Package org.broad.igv.exceptions

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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                }
            }


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


        } catch (IOException ioe) {
            throw new DataLoadException(ioe.getMessage(), inputFile);
        } finally {
            setIsBatchMode(false);
            if (cursorToken != null) WaitCursorManager.removeWaitCursor(cursorToken);
            if (reader != null) {
                try {
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            readHeader();
            log.debug("Done reading header");

        } catch (IOException ex) {
            log.error("Error loading file: " + locator.getPath(), ex);
            throw new DataLoadException("Error loading file: " + ex.toString(), locator.getPath());
        }
        compressionUtils = new CompressionUtils();
    }
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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", file.getAbsolutePath());
            }
            return null;
        }
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            return mutationMap;
        } catch (IOException e) {
            log.error("Error loading mutation file", e);
            throw new DataLoadException("IO Exception: " + e.toString(), locator.getPath());
        } finally {
            reader.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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