Java tutorial
/* * To change this license header, choose License Headers in Project Properties. * To change this template file, choose Tools | Templates * and open the template in the editor. */ package coverageqc.functions; import coverageqc.data.DoNotCall; import coverageqc.data.Variant; import java.awt.Color; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import org.apache.poi.ss.usermodel.Cell; import org.apache.poi.ss.usermodel.PrintOrientation; import org.apache.poi.ss.usermodel.PrintSetup; import org.apache.poi.ss.usermodel.Sheet; import org.apache.poi.ss.util.CellRangeAddress; import org.apache.poi.xssf.usermodel.XSSFCellStyle; import org.apache.poi.xssf.usermodel.XSSFColor; import org.apache.poi.xssf.usermodel.XSSFFont; import org.apache.poi.xssf.usermodel.XSSFPrintSetup; import org.apache.poi.xssf.usermodel.XSSFRow; import org.apache.poi.xssf.usermodel.XSSFSheet; import org.apache.poi.xssf.usermodel.XSSFWorkbook; /** * * @author Tom */ public class MyExcelGenerator { public HashMap<Integer, Integer> tsvRearrangeConversion = null; public HashMap<String, Integer> originalHeadings = null; public String[] originalHeadingsArray = null; public XSSFWorkbook workbookcopy; String headingLine; ArrayList<String> sheetNames; public MyExcelGenerator() { //sheetNames=givenSheetNames; workbookcopy = new XSSFWorkbook(); // for(int i=0; i<givenSheetNames.size(); i++) // { // workbookcopy.createSheet(sheetNames.get(i)); // } } public void excelRowCreator(int currentRowNum, String currentSheet, Variant currentVariant, String variantTsvDataLine, ArrayList<DoNotCall> donotcalls) { XSSFRow currentRow = this.workbookcopy.getSheet(currentSheet).createRow(currentRowNum); //list of possible cells to highlight Boolean filterCell = false; Boolean altVariantFreqCell = false; Boolean consequenceCell = false; Boolean alleleMinorCell = false; Boolean containsDoNotCall = false; //XSSFCellStyle cellStyle = currentRow.getRowStyle(); // Cell cellInterp = currentRow.createCell(0); // XSSFCellStyle cellStyle = (XSSFCellStyle)cellInterp.getCellStyle(); XSSFCellStyle cellStyle = getDefaultCellStyle(currentRow, Color.WHITE); String textOnInterp = ""; //cellStyle.setFillPattern(XSSFCellStyle.SOLID_FOREGROUND); // XSSFColor myColor; // Tom Addition //if any of these the text on Interp is "Do Not Call" if (currentVariant.consequence.contains("synonymous_variant") || currentVariant.altVariantFreq.floatValue() <= 5 || currentVariant.typeOfDoNotCall.equals("Don't call, always")) { textOnInterp = textOnInterp + "Do Not Call -"; // cellStyle.setFillForegroundColor(new XSSFColor(Color.GRAY)); cellStyle = getDefaultCellStyle(currentRow, Color.GRAY); containsDoNotCall = true; if (currentVariant.typeOfDoNotCall.equals("Don't call, always")) { if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + " on lab list of definitive do-not-calls"; } else { textOnInterp = textOnInterp + ", on lab list of definitive do-not-calls"; } } if (currentVariant.consequence.contains("synonymous_variant")) { consequenceCell = true; //if the string size if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + " synonymous variant"; } else { textOnInterp = textOnInterp + ", synonymous variant"; } } if (currentVariant.altVariantFreq.floatValue() <= 5) { altVariantFreqCell = true; if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + " variant <5%"; } else { textOnInterp = textOnInterp + ", variant <5%"; } } } //if any of these the text on Interp is "Warning" if ((currentVariant.onTheDoNotCallList && (!currentVariant.typeOfDoNotCall.equals("Don't call, always"))) || currentVariant.alleleFreqGlobalMinor.floatValue() > 1 || !(currentVariant.filters.equals("PASS"))) { //cellStyle.setFillForegroundColor(new XSSFColor(Color.GRAY)); // System.out.println(currentVariant.gene); if (!containsDoNotCall) { cellStyle = getDefaultCellStyle(currentRow, Color.YELLOW); } if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + "WARNING -"; } else { textOnInterp = textOnInterp + ", WARNING -"; } if ((currentVariant.onTheDoNotCallList && !(currentVariant.typeOfDoNotCall.equals("Don't call, always")))) { if (currentVariant.typeOfDoNotCall.contains("In same location")) { if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + "in same location as lab list of do-not-calls"; } else { textOnInterp = textOnInterp + ", in same location as lab list of do-not-calls"; } } else { if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + "on lab list of possible do-not-calls "; } else { textOnInterp = textOnInterp + ", on lab list of possible do-not-calls - "; } } } if (currentVariant.alleleFreqGlobalMinor > 1) { alleleMinorCell = true; if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + " MAF >1%"; } else { textOnInterp = textOnInterp + ", MAF >1%"; } } if (!(currentVariant.filters.equals("PASS"))) { filterCell = true; if (textOnInterp.lastIndexOf("-") == textOnInterp.length() - 1) { textOnInterp = textOnInterp + " Quality Filter = " + currentVariant.filters; } else { textOnInterp = textOnInterp + ", Quality Filter = " + currentVariant.filters; } } } //end if statement saying it is on Warning //now creating three columns of interps for (int x = 0; x <= 2; x++) { Cell cellInterp = currentRow.createCell(x); cellInterp.setCellStyle(cellStyle); cellInterp.setCellValue(textOnInterp); } //adding TSV dataline to output excel file // row = sheet.createRow(rownum++); // String[] headingsArray = tsvHeadingLine.split("\t"); // HashMap<String, Integer> headings = new HashMap<String, Integer>(); // for(int x = 0; x < headingsArray.length; x++) { // headings.put(headingsArray[x].substring(0, headingsArray[x].indexOf("_")), x); // } String[] dataArray = variantTsvDataLine.split("\t"); for (int x = 0; x < dataArray.length; x++) { Cell cell = currentRow.createCell(x + 3); //System.out.println(x); //System.out.println(this.tsvRearrangeConversion.get(x)); if ((this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)].contains("Filters_") && filterCell) || (this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)] .contains("Allele Freq Global Minor_") && alleleMinorCell)) { // cellStyle.setFillPattern(XSSFCellStyle.SOLID_FOREGROUND); // cellStyle.setFillForegroundColor(new XSSFColor(Color.GRAY)); cellStyle = getDefaultCellStyle(currentRow, Color.YELLOW); } else if ((this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)].contains("Consequence_") && consequenceCell) || (altVariantFreqCell && (this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)] .contains("Alt Variant Freq_")))) { cellStyle = getDefaultCellStyle(currentRow, Color.GRAY); } else { cellStyle = getDefaultCellStyle(currentRow, Color.WHITE); //cellStyle.setFillForegroundColor(new XSSFColor(Color.white)); } cell.setCellStyle(cellStyle); // XSSFCellStyle style = workbookcopy.createCellStyle(); // XSSFColor myColor = new XSSFColor(Color.RED); // style.setFillPattern(XSSFCellStyle.SOLID_FOREGROUND); // style.setFillForegroundColor(myColor); cell.setCellValue(dataArray[this.tsvRearrangeConversion.get(x)]); } // return currentRow; } public void excelHeadingCreator(String specifiedsheet, String headingLine) { XSSFSheet currentSheet = workbookcopy.createSheet(specifiedsheet); XSSFRow currentRow = currentSheet.createRow(0); XSSFCellStyle cellStyle; // String[] originalHeadingsArray = headingLine.split("\t"); this.originalHeadingsArray = headingLine.split("\t"); ; HashMap<String, Integer> headings = new HashMap<String, Integer>(); for (int x = 0; x < originalHeadingsArray.length; x++) { headings.put(originalHeadingsArray[x].substring(0, originalHeadingsArray[x].indexOf("_")), x); } this.setRearrangedHashMap(headings); this.originalHeadings = headings; //the headers for the first three columns for (int x = 0; x < 3; x++) { Cell cell = currentRow.createCell(x); cellStyle = getDefaultCellStyle(currentRow, Color.WHITE); if (x == 0 || x == 1) { cell.setCellStyle(cellStyle); if (x == 0) { cell.setCellValue("Tom's Interpretation"); //cell.setCellValue("Fellow1's Interpretation"); } else { cell.setCellValue("Christina's Interpretation"); //cell.setCellValue("Fellow2's Interpretation"); } } else if (x == 2) { cell.setCellStyle(cellStyle); cell.setCellValue("Attending Pathologist Interpretation"); } } for (int x = 0; x < originalHeadingsArray.length; x++) { //plus three because have three header columns Cell cell = currentRow.createCell(x + 3); cellStyle = getDefaultCellStyle(currentRow, Color.WHITE); // cell.setCellStyle(cellStyle); if (this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)].contains("Gene_") || this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)].contains("Variant_") || this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)].contains("Chr_")) // ||originalHeadingsArray[x].contains("Coordinate_") // ||originalHeadingsArray[x].contains("Type_")) // ||originalHeadingsArray[x-3].contains("Genotype_") // ||originalHeadingsArray[x-3].contains("Coordinate_") // ||originalHeadingsArray[x-3].contains("Filters_")) { cellStyle.setRotation((short) 0); } else { cellStyle.setRotation((short) 90); } cell.setCellStyle(cellStyle); //cell.setCellValue(originalHeadingsArray[x-3]); // this.tsvRearrangeConversion.get(x) cell.setCellValue(this.originalHeadingsArray[this.tsvRearrangeConversion.get(x)]); //cell.setCellValue(headinsArray[headingsConversion.get(x-3)]); } //end for loop //return currentRow; } public void excelFormator(String sheetName, File variantTsvFile) throws IOException { // String[] headingsArray = tsvHeadingLine.split("\t"); // HashMap<String, Integer> headings = new HashMap<String, Integer>(); // for(int x = 0; x < headingsArray.length; x++) { // headings.put(headingsArray[x].substring(0, headingsArray[x].indexOf("_")), x); // } XSSFSheet currentSheet = this.workbookcopy.getSheet(sheetName); XSSFPrintSetup printSetup = (XSSFPrintSetup) currentSheet.getPrintSetup(); File xslxTempFile = new File(variantTsvFile.getCanonicalPath() + ".coverage_qc.xlsx"); currentSheet.getHeader().setLeft(xslxTempFile.getName()); currentSheet.getHeader().setRight("DO NOT DISCARD!!! Keep with patient folder."); //in Dr. Carter's VBA was set at points 18 which is .25 inches currentSheet.setMargin(Sheet.RightMargin, .25); currentSheet.setMargin(Sheet.LeftMargin, .25); printSetup.setOrientation(PrintOrientation.LANDSCAPE); //NOTE: setFitWidth doesn't work for columns, ie can't setFitToPageColumns, this //is the best workaround I can do, it will only looked cramped for those with a lot of calls printSetup.setFitWidth((short) 1); printSetup.setFitHeight((short) 3); currentSheet.setRepeatingRows(CellRangeAddress.valueOf("1")); currentSheet.setFitToPage(true); //making it by default not print the fellow's interp currentSheet.getWorkbook().setPrintArea(0, 2, 20, 0, currentSheet.getLastRowNum()); for (int x = 0; x < currentSheet.getRow(0).getPhysicalNumberOfCells(); x++) { currentSheet.autoSizeColumn(x); if (x > 33) { currentSheet.setColumnHidden(x, true); } } currentSheet.setColumnWidth(0, 10000); currentSheet.setColumnWidth(1, 10000); currentSheet.setColumnWidth(2, 10000); // currentSheet.setColumnWidth(this.tsvRearrangeConversion.get(this.originalHeadings.get("Consequence"))+3, 3500); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Gene"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Variant"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Chr"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Coordinate"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Type"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Genotype"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Exonic"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Filters"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Quality"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("GQX"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Alt Variant Freq"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Read Depth"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Alt Read Depth"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Consequence"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Sift"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("PolyPhen"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allele Freq Global Minor"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Classification"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Inherited From"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allelic Depths"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Custom Annotation"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Custom Gene Annotation"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Num Transcripts"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Transcript"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("cDNA Position"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("CDS Position"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Protein Position"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Amino Acids"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Codons"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("HGNC"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Transcript HGNC"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Canonical"))+3, true); // //currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Sift"))+3, false); // //currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("PolyPhen"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ENSP"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("HGVSc"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("HGVSp"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("dbSNP ID"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Ancestral Allele"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Global Minor Allele"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allele Freq Amr"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allele Freq Asn"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allele Freq Af"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allele Freq Eur"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Allele Freq Evs"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("EVS Coverage"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("EVS Samples"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Conserved Sequence"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("COSMIC ID"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("COSMIC Wildtype"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("COSMIC Allele"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("COSMIC Gene"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("COSMIC Primary Site"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("COSMIC Histology"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Accession"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Ref"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Alleles"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Allele Type"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Significance"))+3, false); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Alternate Alleles"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("Google Scholar"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("PubMed"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("UCSC Browser"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar RS"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Disease Name"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar MedGen"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar OMIM"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar Orphanet"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar GeneReviews"))+3, true); // currentSheet.setColumnHidden(this.tsvRearrangeConversion.get(this.originalHeadings.get("ClinVar SnoMedCt ID"))+3, true); } //If Color.White is specified there is no do not calls or warnings //If Color.Yellow is specified there is no do not calls but there are warnings //If Color.Gray is specifified there are do not calls and there may or may not be warnings private XSSFCellStyle getDefaultCellStyle(XSSFRow currentRow, Color specifiedColor) { XSSFCellStyle cellStyle = currentRow.getSheet().getWorkbook().createCellStyle(); cellStyle.setWrapText(true); cellStyle.setBorderBottom(cellStyle.BORDER_THIN); cellStyle.setBorderLeft(cellStyle.BORDER_THIN); cellStyle.setBorderRight(cellStyle.BORDER_THIN); cellStyle.setBorderTop(cellStyle.BORDER_THIN); XSSFFont myFont = currentRow.getSheet().getWorkbook().createFont(); myFont.setFontHeight(9); cellStyle.setFont(myFont); cellStyle.setFillPattern(XSSFCellStyle.SOLID_FOREGROUND); cellStyle.setFillForegroundColor(new XSSFColor(specifiedColor)); return cellStyle; } public void setRearrangedHashMap(HashMap<String, Integer> originalHeadings) { //illumina TSV columns end in BQ (26 *2) + 17; hence the hashmap should be 69 in length, TSV ends in BQ //HashMap<Integer,Integer> tsvRearrangeConversion; tsvRearrangeConversion = new HashMap<Integer, Integer>(); int x = 0; tsvRearrangeConversion.put(x++, originalHeadings.get("Gene"));//A tsvRearrangeConversion.put(x++, originalHeadings.get("Variant"));//B tsvRearrangeConversion.put(x++, originalHeadings.get("Chr"));//C tsvRearrangeConversion.put(x++, originalHeadings.get("cDNA Position"));//AC tsvRearrangeConversion.put(x++, originalHeadings.get("CDS Position"));//AD tsvRearrangeConversion.put(x++, originalHeadings.get("Protein Position"));//AE tsvRearrangeConversion.put(x++, originalHeadings.get("Coordinate"));//D tsvRearrangeConversion.put(x++, originalHeadings.get("Type"));//E tsvRearrangeConversion.put(x++, originalHeadings.get("Genotype"));//F tsvRearrangeConversion.put(x++, originalHeadings.get("Exonic"));//G tsvRearrangeConversion.put(x++, originalHeadings.get("Filters"));//H tsvRearrangeConversion.put(x++, originalHeadings.get("Quality"));//I tsvRearrangeConversion.put(x++, originalHeadings.get("GQX"));//J tsvRearrangeConversion.put(x++, originalHeadings.get("Alt Variant Freq"));//k tsvRearrangeConversion.put(x++, originalHeadings.get("Read Depth"));//L tsvRearrangeConversion.put(x++, originalHeadings.get("Alt Read Depth"));//M tsvRearrangeConversion.put(x++, originalHeadings.get("Consequence"));//N tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq Global Minor"));//O tsvRearrangeConversion.put(x++, originalHeadings.get("Sift"));//P tsvRearrangeConversion.put(x++, originalHeadings.get("PolyPhen"));//Q tsvRearrangeConversion.put(x++, originalHeadings.get("COSMIC ID"));//R tsvRearrangeConversion.put(x++, originalHeadings.get("COSMIC Primary Site"));//S tsvRearrangeConversion.put(x++, originalHeadings.get("ENSP"));//T tsvRearrangeConversion.put(x++, originalHeadings.get("HGVSc"));//U tsvRearrangeConversion.put(x++, originalHeadings.get("HGVSp"));//V tsvRearrangeConversion.put(x++, originalHeadings.get("dbSNP ID"));//W tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Accession"));//X tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Ref"));//Y tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Alleles"));//Z tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Allele Type"));//AA tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Significance"));//AB tsvRearrangeConversion.put(x++, originalHeadings.get("Classification"));//AF tsvRearrangeConversion.put(x++, originalHeadings.get("Inherited From"));//AG tsvRearrangeConversion.put(x++, originalHeadings.get("Allelic Depths"));//AH tsvRearrangeConversion.put(x++, originalHeadings.get("Custom Annotation"));//AI tsvRearrangeConversion.put(x++, originalHeadings.get("Custom Gene Annotation"));//AJ tsvRearrangeConversion.put(x++, originalHeadings.get("Num Transcripts"));//AK tsvRearrangeConversion.put(x++, originalHeadings.get("Transcript"));//AL tsvRearrangeConversion.put(x++, originalHeadings.get("Amino Acids"));//AM tsvRearrangeConversion.put(x++, originalHeadings.get("Codons"));//AN tsvRearrangeConversion.put(x++, originalHeadings.get("HGNC"));//AO tsvRearrangeConversion.put(x++, originalHeadings.get("Transcript HGNC"));//AP tsvRearrangeConversion.put(x++, originalHeadings.get("Canonical"));//AQ tsvRearrangeConversion.put(x++, originalHeadings.get("Ancestral Allele"));//AR tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq"));//AS tsvRearrangeConversion.put(x++, originalHeadings.get("Global Minor Allele"));//AT tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq Amr"));//AU tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq Asn"));//AV tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq Af"));//AW tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq Eur"));//AX tsvRearrangeConversion.put(x++, originalHeadings.get("Allele Freq Evs"));//AY tsvRearrangeConversion.put(x++, originalHeadings.get("EVS Coverage"));//AZ tsvRearrangeConversion.put(x++, originalHeadings.get("EVS Samples"));//BA tsvRearrangeConversion.put(x++, originalHeadings.get("Conserved Sequence"));//BB tsvRearrangeConversion.put(x++, originalHeadings.get("COSMIC Wildtype"));//BC tsvRearrangeConversion.put(x++, originalHeadings.get("COSMIC Allele"));//BD tsvRearrangeConversion.put(x++, originalHeadings.get("COSMIC Gene"));//BE tsvRearrangeConversion.put(x++, originalHeadings.get("COSMIC Histology"));//BF tsvRearrangeConversion.put(x++, originalHeadings.get("Alternate Alleles"));//BG tsvRearrangeConversion.put(x++, originalHeadings.get("Google Scholar"));//BH tsvRearrangeConversion.put(x++, originalHeadings.get("PubMed"));//BI tsvRearrangeConversion.put(x++, originalHeadings.get("UCSC Browser"));//BJ tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar RS"));//BK tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Disease Name"));//BL tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar MedGen"));//BM tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar OMIM"));//BN tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar Orphanet"));//BO tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar GeneReviews"));//BP tsvRearrangeConversion.put(x++, originalHeadings.get("ClinVar SnoMedCt ID"));//BQ } public XSSFWorkbook getWorkbook() { return this.workbookcopy; } }