s_mart: smart_toolShed/SMART/Java/Sav/PythonHelperReader.java annotate

annotate smart_toolShed/SMART/Java/Sav/PythonHelperReader.java @ 4:1fc014126d55

Uploaded

author	yufei-luo
date	Fri, 18 Jan 2013 04:45:50 -0500
parents	e0f8dcca02ed
children

rev	line source
0 e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	1 /**
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	2 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	3 * Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	4 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	5 * This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	6 * abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	7 * modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	8 * license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	9 * "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	10 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	11 * As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	12 * modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	13 * with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	14 * economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	15 * liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	16 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	17 * In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	18 * with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	19 * software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	20 * that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	21 * therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	22 * professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	23 * encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	24 * requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	25 * data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	26 * same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	27 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	28 * The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	29 * knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	30 *
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	31 */
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	32 import java.util.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	33 import java.io.File;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	34 import java.io.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	35 import java.util.regex.*;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	36
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	37 public class PythonHelperReader {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	38
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	39 String fileName;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	40 Program program;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	41 BufferedReader reader;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	42 String message;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	43
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	44 public PythonHelperReader(String fileName) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	45 this.fileName = fileName;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	46 this.reader = reader;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	47 this.message = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	48 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	49
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	50 public void setReader(BufferedReader reader) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	51 this.reader = reader;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	52 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	53
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	54 public void run() {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	55 this.program = new Program();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	56 boolean inBeginning = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	57 boolean inUsage = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	58 boolean afterUsage = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	59 boolean inDescription = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	60 boolean afterDescription = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	61 boolean inOptions = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	62 boolean inOptionBlank = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	63 boolean inError = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	64 String usage = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	65 String description = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	66 String option = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	67 Vector <String> options = new Vector < String > ();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	68 String[] optionSplitted;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	69
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	70 // Parse file
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	71 try {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	72 String line = null;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	73
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	74 while ((line = reader.readLine()) != null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	75 line = line.trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	76 if (line.startsWith("Traceback")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	77 this.message = "Problem with header of '" + this.fileName + "':\n" + line + "\n";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	78 inError = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	79 inBeginning = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	80 inUsage = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	81 afterUsage = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	82 inDescription = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	83 afterDescription = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	84 inOptions = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	85 inOptionBlank = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	86 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	87 else if (inError) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	88 this.message += line + "\n";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	89 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	90 else if (inBeginning) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	91 if (line.startsWith("Usage:")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	92 inUsage = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	93 inBeginning = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	94 usage = line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	95 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	96 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	97 else if (inUsage) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	98 if ("".equals(line)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	99 inUsage = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	100 afterUsage = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	101 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	102 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	103 usage += " " + line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	104 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	105 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	106 else if (afterUsage) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	107 if (! "".equals(line)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	108 description = line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	109 afterUsage = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	110 inDescription = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	111 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	112 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	113 else if (inDescription) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	114 if ("".equals(line)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	115 inDescription = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	116 afterDescription = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	117 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	118 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	119 description += " " + line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	120 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	121 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	122 else if (afterDescription) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	123 if (! "".equals(line)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	124 afterDescription = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	125 inOptions = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	126 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	127 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	128 else if (inOptions) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	129 if ("".equals(line)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	130 inOptions = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	131 inOptionBlank = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	132 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	133 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	134 if (option == null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	135 option = line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	136 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	137 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	138 if (line.charAt(0) == '-') {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	139 options.add(option);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	140 option = line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	141 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	142 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	143 option += " " + line;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	144 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	145 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	146 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	147 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	148 else if (inOptionBlank) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	149 if (! "".equals(line)) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	150 inOptionBlank = false;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	151 inOptions = true;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	152 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	153 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	154 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	155 this.message = "Something is wrong in the file '" + this.fileName + "'.";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	156 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	157 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	158 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	159
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	160 reader.close();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	161 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	162 catch (FileNotFoundException e) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	163 this.message = "File " + this.fileName + " not found";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	164 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	165 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	166 catch (IOException e) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	167 this.message = "IOException while reading file " + this.fileName;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	168 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	169 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	170
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	171 if (inError) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	172 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	173 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	174
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	175 if (option != null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	176 options.add(option);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	177 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	178
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	179 HashMap < String, ProgramOption > identifierToOptions = new HashMap < String, ProgramOption > ();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	180 HashMap < ProgramOption, String > associatedOption = new HashMap < ProgramOption, String > ();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	181
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	182 if (usage == null) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	183 this.message = "Cannot read the usage of file " + this.fileName;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	184 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	185 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	186 program.setShortName(usage.split(" ")[1].trim());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	187 program.setName(description.split(":")[0].trim());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	188
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	189 Pattern pattern = Pattern.compile("\\[Category: .*\\]");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	190 Matcher matcher = pattern.matcher(description);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	191 if (matcher.find()) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	192 program.setSection(description.substring(matcher.start() + "[Category: ".length(), matcher.end() - 1));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	193 program.setDescription(description.substring(0, matcher.start() - 1).trim());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	194 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	195 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	196 this.message = "Cannot find category in description '" + description + "' in file " + this.fileName;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	197 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	198 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	199 for (int i = 0; i < options.size(); i++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	200 option = options.get(i).replace("\t", " ");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	201 optionSplitted = option.split(" ");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	202 option = "";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	203 for (int j = 3; j < optionSplitted.length; j++) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	204 option += optionSplitted[j] + " ";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	205 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	206
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	207 String identifier = optionSplitted[0].replace("-", "").replace(",", "");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	208 // Skip -h and -v options
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	209 if (("h".equals(identifier)) \|\| ("v".equals(identifier)))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	210 continue;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	211
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	212 ProgramOption programOption = new ProgramOption();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	213 programOption.setIdentifier("-" + identifier);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	214 programOption.setComment(option.substring(0, option.indexOf("[")).trim());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	215 identifierToOptions.put(identifier, programOption);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	216
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	217 pattern = Pattern.compile("\\[[^\\]]*\\]");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	218 matcher = pattern.matcher(option);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	219 while (matcher.find()) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	220 String inner = option.substring(matcher.start()+1, matcher.end()-1);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	221 if (inner.contains(":")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	222 String type = inner.substring(0, inner.indexOf(":")).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	223 String value = inner.substring(inner.indexOf(":")+1).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	224 // Types of the options
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	225 if ("format".compareToIgnoreCase(type) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	226 String currentWord = "";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	227 String rest = "";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	228 if (value.contains(" ")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	229 int pos = value.indexOf(" ");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	230 currentWord = value.substring(0, pos);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	231 rest = value.substring(pos+1);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	232 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	233 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	234 currentWord = value;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	235 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	236 // Output file type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	237 if ("output".compareToIgnoreCase(currentWord) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	238 programOption.setInput(false);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	239 int pos = rest.indexOf(" ");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	240 currentWord = rest.substring(0, pos).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	241 rest = rest.substring(pos+1).trim();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	242 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	243 // File (input or output file)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	244 if ("file".compareToIgnoreCase(currentWord) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	245 programOption.setType("file");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	246 // Format given by an associated option (to be found later)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	247 if (rest.startsWith("in format given by ")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	248 associatedOption.put(programOption, rest.substring(rest.indexOf("format given by ") + "format given by ".length() + 1).trim());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	249 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	250 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	251 if (! rest.startsWith("in ")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	252 this.message = "Descriptor " + option + " does not have a proper format.";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	253 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	254 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	255 rest = rest.substring("in ".length());
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	256 int pos = rest.indexOf(" format");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	257 if (pos == -1) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	258 this.message = "Descriptor " + option + " does not have a proper format.";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	259 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	260 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	261 programOption.setFormat(rest.substring(0, pos).trim().toLowerCase().split(" or "));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	262 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	263 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	264 // Format type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	265 else if (rest.endsWith("file format")) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	266 programOption.setFormat((currentWord + " " + rest.substring(0, rest.indexOf("file format"))).trim().toLowerCase().split(" or "));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	267 programOption.setType("format");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	268 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	269 // Choice type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	270 else if ("choice".compareToIgnoreCase(currentWord) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	271 programOption.setChoices(rest.replace("(", "").replace(")", "").split(", "));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	272 programOption.setType("choice");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	273 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	274 // Boolean type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	275 else if ("bool".compareToIgnoreCase(currentWord) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	276 programOption.setType("boolean");
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	277 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	278 // Other type
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	279 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	280 programOption.setType(currentWord);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	281 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	282 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	283 // Default value
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	284 else if ("default".compareToIgnoreCase(type) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	285 programOption.setDefault(value);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	286 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	287 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	288 this.message = "Do not understand option descriptor '" + inner + "'.";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	289 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	290 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	291 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	292 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	293 // Compulsory option
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	294 if ("compulsory".compareToIgnoreCase(inner) == 0) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	295 programOption.setCompulsory(true);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	296 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	297 else {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	298 this.message = "Do not understand option descriptor '" + inner + "'.";
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	299 return;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	300 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	301 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	302 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	303 program.addOption(programOption);
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	304 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	305
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	306 // Set associated option
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	307 Iterator it = associatedOption.keySet().iterator();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	308 while (it.hasNext()) {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	309 ProgramOption programOption = (ProgramOption) it.next();
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	310 programOption.setAssociatedOption(identifierToOptions.get(associatedOption.get(programOption)));
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	311 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	312 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	313
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	314 public String getMessage () {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	315 return this.message;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	316 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	317
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	318 public Program getProgram () {
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	319 return this.program;
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	320 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	321 }
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	322
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data. yufei-luo parents: diff changeset	323

Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Sav/PythonHelperReader.java @ 4:1fc014126d55