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author basfplant
date Tue, 05 Mar 2013 04:00:19 -0500
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1 package be.cropdesign.iprscan;
2 /**
3 * Converts the *.raw output file of the InterProScan program to an Excel file (*.xlsx)
4 * @author: Katrien Bernaerts and Domantas Motiejunas
5 * @date: 21/06/2012
6 * @affiliation: CropDesign N.V., a BASF Plant Science Company - Technologiepark 3, 9052 Zwijnaarde - Belgium
7 */
8 import java.awt.Color;
9 import java.io.BufferedReader;
10 import java.io.FileNotFoundException;
11 import java.io.FileReader;
12 import java.io.IOException;
13 import java.util.ArrayList;
14 import java.util.regex.Matcher;
15 import java.util.regex.Pattern;
16
17 import org.apache.poi.xssf.usermodel.XSSFCell;
18 import org.apache.poi.xssf.usermodel.XSSFCellStyle;
19 import org.apache.poi.xssf.usermodel.XSSFColor;
20 import org.apache.poi.xssf.usermodel.XSSFDataFormat;
21 import org.apache.poi.xssf.usermodel.XSSFFont;
22 import org.apache.poi.xssf.usermodel.XSSFRow;
23 import org.apache.poi.xssf.usermodel.XSSFSheet;
24 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
25
26 public class RawToExcel {
27
28 private int colnr;
29 private int maxNr;
30 private int rownr;
31 private int maxNrOfGOTerms;
32
33 /**
34 * fields needed to generate Excel
35 */
36 private XSSFWorkbook wb;
37 private XSSFSheet sheet;
38 private XSSFRow myRow;
39 private XSSFCell myCell;
40 private String rawFile;
41 private boolean interproInfo; // this info is not standard in every .raw file, but can occur
42 private boolean GOInfo; // this info is not standard in every .raw file, but can occur
43
44 private ArrayList<String> titles;
45
46 /**
47 * constructor
48 * @param wb
49 * @param sheet3
50 * @param myRow
51 * @param myCell
52 * @param rawFile
53 */
54 public RawToExcel(XSSFWorkbook wb, XSSFSheet sheet3,XSSFRow myRow, XSSFCell myCell, String rawFile){
55 this.wb = wb;
56 this.sheet = sheet3;
57 this.myRow = myRow;
58 this.myCell = myCell;
59 this.rawFile = rawFile;
60 maxNr = 0;
61 maxNrOfGOTerms = 0;
62 interproInfo = false;
63 GOInfo = false;
64 titles = new ArrayList<String>();
65 parseRaw();
66 addHeaderTitles();
67 formatStyle();
68 }
69
70 /**********************************
71 * parsing of the .raw file content
72 **********************************/
73 /**
74 * method to parse the data in the .raw file with a BufferedReader/FileReader. The parsed data
75 * are written to Excel using the Apache POI library.
76 */
77 public void parseRaw() {
78 BufferedReader reader = null;
79 try {
80 reader = new BufferedReader(new FileReader(rawFile));
81
82 String line = reader.readLine();
83
84 /*
85 * start with rownr = 1 to write content because an empty row has to be reserved for the titles
86 * The title row cannot be filled yet at this point because we first have to determine how many
87 * columns are needed, and by consequence, how many titles. The problem is that different .raw files
88 * can have a different amount of columns.
89 * For each line read with the buffered reader, the number of columns is compared to the maxColnr,
90 * because sometimes not all lines of the same file have the same number of columns, e.g. because the
91 * last column is empty. However, if for some rows the last column is empty, a column title is still needed
92 * for the other rows. Therefore, the method getMaxColumns(colnr) is called for each line.
93 */
94 rownr = 1;
95 while(line != null) {
96 String[] splits = line.split("\t"); // tab delimited file
97 myRow = sheet.createRow(rownr);
98 colnr = 0;
99 for (String string : splits){
100 myCell = myRow.createCell(colnr);
101 myCell.setCellValue(string);
102
103 /*
104 * interProScan info is not present in all raw files. For the creation of the right
105 * header titles, it is important to know whether the parsed raw file contained
106 * interProScan info
107 */
108 if (string.contains("IPR")){
109 interproInfo = true;
110 }
111
112 /*
113 * format the cell content as Integer for the columns protein length (colnr=2),
114 * start (colnr=6) or end (colnr=7). To know which input only contains integers,
115 * a regex is used. If only numbers or spaces are found in the input string,
116 * and if the input string is not empty, the corresponding Excel cell is
117 * formatted as Integer.
118 * If the cell content is not formatted as number, sorting etc. via the filters
119 * in the headers does not work correct.
120 */
121 if (checkRegex("^([0-9]+\\s*)*$", string)){
122 myCell.setCellValue(Integer.parseInt(string));
123 }
124
125 /*
126 * create a cell style that formats numbers in scientific notation (exponential)
127 * for the score column (index 8)
128 */
129 if (checkRegex("^[-+]?([0-9]*\\.?[0-9]+([eE][-+]?[0-9]+))*$", string)){
130 formatExponential(string);
131 }
132 /*
133 * split up the line with GO classification information further such
134 * that the splitted line of GO information can be stored in different
135 * Excel cells instead of all information concatenated into one cell (like it is
136 * in the original .raw file generated by iprscan). First the information
137 * in the splitted line is stored in a double array. In a second step (at the end of the
138 * current method, the double array content is written to Excel.
139 */
140 if (string.contains("GO:")){
141 GOInfo = true;
142 splitGOTerms(string);
143 }
144 getMax(colnr);
145 colnr++;
146 }
147 line = reader.readLine();
148 rownr++;
149 myRow = sheet.createRow(rownr);
150 }
151 } catch (FileNotFoundException e) {
152 System.err.println("The .raw file cannot be found.");
153 } catch (IOException e) {
154 System.err.println("An input/output exception occurred while reading the .raw file.");
155 }
156 finally {
157 if (reader != null) {
158 try {
159 reader.close();
160 }
161 catch (IOException e){}
162 }
163 }
164 }
165
166 /**
167 * Helper method for parseRaw()
168 * Split a string containing GO information. A typical string looks like:
169 * "Molecular Function: sequence-specific DNA binding transcription factor activity (GO:0003700), Cellular Component: nucleus (GO:0005634), Biological Process: regulation of transcription, DNA-dependent (GO:0006355), Molecular Function: sequence-specific DNA binding (GO:0043565)"
170 * or in more general terms:
171 * "Title1: description1 (GO number1), Title2: description2 (GO number2), Title3: description3 (GO number3)"
172 * The string should be splitted in three parts: title, description and GO number.
173 * In fact we are dealing with comma delimited strings, but split may not happen at every comma,
174 * only when comma is preceded by (
175 * Split may for example not happen at the comma in case of "Molecular Function: transferase activity,
176 * transferring phosphorus-containing groups (GO:0016772)"
177 * In order to assure that the splitting occurs at the right place, the comma's at the places where splitting has to
178 * occur are replaced by the unique splitting character ;
179 * @return
180 */
181 public void splitGOTerms(String string){
182 if (string != null &&!string.isEmpty() && !string.trim().isEmpty()){
183
184 String modifiedString = string.replace("),", ");");
185 /*
186 * the modifiedString is splitted at the ;
187 */
188 String[] splitsClassification = modifiedString.split("; ");
189 int numberOfGoTerms = splitsClassification.length;
190 getMaxNrOfGOTerms(numberOfGoTerms);
191 for (int i = 0; i < splitsClassification.length; i++){
192 myCell = myRow.createCell(colnr);
193 myCell.setCellValue(splitsClassification[i].substring(0, splitsClassification[i].indexOf(':'))); //title
194 colnr++;
195 myCell = myRow.createCell(colnr);
196 myCell.setCellValue(splitsClassification[i].substring(splitsClassification[i].indexOf('(')+1, splitsClassification[i].indexOf(')'))); // GO term
197 colnr++;
198 myCell = myRow.createCell(colnr);
199 myCell.setCellValue(splitsClassification[i].substring(splitsClassification[i].indexOf(':')+2, splitsClassification[i].indexOf('('))); // description)
200 colnr++;
201 }
202 }
203 }
204
205 /**
206 * Helper method for parseRaw()
207 * Check whether a certain input string (stringToMatch) matches a certain regular expression.
208 * @param regex
209 * @param stringToMatch
210 * @return
211 */
212 public boolean checkRegex(String regex, String stringToMatch){
213 Pattern p = Pattern.compile(regex);
214 Matcher m = p.matcher(stringToMatch);
215 if(m.matches() && stringToMatch != null &&!stringToMatch.isEmpty() && !stringToMatch.trim().isEmpty()){
216 return true;
217 } else {
218 return false;
219 }
220 }
221
222 /**********************************
223 * header titles of the Excel sheet
224 *********************************/
225 /**
226 * the header titles are generated in the first row (index 0) of the spreadsheet
227 * All the potential column titles are added to the titles ArrayList. The .raw file always contains
228 * some fixed part (standard titles), but can also contain more information (titles which are not
229 * required for every .raw file).
230 * This last category of headers is only added in case the information occurs in the .raw file.
231 */
232 public void addHeaderTitles(){
233 /*
234 * standard titles
235 */
236 titles.add("protein ID");
237 titles.add("protein crc64");
238 titles.add("protein length");
239 titles.add("match dbname");
240 titles.add("classification id");
241 titles.add("classification description");
242 titles.add("start");
243 titles.add("end");
244 titles.add("score");
245 titles.add("status");
246 titles.add("date");
247 /*
248 * titles which are not required for every .raw file
249 */
250 if (interproInfo){ // only if the .raw file contains "IPR" boolean interproInfo becomes true
251 titles.add("interpro ID");
252 titles.add("interpro name");
253 }
254
255 if (GOInfo){
256 for (int i = 0; i < maxNrOfGOTerms; i++){
257 titles.add("title");
258 titles.add("GO number");
259 titles.add("description");
260 }
261 }
262
263 myRow = sheet.createRow(0);
264 // show the headers in the table
265 for (int i = 0; i < titles.size() ; i ++){
266 myCell = myRow.createCell(i);
267 myCell.setCellValue(titles.get(i)); // content of the headercell
268 formatHeader(); // color of the headercell
269 }
270 }
271
272 /**
273 * method to find the number of Excel columns needed for the GO terms information (title, description and GO number)n
274 * The method looks for the maximal number of columns needed, because sometimes there are
275 * rows with no GO information and other rows which have GO information.
276 * As long as in one Excel sheet there is one row with GO information, the titles for the GO information
277 * have to be showed correctly. The method getNrOfGOTerms helps in this task.
278 */
279 public void getMaxNrOfGOTerms(int nr){
280 if (nr > maxNrOfGOTerms){
281 maxNrOfGOTerms = nr;
282 }
283 }
284
285
286 /*******************************
287 * formatting of the Excel sheet
288 ******************************/
289 /**
290 * method to apply all formatting to the Excel tabsheet containing the .raw data
291 */
292 public void formatStyle(){
293 setAutoFilters();
294 autoSizeColumns();
295 freezeRow();
296 }
297
298 /**
299 * make autofilters of the column headers in Excel
300 * ref: http://stackoverflow.com/questions/3114220/poi-auto-filter
301 */
302 public void setAutoFilters(){
303 if (GOInfo){
304 /*
305 * for some reason, the first empty column contains an autofilter in the case there is
306 * GO information. However, only the columns which are not empty should have and autofilter.
307 * In order to avoid this small bug, the autofilter method was changed
308 * slightly: maxNr -1 instead of maxNr
309 * method: public XSSFAutoFilter setAutoFilter(CellRangeAddress, range);
310 */
311 sheet.setAutoFilter(org.apache.poi.ss.util.CellRangeAddress.valueOf("A1:"+ (Character.toString((char)( 65+maxNr-1)))+"1"));
312 } else {
313 sheet.setAutoFilter(org.apache.poi.ss.util.CellRangeAddress.valueOf("A1:"+ (Character.toString((char)( 65+maxNr)))+"1"));
314 }
315 }
316
317 /**
318 * set the column width automatically to the width of the content
319 */
320 public void autoSizeColumns(){
321 for(int column = 0; column < maxNr; column++){
322 sheet.autoSizeColumn(column);
323 }
324 }
325
326 /**
327 * helper method for setAutoFilters() and autoSizeColumns() to find the number
328 * of columns present in the tab sheet of the Excel file.
329 * Sometimes, there are columns which are empty in a certain row, but filled in
330 * another row. We always have to cope with the most extreme situation. Therefore,
331 * the maximum number of columns is determined.
332 * @param nr
333 */
334 public void getMax(int nr){
335 if (nr > maxNr){
336 maxNr = nr;
337 }
338 }
339
340 /**
341 * give the header cells a blue color and bold formatting
342 */
343 public void formatHeader(){
344 XSSFCellStyle style = wb.createCellStyle();
345 XSSFFont font = wb.createFont();
346 font.setColor(new XSSFColor(Color.BLUE));
347 font.setBold(true);
348 style.setFont(font);
349 myCell.setCellStyle(style);
350 }
351
352 /**
353 * freeze the header row
354 * method: public void createFreezePane(int colSplit, int rowSplit, intleftmostColumn, int topRow)
355 */
356 public void freezeRow(){
357 sheet.createFreezePane(0, 1, 0, 1);
358 }
359
360 /**
361 * create a cell style that formats numbers in scientific notation (exponential)
362 * for the score column (index 8)
363 * Differentiate the text content (NA) from the exponential values via an if ... else
364 * because otherwise the formatting as exponential value is not OK.
365 */
366 public void formatExponential(String s){
367 if (s.equals("NA")){
368 myCell.setCellValue("NA");
369 }
370 else {
371 XSSFCellStyle cs = wb.createCellStyle();
372 XSSFDataFormat df = wb.createDataFormat();
373 cs.setDataFormat(df.getFormat("0.0E+0"));
374 myCell.setCellValue(Double.parseDouble(s));
375 myCell.setCellStyle(cs);
376 }
377 }
378
379 /*********************
380 * getters and setters
381 *********************/
382 public void setColnr(int colnr) {
383 this.colnr = colnr;
384 }
385
386 public int getColnr() {
387 return colnr;
388 }
389
390 /**
391 * @param nrOfGOTerms the nrOfGOTerms to set
392 */
393 public void setNrOfGOTerms(int nrOfGOTerms) {
394 this.maxNrOfGOTerms = nrOfGOTerms;
395 }
396
397 /**
398 * @return the nrOfGOTerms
399 */
400 public int getNrOfGOTerms() {
401 return maxNrOfGOTerms;
402 }
403 }