Examples of DataLoadException

Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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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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Examples of org.broad.igv.exceptions.DataLoadException

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                        sequenceWindow.remove();
                }
            }
        }
        catch (IOException e) {
            throw new DataLoadException(e.getMessage(), inputFile);
        }
        finally {
            try {
                bfr.close();
            } catch (IOException e) {
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Examples of org.broad.igv.exceptions.DataLoadException

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                }
            }


            if (IGV_DIRECTORY == null || !IGV_DIRECTORY.canRead()) {
                throw new DataLoadException("Cannot read from user directory", IGV_DIRECTORY.getAbsolutePath());
            } else if (!canWrite(IGV_DIRECTORY)) {
                throw new DataLoadException("Cannot write to user directory", IGV_DIRECTORY.getAbsolutePath());
            }

            log.info("IGV Directory: " + IGV_DIRECTORY.getAbsolutePath());
        }
        return IGV_DIRECTORY;
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Examples of org.broad.igv.exceptions.DataLoadException

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            GENOME_CACHE_DIRECTORY = new File(getIgvDirectory(), "genomes");
            if (!GENOME_CACHE_DIRECTORY.exists()) {
                GENOME_CACHE_DIRECTORY.mkdir();
            }
            if (!GENOME_CACHE_DIRECTORY.canRead()) {
                throw new DataLoadException("Cannot read from user directory", GENOME_CACHE_DIRECTORY.getAbsolutePath());
            } else if (!GENOME_CACHE_DIRECTORY.canWrite()) {
                throw new DataLoadException("Cannot write to user directory", GENOME_CACHE_DIRECTORY.getAbsolutePath());
            }
        }
        return GENOME_CACHE_DIRECTORY;
    }
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