
            groupCache.put(rootGroup.getName(), rootGroup);

        } catch (IOException ex) {
            log.error("Error opening output stream to file: " + file, ex);
            throw new DataLoadException("Error creating file", "" + file);
        }

        compressionUtils = new CompressionUtils();
    }
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                parseDocument(dom, chr, features);
                FeatureUtils.sortFeatureList(features);
                return features;

            } catch (IOException ioe) {
                throw new DataLoadException("Failed to reconnect with server", serverURL);
            }
        }
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                        dasDoc.getDocumentElement(), NodeFilter.SHOW_ELEMENT, null, true);
                parseTree(treewalker, "FEATURE", chr, features);

            } catch (Exception ex) {
                log.error(ex);
                throw new DataLoadException("Error loading DAS resource (" + ex.toString() + ")", getPath());
            }
        }
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            }
            boolean normalizeCounts = PreferenceManager.getInstance().getAsBoolean(PreferenceManager.NORMALIZE_COVERAGE);
            setNormalize(normalizeCounts);
        } catch (IOException ex) {
            LOG.error("Error loading file: " + filename, ex);
            throw new DataLoadException("Error loading goby counts archive file: " + ex.toString(), filename);
        }
    }
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            result.add(new BasicScore(position, endLocation, 0.0f));

            return result;
        } catch (IOException e) {
            LOG.error(e);
            throw new DataLoadException(
                    String.format("Error getting summary scores for range %s:%d-%d in goby counts archive file %s %n",
                            chr, startLocation, endLocation, filename), filename);

        }
    }
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                buf.append(e.getMessage());
                buf.append("<br><br>Note: igvtools can be used to sort the file, select \"File > Run igvtools...\".");
                MessageUtils.showMessage(buf.toString());
            }
        } else {
            throw new DataLoadException("Unknown File Type", ifile);
        }
        userMessageWriter.flush();
        return outputFileName;

    }
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                result +=
                        Integer.toString((b[i] & 0xff) + 0x100, 16).substring(1);
            }
            return result;
        }
        throw new DataLoadException("No file found", filename);
    }
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                if (iPath.getName().endsWith(".txt")) {
                    chromosome = iPath.getName().replace(".txt", "");
                    CalculatePercent(iPath.getAbsolutePath(), pw);
                }
            } else {
                throw new DataLoadException("Unable to load files", inPath);
            }
        } catch (IOException e) {
            log.error("Error during load", e);
        } finally {
            pw.close();
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Related Classes of org.broad.igv.exceptions.DataLoadException

  • org.broad.igv.batch.BatchRunner
  • org.broad.igv.das.DASFeatureSource
  • org.broad.igv.das.DASFeatureSource$DasReader
  • org.broad.igv.data.cufflinks.CufflinksCodec
  • org.broad.igv.DirectoryManager
  • org.broad.igv.feature.genome.FastaUtils
  • org.broad.igv.feature.MutationTrackLoader
  • org.broad.igv.feature.tribble.MUTCodec
  • org.broad.igv.goby.GobyCountArchiveDataSource
  • org.broad.igv.sam.reader.AlignmentReaderFactory
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