Package org.broad.igv.lists

Examples of org.broad.igv.lists.GeneList

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    }

    private void writeGeneList(Element globalElement, Document document) {

        GeneList geneList = session.getCurrentGeneList();

        if (geneList != null) {

            Element geneListElement = document.createElement(SessionElement.GENE_LIST.getText());
            geneListElement.setAttribute(IGVSessionReader.SessionAttribute.NAME.getText(), geneList.getName());

            StringBuffer genes = new StringBuffer();
            for (String gene : geneList.getLoci()) {
                genes.append(gene);
                genes.append("\n");
            }

            geneListElement.setTextContent(genes.toString());
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                        end += Math.abs(start);
                        start = 0;
                    }
                    loci.add(new RegionOfInterest(roi.getChr(), start, end, roi.getDescription()).getLocusString());
                }
                GeneList geneList = new GeneList("Regions of Interest", loci, false);
                IGV.getInstance().getSession().setCurrentGeneList(geneList);
                IGV.getInstance().resetFrames();

            }
            updateButtonsEnabled();
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Related Classes of org.broad.igv.lists.GeneList

  • org.broad.igv.cbio.FilterGeneNetworkUI
  • org.broad.igv.sam.AlignmentTrack
  • org.broad.igv.session.IGVSessionReader
  • org.broad.igv.session.SessionWriter
  • org.broad.igv.track.TrackLoader
  • org.broad.igv.ui.action.SearchCommand
  • org.broad.igv.ui.IGV
  • org.broad.igv.ui.panel.HeaderPanelContainer
  • org.broad.igv.ui.panel.ReferenceFrameTest
  • org.broad.igv.ui.panel.ReferenceFrameTestHeaded
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