Examples of org.broad.igv.data.CharArrayList

            } catch (EOFException e) {
                // This is expected when there is no data available for this chromosome.
                return;
            }
            while (c != '\n') {
                CharArrayList chars = new CharArrayList(10);
                while (c != '\t') {
                    chars.add(c);
                    c = is.readChar();
                }
                String nm = new String(chars.toArray()).trim();
                tmp.add(nm);
                c = is.readChar();
            }


            sampleNames = tmp.toArray(new String[]{});

                splicedInsertionBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.insertionBlock));
                splicedInsertionBlocks.addAll(insertionBlocks);
                spliceHeadAlignment.insertionBlock = splicedInsertionBlocks.toArray(new AlignmentBlock[splicedInsertionBlocks.size()]);


                if (spliceHeadAlignment.gapTypes == null) {
                    spliceHeadAlignment.gapTypes = new CharArrayList(10);
                }
                spliceHeadAlignment.gapTypes.add(SAMAlignment.SKIPPED_REGION);


                // Since the previous alignment carries this information, we clear up block and insertionBlock
                // in this alignment, but keep any softClips:

Related Classes of org.broad.igv.data.CharArrayList

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