├── CircView.tar.gz ├── LICENSE ├── README.md ├── UserGuide.pdf ├── image ├── circrna-clear.png ├── circrna-files-add.png ├── circrna-load.png ├── circrna-mre-rbp-details.png ├── circrna-mre-rbp.png ├── comparison-table.png ├── dblink.png ├── mre-clear.png ├── mre-load.png ├── one-circrna.png ├── species-add.png ├── species-default.png ├── species-del.png ├── tool-add.png ├── tool-del.png └── whole-circrna.png ├── src └── cn │ └── edu │ └── whu │ ├── CircRna.java │ ├── CircRnaTool.java │ ├── CircView.java │ ├── Exon.java │ ├── Gene.java │ ├── GeneTranscript.java │ ├── MainData.java │ ├── exception │ └── FileReadException.java │ ├── ui │ ├── AboutDialog.java │ ├── CircRnaDataClearDialog.java │ ├── CircRnaDataLoadDialog.java │ ├── CircRnaImagePanel.java │ ├── CircRnaToolAddDialog.java │ ├── CircRnaToolDelDialog.java │ ├── ComparisonFrame.java │ ├── CsvSaveFileChooser.java │ ├── DataLoadingDialog.java │ ├── DataLoadingProgressDialog.java │ ├── DetailsResultDialog.java │ ├── ImageSaveFileChooser.java │ ├── MreClearDialog.java │ ├── MreLoadDialog.java │ ├── OpenFileChooser.java │ ├── ProgressDialog.java │ ├── RbpClearDialog.java │ ├── RbpLoadDialog.java │ ├── SaveImageDialog.java │ ├── SpeciesAddDialog.java │ └── SpeciesDelDialog.java │ └── util │ ├── CloneUtils.java │ ├── Constant.java │ ├── DbConfig.java │ ├── DbUtil.java │ ├── EvenOddRenderer.java │ ├── MyMath.java │ ├── RuntimeUtils.java │ └── TextAreaCellRenderer.java └── testdata └── human.tar.gz /CircView.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GeneFeng/CircView/299fde303bdde161bcf9f0cb0248d5c5faec9812/CircView.tar.gz -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | **1. BEST PRACTISE** 2 | > **1.1. Basic Feature: CircRNAs Visualization** 3 | > 1.1.1 Java Virtual Machine needs to be installed before running this program. See **7 HOW TO INSTALL JAVA VIRTUAL MACHINE**. 4 | > 1.1.2 Download and decompress "CircView.tar.gz" from http://github.com/GeneFeng/CircView/blob/master/CircView.tar.gz 5 | > Double click CircView.jar to launch the program. 6 | > 1.1.3 Download and decompress circRNA data from https://github.com/GeneFeng/CircView/blob/master/testdata/human.tar.gz 7 | > 1.1.4 Click “CircRNA”->”Load Data” to load circRNA files according species and tools. 8 | > 9 | > 1.1.5 Click gene transcript name on list panel to view the image of the circRNAs. 10 | > 11 | > 1.1.6 Gene transcript can be searched by name or location. 12 | > 1.1.7 Click one "Circle" to view details of each circRNA. 13 | > 14 | > 1.1.8 Detailed information and image of circRNAs can be saved for further use. 15 | > 1.1.9 Click "Analysis"->"Comparison" to make a comparison between circRNAs with different samples and/or tools. 16 | > 17 | > Click "Save as" button to export results to a ".csv" file for further use. 18 | 19 | > **1.2. Advanced Feature: MRE and RBP sites Visualization on CircRNAs** 20 | > 1.2.1 MySQL needs to be installed, see **8 HOW TO INSTALL MYSQL**. 21 | > 1.2.2 Restart CircView.jar 22 | > 1.2.3 Download and decompress MRE data from http://gb.whu.edu.cn/CircView/testdata/mre_human.tar.gz 23 | > 1.2.4 Click “MRE”->”Load Data” to load MRE file. 24 | > 1.2.5 Download and decompress RBP data from http://gb.whu.edu.cn/CircView/testdata/rbp_human.tar.gz 25 | > 1.2.6 Click “RBP”->”Load Data” to load RBP file. 26 | > 1.2.7 Load circRNAs data, see 1.1.4 27 | > 1.2.8 Check MRE or RBP to add MRE sites (blue lines) or RBP sites (red triangles) to CircRNAs. 28 | > 29 | > 1.2.9 Click "Details" button to see detailed information of MRE and RBP sites. 30 | > 31 | 32 | **2. HOW TO GET CIRCVIEW AND TEST DATA** 33 | > Download CircView application from http://github.com/GeneFeng/CircView/blob/master/CircView.tar.gz 34 | > Download circRNAs test data from https://github.com/GeneFeng/CircView/blob/master/testdata 35 | > Download MRE data from http://gb.whu.edu.cn/CircView/testdata/mre_human.tar.gz 36 | > Download RBP data from http://gb.whu.edu.cn/CircView/testdata/rbp_human.tar.gz 37 | 38 | **3. HOW TO MANAGE CIRCRNAS DATA** 39 | > **3.1. CircRNAs Identification Tool Management** 40 | > CircView integrates 6 CircRNAs identification tools (CIRCexplorer, circRNA_finder, CIRI, find_circ, Mapsplice, and UROBORUB) by default. 41 | > Users can add or delete tool by using menu “CircRNA”->”Add Tool” or “CircRNA”->”Delete Tool”. 42 | >      43 | > 44 | >**3.2. CircRNAs Data Management** 45 | > CircView can load CircRNAs data directly from output of default 6 CircRNAs identification tools. 46 | > Users can also import circRNAs identified by other tools with six tab delimited columns, including chromosome, start point, end point, running number/name, junction reads and strand. 47 | >      48 | 49 | **4. HOW TO MANAGE SPECIES DATA** 50 | > CircView provides 7 species (Human (hg38), Human (hg19), Mouse (mm10), Mouse (mm9), Zebrafish (zv9), Fly (dm6), C.elegans (ce10)) by default. 51 | > 52 | > Users can also add or delete species annotation data with compatible format by using menu “Species”->”Add Species” or “Species”->”Delete Species”. 53 | >      54 | 55 | **5. HOW TO FIND CIRCRNA DATABASES** 56 | > CircView provides links to existing circRNA databases, including Circ2Traits, CircBase, CircInteractome, CircNet, circRNADb, StarBase, and TSCD. 57 | > 58 | 59 | **6. HOW TO MANAGE MRE AND RBP DATA** 60 | > CircRNAs mainly function as sponges for the regulatory elements, such as miRNA respond elements (MREs) and RNA binding proteins (RBPs). CircView provides advanced features to display regulatory elements. 61 | > This module requires the users to install MySQL locally, see **8 HOW TO INSTALL MYSQL**. Users can load and display the MRE data identified by TargetScan (http://targetscan.org/) and/or the RBP data identified by starBase (http://starbase.sysu.edu.cn/) or any other tool. The format requires five tab delimited columns, including chromosome, start site, end site, MRE/RBP name and description. 62 | > Load MRE or RBP file will create table and deposit data into MySQL database, and Clear MRE or RBP will remove data from the database. As the data are persistent, users should not load the same data for more than once. 63 | >      64 | 65 | **7. HOW TO INSTALL JAVA VIRTUAL MACHINE** 66 | > Java Virtual Machine needs to be installed before running this program. Simply access http://www.java.com, download Java, and install it. 67 | 68 | **8. HOW TO INSTALL MYSQL** 69 | > **8.1. For Windows** 70 | > 8.1.1 Download and decompress MySQL Installation file from http://gb.whu.edu.cn/CircView/MySQL/mysql_windows.tar.gz 71 | > 8.1.2 Double click “NDP46-KB3045557-x86-x64-AllOS-ENU.exe” to install .NET Framework. 72 | > 8.1.3 Double click “mysql-installer-community-5.7.16.0.msi” to install MySQL. Please create password “12345” for user root during installation. 73 | > 74 | > **8.2. For Mac OS** 75 | > 8.2.1 Download MySQL Installation file from http://gb.whu.edu.cn/CircView/MySQL/mysql-5.7.17-macos10.12-x86_64.dmg 76 | > 8.2.2 Double click “mysql-5.7.17-macos10.12-x86_64.dmg” to install MySQL. 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private String chrom; 25 | 26 | /** 27 | * circRNA start point; 28 | */ 29 | private long startPoint; 30 | 31 | /** 32 | * circRNA end point; 33 | */ 34 | private long endPoint; 35 | 36 | /** 37 | * strand 38 | */ 39 | private String strand; 40 | 41 | /** 42 | * junction reads 43 | */ 44 | private int junctionReads; 45 | 46 | /** 47 | * "geneName transcriptName" "geneName transcriptName" pair 48 | */ 49 | private TreeMap geneTranscrpits; 50 | 51 | /** 52 | * Repeat Times 53 | */ 54 | // private int repeat; 55 | 56 | private TreeMap samples; 57 | private TreeMap circTools; 58 | private TreeMap files; 59 | 60 | /** 61 | * exon or intron or intergenic 62 | */ 63 | private String region; 64 | 65 | /** 66 | * mRNA or lncRNA or unknown 67 | */ 68 | private String circRnaType; 69 | 70 | /** 71 | * Constructor of CircRna 72 | * 73 | * @param geneName 74 | */ 75 | public CircRna(String circRnaID) { 76 | this.circRnaID = circRnaID; 77 | geneTranscrpits = new TreeMap(); 78 | samples = new TreeMap(); 79 | circTools = new TreeMap(); 80 | files = new TreeMap(); 81 | } 82 | 83 | public String getCircRnaID() { 84 | return circRnaID; 85 | } 86 | 87 | public void setCircRnaID(String circRnaID) { 88 | this.circRnaID = circRnaID; 89 | } 90 | 91 | public String getChrom() { 92 | return chrom; 93 | } 94 | 95 | public void setChrom(String chrom) { 96 | this.chrom = chrom; 97 | } 98 | 99 | public long getStartPoint() { 100 | return startPoint; 101 | } 102 | 103 | public void setStartPoint(long startPoint) { 104 | this.startPoint = startPoint; 105 | } 106 | 107 | public long getEndPoint() { 108 | return endPoint; 109 | } 110 | 111 | public void setEndPoint(long endPoint) { 112 | this.endPoint = endPoint; 113 | } 114 | 115 | public String getStrand() { 116 | return strand; 117 | } 118 | 119 | public void setStrand(String strand) { 120 | this.strand = strand; 121 | } 122 | 123 | public int getJunctionReads() { 124 | return junctionReads; 125 | } 126 | 127 | public void setJunctionReads(int junctionReads) { 128 | this.junctionReads = junctionReads; 129 | } 130 | 131 | public String getRegion() { 132 | return region; 133 | } 134 | 135 | public void setRegion(String region) { 136 | this.region = region; 137 | } 138 | 139 | public String getCircRnaType() { 140 | return circRnaType; 141 | } 142 | 143 | public void setCircRnaType(String circRnaType) { 144 | this.circRnaType = circRnaType; 145 | } 146 | 147 | /** 148 | * @return the geneTranscrpits 149 | */ 150 | public TreeMap getGeneTranscrpits() { 151 | return geneTranscrpits; 152 | } 153 | 154 | /** 155 | * @param geneTranscrpits 156 | * the geneTranscrpits to set 157 | */ 158 | public void setGeneTranscrpits(TreeMap geneTranscrpits) { 159 | this.geneTranscrpits = geneTranscrpits; 160 | } 161 | 162 | /** 163 | * @return the samples 164 | */ 165 | public TreeMap getSamples() { 166 | return samples; 167 | } 168 | 169 | /** 170 | * @param samples 171 | * the samples to set 172 | */ 173 | public void setSamples(TreeMap samples) { 174 | this.samples = samples; 175 | } 176 | 177 | /** 178 | * @return the circTools 179 | */ 180 | public TreeMap getCircTools() { 181 | return circTools; 182 | } 183 | 184 | /** 185 | * @param circTools 186 | * the circTools to set 187 | */ 188 | public void setCircTools(TreeMap circTools) { 189 | this.circTools = circTools; 190 | } 191 | 192 | /** 193 | * @return the files 194 | */ 195 | public TreeMap getFiles() { 196 | return files; 197 | } 198 | 199 | /** 200 | * @param files 201 | * the files to set 202 | */ 203 | public void setFiles(TreeMap files) { 204 | this.files = files; 205 | } 206 | 207 | // /** 208 | // * @return the repeat 209 | // */ 210 | // public int getRepeat() { 211 | // return repeat; 212 | // } 213 | // 214 | // /** 215 | // * @param repeat the repeat to set 216 | // */ 217 | // public void setRepeat(int repeat) { 218 | // this.repeat = repeat; 219 | // } 220 | } 221 | -------------------------------------------------------------------------------- /src/cn/edu/whu/CircRnaTool.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu; 2 | 3 | import java.io.BufferedReader; 4 | import java.io.File; 5 | import java.io.FileReader; 6 | import java.io.Serializable; 7 | import java.util.ArrayList; 8 | import java.util.Collections; 9 | import java.util.TreeMap; 10 | import java.util.Vector; 11 | 12 | import cn.edu.whu.exception.FileReadException; 13 | import cn.edu.whu.util.Constant; 14 | 15 | public class CircRnaTool implements Serializable { 16 | private static final long serialVersionUID = 1L; 17 | 18 | public CircRnaTool() { 19 | } 20 | 21 | public static boolean initSpeciesDataFromFile(File file, TreeMap genes) { 22 | return parseGeneTranscriptFile(file, genes); 23 | } 24 | 25 | public static boolean initCircRnaDataFromFiles(Vector> fileTableData, String speciesName, 26 | TreeMap genes) throws FileReadException { 27 | return addCircRnaData(fileTableData, speciesName, genes); 28 | } 29 | 30 | private static boolean addCircRnaData(Vector> fileTableData, String speciesName, 31 | TreeMap genes) throws FileReadException { 32 | TreeMap circRnas = new TreeMap(); 33 | for (Vector rowData : fileTableData) { 34 | String species = rowData.get(0); 35 | if (!species.equalsIgnoreCase(speciesName)) { 36 | continue; 37 | } 38 | String toolName = rowData.get(1); 39 | String fileName = rowData.get(2); 40 | String filePath = rowData.get(3); 41 | String[] tmp = fileName.split("\\."); 42 | String sampleName = tmp[0]; 43 | File file = new File(filePath); 44 | if (toolName.equalsIgnoreCase(Constant.TOOL_CIRCRNAFINDER) 45 | || toolName.equalsIgnoreCase(Constant.TOOL_FIND_CIRC)) { 46 | if (!parseCircRnaFinderFile(file, circRnas, sampleName, toolName, fileName)) { 47 | throw new FileReadException("Can not open [" + file.getName() + "] or file FORMAT ERROR!"); 48 | } 49 | } else if (toolName.equalsIgnoreCase(Constant.TOOL_CIRI)) { 50 | if (!parseCiriFile(file, circRnas, sampleName, toolName, fileName)) { 51 | throw new FileReadException("Can not open [" + file.getName() + "] or file FORMAT ERROR!"); 52 | } 53 | } else if (toolName.equalsIgnoreCase(Constant.TOOL_CIRCEXPLORER)) { 54 | if (!parseCircExplorerFile(file, circRnas, sampleName, toolName, fileName)) { 55 | throw new FileReadException("Can not open [" + file.getName() + "] or file FORMAT ERROR!"); 56 | } 57 | } else if (toolName.equalsIgnoreCase(Constant.TOOL_MAPSPLICE)) { 58 | if (!parseMapspliceFile(file, circRnas, sampleName, toolName, fileName)) { 59 | throw new FileReadException("Can not open [" + file.getName() + "] or file FORMAT ERROR!"); 60 | } 61 | } else if (toolName.equalsIgnoreCase(Constant.TOOL_UROBORUS)) { 62 | if (!parseUroborusFile(file, circRnas, sampleName, toolName, fileName)) { 63 | throw new FileReadException("Can not open [" + file.getName() + "] or file FORMAT ERROR!"); 64 | } 65 | } else { 66 | if (!parseCircRnaFinderFile(file, circRnas, sampleName, toolName, fileName)) { 67 | throw new FileReadException("Can not open [" + file.getName() + "] or file FORMAT ERROR!"); 68 | } 69 | 70 | } 71 | } 72 | CircView.log.info("Genes number: " + genes.size()); 73 | CircView.log.info("CircRNAs number: " + circRnas.size()); 74 | assignAll(genes, circRnas); 75 | return true; 76 | } 77 | 78 | private static boolean parseGeneTranscriptFile(File file, TreeMap genes) { 79 | boolean ret = true; 80 | CircView.log.info("Parsing " + file.getName()); 81 | BufferedReader reader = null; 82 | try { 83 | if (file.isFile() && file.exists()) { 84 | reader = new BufferedReader(new FileReader(file)); 85 | String lineTxt = null; 86 | int lineNum = 0; 87 | while ((lineTxt = reader.readLine()) != null) { 88 | lineNum++; 89 | if (lineTxt.toLowerCase().contains("gene")) { 90 | continue; 91 | } 92 | String[] parts = lineTxt.split("\t"); 93 | // parts[0] Gene Name 94 | // parts[1] Gene Transcript Name 95 | // parts[2] Chromosome name 96 | // parts[3] + or - for strand 97 | // parts[4] Transcription start position 98 | // parts[5] Transcription end position 99 | // parts[6] Coding region start 100 | // parts[7] Coding region end 101 | // parts[8] Number of exons 102 | // parts[9] Exon start postions 103 | // parts[10] Exon end postions 104 | if (parts[3].contains("+") || parts[3].contains("-")) { 105 | } else if (1 == lineNum) { 106 | continue; 107 | } else { 108 | reader.close(); 109 | return false; 110 | } 111 | String geneName = parts[0]; 112 | GeneTranscript geneTranscript = new GeneTranscript(geneName); 113 | geneTranscript.setTranscriptName(parts[1]); 114 | geneTranscript.setChrom(parts[2]); 115 | geneTranscript.setStrand(parts[3]); 116 | geneTranscript.setTxStart(Long.parseLong(parts[4])); 117 | geneTranscript.setTxEnd(Long.parseLong(parts[5])); 118 | geneTranscript.setCdsStart(Long.parseLong(parts[6])); 119 | geneTranscript.setCdsEnd(Long.parseLong(parts[7])); 120 | geneTranscript.setExonCount(Integer.parseInt(parts[8])); 121 | String[] exonStarts = parts[9].split(","); 122 | for (int i = 0; i < exonStarts.length; i++) { 123 | geneTranscript.getExonStarts().addElement(Long.parseLong(exonStarts[i])); 124 | } 125 | String[] exonEnds = parts[10].split(","); 126 | for (int i = 0; i < exonEnds.length; i++) { 127 | geneTranscript.getExonEnds().addElement(Long.parseLong(exonEnds[i])); 128 | } 129 | if (genes.containsKey(geneName.toUpperCase())) { 130 | genes.get(geneName.toUpperCase()).getGeneTranscripts().put(geneTranscript.getTranscriptName(), 131 | geneTranscript); 132 | } else { 133 | Gene gene = new Gene(geneName); 134 | gene.getGeneTranscripts().put(geneTranscript.getTranscriptName(), geneTranscript); 135 | genes.put(geneName.toUpperCase(), gene); 136 | } 137 | } 138 | reader.close(); 139 | } else { 140 | ret = false; 141 | CircView.log.info("Can't open the file: " + file.getName()); 142 | } 143 | } catch (Exception e) { 144 | ret = false; 145 | CircView.log.warn(e.getMessage()); 146 | } 147 | return ret; 148 | } 149 | 150 | private static boolean parseCircRnaFinderFile(File file, TreeMap circRnas, String sampleName, 151 | String circTool, String fileName) { 152 | boolean ret = true; 153 | CircView.log.info("Parsing " + file.getName()); 154 | BufferedReader reader = null; 155 | try { 156 | if (file.isFile() && file.exists()) { 157 | reader = new BufferedReader(new FileReader(file)); 158 | String lineTxt = null; 159 | int lineNum = 0; 160 | while ((lineTxt = reader.readLine()) != null) { 161 | lineNum++; 162 | if (lineTxt.toLowerCase().contains("strand")) { 163 | continue; 164 | } 165 | String[] parts = lineTxt.split("\t"); 166 | // parts[0] Chromosome name 167 | // parts[1] start position 168 | // parts[2] end position 169 | // parts[3] 170 | // parts[4] junction reads 171 | // parts[5] + or - for strand 172 | if (parts[5].contains("+") || parts[5].contains("-")) { 173 | } else if (1 == lineNum) { 174 | continue; 175 | } else { 176 | reader.close(); 177 | return false; 178 | } 179 | String circRnaId = parts[0] + ":" + parts[1] + "|" + parts[2]; 180 | CircRna circRna = new CircRna(circRnaId); 181 | circRna.setChrom(parts[0]); 182 | circRna.setStartPoint(Long.parseLong(parts[1])); 183 | circRna.setEndPoint(Long.parseLong(parts[2])); 184 | circRna.setJunctionReads((int) Long.parseLong(parts[4])); 185 | circRna.setStrand(parts[5]); 186 | if (circRnas.containsKey(circRnaId.toUpperCase())) { 187 | if (null != circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName)) { 188 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 189 | circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName) + 1); 190 | } else { 191 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 1); 192 | } 193 | if (null != circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool)) { 194 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 195 | circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool) + 1); 196 | } else { 197 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 1); 198 | } 199 | if (null != circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName)) { 200 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 201 | circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName) + 1); 202 | } else { 203 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 1); 204 | } 205 | // Save the Max Junction reads 206 | if (circRna.getJunctionReads() > circRnas.get(circRnaId.toUpperCase()).getJunctionReads()) { 207 | circRnas.get(circRnaId.toUpperCase()).setJunctionReads(circRna.getJunctionReads()); 208 | } 209 | } else { 210 | circRna.getSamples().put(sampleName, 1); 211 | circRna.getCircTools().put(circTool, 1); 212 | circRna.getFiles().put(fileName, 1); 213 | circRnas.put(circRnaId.toUpperCase(), circRna); 214 | } 215 | } 216 | reader.close(); 217 | } else { 218 | CircView.log.warn("Can't find the file: " + file.getName()); 219 | } 220 | } catch (Exception e) { 221 | CircView.log.warn(e.getMessage()); 222 | ret = false; 223 | } 224 | return ret; 225 | } 226 | 227 | private static boolean parseCircExplorerFile(File file, TreeMap circRnas, String sampleName, 228 | String circTool, String fileName) { 229 | boolean ret = true; 230 | CircView.log.info("Parsing " + file.getName()); 231 | BufferedReader reader = null; 232 | try { 233 | if (file.isFile() && file.exists()) { 234 | reader = new BufferedReader(new FileReader(file)); 235 | String lineTxt = null; 236 | int lineNum = 0; 237 | while ((lineTxt = reader.readLine()) != null) { 238 | lineNum++; 239 | String[] parts = lineTxt.split("\t"); 240 | // parts[0] Chromosome name 241 | // parts[1] start position 242 | // parts[2] end position 243 | // parts[3] CircRNA/junction reads 244 | // parts[4] 245 | // parts[5] + or - for strand 246 | if (parts[5].contains("+") || parts[5].contains("-")) { 247 | } else if (1 == lineNum) { 248 | continue; 249 | } else { 250 | reader.close(); 251 | return false; 252 | } 253 | String circRnaId = parts[0] + ":" + parts[1] + "|" + parts[2]; 254 | CircRna circRna = new CircRna(circRnaId); 255 | circRna.setChrom(parts[0]); 256 | circRna.setStartPoint(Long.parseLong(parts[1])); 257 | circRna.setEndPoint(Long.parseLong(parts[2])); 258 | String tmp = parts[3]; 259 | String[] junc = tmp.split("/"); 260 | circRna.setJunctionReads((int) Long.parseLong(junc[1])); 261 | circRna.setStrand(parts[5]); 262 | if (circRnas.containsKey(circRnaId.toUpperCase())) { 263 | if (null != circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName)) { 264 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 265 | circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName) + 1); 266 | } else { 267 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 1); 268 | } 269 | if (null != circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool)) { 270 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 271 | circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool) + 1); 272 | } else { 273 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 1); 274 | } 275 | if (null != circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName)) { 276 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 277 | circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName) + 1); 278 | } else { 279 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 1); 280 | } 281 | // Save the Max Junction reads 282 | if (circRna.getJunctionReads() > circRnas.get(circRnaId.toUpperCase()).getJunctionReads()) { 283 | circRnas.get(circRnaId.toUpperCase()).setJunctionReads(circRna.getJunctionReads()); 284 | } 285 | } else { 286 | circRna.getSamples().put(sampleName, 1); 287 | circRna.getCircTools().put(circTool, 1); 288 | circRna.getFiles().put(fileName, 1); 289 | circRnas.put(circRnaId.toUpperCase(), circRna); 290 | } 291 | } 292 | reader.close(); 293 | } else { 294 | CircView.log.warn("Can't find the file: " + file.getName()); 295 | } 296 | } catch (Exception e) { 297 | CircView.log.warn(e.getMessage()); 298 | ret = false; 299 | } 300 | return ret; 301 | } 302 | 303 | private static boolean parseCiriFile(File file, TreeMap circRnas, String sampleName, 304 | String circTool, String fileName) { 305 | boolean ret = true; 306 | CircView.log.info("Parsing " + file.getName()); 307 | BufferedReader reader = null; 308 | try { 309 | if (file.isFile() && file.exists()) { 310 | reader = new BufferedReader(new FileReader(file)); 311 | String lineTxt = null; 312 | int lineNum = 0; 313 | while ((lineTxt = reader.readLine()) != null) { 314 | lineNum++; 315 | String[] parts = lineTxt.split("\t"); 316 | // parts[0] CircRNA ID 317 | // parts[1] Chromosome name 318 | // parts[2] start position 319 | // parts[3] end position 320 | // parts[4] junction reads 321 | // parts[10] + or - for strand 322 | if (parts[10].contains("+") || parts[10].contains("-")) { 323 | } else if (1 == lineNum) { 324 | continue; 325 | } else { 326 | reader.close(); 327 | return false; 328 | } 329 | String circRnaId = parts[0]; 330 | CircRna circRna = new CircRna(circRnaId); 331 | circRna.setChrom(parts[1]); 332 | circRna.setStartPoint(Long.parseLong(parts[2])); 333 | circRna.setEndPoint(Long.parseLong(parts[3])); 334 | circRna.setJunctionReads((int) Long.parseLong(parts[4])); 335 | circRna.setStrand(parts[10]); 336 | if (circRnas.containsKey(circRnaId.toUpperCase())) { 337 | if (null != circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName)) { 338 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 339 | circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName) + 1); 340 | } else { 341 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 1); 342 | } 343 | if (null != circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool)) { 344 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 345 | circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool) + 1); 346 | } else { 347 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 1); 348 | } 349 | if (null != circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName)) { 350 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 351 | circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName) + 1); 352 | } else { 353 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 1); 354 | } 355 | // Save the Max Junction reads 356 | if (circRna.getJunctionReads() > circRnas.get(circRnaId.toUpperCase()).getJunctionReads()) { 357 | circRnas.get(circRnaId.toUpperCase()).setJunctionReads(circRna.getJunctionReads()); 358 | } 359 | } else { 360 | circRna.getSamples().put(sampleName, 1); 361 | circRna.getCircTools().put(circTool, 1); 362 | circRna.getFiles().put(fileName, 1); 363 | circRnas.put(circRnaId.toUpperCase(), circRna); 364 | } 365 | } 366 | reader.close(); 367 | } else { 368 | CircView.log.warn("Can't find the file: " + file.getName()); 369 | ret = false; 370 | } 371 | } catch (Exception e) { 372 | CircView.log.warn(e.getMessage()); 373 | ret = false; 374 | } 375 | return ret; 376 | } 377 | 378 | private static boolean parseMapspliceFile(File file, TreeMap circRnas, String sampleName, 379 | String circTool, String fileName) { 380 | boolean ret = true; 381 | CircView.log.info("Parsing " + file.getName()); 382 | BufferedReader reader = null; 383 | try { 384 | if (file.isFile() && file.exists()) { 385 | reader = new BufferedReader(new FileReader(file)); 386 | String lineTxt = null; 387 | int lineNum = 0; 388 | while ((lineTxt = reader.readLine()) != null) { 389 | lineNum++; 390 | if (lineTxt.toLowerCase().contains("circ")) { 391 | continue; 392 | } 393 | String[] parts = lineTxt.split("\t"); 394 | // parts[0] Chromosome name 395 | // parts[1] start position 396 | // parts[2] end position 397 | // parts[3] 398 | // parts[4] junction reads 399 | // parts[5] + or - for strand 400 | // parts[6] 401 | if (parts[5].contains("+") || parts[5].contains("-")) { 402 | } else if (1 == lineNum) { 403 | continue; 404 | } else { 405 | reader.close(); 406 | return false; 407 | } 408 | String[] tmp = parts[0].split("~"); 409 | String chr = tmp[0]; 410 | String circRnaId = chr + ":" + parts[1] + "|" + parts[2]; 411 | CircRna circRna = new CircRna(circRnaId); 412 | circRna.setChrom(chr); 413 | circRna.setStartPoint(Long.parseLong(parts[1])); 414 | circRna.setEndPoint(Long.parseLong(parts[2])); 415 | circRna.setStrand(parts[5].substring(0, 1)); 416 | circRna.setJunctionReads((int) Long.parseLong(parts[4])); 417 | if (circRnas.containsKey(circRnaId.toUpperCase())) { 418 | if (null != circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName)) { 419 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 420 | circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName) + 1); 421 | } else { 422 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 1); 423 | } 424 | if (null != circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool)) { 425 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 426 | circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool) + 1); 427 | } else { 428 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 1); 429 | } 430 | if (null != circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName)) { 431 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 432 | circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName) + 1); 433 | } else { 434 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 1); 435 | } 436 | // Save the Max Junction reads 437 | if (circRna.getJunctionReads() > circRnas.get(circRnaId.toUpperCase()).getJunctionReads()) { 438 | circRnas.get(circRnaId.toUpperCase()).setJunctionReads(circRna.getJunctionReads()); 439 | } 440 | } else { 441 | circRna.getSamples().put(sampleName, 1); 442 | circRna.getCircTools().put(circTool, 1); 443 | circRna.getFiles().put(fileName, 1); 444 | circRnas.put(circRnaId.toUpperCase(), circRna); 445 | } 446 | } 447 | reader.close(); 448 | } else { 449 | CircView.log.warn("Can't find the file: " + file.getName()); 450 | } 451 | } catch (Exception e) { 452 | CircView.log.warn(e.getMessage()); 453 | ret = false; 454 | } 455 | return ret; 456 | } 457 | 458 | private static boolean parseUroborusFile(File file, TreeMap circRnas, String sampleName, 459 | String circTool, String fileName) { 460 | boolean ret = true; 461 | CircView.log.info("Parsing " + file.getName()); 462 | BufferedReader reader = null; 463 | try { 464 | if (file.isFile() && file.exists()) { 465 | reader = new BufferedReader(new FileReader(file)); 466 | String lineTxt = null; 467 | int lineNum = 0; 468 | while ((lineTxt = reader.readLine()) != null) { 469 | lineNum++; 470 | if (lineTxt.toLowerCase().contains("circ")) { 471 | continue; 472 | } 473 | String[] parts = lineTxt.split("\t"); 474 | // parts[0] Chromosome name 475 | // parts[1] start position 476 | // parts[2] end position 477 | // parts[3] + or - for strand 478 | // parts[4] 479 | // parts[5] 480 | // parts[6] junction reads 481 | if (parts[3].contains("+") || parts[3].contains("-")) { 482 | } else if (1 == lineNum) { 483 | continue; 484 | } else { 485 | reader.close(); 486 | return false; 487 | } 488 | String circRnaId = parts[0] + ":" + parts[1] + "|" + parts[2]; 489 | CircRna circRna = new CircRna(circRnaId); 490 | circRna.setChrom(parts[0]); 491 | circRna.setStartPoint(Long.parseLong(parts[1])); 492 | circRna.setEndPoint(Long.parseLong(parts[2])); 493 | circRna.setStrand(parts[3]); 494 | circRna.setJunctionReads((int) Long.parseLong(parts[6])); 495 | if (circRnas.containsKey(circRnaId.toUpperCase())) { 496 | if (null != circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName)) { 497 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 498 | circRnas.get(circRnaId.toUpperCase()).getSamples().get(sampleName) + 1); 499 | } else { 500 | circRnas.get(circRnaId.toUpperCase()).getSamples().put(sampleName, 1); 501 | } 502 | if (null != circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool)) { 503 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 504 | circRnas.get(circRnaId.toUpperCase()).getCircTools().get(circTool) + 1); 505 | } else { 506 | circRnas.get(circRnaId.toUpperCase()).getCircTools().put(circTool, 1); 507 | } 508 | if (null != circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName)) { 509 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 510 | circRnas.get(circRnaId.toUpperCase()).getFiles().get(fileName) + 1); 511 | } else { 512 | circRnas.get(circRnaId.toUpperCase()).getFiles().put(fileName, 1); 513 | } 514 | // Save the Max Junction reads 515 | if (circRna.getJunctionReads() > circRnas.get(circRnaId.toUpperCase()).getJunctionReads()) { 516 | circRnas.get(circRnaId.toUpperCase()).setJunctionReads(circRna.getJunctionReads()); 517 | } 518 | } else { 519 | circRna.getSamples().put(sampleName, 1); 520 | circRna.getCircTools().put(circTool, 1); 521 | circRna.getFiles().put(fileName, 1); 522 | circRnas.put(circRnaId.toUpperCase(), circRna); 523 | } 524 | } 525 | reader.close(); 526 | } else { 527 | CircView.log.warn("Can't find the file: " + file.getName()); 528 | } 529 | } catch (Exception e) { 530 | CircView.log.warn(e.getMessage()); 531 | ret = false; 532 | } 533 | return ret; 534 | } 535 | 536 | private static void preAssign(TreeMap allGene, TreeMap> txStartMap, 537 | TreeMap> txEndMap, TreeMap> txStart2Name, 538 | TreeMap> txEnd2Name) { 539 | 540 | // Init Maps 541 | txStartMap.clear(); 542 | txEndMap.clear(); 543 | txStart2Name.clear(); 544 | txEnd2Name.clear(); 545 | 546 | // Create Chrom -- > txStart-geneNames pair 547 | for (String geneName : allGene.keySet()) { 548 | String chrom = ""; 549 | TreeMap tmpUniqueStart = new TreeMap(); 550 | TreeMap tmpUniqueEnd = new TreeMap(); 551 | TreeMap transcripts = allGene.get(geneName.toUpperCase()).getGeneTranscripts(); 552 | for (String transcriptName : transcripts.keySet()) { 553 | GeneTranscript transcript = transcripts.get(transcriptName); 554 | chrom = transcript.getChrom(); 555 | Long txStart = transcript.getTxStart(); 556 | Long txEnd = transcript.getTxEnd(); 557 | if (txStart2Name.get(txStart) != null) { 558 | TreeMap genesTmp = txStart2Name.get(txStart); 559 | genesTmp.put(geneName, geneName); 560 | txStart2Name.put(txStart, genesTmp); 561 | } else { 562 | TreeMap genesTmp = new TreeMap(); 563 | genesTmp.put(geneName, geneName); 564 | txStart2Name.put(txStart, genesTmp); 565 | } 566 | if (txEnd2Name.get(txEnd) != null) { 567 | TreeMap genesTmp = txEnd2Name.get(txEnd); 568 | genesTmp.put(geneName, geneName); 569 | txEnd2Name.put(txEnd, genesTmp); 570 | } else { 571 | TreeMap genesTmp = new TreeMap(); 572 | genesTmp.put(geneName, geneName); 573 | txEnd2Name.put(txEnd, genesTmp); 574 | } 575 | tmpUniqueStart.put(txStart, 1); 576 | tmpUniqueEnd.put(txEnd, 1); 577 | } 578 | // Create Unique txStart and txEnd list 579 | ArrayList uniqueStartList = new ArrayList(); 580 | ArrayList uniqueEndList = new ArrayList(); 581 | for (Long txStart : tmpUniqueStart.keySet()) { 582 | uniqueStartList.add(txStart); 583 | } 584 | for (Long txEnd : tmpUniqueEnd.keySet()) { 585 | uniqueEndList.add(txEnd); 586 | } 587 | // Create Chrom --> Unique List 588 | if (txStartMap.get(chrom) != null) { 589 | txStartMap.get(chrom).addAll(uniqueStartList); 590 | } else { 591 | txStartMap.put(chrom, uniqueStartList); 592 | } 593 | if (txEndMap.get(chrom) != null) { 594 | txEndMap.get(chrom).addAll(uniqueEndList); 595 | } else { 596 | txEndMap.put(chrom, uniqueEndList); 597 | } 598 | } 599 | 600 | // Sort Unique List 601 | for (String chr : txStartMap.keySet()) { 602 | Collections.sort(txStartMap.get(chr)); 603 | } 604 | for (String chr : txEndMap.keySet()) { 605 | Collections.sort(txEndMap.get(chr)); 606 | } 607 | } 608 | 609 | private static void assign(CircRna circRna, TreeMap allGene, 610 | TreeMap> chr2StartList, TreeMap> chr2EndList, 611 | TreeMap> txStart2Name, TreeMap> txEnd2Name) { 612 | String chrom = circRna.getChrom(); 613 | Long startPoint = circRna.getStartPoint(); 614 | Long endPoint = circRna.getEndPoint(); 615 | ArrayList txStartList = chr2StartList.get(chrom); 616 | if (txStartList == null) { 617 | CircView.log.info("circRNA_ID [" + circRna.getCircRnaID() + "] can not find related chrom"); 618 | return; 619 | } 620 | ArrayList txEndList = chr2EndList.get(chrom); 621 | if (txEndList == null) { 622 | CircView.log.info("circRNA_ID [" + circRna.getCircRnaID() + "] can not find related chrom"); 623 | return; 624 | } 625 | // Binary search to find index of txStart 626 | int indexByTxStart = splitHalfByTxStart(txStartList, startPoint.longValue(), 0, txStartList.size() - 1); 627 | // index boundary control 628 | indexByTxStart = (indexByTxStart < 0) ? 0 : indexByTxStart; 629 | indexByTxStart = (indexByTxStart > txStartList.size() - 1) ? txStartList.size() - 1 : indexByTxStart; 630 | // Binary search to find index of txEnd 631 | int indexByTxEnd = splitHalfByTxEnd(txEndList, endPoint.longValue(), 0, txEndList.size() - 1); 632 | // index boundary control 633 | indexByTxEnd = (indexByTxEnd <= 1) ? 0 : indexByTxEnd; 634 | indexByTxEnd = (indexByTxEnd > txEndList.size() - 1) ? txEndList.size() - 1 : indexByTxEnd; 635 | 636 | TreeMap geneNames = new TreeMap(); 637 | // Compare indexByTxStart and indexByTxEnd 638 | if ((indexByTxStart + 1) < (txEndList.size() - indexByTxEnd)) { 639 | // Select indexByTxStart 640 | for (int index = 0; index <= indexByTxStart; index++) { 641 | for (String name : txStart2Name.get(txStartList.get(index)).keySet()) { 642 | geneNames.put(name, 1); 643 | } 644 | } 645 | } else { 646 | // Select indexByTxEnd 647 | for (int index = indexByTxEnd; index < txEndList.size(); index++) { 648 | for (String name : txEnd2Name.get(txEndList.get(index)).keySet()) { 649 | geneNames.put(name, 1); 650 | } 651 | } 652 | } 653 | 654 | // gene location, circRNA type, region 655 | TreeMap geneLocation = new TreeMap(); 656 | TreeMap region = new TreeMap(); 657 | int exonSign = 0; 658 | for (String name : geneNames.keySet()) { 659 | int geneLocationSign = 0; 660 | int mRnaSign = 0; 661 | int lncRnaSign = 0; 662 | Gene gene = allGene.get(name.toUpperCase()); 663 | TreeMap transcripts; 664 | if (gene != null) { 665 | transcripts = gene.getGeneTranscripts(); 666 | } else { 667 | return; 668 | } 669 | for (String transcriptName : transcripts.keySet()) { 670 | GeneTranscript trans = transcripts.get(transcriptName); 671 | if ((trans.getTxStart().longValue() <= startPoint.longValue()) 672 | && (endPoint.longValue() <= trans.getTxEnd().longValue())) { 673 | geneLocationSign++; 674 | geneLocation.put(name + " " + trans.getTranscriptName(), 1); 675 | 676 | if (trans.getCircRnas().get(circRna.getCircRnaID()) == null) { 677 | trans.getCircRnas().put(circRna.getCircRnaID(), circRna); 678 | } 679 | int repeat = 0; 680 | for (String fileName : circRna.getFiles().keySet()) { 681 | repeat += circRna.getFiles().get(fileName); 682 | } 683 | trans.getCircRnasNum().put(circRna.getCircRnaID(), repeat); 684 | trans.setTotalJunctionReads(trans.getTotalJunctionReads() + circRna.getJunctionReads()); 685 | } 686 | if (trans.getCdsStart().longValue() < trans.getCdsEnd().longValue()) { 687 | mRnaSign++; 688 | } else { 689 | lncRnaSign++; 690 | } 691 | for (int i = 0; i < trans.getExonCount(); i++) { 692 | Long exonStart = trans.getExonStarts().get(i); 693 | Long exonEnd = trans.getExonEnds().get(i); 694 | if (((exonStart.longValue() - Constant.ASSIGN_TOLERATION <= startPoint.longValue()) 695 | && (startPoint.longValue() < exonEnd.longValue() + Constant.ASSIGN_TOLERATION)) 696 | || ((exonStart.longValue() - Constant.ASSIGN_TOLERATION < endPoint.longValue()) 697 | && (endPoint.longValue() <= exonEnd.longValue() + Constant.ASSIGN_TOLERATION)) 698 | || ((startPoint.longValue() < exonStart.longValue() - Constant.ASSIGN_TOLERATION) 699 | && (exonEnd.longValue() < endPoint.longValue() + Constant.ASSIGN_TOLERATION))) { 700 | exonSign++; 701 | } 702 | } 703 | } 704 | if (geneLocationSign > 0) { 705 | if (mRnaSign > 0) { 706 | region.put("mRNA", 1); 707 | } else { 708 | region.put("lncRNA", 1); 709 | } 710 | } 711 | } 712 | 713 | if (geneLocation.size() > 0) { 714 | for (String n : geneLocation.keySet()) { 715 | circRna.getGeneTranscrpits().put(n, n); 716 | } 717 | if (exonSign > 0) { 718 | circRna.setCircRnaType("exon"); 719 | } else { 720 | circRna.setCircRnaType("intron"); 721 | } 722 | if ((region.get("mRNA") != null) && (region.get("lncRNA") == null)) { 723 | circRna.setRegion("mRNA"); 724 | } else if ((region.get("mRNA") == null) && (region.get("lncRNA") != null)) { 725 | circRna.setRegion("lncRNA"); 726 | } 727 | if ((region.get("mRNA") != null) && (region.get("lncRNA") != null)) { 728 | circRna.setRegion("mRNA,lncRNA"); 729 | } 730 | } else { 731 | circRna.getGeneTranscrpits().put("n/a", "n/a"); 732 | circRna.setCircRnaType("intergenic"); 733 | circRna.setRegion("Unknown"); 734 | } 735 | } 736 | 737 | private static void assignAll(TreeMap allGene, TreeMap allCircRna) { 738 | TreeMap> chr2StartList = new TreeMap>(); 739 | TreeMap> chr2EndList = new TreeMap>(); 740 | TreeMap> txStart2Name = new TreeMap>(); 741 | TreeMap> txEnd2Name = new TreeMap>(); 742 | 743 | if (allGene != null && allCircRna != null) { 744 | preAssign(allGene, chr2StartList, chr2EndList, txStart2Name, txEnd2Name); 745 | } 746 | int num = 0; 747 | 748 | for (String circRnaId : allCircRna.keySet()) { 749 | if (0 == (++num % 1000)) { 750 | CircView.log.info("Mapping: [" + num + "|" + allCircRna.size() + "]"); 751 | } 752 | CircRna circRna = allCircRna.get(circRnaId); 753 | assign(circRna, allGene, chr2StartList, chr2EndList, txStart2Name, txEnd2Name); 754 | } 755 | } 756 | 757 | private static int splitHalfByTxStart(ArrayList arrayData, Long txStart, int start, int end) { 758 | int index = (start + end) / 2; 759 | Long data = arrayData.get(index); 760 | if (start > end) { 761 | return end; 762 | } 763 | if (data.longValue() == txStart.longValue()) { 764 | return index; 765 | } else { 766 | if (data.longValue() < txStart.longValue()) { 767 | return splitHalfByTxStart(arrayData, txStart, index + 1, end); 768 | } else { 769 | return splitHalfByTxStart(arrayData, txStart, start, index - 1); 770 | } 771 | } 772 | } 773 | 774 | private static int splitHalfByTxEnd(ArrayList arrayData, Long txEnd, int start, int end) { 775 | int index = (start + end) / 2; 776 | Long data = arrayData.get(index); 777 | if (start > end) { 778 | return start; 779 | } 780 | if (data.longValue() == txEnd.longValue()) { 781 | return index; 782 | } else { 783 | if (data.longValue() < txEnd.longValue()) { 784 | return splitHalfByTxEnd(arrayData, txEnd, index + 1, end); 785 | } else { 786 | return splitHalfByTxEnd(arrayData, txEnd, start, index - 1); 787 | } 788 | } 789 | } 790 | } 791 | -------------------------------------------------------------------------------- /src/cn/edu/whu/Exon.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu; 2 | 3 | public class Exon { 4 | private long startPoint; 5 | private long endPoint; 6 | 7 | public Exon(long startPoint, long endPoint) { 8 | this.startPoint = startPoint; 9 | this.endPoint = endPoint; 10 | } 11 | 12 | public long getStartPoint() { 13 | return startPoint; 14 | } 15 | 16 | public void setStartPoint(long startPoint) { 17 | this.startPoint = startPoint; 18 | } 19 | 20 | public long getEndPoint() { 21 | return endPoint; 22 | } 23 | 24 | public void setEndPoint(long endPoint) { 25 | this.endPoint = endPoint; 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /src/cn/edu/whu/Gene.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu; 2 | 3 | import java.io.Serializable; 4 | import java.util.TreeMap; 5 | import java.util.Vector; 6 | 7 | /** 8 | * Gene class 9 | * 10 | * @author Gene 11 | * 12 | */ 13 | public class Gene implements Serializable{ 14 | 15 | private static final long serialVersionUID = 1L; 16 | /** 17 | * gene's name 18 | */ 19 | private String geneName; 20 | /** 21 | * gene's transcripts 22 | */ 23 | private TreeMap geneTranscripts; 24 | /** 25 | * gene's circRNA samples 26 | */ 27 | 28 | private Vector allExons; 29 | /** 30 | * gene's reference 31 | */ 32 | private GeneTranscript geneReference; 33 | 34 | /** 35 | * Constructor of Gene 36 | * 37 | * @param geneName 38 | */ 39 | public Gene(String geneName) { 40 | this.setGeneName(geneName); 41 | geneTranscripts = new TreeMap(); 42 | allExons = new Vector(); 43 | geneReference = new GeneTranscript(geneName); 44 | } 45 | 46 | /** 47 | * get Gene's name 48 | * 49 | * @return geneName 50 | */ 51 | public String getGeneName() { 52 | return geneName; 53 | } 54 | 55 | /** 56 | * set Gene's name 57 | * 58 | * @param geneName 59 | */ 60 | public void setGeneName(String geneName) { 61 | this.geneName = geneName; 62 | } 63 | 64 | /** 65 | * get gene's transcripts 66 | * 67 | * @return geneTranscripts 68 | */ 69 | public TreeMap getGeneTranscripts() { 70 | return geneTranscripts; 71 | } 72 | 73 | /** 74 | * set gene's transcripts 75 | * 76 | * @param geneTranscripts 77 | */ 78 | public void setGeneTranscripts(TreeMap geneTranscripts) { 79 | this.geneTranscripts = geneTranscripts; 80 | } 81 | 82 | /** 83 | * get all exons 84 | * 85 | * @return allExons 86 | */ 87 | public Vector getAllExons() { 88 | return allExons; 89 | } 90 | 91 | /** 92 | * set all exons 93 | * 94 | * @param allExons 95 | */ 96 | public void setAllExons(Vector allExons) { 97 | this.allExons = allExons; 98 | } 99 | 100 | /** 101 | * get gene's reference 102 | * 103 | * @return geneReference 104 | */ 105 | public GeneTranscript getGeneReference() { 106 | return geneReference; 107 | } 108 | 109 | /** 110 | * set gene's reference 111 | * 112 | * @param geneReference 113 | */ 114 | public void setGeneReference(GeneTranscript geneReference) { 115 | this.geneReference = geneReference; 116 | } 117 | 118 | } 119 | -------------------------------------------------------------------------------- /src/cn/edu/whu/GeneTranscript.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu; 2 | 3 | import java.io.ByteArrayInputStream; 4 | import java.io.ByteArrayOutputStream; 5 | import java.io.IOException; 6 | import java.io.ObjectInputStream; 7 | import java.io.ObjectOutputStream; 8 | import java.io.Serializable; 9 | import java.util.TreeMap; 10 | import java.util.Vector; 11 | 12 | /** 13 | * GeneTranscript 14 | * 15 | * @author Gene deal refFlat format file 16 | */ 17 | public class GeneTranscript implements Serializable { 18 | 19 | private static final long serialVersionUID = 1L; 20 | /** 21 | * Name of gene as it appears in Genome Browser 22 | */ 23 | private String geneName; 24 | /** 25 | * Name of gene 26 | */ 27 | private String transcriptName; 28 | /** 29 | * Chromosome name 30 | */ 31 | private String chrom; 32 | /** 33 | * + or - for strand 34 | */ 35 | private String strand; 36 | /** 37 | * Transcription start position 38 | */ 39 | private Long txStart; 40 | /** 41 | * Transcription end position 42 | */ 43 | private Long txEnd; 44 | /** 45 | * Coding region start 46 | */ 47 | private Long cdsStart; 48 | /** 49 | * Coding region end 50 | */ 51 | private Long cdsEnd; 52 | /** 53 | * Number of exons 54 | */ 55 | private Integer exonCount; 56 | /** 57 | * Exon start postions 58 | */ 59 | private Vector exonStarts; 60 | /** 61 | * Exon end positons 62 | */ 63 | private Vector exonEnds; 64 | 65 | private TreeMap circRnas; 66 | private TreeMap circRnasNum; 67 | private int totalJunctionReads; 68 | 69 | /** 70 | * Constructor of class GeneTranscript 71 | * 72 | * @param geneName 73 | */ 74 | public GeneTranscript(String geneName) { 75 | this.setGeneName(geneName); 76 | exonStarts = new Vector(); 77 | exonEnds = new Vector(); 78 | setCircRnas(new TreeMap()); 79 | setCircRnasNum(new TreeMap()); 80 | setTotalJunctionReads(0); 81 | } 82 | 83 | /** 84 | * get gene name 85 | * 86 | * @return geneName 87 | */ 88 | public String getGeneName() { 89 | return geneName; 90 | } 91 | 92 | /** 93 | * set gene name 94 | * 95 | * @param geneName 96 | */ 97 | public void setGeneName(String geneName) { 98 | this.geneName = geneName; 99 | } 100 | 101 | /** 102 | * get transcript name 103 | * 104 | * @return transcriptName 105 | */ 106 | public String getTranscriptName() { 107 | return transcriptName; 108 | } 109 | 110 | /** 111 | * set transcript name 112 | * 113 | * @param transcriptName 114 | */ 115 | public void setTranscriptName(String transcriptName) { 116 | this.transcriptName = transcriptName; 117 | } 118 | 119 | /** 120 | * get chrom 121 | * 122 | * @return chrom 123 | */ 124 | public String getChrom() { 125 | return chrom; 126 | } 127 | 128 | /** 129 | * set chrom 130 | * 131 | * @param chrom 132 | */ 133 | public void setChrom(String chrom) { 134 | this.chrom = chrom; 135 | } 136 | 137 | /** 138 | * get strand 139 | * 140 | * @return strand 141 | */ 142 | public String getStrand() { 143 | return strand; 144 | } 145 | 146 | /** 147 | * set strand 148 | * 149 | * @param strand 150 | */ 151 | public void setStrand(String strand) { 152 | this.strand = strand; 153 | } 154 | 155 | /** 156 | * get Tx start 157 | * 158 | * @return txStart 159 | */ 160 | public Long getTxStart() { 161 | return txStart; 162 | } 163 | 164 | /** 165 | * set Tx start 166 | * 167 | * @param txStart 168 | */ 169 | public void setTxStart(Long txStart) { 170 | this.txStart = txStart; 171 | } 172 | 173 | /** 174 | * get Tx end 175 | * 176 | * @return txEnd 177 | */ 178 | public Long getTxEnd() { 179 | return txEnd; 180 | } 181 | 182 | /** 183 | * set Tx end 184 | * 185 | * @param txEnd 186 | */ 187 | public void setTxEnd(Long txEnd) { 188 | this.txEnd = txEnd; 189 | } 190 | 191 | /** 192 | * get CDS start 193 | * 194 | * @return cdsStart 195 | */ 196 | public Long getCdsStart() { 197 | return cdsStart; 198 | } 199 | 200 | /** 201 | * set CDS start 202 | * 203 | * @param cdsStart 204 | */ 205 | public void setCdsStart(Long cdsStart) { 206 | this.cdsStart = cdsStart; 207 | } 208 | 209 | /** 210 | * get CDS end 211 | * 212 | * @return cdsEnd 213 | */ 214 | public Long getCdsEnd() { 215 | return cdsEnd; 216 | } 217 | 218 | /** 219 | * set CDS end 220 | * 221 | * @param cdsEnd 222 | */ 223 | public void setCdsEnd(Long cdsEnd) { 224 | this.cdsEnd = cdsEnd; 225 | } 226 | 227 | /** 228 | * get exon count 229 | * 230 | * @return exonCount 231 | */ 232 | public Integer getExonCount() { 233 | return exonCount; 234 | } 235 | 236 | /** 237 | * set exon count 238 | * 239 | * @param exonCount 240 | */ 241 | public void setExonCount(Integer exonCount) { 242 | this.exonCount = exonCount; 243 | } 244 | 245 | /** 246 | * get exon starts 247 | * 248 | * @return exonStarts 249 | */ 250 | public Vector getExonStarts() { 251 | return exonStarts; 252 | } 253 | 254 | /** 255 | * set exon starts 256 | * 257 | * @param exonStarts 258 | */ 259 | public void setExonStarts(Vector exonStarts) { 260 | this.exonStarts = exonStarts; 261 | } 262 | 263 | /** 264 | * get exon ends 265 | * 266 | * @return exonEnds 267 | */ 268 | public Vector getExonEnds() { 269 | return exonEnds; 270 | } 271 | 272 | /** 273 | * set exon ends 274 | * 275 | * @param exonEnds 276 | */ 277 | public void setExonEnds(Vector exonEnds) { 278 | this.exonEnds = exonEnds; 279 | } 280 | 281 | /** 282 | * @return the circRnaNum 283 | */ 284 | public TreeMap getCircRnasNum() { 285 | return circRnasNum; 286 | } 287 | 288 | /** 289 | * @param circRnaNum 290 | * the circRnaNum to set 291 | */ 292 | public void setCircRnasNum(TreeMap circRnasNum) { 293 | this.circRnasNum = circRnasNum; 294 | } 295 | 296 | /** 297 | * @return the totalJunctionReads 298 | */ 299 | public int getTotalJunctionReads() { 300 | return totalJunctionReads; 301 | } 302 | 303 | /** 304 | * @param totalJunctionReads the totalJunctionReads to set 305 | */ 306 | public void setTotalJunctionReads(int totalJunctionReads) { 307 | this.totalJunctionReads = totalJunctionReads; 308 | } 309 | 310 | /** 311 | * @return the circRnas 312 | */ 313 | public TreeMap getCircRnas() { 314 | return circRnas; 315 | } 316 | 317 | /** 318 | * @param circRnas 319 | * the circRnas to set 320 | */ 321 | public void setCircRnas(TreeMap circRnas) { 322 | this.circRnas = circRnas; 323 | } 324 | 325 | public GeneTranscript deepClone() { 326 | ByteArrayOutputStream byteOut = null; 327 | ObjectOutputStream objOut = null; 328 | ByteArrayInputStream byteIn = null; 329 | ObjectInputStream objIn = null; 330 | 331 | try { 332 | byteOut = new ByteArrayOutputStream(); 333 | objOut = new ObjectOutputStream(byteOut); 334 | objOut.writeObject(this); 335 | 336 | byteIn = new ByteArrayInputStream(byteOut.toByteArray()); 337 | objIn = new ObjectInputStream(byteIn); 338 | 339 | return (GeneTranscript) objIn.readObject(); 340 | } catch (IOException e) { 341 | throw new RuntimeException("Clone Object failed in IO.", e); 342 | } catch (ClassNotFoundException e) { 343 | throw new RuntimeException("Class not found.", e); 344 | } finally { 345 | try { 346 | byteIn = null; 347 | byteOut = null; 348 | if (objOut != null) 349 | objOut.close(); 350 | if (objIn != null) 351 | objIn.close(); 352 | } catch (IOException e) { 353 | } 354 | } 355 | } 356 | 357 | } 358 | -------------------------------------------------------------------------------- /src/cn/edu/whu/MainData.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu; 2 | 3 | import java.io.File; 4 | import java.io.FileInputStream; 5 | import java.io.FileOutputStream; 6 | import java.io.IOException; 7 | import java.io.InputStream; 8 | import java.io.OutputStream; 9 | import java.util.Properties; 10 | import java.util.TreeMap; 11 | import java.util.Vector; 12 | 13 | import cn.edu.whu.util.Constant; 14 | import cn.edu.whu.util.DbConfig; 15 | 16 | public class MainData { 17 | private static TreeMap speciesFile; // SpeciesName - Species 18 | // Data File Path 19 | private static TreeMap> speciesData; // SpeciesName 20 | // - 21 | // Loaded 22 | // Species 23 | // Data 24 | private static Vector speciesNames; // Tool Names 25 | private static Vector circRnaToolNames; // Tool Names 26 | private static Vector> circRnaFilesInfo; 27 | private static Properties properties; 28 | private static DbConfig dbConfig; 29 | 30 | public MainData() { 31 | speciesFile = new TreeMap(); 32 | speciesData = new TreeMap>(); 33 | speciesNames = new Vector(); 34 | circRnaToolNames = new Vector(); 35 | circRnaFilesInfo = new Vector>(); 36 | properties = new Properties(); 37 | dbConfig = new DbConfig(); 38 | configure(); 39 | } 40 | 41 | private void configure() { 42 | File file = new File(Constant.CONFIG_FILE); 43 | if (file.exists()) { 44 | readDbConfig(); 45 | } else { 46 | initDbConfig(); 47 | writeDbConfig(); 48 | } 49 | initSpeciesFile(); 50 | initTools(); 51 | } 52 | 53 | private void initSpeciesFile() { 54 | // Init Default Species Config 55 | for (String speciesName : Constant.SPECIES) { 56 | File file = new File(Constant.SPECIES_FILE.get(speciesName)); 57 | if (file.exists()) { 58 | speciesNames.add(speciesName); 59 | speciesFile.put(speciesName, Constant.SPECIES_FILE.get(speciesName)); 60 | } else { 61 | CircView.log.info("Can not find annotation file " + file.getName()); 62 | } 63 | } 64 | } 65 | 66 | private void initTools() { 67 | // Init Default CircRNA Tools Config 68 | for (String circRnaToolName : Constant.CIRCRNA_TOOLS) { 69 | circRnaToolNames.add(circRnaToolName); 70 | } 71 | } 72 | 73 | private void initDbConfig() { 74 | CircView.log.info("Init Default Config"); 75 | // Init Default Database Config 76 | dbConfig.setDbServer(Constant.DEFAULT_DB_SERVER); 77 | dbConfig.setDbPort(Constant.DEFAULT_DB_PORT); 78 | dbConfig.setDbUser(Constant.DEFAULT_DB_USER); 79 | dbConfig.setDbPasswd(Constant.DEFAULT_DB_PASSWD); 80 | dbConfig.setDbName(Constant.DEFAULT_DB_NAME); 81 | } 82 | 83 | public static void readDbConfig() { 84 | // Read Configure File 85 | CircView.log.info(Constant.CONFIG_FILE + " is loaded"); 86 | try { 87 | InputStream in = new FileInputStream(Constant.CONFIG_FILE); 88 | properties.load(in); 89 | dbConfig.setDbServer(properties.getProperty(Constant.CONFIG_DB_SERVER)); 90 | dbConfig.setDbPort(properties.getProperty(Constant.CONFIG_DB_PORT)); 91 | dbConfig.setDbUser(properties.getProperty(Constant.CONFIG_DB_USER)); 92 | dbConfig.setDbPasswd(properties.getProperty(Constant.CONFIG_DB_PASSWD)); 93 | dbConfig.setDbName(properties.getProperty(Constant.CONFIG_DB_NAME)); 94 | } catch (IOException e) { 95 | CircView.log.info(e.getMessage()); 96 | } 97 | } 98 | 99 | public static void writeDbConfig() { 100 | try { 101 | properties.setProperty(Constant.CONFIG_DB_SERVER, Constant.DEFAULT_DB_SERVER); 102 | properties.setProperty(Constant.CONFIG_DB_PORT, Constant.DEFAULT_DB_PORT); 103 | properties.setProperty(Constant.CONFIG_DB_USER, Constant.DEFAULT_DB_USER); 104 | properties.setProperty(Constant.CONFIG_DB_PASSWD, Constant.DEFAULT_DB_PASSWD); 105 | properties.setProperty(Constant.CONFIG_DB_NAME, Constant.DEFAULT_DB_NAME); 106 | // Write Config File 107 | OutputStream os = new FileOutputStream(Constant.CONFIG_FILE); 108 | properties.store(os, "Save Config File"); 109 | } catch (IOException e) { 110 | CircView.log.error(e.getMessage()); 111 | } 112 | } 113 | 114 | public static TreeMap> getSpeciesData() { 115 | return speciesData; 116 | } 117 | 118 | public static void setSpeciesData(TreeMap> speciesData) { 119 | MainData.speciesData = speciesData; 120 | } 121 | 122 | public static TreeMap getSpeciesFile() { 123 | return speciesFile; 124 | } 125 | 126 | public static void setSpeciesFile(TreeMap speciesFile) { 127 | MainData.speciesFile = speciesFile; 128 | } 129 | 130 | public static Vector getSpeciesNames() { 131 | return speciesNames; 132 | } 133 | 134 | public static void setSpeciesNames(Vector speciesNames) { 135 | MainData.speciesNames = speciesNames; 136 | } 137 | 138 | public static Vector getCircRnaToolNames() { 139 | return circRnaToolNames; 140 | } 141 | 142 | public static void setCircRnaToolNames(Vector circRnaToolNames) { 143 | MainData.circRnaToolNames = circRnaToolNames; 144 | } 145 | 146 | public static Vector> getCircRnaFilesInfo() { 147 | return circRnaFilesInfo; 148 | } 149 | 150 | public static void setCircRnaFilesInfo(Vector> circRnaFilesInfo) { 151 | MainData.circRnaFilesInfo = circRnaFilesInfo; 152 | } 153 | 154 | public static Properties getProperties() { 155 | return properties; 156 | } 157 | 158 | public static void setProperties(Properties properties) { 159 | MainData.properties = properties; 160 | } 161 | 162 | public static DbConfig getDbConfig() { 163 | return dbConfig; 164 | } 165 | 166 | public static void setDbConfig(DbConfig dbConfig) { 167 | MainData.dbConfig = dbConfig; 168 | } 169 | 170 | } 171 | -------------------------------------------------------------------------------- /src/cn/edu/whu/exception/FileReadException.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.exception; 2 | 3 | public class FileReadException extends Exception { 4 | 5 | private static final long serialVersionUID = 1L; 6 | 7 | public FileReadException(String message) { 8 | super(message); 9 | } 10 | } 11 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/AboutDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.Rectangle; 5 | import java.awt.event.ActionEvent; 6 | import java.awt.event.ActionListener; 7 | 8 | import javax.swing.Box; 9 | import javax.swing.JButton; 10 | import javax.swing.JDialog; 11 | import javax.swing.JLabel; 12 | import javax.swing.JPanel; 13 | import cn.edu.whu.CircView; 14 | import cn.edu.whu.util.Constant; 15 | 16 | public class AboutDialog extends JDialog { 17 | 18 | private static final long serialVersionUID = 1L; 19 | 20 | public AboutDialog() { 21 | super(CircView.frame); 22 | initUi(); 23 | setTitle("About CircView"); 24 | // setResizable(false); 25 | setSize(250, 150); 26 | centerScreen(); 27 | } 28 | 29 | private void centerScreen() { 30 | Dimension dim = getToolkit().getScreenSize(); 31 | Rectangle abounds = getBounds(); 32 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 33 | super.setVisible(true); 34 | requestFocus(); 35 | } 36 | 37 | private void initUi() { 38 | Box b = Box.createVerticalBox(); 39 | b.add(Box.createGlue()); 40 | b.add(new JLabel(Constant.ABOUT)); 41 | b.add(new JLabel(Constant.VERSION)); 42 | b.add(new JLabel(Constant.AUTHOR)); 43 | b.add(Box.createGlue()); 44 | getContentPane().add(b, "Center"); 45 | 46 | JPanel p = new JPanel(); 47 | JButton btClose = new JButton("Close"); 48 | p.add(btClose); 49 | getContentPane().add(p, "South"); 50 | 51 | btClose.addActionListener(new ActionListener() { 52 | public void actionPerformed(ActionEvent e) { 53 | AboutDialog.this.dispose(); 54 | } 55 | }); 56 | } 57 | } 58 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/CircRnaDataClearDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.util.Vector; 9 | 10 | import javax.swing.JButton; 11 | import javax.swing.JComboBox; 12 | import javax.swing.JDialog; 13 | import cn.edu.whu.MainData; 14 | import cn.edu.whu.CircView; 15 | 16 | public class CircRnaDataClearDialog extends JDialog { 17 | 18 | private static final long serialVersionUID = 1L; 19 | 20 | public CircRnaDataClearDialog() { 21 | super(CircView.frame); 22 | initUi(); 23 | setTitle("Clear CircRNA Data for:"); 24 | setResizable(false); 25 | setSize(300, 65); 26 | this.setLayout(new FlowLayout()); 27 | centerScreen(); 28 | } 29 | 30 | private void centerScreen() { 31 | Dimension dim = getToolkit().getScreenSize(); 32 | Rectangle abounds = getBounds(); 33 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 34 | super.setVisible(true); 35 | requestFocus(); 36 | } 37 | 38 | private void initUi() { 39 | // ComboBox 40 | final JComboBox cbSpecies = new JComboBox(); 41 | final JButton btClear = new JButton("Clear"); 42 | 43 | cbSpecies.setPreferredSize(new Dimension(160, 28)); 44 | for (String speciesName : MainData.getSpeciesData().keySet()) { 45 | cbSpecies.addItem(speciesName); 46 | } 47 | 48 | getContentPane().add(cbSpecies); 49 | getContentPane().add(btClear); 50 | 51 | // Button 52 | btClear.addActionListener(new ActionListener() { 53 | public void actionPerformed(ActionEvent e) { 54 | if (null == cbSpecies.getSelectedItem()) { 55 | return; 56 | } 57 | String delSpecies = cbSpecies.getSelectedItem().toString(); 58 | // Delete Species Data 59 | if (null != MainData.getSpeciesData().get(delSpecies)) { 60 | MainData.getSpeciesData().remove(delSpecies); 61 | } 62 | CircView.log.error("CircRNA Data for " + delSpecies + " is CLEARED"); 63 | // Delete CircRNA File Info for this Species 64 | for (int i = MainData.getCircRnaFilesInfo().size() - 1; i >= 0; i--) { 65 | Vector rowData = MainData.getCircRnaFilesInfo().get(i); 66 | String sname = rowData.get(0); 67 | if (delSpecies.equalsIgnoreCase(sname)) { 68 | MainData.getCircRnaFilesInfo().remove(i); 69 | } 70 | } 71 | CircView.log.error("CircRNA files for " + delSpecies + " is DELETED"); 72 | 73 | CircView.updateSpeciesCombo(); 74 | CircView.updateCircRnaToolsCombo(); 75 | CircView.updateSamplesCombo(); 76 | CircView.updateCbChrom(); 77 | CircView.updateGeneTransList(); 78 | CircRnaDataClearDialog.this.dispose(); 79 | } 80 | 81 | }); 82 | } 83 | } 84 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/CircRnaDataLoadDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.BorderLayout; 4 | import java.awt.Dimension; 5 | import java.awt.FlowLayout; 6 | import java.awt.Rectangle; 7 | import java.awt.event.ActionEvent; 8 | import java.awt.event.ActionListener; 9 | import java.io.File; 10 | import java.util.TreeMap; 11 | import java.util.Vector; 12 | 13 | import javax.swing.JButton; 14 | import javax.swing.JComboBox; 15 | import javax.swing.JDialog; 16 | import javax.swing.JFileChooser; 17 | import javax.swing.JOptionPane; 18 | import javax.swing.JPanel; 19 | import javax.swing.JScrollPane; 20 | import javax.swing.JTable; 21 | import javax.swing.table.DefaultTableModel; 22 | 23 | import cn.edu.whu.CircRnaTool; 24 | import cn.edu.whu.CircView; 25 | import cn.edu.whu.Gene; 26 | import cn.edu.whu.MainData; 27 | import cn.edu.whu.exception.FileReadException; 28 | 29 | public class CircRnaDataLoadDialog extends JDialog { 30 | private static final long serialVersionUID = 1L; 31 | 32 | private JTable table; 33 | private Vector> tableData; 34 | private JComboBox cbSpecies; 35 | private JComboBox cbCircRnaTool; 36 | 37 | public CircRnaDataLoadDialog() { 38 | super(CircView.frame); 39 | setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); 40 | setLayout(new BorderLayout()); 41 | initUi(); 42 | setTitle("Load CircRNA files"); 43 | setResizable(false); 44 | setSize(600, 400); 45 | centerScreen(); 46 | } 47 | 48 | private void centerScreen() { 49 | Dimension dim = getToolkit().getScreenSize(); 50 | Rectangle abounds = getBounds(); 51 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 52 | super.setVisible(true); 53 | requestFocus(); 54 | } 55 | 56 | private void initUi() { 57 | // North 58 | JPanel jpNorth = new JPanel(new FlowLayout()); 59 | cbSpecies = new JComboBox(); 60 | cbCircRnaTool = new JComboBox(); 61 | JButton btAdd = new JButton("Add Files"); 62 | cbSpecies.setPreferredSize(new Dimension(200, 28)); 63 | cbCircRnaTool.setPreferredSize(new Dimension(200, 28)); 64 | jpNorth.add(cbSpecies); 65 | jpNorth.add(cbCircRnaTool); 66 | jpNorth.add(btAdd); 67 | getContentPane().add(jpNorth, BorderLayout.NORTH); 68 | 69 | for (String speciesName : MainData.getSpeciesNames()) { 70 | cbSpecies.addItem(speciesName); 71 | } 72 | for (String circRnaToolName : MainData.getCircRnaToolNames()) { 73 | cbCircRnaTool.addItem(circRnaToolName); 74 | } 75 | 76 | // Center 77 | final Vector colName = new Vector(); 78 | colName.addElement("Species"); 79 | colName.addElement("CircRNA Tool"); 80 | colName.addElement("File Name"); 81 | colName.addElement("File Path"); 82 | tableData = new Vector>(); 83 | final DefaultTableModel model = new DefaultTableModel(); 84 | table = new JTable(model); 85 | model.setDataVector(tableData, colName); 86 | JScrollPane jsPane = new JScrollPane(table); 87 | getContentPane().add(jsPane, BorderLayout.CENTER); 88 | 89 | // South 90 | JPanel jpSouth = new JPanel(new FlowLayout()); 91 | JButton btOpen = new JButton("Open"); 92 | JButton btClear = new JButton("Clear"); 93 | jpSouth.add(btOpen); 94 | jpSouth.add(btClear); 95 | getContentPane().add(jpSouth, BorderLayout.SOUTH); 96 | 97 | btAdd.addActionListener(new ActionListener() { 98 | public void actionPerformed(ActionEvent e) { 99 | if(null == cbSpecies.getSelectedItem()) { 100 | JOptionPane.showMessageDialog(CircView.frame, "Species Name is needed"); 101 | return; 102 | } 103 | if(null == cbCircRnaTool.getSelectedItem()) { 104 | JOptionPane.showMessageDialog(CircView.frame, "Tool Name is needed"); 105 | return; 106 | } 107 | String speciesName = cbSpecies.getSelectedItem().toString(); 108 | String circRnaToolName = cbCircRnaTool.getSelectedItem().toString(); 109 | String pattern = "\\s+"; 110 | if (speciesName.matches(pattern)) { 111 | JOptionPane.showMessageDialog(CircView.frame, "Species Name is needed"); 112 | return; 113 | } 114 | if (circRnaToolName.matches(pattern)) { 115 | JOptionPane.showMessageDialog(CircView.frame, "Tool Name is needed"); 116 | return; 117 | } 118 | 119 | OpenFileChooser openFile = new OpenFileChooser("Open CircRNA Files"); 120 | openFile.setMultiSelectionEnabled(true); 121 | openFile.setFileSelectionMode(JFileChooser.FILES_ONLY); 122 | openFile.setFileHidingEnabled(true); 123 | int returnValue = openFile.showOpenDialog(null); 124 | if (returnValue == JFileChooser.APPROVE_OPTION) { 125 | File[] files = null; 126 | files = openFile.getSelectedFiles(); 127 | for (File file : files) { 128 | Vector rowData = new Vector(); 129 | rowData.addElement(speciesName); 130 | rowData.addElement(circRnaToolName); 131 | rowData.addElement(file.getName()); 132 | rowData.addElement(file.getPath()); 133 | tableData.addElement(rowData); 134 | model.setDataVector(tableData, colName); 135 | } 136 | } 137 | } 138 | }); 139 | 140 | btClear.addActionListener(new ActionListener() { 141 | public void actionPerformed(ActionEvent e) { 142 | tableData.removeAllElements(); 143 | model.setDataVector(tableData, colName); 144 | } 145 | }); 146 | 147 | btOpen.addActionListener(new ActionListener() { 148 | public void actionPerformed(ActionEvent e) { 149 | DataLoadingDialog dataLoadingDialog = new DataLoadingDialog(CircView.frame, "Loading CircRNA Data ..."); 150 | setVisible(false); 151 | TreeMap uniqSpecies = new TreeMap(); 152 | for (Vector rowData : tableData) { 153 | String speciesName = rowData.get(0); 154 | uniqSpecies.put(speciesName, speciesName); 155 | } 156 | boolean hasSpecies = true; 157 | for (String speciesName : uniqSpecies.keySet()) { 158 | if (null == MainData.getSpeciesData().get(speciesName)) { 159 | // Load Species Data 160 | TreeMap genes = new TreeMap(); 161 | File speciesFile = new File(MainData.getSpeciesFile().get(speciesName)); 162 | if (CircRnaTool.initSpeciesDataFromFile(speciesFile, genes)) { 163 | MainData.getSpeciesData().put(speciesName, genes); 164 | CircView.log.info(speciesName + " Data Loaded"); 165 | } else { 166 | hasSpecies = false; 167 | JOptionPane.showMessageDialog(CircView.frame, 168 | "[" + speciesFile.getPath() + "] does NOT EXIST or file FORMAT ERROR!"); 169 | CircView.log.error("[" + speciesFile.getPath() + "] does NOT EXIST or file FORMAT ERROR!"); 170 | dataLoadingDialog.setVisible(false); 171 | CircRnaDataLoadDialog.this.dispose(); 172 | } 173 | } 174 | } 175 | if (hasSpecies) { 176 | for (String speciesName : uniqSpecies.keySet()) { 177 | TreeMap genes = MainData.getSpeciesData().get(speciesName); 178 | try { 179 | // Load CircRNA Data 180 | CircRnaTool.initCircRnaDataFromFiles(tableData, speciesName, genes); 181 | // Save CircRNA File Info 182 | for (Vector rowData : tableData) { 183 | String sname = rowData.get(0); 184 | if (sname.equalsIgnoreCase(speciesName)) { 185 | MainData.getCircRnaFilesInfo().add(rowData); 186 | } 187 | } 188 | // Update UI 189 | CircView.updateSpeciesCombo(); 190 | CircView.updateCircRnaToolsCombo(); 191 | CircView.updateSamplesCombo(); 192 | CircView.updateCbChrom(); 193 | CircView.updateGeneTransList(); 194 | } catch (FileReadException e1) { 195 | JOptionPane.showMessageDialog(CircView.frame, e1.getMessage()); 196 | CircView.log.error(e1.getMessage()); 197 | dataLoadingDialog.setVisible(false); 198 | CircRnaDataLoadDialog.this.dispose(); 199 | } 200 | 201 | } 202 | } 203 | dataLoadingDialog.setVisible(false); 204 | CircRnaDataLoadDialog.this.dispose(); 205 | } 206 | }); 207 | } 208 | } 209 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/CircRnaToolAddDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import javax.swing.JButton; 9 | import javax.swing.JComboBox; 10 | import javax.swing.JDialog; 11 | import javax.swing.JLabel; 12 | import javax.swing.JOptionPane; 13 | import javax.swing.JTextField; 14 | 15 | import com.mysql.jdbc.StringUtils; 16 | 17 | import cn.edu.whu.MainData; 18 | import cn.edu.whu.CircView; 19 | 20 | public class CircRnaToolAddDialog extends JDialog { 21 | 22 | private static final long serialVersionUID = 1L; 23 | 24 | public CircRnaToolAddDialog() { 25 | super(CircView.frame); 26 | initUi(); 27 | setTitle("Add CircRNA Tools Name"); 28 | setResizable(false); 29 | setSize(400, 65); 30 | this.setLayout(new FlowLayout()); 31 | centerScreen(); 32 | } 33 | 34 | private void centerScreen() { 35 | Dimension dim = getToolkit().getScreenSize(); 36 | Rectangle abounds = getBounds(); 37 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 38 | super.setVisible(true); 39 | requestFocus(); 40 | } 41 | 42 | private void initUi() { 43 | // ComboBox 44 | final JTextField tfTools = new JTextField(); 45 | final JLabel lbAdd = new JLabel("->"); 46 | final JComboBox cbTools = new JComboBox(); 47 | final JButton btAdd = new JButton("Add"); 48 | 49 | cbTools.setPreferredSize(new Dimension(150, 28)); 50 | for (String toolName : MainData.getCircRnaToolNames()) { 51 | cbTools.addItem(toolName); 52 | } 53 | tfTools.setPreferredSize(new Dimension(120, 28)); 54 | 55 | getContentPane().add(tfTools); 56 | getContentPane().add(lbAdd); 57 | getContentPane().add(cbTools); 58 | getContentPane().add(btAdd); 59 | 60 | // Button 61 | btAdd.addActionListener(new ActionListener() { 62 | public void actionPerformed(ActionEvent e) { 63 | String newTool = tfTools.getText(); 64 | if (StringUtils.isEmptyOrWhitespaceOnly(newTool)) { 65 | JOptionPane.showMessageDialog(CircRnaToolAddDialog.this, "CircRNA Tool Name is Needed", "warning", 66 | JOptionPane.ERROR_MESSAGE); 67 | return; 68 | } 69 | boolean existed = false; 70 | for (String oldTool : MainData.getCircRnaToolNames()) { 71 | if (newTool.equals(oldTool)) { 72 | existed = true; 73 | } 74 | } 75 | if (existed) { 76 | // Species Name already exists 77 | JOptionPane.showMessageDialog(CircRnaToolAddDialog.this, "CircRNA Tools already exsits", "warning", 78 | JOptionPane.ERROR_MESSAGE); 79 | } else { 80 | MainData.getCircRnaToolNames().add(newTool); 81 | cbTools.addItem(newTool); 82 | tfTools.setText(""); 83 | MainData.writeDbConfig(); 84 | CircView.log.info("New CircRnaTool [" + newTool + "] Added."); 85 | } 86 | } 87 | }); 88 | } 89 | } 90 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/CircRnaToolDelDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import javax.swing.JButton; 9 | import javax.swing.JComboBox; 10 | import javax.swing.JDialog; 11 | import cn.edu.whu.MainData; 12 | import cn.edu.whu.CircView; 13 | 14 | public class CircRnaToolDelDialog extends JDialog { 15 | 16 | private static final long serialVersionUID = 1L; 17 | 18 | public CircRnaToolDelDialog() { 19 | super(); 20 | initUi(); 21 | setTitle("Del CircRNA Tools Name"); 22 | setResizable(false); 23 | setSize(300, 65); 24 | this.setLayout(new FlowLayout()); 25 | centerScreen(); 26 | } 27 | 28 | private void centerScreen() { 29 | Dimension dim = getToolkit().getScreenSize(); 30 | Rectangle abounds = getBounds(); 31 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 32 | super.setVisible(true); 33 | requestFocus(); 34 | } 35 | 36 | private void initUi() { 37 | // ComboBox 38 | final JComboBox cbTools = new JComboBox(); 39 | final JButton btDel = new JButton("Delete"); 40 | 41 | cbTools.setPreferredSize(new Dimension(150, 28)); 42 | for (String toolName : MainData.getCircRnaToolNames()) { 43 | cbTools.addItem(toolName); 44 | } 45 | getContentPane().add(cbTools); 46 | getContentPane().add(btDel); 47 | 48 | // Button 49 | btDel.addActionListener(new ActionListener() { 50 | public void actionPerformed(ActionEvent e) { 51 | if (null != cbTools.getSelectedItem()) { 52 | String delTool = cbTools.getSelectedItem().toString(); 53 | int index = cbTools.getSelectedIndex(); 54 | cbTools.removeItemAt(index); 55 | MainData.getCircRnaToolNames().remove(delTool); 56 | MainData.writeDbConfig(); 57 | CircView.log.info("CircRna Tool [" + delTool + "] Deleted."); 58 | CircRnaToolDelDialog.this.dispose(); 59 | } 60 | } 61 | }); 62 | } 63 | } 64 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/ComparisonFrame.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.BorderLayout; 4 | import java.awt.Dimension; 5 | import java.awt.Rectangle; 6 | import java.awt.Toolkit; 7 | import java.awt.event.ActionEvent; 8 | import java.awt.event.ActionListener; 9 | import java.awt.event.ItemEvent; 10 | import java.awt.event.ItemListener; 11 | import java.awt.event.MouseAdapter; 12 | import java.awt.event.MouseEvent; 13 | import java.awt.event.MouseListener; 14 | import java.io.BufferedWriter; 15 | import java.io.File; 16 | import java.io.FileWriter; 17 | import java.io.IOException; 18 | import java.util.TreeMap; 19 | import java.util.Vector; 20 | 21 | import javax.swing.BoxLayout; 22 | import javax.swing.JButton; 23 | import javax.swing.JComboBox; 24 | import javax.swing.JDialog; 25 | import javax.swing.JFileChooser; 26 | import javax.swing.JFrame; 27 | import javax.swing.JLabel; 28 | import javax.swing.JList; 29 | import javax.swing.JOptionPane; 30 | import javax.swing.JPanel; 31 | import javax.swing.JScrollPane; 32 | import javax.swing.JTable; 33 | import javax.swing.ListSelectionModel; 34 | import javax.swing.table.DefaultTableModel; 35 | 36 | import cn.edu.whu.CircRna; 37 | import cn.edu.whu.CircView; 38 | import cn.edu.whu.Gene; 39 | import cn.edu.whu.GeneTranscript; 40 | import cn.edu.whu.MainData; 41 | import cn.edu.whu.util.Constant; 42 | import cn.edu.whu.util.EvenOddRenderer; 43 | 44 | public class ComparisonFrame extends JFrame { 45 | private static final long serialVersionUID = 1L; 46 | private JComboBox cbSpecies; 47 | private JComboBox cbTolerate; 48 | private JList jlUnSelected; 49 | private JList jlSelected; 50 | private Vector unSelected; 51 | private Vector selected; 52 | private JScrollPane scrollUnSelected; 53 | private JScrollPane scrollSelected; 54 | private DefaultTableModel model; 55 | private JTable tbResult; 56 | private Vector colName; 57 | private Vector> tableData; 58 | Dimension screenSize; 59 | 60 | public ComparisonFrame() { 61 | super(); 62 | setExtendedState(JFrame.MAXIMIZED_BOTH); 63 | setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); 64 | setLayout(new BorderLayout()); 65 | setResizable(true); 66 | setTitle("Comparison Setting"); 67 | 68 | screenSize = Toolkit.getDefaultToolkit().getScreenSize(); 69 | setBounds(0, 100, (int) screenSize.getWidth(), (int) screenSize.getHeight() - 100); 70 | centerScreen(); 71 | initUi(); 72 | } 73 | 74 | private void centerScreen() { 75 | Dimension dim = getToolkit().getScreenSize(); 76 | Rectangle abounds = getBounds(); 77 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 78 | super.setVisible(true); 79 | requestFocus(); 80 | } 81 | 82 | private void initUi() { 83 | JPanel northPanel = new JPanel(); 84 | northPanel.setLayout(new BorderLayout()); 85 | JPanel jpWest = new JPanel(); 86 | jpWest.setLayout(new BoxLayout(jpWest, BoxLayout.Y_AXIS)); 87 | cbSpecies = new JComboBox(); 88 | cbSpecies.setPreferredSize(new Dimension(200, 28)); 89 | JPanel jpTmp = new JPanel(); 90 | JLabel lbTolerate = new JLabel("Compare Overlap"); 91 | cbTolerate = new JComboBox(); 92 | cbTolerate.setPreferredSize(new Dimension(80, 28)); 93 | // cbTolerate.setEditable(true); 94 | JLabel lbBp = new JLabel("bp"); 95 | jpTmp.add(lbTolerate); 96 | jpTmp.add(cbTolerate); 97 | jpTmp.add(lbBp); 98 | jpWest.add(new JLabel(" ")); 99 | jpWest.add(cbSpecies); 100 | jpWest.add(jpTmp); 101 | northPanel.add(jpWest, BorderLayout.WEST); 102 | 103 | JPanel jpCenter = new JPanel(); 104 | jpCenter.setLayout(new BoxLayout(jpCenter, BoxLayout.X_AXIS)); 105 | final JLabel lbUnSelected = new JLabel("Sample List"); 106 | final JLabel lbSelected = new JLabel("Sample selected"); 107 | jlUnSelected = new JList(); 108 | jlSelected = new JList(); 109 | unSelected = new Vector(); 110 | selected = new Vector(); 111 | jlUnSelected.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); 112 | jlSelected.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION); 113 | scrollUnSelected = new JScrollPane(jlUnSelected); 114 | scrollSelected = new JScrollPane(jlSelected); 115 | scrollUnSelected.setPreferredSize(new Dimension((int) jpCenter.getWidth() / 2, 100)); 116 | scrollSelected.setPreferredSize(new Dimension((int) jpCenter.getWidth() / 2, 100)); 117 | JPanel jpLeft = new JPanel(); 118 | JPanel jpRight = new JPanel(); 119 | jpLeft.setLayout(new BoxLayout(jpLeft, BoxLayout.Y_AXIS)); 120 | jpRight.setLayout(new BoxLayout(jpRight, BoxLayout.Y_AXIS)); 121 | jpLeft.add(lbUnSelected); 122 | jpLeft.add(scrollUnSelected); 123 | jpRight.add(lbSelected); 124 | jpRight.add(scrollSelected); 125 | jpCenter.add(jpLeft); 126 | jpCenter.add(jpRight); 127 | northPanel.add(jpCenter, BorderLayout.CENTER); 128 | 129 | final JButton btCompare = new JButton("Compare"); 130 | JButton btReset = new JButton("Reset"); 131 | JButton btSave = new JButton("Save as"); 132 | JPanel jpEast = new JPanel(); 133 | jpEast.setLayout(new BoxLayout(jpEast, BoxLayout.Y_AXIS)); 134 | jpEast.add(new JLabel(" ")); 135 | jpEast.add(btCompare); 136 | jpEast.add(btReset); 137 | jpEast.add(btSave); 138 | northPanel.add(jpEast, BorderLayout.EAST); 139 | getContentPane().add(northPanel, BorderLayout.NORTH); 140 | 141 | model = new DefaultTableModel(); 142 | tbResult = new JTable(model); 143 | colName = new Vector(); 144 | tableData = new Vector>(); 145 | JScrollPane jsResult = new JScrollPane(tbResult); 146 | tbResult.setDefaultRenderer(Object.class, new EvenOddRenderer()); 147 | tbResult.setAutoCreateRowSorter(true); 148 | tbResult.setAutoscrolls(true); 149 | tbResult.setEnabled(false); 150 | getContentPane().add(jsResult, BorderLayout.CENTER); 151 | 152 | colName.addElement("No."); 153 | colName.addElement("gene name"); 154 | colName.addElement("circRNA ID"); 155 | colName.addElement("chromosome"); 156 | colName.addElement("donor site"); 157 | colName.addElement("acceptor site"); 158 | colName.addElement("junction reads"); 159 | colName.addElement("strand"); 160 | colName.addElement("tissue name"); 161 | colName.addElement("tissue num"); 162 | colName.addElement("sample name"); 163 | colName.addElement("sample num"); 164 | colName.addElement("tool name"); 165 | colName.addElement("tool num"); 166 | colName.addElement("circRNA type"); 167 | colName.addElement("circRNA region"); 168 | 169 | cbSpecies.addItemListener(new ItemListener() { 170 | public void itemStateChanged(ItemEvent e) { 171 | if (e.getStateChange() == ItemEvent.SELECTED) { 172 | unSelected.removeAllElements(); 173 | selected.removeAllElements(); 174 | if(null == cbSpecies.getSelectedItem()) { 175 | return; 176 | } 177 | String species = cbSpecies.getSelectedItem().toString(); 178 | TreeMap tools = new TreeMap(); 179 | for(Vector rowData : MainData.getCircRnaFilesInfo()) { 180 | String sname = rowData.get(0); 181 | String fname = rowData.get(2); 182 | if(species.equalsIgnoreCase(sname)) { 183 | tools.put(fname, fname); 184 | } 185 | } 186 | for(String tool : tools.keySet()) { 187 | unSelected.add(tool); 188 | } 189 | 190 | jlUnSelected.setListData(unSelected); 191 | jlSelected.setListData(selected); 192 | } 193 | } 194 | }); 195 | 196 | jlUnSelected.addMouseListener(new MouseListener() { 197 | public void mouseClicked(MouseEvent e) { 198 | JList theList = (JList) e.getSource(); 199 | int index = theList.locationToIndex(e.getPoint()); 200 | if (index >= 0) { 201 | String slct = theList.getModel().getElementAt(index); 202 | for (String name : unSelected) { 203 | if (name.equalsIgnoreCase(slct)) { 204 | unSelected.remove(name); 205 | break; 206 | } 207 | } 208 | selected.addElement(slct); 209 | jlUnSelected.removeAll(); 210 | jlSelected.removeAll(); 211 | jlUnSelected.setListData(unSelected); 212 | jlSelected.setListData(selected); 213 | } 214 | } 215 | 216 | public void mousePressed(MouseEvent e) { 217 | } 218 | 219 | public void mouseReleased(MouseEvent e) { 220 | } 221 | 222 | public void mouseEntered(MouseEvent e) { 223 | } 224 | 225 | public void mouseExited(MouseEvent e) { 226 | } 227 | }); 228 | 229 | jlSelected.addMouseListener(new MouseListener() { 230 | public void mouseClicked(MouseEvent e) { 231 | JList theList = (JList) e.getSource(); 232 | int index = theList.locationToIndex(e.getPoint()); 233 | if (index >= 0) { 234 | String slct = theList.getModel().getElementAt(index); 235 | for (String name : selected) { 236 | if (name.equalsIgnoreCase(slct)) { 237 | selected.remove(name); 238 | break; 239 | } 240 | } 241 | unSelected.addElement(slct); 242 | jlUnSelected.removeAll(); 243 | jlSelected.removeAll(); 244 | jlUnSelected.setListData(unSelected); 245 | jlSelected.setListData(selected); 246 | } 247 | } 248 | 249 | public void mousePressed(MouseEvent e) { 250 | } 251 | 252 | public void mouseReleased(MouseEvent e) { 253 | } 254 | 255 | public void mouseEntered(MouseEvent e) { 256 | } 257 | 258 | public void mouseExited(MouseEvent e) { 259 | } 260 | }); 261 | 262 | btCompare.addActionListener(new ActionListener() { 263 | public void actionPerformed(ActionEvent e) { 264 | String species = (String) cbSpecies.getSelectedItem(); 265 | if (null == species || species.equals("")) { 266 | return; 267 | } 268 | fillTable(); 269 | } 270 | }); 271 | 272 | btReset.addActionListener(new ActionListener() { 273 | public void actionPerformed(ActionEvent e) { 274 | unSelected.removeAllElements(); 275 | selected.removeAllElements(); 276 | jlUnSelected.setListData(unSelected); 277 | jlSelected.setListData(selected); 278 | tableData.removeAllElements(); 279 | model.setDataVector(tableData, colName); 280 | } 281 | }); 282 | 283 | btSave.addActionListener(new ActionListener() { 284 | public void actionPerformed(ActionEvent e) { 285 | CsvSaveFileChooser saveFile = new CsvSaveFileChooser("Save as ..."); 286 | saveFile.setFileSelectionMode(JFileChooser.FILES_ONLY); 287 | saveFile.setMultiSelectionEnabled(false); 288 | int returnValue = saveFile.showSaveDialog(null); 289 | if (returnValue == JFileChooser.APPROVE_OPTION) { 290 | File fileOut = saveFile.getSelectedFile(); 291 | String type = "csv"; 292 | String fileName = fileOut.getAbsolutePath() + "." + type; 293 | try { 294 | BufferedWriter out = new BufferedWriter(new FileWriter(fileName)); 295 | for (int i = 0; i < tbResult.getColumnCount(); i++) { 296 | out.write(tbResult.getColumnName(i) + "\t"); 297 | } 298 | out.newLine(); 299 | for (int i = 0; i < tbResult.getRowCount(); i++) { 300 | for (int j = 0; j < tbResult.getColumnCount(); j++) { 301 | out.write(tbResult.getValueAt(i, j).toString() + "\t"); 302 | } 303 | out.newLine(); 304 | } 305 | out.close(); 306 | JOptionPane.showMessageDialog(null, "Export Data Successfully!"); 307 | } catch (IOException e1) { 308 | CircView.log.warn(e1.getMessage()); 309 | } 310 | } 311 | } 312 | }); 313 | 314 | tbResult.addMouseMotionListener(new MouseAdapter() { 315 | public void mouseMoved(MouseEvent e) { 316 | int row = tbResult.rowAtPoint(e.getPoint()); 317 | int col = tbResult.columnAtPoint(e.getPoint()); 318 | if (row >= 0 && col >= 0) { 319 | Object value = tbResult.getValueAt(row, col); 320 | if (null != value && !value.equals("")) { 321 | tbResult.setToolTipText(value.toString()); 322 | } else { 323 | tbResult.setToolTipText(null); 324 | } 325 | } 326 | } 327 | }); 328 | 329 | for (String speciesName : MainData.getSpeciesData().keySet()) { 330 | cbSpecies.addItem(speciesName); 331 | } 332 | for (int i = 0; i <= Constant.BP_MATCH_TOLERATE; i++) { 333 | cbTolerate.addItem(i + ""); 334 | } 335 | 336 | } 337 | 338 | private void fillTable() { 339 | tableData.removeAllElements(); 340 | if (selected.size() > 0) { 341 | fillTableOr(); 342 | } 343 | model.setDataVector(tableData, colName); 344 | } 345 | 346 | private void fillTableOr() { 347 | int tolerate = Integer.parseInt((String) cbTolerate.getSelectedItem()); 348 | int num = 0; 349 | String species = (String) cbSpecies.getSelectedItem(); 350 | if ((null == species) || (species.equals(""))) { 351 | return; 352 | } 353 | TreeMap genes = MainData.getSpeciesData().get(species); 354 | for (String geneName : genes.keySet()) { 355 | Gene gene = genes.get(geneName); 356 | TreeMap geneTrans = gene.getGeneTranscripts(); 357 | for (String geneTransName : geneTrans.keySet()) { 358 | GeneTranscript gt = geneTrans.get(geneTransName); 359 | TreeMap circRnas = gt.getCircRnas(); 360 | Vector circIds = new Vector(); 361 | for (String circId : circRnas.keySet()) { 362 | circIds.addElement(circId); 363 | } 364 | TreeMap> matched = new TreeMap>(); 365 | TreeMap deleted = new TreeMap(); 366 | for (int i = 0; i < circIds.size() - 1; i++) { 367 | for (int j = i + 1; j < circIds.size(); j++) { 368 | if ((null != deleted.get(i)) || (null != deleted.get(j))) { 369 | continue; 370 | } 371 | CircRna majorCirc = circRnas.get(circIds.get(i)); 372 | CircRna minorCirc = circRnas.get(circIds.get(j)); 373 | if ((Math.abs(majorCirc.getStartPoint() - minorCirc.getStartPoint()) <= tolerate) 374 | && (Math.abs(majorCirc.getEndPoint() - minorCirc.getEndPoint()) <= tolerate)) { 375 | if (null != matched.get(majorCirc.getCircRnaID())) { 376 | Vector sameCircs = matched.get(majorCirc.getCircRnaID()); 377 | sameCircs.addElement(minorCirc.getCircRnaID()); 378 | matched.put(majorCirc.getCircRnaID(), sameCircs); 379 | deleted.put(j, minorCirc.getCircRnaID()); 380 | } else { 381 | Vector sameCircs = new Vector(); 382 | sameCircs.addElement(minorCirc.getCircRnaID()); 383 | matched.put(majorCirc.getCircRnaID(), sameCircs); 384 | deleted.put(j, minorCirc.getCircRnaID()); 385 | } 386 | } 387 | } 388 | } 389 | 390 | for (int i = 0; i < circIds.size(); i++) { 391 | if (null != deleted.get(i)) { 392 | continue; 393 | } 394 | String circId = circIds.get(i); 395 | // tissues name, smaples name, tools name from circRNA info 396 | TreeMap files = new TreeMap(); 397 | TreeMap tissues = new TreeMap(); 398 | TreeMap samples = new TreeMap(); 399 | TreeMap tools = new TreeMap(); 400 | for (String fileName : gt.getCircRnas().get(circId).getFiles().keySet()) { 401 | files.put(fileName, 1); 402 | } 403 | for (String sampleName : gt.getCircRnas().get(circId).getSamples().keySet()) { 404 | samples.put(sampleName, 1); 405 | } 406 | for (String toolName : gt.getCircRnas().get(circId).getCircTools().keySet()) { 407 | tools.put(toolName, 1); 408 | } 409 | Vector sameCircs = matched.get(circId); 410 | if (null != sameCircs) { 411 | for (String sameCircId : sameCircs) { 412 | for (String fileName : gt.getCircRnas().get(sameCircId).getFiles().keySet()) { 413 | files.put(fileName, 1); 414 | } 415 | for (String sampleName : gt.getCircRnas().get(sameCircId).getSamples().keySet()) { 416 | samples.put(sampleName, 1); 417 | } 418 | for (String toolName : gt.getCircRnas().get(sameCircId).getCircTools().keySet()) { 419 | tools.put(toolName, 1); 420 | } 421 | } 422 | } 423 | for (String sampleName : samples.keySet()) { 424 | String[] tmp = sampleName.split("_"); 425 | tissues.put(tmp[0], 1); 426 | } 427 | 428 | // tissues name, smaples name, tools name from file table 429 | TreeMap fTissues = new TreeMap(); 430 | TreeMap fSamples = new TreeMap(); 431 | TreeMap fTools = new TreeMap(); 432 | for (String name : selected) { 433 | for (Vector rowData : MainData.getCircRnaFilesInfo()) { 434 | String sname = rowData.get(0); 435 | String tname = rowData.get(1); 436 | String fname = rowData.get(2); 437 | if(species.equalsIgnoreCase(sname) && fname.equalsIgnoreCase(name)) { 438 | String[] tmp = fname.split("_"); 439 | fTissues.put(tmp[0], 1); 440 | tmp = fname.split("\\."); 441 | fSamples.put(tmp[0], 1); 442 | fTools.put(tname, 1); 443 | } 444 | } 445 | } 446 | 447 | boolean hasFile = false; 448 | for (String name : files.keySet()) { 449 | for (String file : selected) { 450 | if (file.equalsIgnoreCase(name)) { 451 | hasFile = true; 452 | break; 453 | } 454 | } 455 | if (hasFile) { 456 | break; 457 | } 458 | } 459 | if (!hasFile) { 460 | continue; 461 | } 462 | 463 | num++; 464 | Vector one = new Vector(); 465 | // Number 466 | one.addElement(num + ""); 467 | // Gene Name 468 | one.addElement(gene.getGeneName()); 469 | // CircRNA ID 470 | String id = circId; 471 | if (null != sameCircs) { 472 | for (int j = 0; j < sameCircs.size(); j++) { 473 | if (0 == j) { 474 | id += "("; 475 | } 476 | id += sameCircs.get(j) + ","; 477 | if ((sameCircs.size() - 1) == j) { 478 | id += ")"; 479 | } 480 | } 481 | } 482 | one.addElement(id); 483 | one.addElement(gt.getCircRnas().get(circId).getChrom()); 484 | // Start Point 485 | String startP = gt.getCircRnas().get(circId).getStartPoint() + ""; 486 | if (null != sameCircs) { 487 | for (int j = 0; j < sameCircs.size(); j++) { 488 | if (0 == j) { 489 | startP += "("; 490 | } 491 | startP += gt.getCircRnas().get(sameCircs.get(j)).getStartPoint() + ","; 492 | if ((sameCircs.size() - 1) == j) { 493 | startP += ")"; 494 | } 495 | } 496 | } 497 | one.addElement(startP); 498 | // End Point 499 | String endP = gt.getCircRnas().get(circId).getEndPoint() + ""; 500 | if (null != sameCircs) { 501 | for (int j = 0; j < sameCircs.size(); j++) { 502 | if (0 == j) { 503 | endP += "("; 504 | } 505 | endP += gt.getCircRnas().get(sameCircs.get(j)).getEndPoint() + ","; 506 | if ((sameCircs.size() - 1) == j) { 507 | endP += ")"; 508 | } 509 | } 510 | } 511 | one.addElement(endP); 512 | // Junction Reads 513 | String reads = gt.getCircRnas().get(circId).getJunctionReads() + ""; 514 | if (null != sameCircs) { 515 | for (int j = 0; j < sameCircs.size(); j++) { 516 | if (0 == j) { 517 | reads += "("; 518 | } 519 | reads += gt.getCircRnas().get(sameCircs.get(j)).getJunctionReads() + ","; 520 | if ((sameCircs.size() - 1) == j) { 521 | reads += ")"; 522 | } 523 | } 524 | } 525 | one.addElement(reads); 526 | // Strand 527 | one.addElement(gt.getCircRnas().get(circId).getStrand()); 528 | // CircRNA Tissues 529 | String tissue = ""; 530 | int tissueNum = 0; 531 | for (String tissueName : fTissues.keySet()) { 532 | if (null != tissues.get(tissueName)) { 533 | tissue += tissueName + ","; 534 | tissueNum++; 535 | } 536 | } 537 | one.addElement(tissue); 538 | one.addElement(tissueNum + ""); 539 | // CircRNA Sample Name 540 | String sample = ""; 541 | int sampleNum = 0; 542 | for (String sampleName : fSamples.keySet()) { 543 | if (null != samples.get(sampleName)) { 544 | sample += sampleName + ","; 545 | sampleNum++; 546 | } 547 | 548 | } 549 | one.addElement(sample); 550 | one.addElement(sampleNum + ""); 551 | // CircRNA Tools or Algorithm 552 | String tool = ""; 553 | int toolNum = 0; 554 | for (String toolName : fTools.keySet()) { 555 | if (null != tools.get(toolName)) { 556 | tool += toolName + ","; 557 | toolNum++; 558 | } 559 | } 560 | one.addElement(tool); 561 | one.addElement(toolNum + ""); 562 | // CircRNA Type 563 | one.addElement(gt.getCircRnas().get(circId).getCircRnaType()); 564 | // CircRNA Region 565 | one.addElement(gt.getCircRnas().get(circId).getRegion()); 566 | tableData.addElement(one); 567 | } 568 | break; 569 | } 570 | } 571 | } 572 | 573 | } 574 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/CsvSaveFileChooser.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.io.File; 4 | 5 | import javax.swing.JFileChooser; 6 | import javax.swing.filechooser.FileFilter; 7 | 8 | public class CsvSaveFileChooser extends JFileChooser { 9 | 10 | private static final long serialVersionUID = 1L; 11 | 12 | public CsvSaveFileChooser(String title) { 13 | super(title); 14 | addFileFilter(); 15 | // Set default Dir 16 | this.setCurrentDirectory(new File(System.getProperty("user.dir"))); 17 | } 18 | 19 | private void addFileFilter() { 20 | 21 | addChoosableFileFilter(new FileFilter() { 22 | public boolean accept(File f) { 23 | return f.getName().endsWith("csv"); 24 | } 25 | 26 | public String getDescription() { 27 | return "csv"; 28 | } 29 | }); 30 | } 31 | 32 | } 33 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/DataLoadingDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Frame; 6 | import java.awt.Rectangle; 7 | 8 | import javax.swing.JDialog; 9 | 10 | public class DataLoadingDialog extends JDialog { 11 | private static final long serialVersionUID = 1L; 12 | 13 | public DataLoadingDialog(Frame owner, String title) { 14 | super(owner, title); 15 | initUI(); 16 | setTitle(title); 17 | setResizable(false); 18 | setSize(300, 1); 19 | this.setLayout(new FlowLayout()); 20 | centerScreen(); 21 | } 22 | 23 | private void centerScreen() { 24 | Dimension dim = getToolkit().getScreenSize(); 25 | Rectangle abounds = getBounds(); 26 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 27 | super.setVisible(true); 28 | requestFocus(); 29 | } 30 | 31 | private void initUI() { 32 | } 33 | } 34 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/DataLoadingProgressDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Color; 4 | import java.awt.Dimension; 5 | import java.awt.FlowLayout; 6 | import java.awt.Frame; 7 | import java.awt.Rectangle; 8 | import java.awt.event.ActionEvent; 9 | import java.awt.event.ActionListener; 10 | 11 | import javax.swing.JDialog; 12 | import javax.swing.JPanel; 13 | import javax.swing.JProgressBar; 14 | import javax.swing.Timer; 15 | import javax.swing.border.EmptyBorder; 16 | 17 | public class DataLoadingProgressDialog extends JDialog { 18 | private static final long serialVersionUID = 1L; 19 | private Timer timer; 20 | public static JProgressBar process; 21 | 22 | public DataLoadingProgressDialog(Frame owner, String title) { 23 | super(owner, title); 24 | setTitle(title); 25 | setResizable(false); 26 | setSize(300, 300); 27 | this.setLayout(new FlowLayout()); 28 | centerScreen(); 29 | initUI(); 30 | } 31 | 32 | private void centerScreen() { 33 | Dimension dim = getToolkit().getScreenSize(); 34 | Rectangle abounds = getBounds(); 35 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 36 | super.setVisible(true); 37 | requestFocus(); 38 | } 39 | 40 | private void initUI() { 41 | JPanel panel = new JPanel(); 42 | panel.setBorder(new EmptyBorder(5, 5, 5, 5)); 43 | panel.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 5)); 44 | getContentPane().add(panel); 45 | process = new JProgressBar(0, 100); 46 | process.setStringPainted(true); 47 | process.setBackground(Color.GREEN); 48 | process.setPreferredSize(new Dimension(200, 40)); 49 | process.setValue(0); 50 | panel.add(process); 51 | 52 | timer = new Timer(100, new ActionListener() { 53 | public void actionPerformed(ActionEvent e) { 54 | int loadingValue = process.getValue(); 55 | if (loadingValue < 100) { 56 | process.setValue(loadingValue); 57 | } else { 58 | timer.stop(); 59 | } 60 | } 61 | }); 62 | timer.start(); 63 | } 64 | 65 | public static JProgressBar getProcess() { 66 | return process; 67 | } 68 | 69 | public static void setProcess(JProgressBar process) { 70 | DataLoadingProgressDialog.process = process; 71 | } 72 | 73 | } 74 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/DetailsResultDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.Rectangle; 5 | 6 | import javax.swing.JDialog; 7 | import javax.swing.JScrollPane; 8 | import javax.swing.JTextArea; 9 | 10 | import cn.edu.whu.CircView; 11 | 12 | public class DetailsResultDialog extends JDialog { 13 | private static final long serialVersionUID = 1L; 14 | 15 | public DetailsResultDialog(String contents) { 16 | super(CircView.frame); 17 | setTitle("Details"); 18 | setResizable(true); 19 | setSize(600, 400); 20 | centerScreen(); 21 | 22 | JTextArea detailsTextArea = new JTextArea(); 23 | detailsTextArea.setSize(new Dimension(this.getContentPane().getWidth(), this.getContentPane().getWidth())); 24 | detailsTextArea.setEditable(false); 25 | detailsTextArea.setText(contents); 26 | JScrollPane sp = new JScrollPane(detailsTextArea); 27 | sp.setPreferredSize(new Dimension(this.getContentPane().getWidth(), this.getContentPane().getWidth())); 28 | this.getContentPane().add(sp); 29 | this.setVisible(true); 30 | this.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); 31 | } 32 | 33 | private void centerScreen() { 34 | Dimension dim = getToolkit().getScreenSize(); 35 | Rectangle abounds = getBounds(); 36 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 37 | super.setVisible(true); 38 | requestFocus(); 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/ImageSaveFileChooser.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.io.File; 4 | 5 | import javax.swing.JFileChooser; 6 | import javax.swing.filechooser.FileFilter; 7 | 8 | public class ImageSaveFileChooser extends JFileChooser { 9 | 10 | private static final long serialVersionUID = 1L; 11 | 12 | public ImageSaveFileChooser(String title) { 13 | super(title); 14 | addFileFilter(); 15 | // Set default Dir 16 | this.setCurrentDirectory(new File(System.getProperty("user.dir"))); 17 | } 18 | 19 | private void addFileFilter() { 20 | 21 | addChoosableFileFilter(new FileFilter() { 22 | public boolean accept(File f) { 23 | return f.getName().endsWith("png"); 24 | } 25 | 26 | public String getDescription() { 27 | return "png"; 28 | } 29 | }); 30 | } 31 | 32 | } 33 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/MreClearDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.awt.event.ItemEvent; 9 | import java.awt.event.ItemListener; 10 | import java.sql.Connection; 11 | import java.sql.SQLException; 12 | import javax.swing.JButton; 13 | import javax.swing.JComboBox; 14 | import javax.swing.JDialog; 15 | import javax.swing.JOptionPane; 16 | 17 | import cn.edu.whu.MainData; 18 | import cn.edu.whu.CircView; 19 | import cn.edu.whu.util.DbUtil; 20 | 21 | public class MreClearDialog extends JDialog { 22 | 23 | private static final long serialVersionUID = 1L; 24 | Connection conn; 25 | 26 | public MreClearDialog(Connection conn) { 27 | super(CircView.frame); 28 | this.conn = conn; 29 | initUi(); 30 | setTitle("Clear MRE Data"); 31 | setResizable(false); 32 | setSize(300, 65); 33 | this.setLayout(new FlowLayout()); 34 | centerScreen(); 35 | } 36 | 37 | private void centerScreen() { 38 | Dimension dim = getToolkit().getScreenSize(); 39 | Rectangle abounds = getBounds(); 40 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 41 | super.setVisible(true); 42 | requestFocus(); 43 | } 44 | 45 | private void initUi() { 46 | // ComboBox 47 | final JComboBox cbSpecies = new JComboBox(); 48 | cbSpecies.setPreferredSize(new Dimension(150, 28)); 49 | getContentPane().add(cbSpecies); 50 | // Add ItemListener to Speicies 51 | cbSpecies.addItemListener(new ItemListener() { 52 | public void itemStateChanged(ItemEvent e) { 53 | if (e.getStateChange() == ItemEvent.SELECTED) { 54 | } 55 | } 56 | }); 57 | for (String speciesName : MainData.getSpeciesNames()) { 58 | cbSpecies.addItem(speciesName); 59 | } 60 | // Button 61 | JButton btOpen = new JButton("Clear MRE Data"); 62 | getContentPane().add(btOpen); 63 | btOpen.addActionListener(new ActionListener() { 64 | public void actionPerformed(ActionEvent e) { 65 | setVisible(false); 66 | int dialogButton = JOptionPane.showConfirmDialog(CircView.frame, 67 | "All MRE Data for " + cbSpecies.getSelectedItem() + " WILL BE ERASE!"); 68 | if (dialogButton == JOptionPane.YES_OPTION) { 69 | DataLoadingDialog clearDialog = new DataLoadingDialog(CircView.frame, "Erasing MRE ..."); 70 | // Delete MRE data for selected Species 71 | String species = cbSpecies.getSelectedItem().toString(); 72 | try { 73 | String tableName = "mre_" + DbUtil.species2TableName(species); 74 | DbUtil.dropTable(conn, tableName); 75 | } catch (ClassNotFoundException | SQLException ex) { 76 | JOptionPane.showMessageDialog(CircView.frame, "MRE Data Clear Failed!"); 77 | CircView.log.warn(ex.getMessage()); 78 | } 79 | CircView.log.info("MRE Data for " + species + " Deleted"); 80 | CircView.updateRbpMreStatus(); 81 | clearDialog.setVisible(false); 82 | } 83 | MreClearDialog.this.dispose(); 84 | } 85 | }); 86 | } 87 | } 88 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/MreLoadDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.awt.event.ItemEvent; 9 | import java.awt.event.ItemListener; 10 | import java.io.File; 11 | import java.sql.Connection; 12 | import java.sql.SQLException; 13 | import javax.swing.JButton; 14 | import javax.swing.JComboBox; 15 | import javax.swing.JDialog; 16 | import javax.swing.JFileChooser; 17 | import javax.swing.JOptionPane; 18 | 19 | import cn.edu.whu.MainData; 20 | import cn.edu.whu.CircView; 21 | import cn.edu.whu.util.DbUtil; 22 | 23 | public class MreLoadDialog extends JDialog { 24 | 25 | private static final long serialVersionUID = 1L; 26 | 27 | private File[] files; 28 | Connection conn; 29 | 30 | public MreLoadDialog(Connection conn) { 31 | super(CircView.frame); 32 | this.conn = conn; 33 | initUi(); 34 | setTitle("Load MRE files"); 35 | setResizable(false); 36 | setSize(300, 65); 37 | this.setLayout(new FlowLayout()); 38 | centerScreen(); 39 | } 40 | 41 | private void centerScreen() { 42 | Dimension dim = getToolkit().getScreenSize(); 43 | Rectangle abounds = getBounds(); 44 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 45 | super.setVisible(true); 46 | requestFocus(); 47 | } 48 | 49 | private void initUi() { 50 | // ComboBox 51 | final JComboBox cbSpecies = new JComboBox(); 52 | cbSpecies.setPreferredSize(new Dimension(150, 28)); 53 | getContentPane().add(cbSpecies); 54 | // Add ItemListener to Speicies 55 | cbSpecies.addItemListener(new ItemListener() { 56 | public void itemStateChanged(ItemEvent e) { 57 | if (e.getStateChange() == ItemEvent.SELECTED) { 58 | } 59 | } 60 | }); 61 | for (String speciesName : MainData.getSpeciesNames()) { 62 | cbSpecies.addItem(speciesName); 63 | } 64 | // Button 65 | JButton btOpen = new JButton("Open MRE files"); 66 | getContentPane().add(btOpen); 67 | btOpen.addActionListener(new ActionListener() { 68 | public void actionPerformed(ActionEvent e) { 69 | MreLoadDialog.this.setVisible(false); 70 | OpenFileChooser openFile = new OpenFileChooser("Open MRE Files"); 71 | openFile.setMultiSelectionEnabled(true); 72 | openFile.setFileSelectionMode(JFileChooser.FILES_ONLY); 73 | openFile.setFileHidingEnabled(true); 74 | int returnValue = openFile.showOpenDialog(null); 75 | if (returnValue == JFileChooser.APPROVE_OPTION) { 76 | String species = cbSpecies.getSelectedItem().toString(); 77 | files = openFile.getSelectedFiles(); 78 | DataLoadingDialog dataLoadingDialog = new DataLoadingDialog(CircView.frame, "Loading MRE Data ..."); 79 | save2Db(species, files); 80 | CircView.updateRbpMreStatus(); 81 | dataLoadingDialog.setVisible(false); 82 | } 83 | MreLoadDialog.this.dispose(); 84 | } 85 | }); 86 | } 87 | 88 | private void save2Db(String species, File[] files) { 89 | if (null == conn) { 90 | try { 91 | conn = DbUtil.connectDb(); 92 | } catch (ClassNotFoundException | SQLException e) { 93 | CircView.log.warn(e.getMessage()); 94 | JOptionPane.showConfirmDialog(CircView.frame, "Can't Connect to the Database!"); 95 | return; 96 | } 97 | } 98 | try { 99 | String tableName = "mre_" + DbUtil.species2TableName(species); 100 | if (!DbUtil.existTable(conn, tableName)) { 101 | DbUtil.createMreTable(conn, tableName); 102 | } 103 | for (int i = 0; i < files.length; i++) { 104 | DbUtil.file2Db(conn, files[i].getAbsolutePath(), tableName); 105 | } 106 | } catch (ClassNotFoundException | SQLException e) { 107 | CircView.log.warn(e.getMessage()); 108 | JOptionPane.showMessageDialog(CircView.frame, "File FORMAT ERROR!"); 109 | } 110 | CircView.log.info("MRE Data for " + species + " Loaded"); 111 | } 112 | } 113 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/OpenFileChooser.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.io.File; 4 | 5 | import javax.swing.JFileChooser; 6 | 7 | public class OpenFileChooser extends JFileChooser { 8 | private static final long serialVersionUID = 1L; 9 | 10 | public OpenFileChooser(String title) { 11 | super(title); 12 | // addFileFilter(); 13 | setAcceptAllFileFilterUsed(false); 14 | 15 | // Set default Dir 16 | this.setCurrentDirectory(new File(System.getProperty("user.dir"))); 17 | } 18 | 19 | // private void addFileFilter() { 20 | // 21 | // for (final String circRnaTool : Constant.CIRCRNA_TOOLS.keySet()) { 22 | // for (final String species : Constant.SPECIES.keySet()) { 23 | // addChoosableFileFilter(new FileFilter() { 24 | // public boolean accept(File f) { 25 | // return f.getName().endsWith(""); 26 | // } 27 | // 28 | // public String getDescription() { 29 | // return circRnaTool + " in " + species; 30 | // } 31 | // }); 32 | // } 33 | // } 34 | // } 35 | } 36 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/ProgressDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.BorderLayout; 4 | import java.awt.Dimension; 5 | import java.awt.Rectangle; 6 | import javax.swing.JDialog; 7 | import javax.swing.JPanel; 8 | import javax.swing.JProgressBar; 9 | import cn.edu.whu.CircView; 10 | 11 | public class ProgressDialog extends JDialog { 12 | private static final long serialVersionUID = 1L; 13 | private static JProgressBar progressBar; 14 | 15 | public ProgressDialog() { 16 | super(CircView.frame); 17 | setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE); 18 | setLayout(new BorderLayout()); 19 | setSize(600, 400); 20 | setResizable(false); 21 | setTitle("Load Data ..."); 22 | centerScreen(); 23 | progressBar = new JProgressBar(0, 100); 24 | progressBar.setValue(0); 25 | progressBar.setStringPainted(true); 26 | JPanel panel = new JPanel(); 27 | panel.add(progressBar); 28 | this.getContentPane().add(panel); 29 | start(); 30 | } 31 | 32 | public void start() { 33 | while (progressBar.getValue() < 100) { 34 | try { 35 | Thread.sleep(500); 36 | repaint(); 37 | } catch (InterruptedException e) { 38 | CircView.log.info(e.getMessage()); 39 | } 40 | } 41 | } 42 | 43 | private void centerScreen() { 44 | Dimension dim = getToolkit().getScreenSize(); 45 | Rectangle abounds = getBounds(); 46 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 47 | super.setVisible(true); 48 | requestFocus(); 49 | } 50 | 51 | public static JProgressBar getProgressBar() { 52 | return progressBar; 53 | } 54 | 55 | public static void setProgressBar(JProgressBar progressBar) { 56 | ProgressDialog.progressBar = progressBar; 57 | } 58 | } 59 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/RbpClearDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.awt.event.ItemEvent; 9 | import java.awt.event.ItemListener; 10 | import java.sql.Connection; 11 | import java.sql.SQLException; 12 | import javax.swing.JButton; 13 | import javax.swing.JComboBox; 14 | import javax.swing.JDialog; 15 | import javax.swing.JOptionPane; 16 | 17 | import cn.edu.whu.MainData; 18 | import cn.edu.whu.CircView; 19 | import cn.edu.whu.util.DbUtil; 20 | 21 | public class RbpClearDialog extends JDialog { 22 | 23 | private static final long serialVersionUID = 1L; 24 | Connection conn; 25 | 26 | public RbpClearDialog(Connection conn) { 27 | super(CircView.frame); 28 | this.conn = conn; 29 | initUi(); 30 | setTitle("Clear RBP Data"); 31 | setResizable(false); 32 | setSize(300, 65); 33 | this.setLayout(new FlowLayout()); 34 | centerScreen(); 35 | } 36 | 37 | private void centerScreen() { 38 | Dimension dim = getToolkit().getScreenSize(); 39 | Rectangle abounds = getBounds(); 40 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 41 | super.setVisible(true); 42 | requestFocus(); 43 | } 44 | 45 | private void initUi() { 46 | // ComboBox 47 | final JComboBox cbSpecies = new JComboBox(); 48 | cbSpecies.setPreferredSize(new Dimension(150, 28)); 49 | getContentPane().add(cbSpecies); 50 | // Add ItemListener to Speicies 51 | cbSpecies.addItemListener(new ItemListener() { 52 | public void itemStateChanged(ItemEvent e) { 53 | if (e.getStateChange() == ItemEvent.SELECTED) { 54 | } 55 | } 56 | }); 57 | for (String speciesName : MainData.getSpeciesNames()) { 58 | cbSpecies.addItem(speciesName); 59 | } 60 | // Button 61 | JButton btOpen = new JButton("Clear RBP Data"); 62 | getContentPane().add(btOpen); 63 | btOpen.addActionListener(new ActionListener() { 64 | public void actionPerformed(ActionEvent e) { 65 | RbpClearDialog.this.setVisible(false); 66 | int dialogButton = JOptionPane.showConfirmDialog(CircView.frame, 67 | "All RBP Data for " + cbSpecies.getSelectedItem() + " WILL BE ERASE!"); 68 | if (dialogButton == JOptionPane.YES_OPTION) { 69 | DataLoadingDialog clearDialog = new DataLoadingDialog(CircView.frame, "Erasing RBP ..."); 70 | // Delete RBP data for selected Species 71 | String species = cbSpecies.getSelectedItem().toString(); 72 | try { 73 | String tableName = "rbp_" + DbUtil.species2TableName(species); 74 | DbUtil.dropTable(conn, tableName); 75 | } catch (ClassNotFoundException | SQLException ex) { 76 | JOptionPane.showMessageDialog(CircView.frame, "RBP Data Clear Failed!"); 77 | CircView.log.warn(ex.getMessage()); 78 | } 79 | CircView.log.info("RBP Data for " + species + " Deleted"); 80 | CircView.updateRbpMreStatus(); 81 | clearDialog.setVisible(false); 82 | } 83 | RbpClearDialog.this.dispose(); 84 | } 85 | }); 86 | } 87 | } 88 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/RbpLoadDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.awt.event.ItemEvent; 9 | import java.awt.event.ItemListener; 10 | import java.io.File; 11 | import java.sql.Connection; 12 | import java.sql.SQLException; 13 | import javax.swing.JButton; 14 | import javax.swing.JComboBox; 15 | import javax.swing.JDialog; 16 | import javax.swing.JFileChooser; 17 | import javax.swing.JOptionPane; 18 | 19 | import cn.edu.whu.MainData; 20 | import cn.edu.whu.CircView; 21 | import cn.edu.whu.util.DbUtil; 22 | 23 | public class RbpLoadDialog extends JDialog { 24 | 25 | private static final long serialVersionUID = 1L; 26 | 27 | private File[] files; 28 | Connection conn; 29 | 30 | public RbpLoadDialog(Connection conn) { 31 | super(CircView.frame); 32 | this.conn = conn; 33 | initUi(); 34 | setTitle("Load RBP files"); 35 | setResizable(false); 36 | setSize(300, 65); 37 | this.setLayout(new FlowLayout()); 38 | centerScreen(); 39 | } 40 | 41 | private void centerScreen() { 42 | Dimension dim = getToolkit().getScreenSize(); 43 | Rectangle abounds = getBounds(); 44 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 45 | super.setVisible(true); 46 | requestFocus(); 47 | } 48 | 49 | private void initUi() { 50 | // ComboBox 51 | final JComboBox cbSpecies = new JComboBox(); 52 | cbSpecies.setPreferredSize(new Dimension(150, 28)); 53 | getContentPane().add(cbSpecies); 54 | // Add ItemListener to Speicies 55 | cbSpecies.addItemListener(new ItemListener() { 56 | public void itemStateChanged(ItemEvent e) { 57 | if (e.getStateChange() == ItemEvent.SELECTED) { 58 | } 59 | } 60 | }); 61 | for (String speciesName : MainData.getSpeciesNames()) { 62 | cbSpecies.addItem(speciesName); 63 | } 64 | // Button 65 | JButton btOpen = new JButton("Open RBP files"); 66 | getContentPane().add(btOpen); 67 | btOpen.addActionListener(new ActionListener() { 68 | public void actionPerformed(ActionEvent e) { 69 | RbpLoadDialog.this.setVisible(false); 70 | OpenFileChooser openFile = new OpenFileChooser("Open RBP Files"); 71 | openFile.setMultiSelectionEnabled(true); 72 | openFile.setFileSelectionMode(JFileChooser.FILES_ONLY); 73 | openFile.setFileHidingEnabled(true); 74 | int returnValue = openFile.showOpenDialog(null); 75 | if (returnValue == JFileChooser.APPROVE_OPTION) { 76 | String species = cbSpecies.getSelectedItem().toString(); 77 | files = openFile.getSelectedFiles(); 78 | DataLoadingDialog dataLoadingDialog = new DataLoadingDialog(CircView.frame, "Loading RBP Data ..."); 79 | save2Db(species, files); 80 | CircView.updateRbpMreStatus(); 81 | dataLoadingDialog.setVisible(false); 82 | } 83 | RbpLoadDialog.this.dispose(); 84 | } 85 | }); 86 | } 87 | 88 | private void save2Db(String species, File[] files) { 89 | if (null == conn) { 90 | try { 91 | conn = DbUtil.connectDb(); 92 | } catch (ClassNotFoundException | SQLException e) { 93 | CircView.log.warn(e.getMessage()); 94 | JOptionPane.showConfirmDialog(CircView.frame, "Can't Connect to the Database!"); 95 | return; 96 | } 97 | } 98 | try { 99 | String tableName = "rbp_" + DbUtil.species2TableName(species); 100 | if (!DbUtil.existTable(conn, tableName)) { 101 | DbUtil.createRbpTable(conn, tableName); 102 | } 103 | for (int i = 0; i < files.length; i++) { 104 | DbUtil.file2Db(conn, files[i].getAbsolutePath(), tableName); 105 | } 106 | } catch (ClassNotFoundException | SQLException e) { 107 | CircView.log.warn(e.getMessage()); 108 | JOptionPane.showMessageDialog(CircView.frame, "File FORMAT ERROR!"); 109 | } 110 | CircView.log.info("RBP Data for " + species + " Loaded"); 111 | } 112 | } 113 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/SaveImageDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.io.File; 9 | import javax.swing.JButton; 10 | import javax.swing.JDialog; 11 | import javax.swing.JFileChooser; 12 | import javax.swing.JLabel; 13 | import javax.swing.JOptionPane; 14 | import javax.swing.JTextField; 15 | 16 | import cn.edu.whu.CircView; 17 | 18 | public class SaveImageDialog extends JDialog { 19 | 20 | private static final long serialVersionUID = 1L; 21 | private static CircRnaImagePanel circRnaImage; 22 | 23 | public SaveImageDialog(CircRnaImagePanel image) { 24 | super(CircView.frame); 25 | circRnaImage = image; 26 | initUi(); 27 | setTitle("Save Image as File"); 28 | setResizable(false); 29 | setSize(450, 65); 30 | this.setLayout(new FlowLayout()); 31 | centerScreen(); 32 | } 33 | 34 | private void centerScreen() { 35 | Dimension dim = getToolkit().getScreenSize(); 36 | Rectangle abounds = getBounds(); 37 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 38 | super.setVisible(true); 39 | requestFocus(); 40 | } 41 | 42 | private void initUi() { 43 | // ComboBox 44 | final JLabel lbWidth = new JLabel("Width"); 45 | final JTextField tfWidth = new JTextField(); 46 | final JLabel lbHeight = new JLabel("Height"); 47 | final JTextField tfHeight = new JTextField(); 48 | final JLabel lbpx = new JLabel("px"); 49 | JButton btSave = new JButton("Save as"); 50 | 51 | tfWidth.setPreferredSize(new Dimension(100, 28)); 52 | tfHeight.setPreferredSize(new Dimension(100, 28)); 53 | getContentPane().add(lbWidth); 54 | getContentPane().add(tfWidth); 55 | getContentPane().add(lbHeight); 56 | getContentPane().add(tfHeight); 57 | getContentPane().add(lbpx); 58 | getContentPane().add(btSave); 59 | 60 | tfWidth.setText(circRnaImage.getWidth() * 2 + ""); 61 | tfHeight.setText(circRnaImage.getHeight() * 2 + ""); 62 | 63 | // Button 64 | btSave.addActionListener(new ActionListener() { 65 | public void actionPerformed(ActionEvent e) { 66 | int w = Integer.parseInt(tfWidth.getText()); 67 | int h = Integer.parseInt(tfHeight.getText()); 68 | if (w * h > 20000 * 10000) { 69 | JOptionPane.showMessageDialog(CircView.frame, "Image Size MUST Be Smaller than 20000 * 10000"); 70 | } else if (w > 0 && h > 0) { 71 | SaveImageDialog.this.setVisible(false); 72 | ImageSaveFileChooser saveFile = new ImageSaveFileChooser("Save Image as ..."); 73 | saveFile.setFileSelectionMode(JFileChooser.FILES_ONLY); 74 | saveFile.setMultiSelectionEnabled(false); 75 | int returnValue = saveFile.showSaveDialog(null); 76 | if (returnValue == JFileChooser.APPROVE_OPTION) { 77 | File fileOut = saveFile.getSelectedFile(); 78 | String type = "png"; 79 | String fileName = fileOut.getAbsolutePath() + "." + type; 80 | circRnaImage.saveImage(circRnaImage.getGt(), new File(fileName), type, w, h); 81 | } 82 | SaveImageDialog.this.dispose(); 83 | } 84 | } 85 | }); 86 | } 87 | } 88 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/SpeciesAddDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import java.io.File; 9 | import javax.swing.JButton; 10 | import javax.swing.JDialog; 11 | import javax.swing.JFileChooser; 12 | import javax.swing.JLabel; 13 | import javax.swing.JOptionPane; 14 | import javax.swing.JTextField; 15 | 16 | import cn.edu.whu.MainData; 17 | import cn.edu.whu.CircView; 18 | 19 | public class SpeciesAddDialog extends JDialog { 20 | private static final long serialVersionUID = 1L; 21 | private File speciesFile; 22 | 23 | public SpeciesAddDialog() { 24 | super(CircView.frame); 25 | initUi(); 26 | setTitle("Add Species"); 27 | setResizable(false); 28 | setSize(600, 65); 29 | this.setLayout(new FlowLayout()); 30 | centerScreen(); 31 | } 32 | 33 | private void centerScreen() { 34 | Dimension dim = getToolkit().getScreenSize(); 35 | Rectangle abounds = getBounds(); 36 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 37 | super.setVisible(true); 38 | requestFocus(); 39 | } 40 | 41 | private void initUi() { 42 | // ComboBox 43 | final JLabel lbName = new JLabel("Name:"); 44 | final JTextField tfSpecies = new JTextField(); 45 | final JLabel lbFile = new JLabel(""); 46 | final JTextField tfFile = new JTextField(); 47 | tfFile.setEditable(false); 48 | final JButton btChoose = new JButton("Choose File"); 49 | final JButton btAdd = new JButton("Add"); 50 | 51 | tfSpecies.setPreferredSize(new Dimension(100, 28)); 52 | tfFile.setPreferredSize(new Dimension(150, 28)); 53 | 54 | getContentPane().add(lbName); 55 | getContentPane().add(tfSpecies); 56 | getContentPane().add(lbFile); 57 | getContentPane().add(tfFile); 58 | getContentPane().add(btChoose); 59 | getContentPane().add(btAdd); 60 | 61 | // Button 62 | btChoose.addActionListener(new ActionListener() { 63 | public void actionPerformed(ActionEvent e) { 64 | OpenFileChooser openFile = new OpenFileChooser("Select Gene Annotation File"); 65 | openFile.setMultiSelectionEnabled(false); 66 | openFile.setFileSelectionMode(JFileChooser.FILES_ONLY); 67 | openFile.setFileHidingEnabled(true); 68 | int returnValue = openFile.showOpenDialog(null); 69 | if (returnValue == JFileChooser.APPROVE_OPTION) { 70 | tfFile.setText(openFile.getSelectedFile().getName()); 71 | speciesFile = openFile.getSelectedFile(); 72 | } 73 | } 74 | }); 75 | btAdd.addActionListener(new ActionListener() { 76 | public void actionPerformed(ActionEvent e) { 77 | String speciesName = tfSpecies.getText(); 78 | String pattern = "\\s+"; 79 | if (speciesName.matches(pattern)) { 80 | JOptionPane.showMessageDialog(CircView.frame, "Species Name is needed"); 81 | return; 82 | } 83 | if (null == speciesFile || speciesFile.getPath().matches(pattern)) { 84 | JOptionPane.showMessageDialog(CircView.frame, 85 | "Annotation file for [" + speciesName + "] is needed"); 86 | return; 87 | } 88 | 89 | if (null != MainData.getSpeciesFile().get(speciesName)) { 90 | JOptionPane.showMessageDialog(CircView.frame, "Species [" + speciesName + "] already exists"); 91 | return; 92 | } else { 93 | MainData.getSpeciesNames().add(speciesName); 94 | MainData.getSpeciesFile().put(speciesName, speciesFile.getPath()); 95 | CircView.log.error(speciesName + " " + speciesFile.getPath() + " is added."); 96 | JOptionPane.showMessageDialog(CircView.frame, 97 | speciesName + " " + speciesFile.getName() + " is added."); 98 | SpeciesAddDialog.this.dispose(); 99 | } 100 | } 101 | }); 102 | } 103 | } 104 | -------------------------------------------------------------------------------- /src/cn/edu/whu/ui/SpeciesDelDialog.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.ui; 2 | 3 | import java.awt.Dimension; 4 | import java.awt.FlowLayout; 5 | import java.awt.Rectangle; 6 | import java.awt.event.ActionEvent; 7 | import java.awt.event.ActionListener; 8 | import javax.swing.JButton; 9 | import javax.swing.JComboBox; 10 | import javax.swing.JDialog; 11 | import cn.edu.whu.MainData; 12 | import cn.edu.whu.CircView; 13 | 14 | public class SpeciesDelDialog extends JDialog { 15 | 16 | private static final long serialVersionUID = 1L; 17 | 18 | public SpeciesDelDialog() { 19 | super(CircView.frame); 20 | initUi(); 21 | setTitle("Delete Species"); 22 | setResizable(false); 23 | setSize(300, 65); 24 | this.setLayout(new FlowLayout()); 25 | centerScreen(); 26 | } 27 | 28 | private void centerScreen() { 29 | Dimension dim = getToolkit().getScreenSize(); 30 | Rectangle abounds = getBounds(); 31 | setLocation((dim.width - abounds.width) / 2, (dim.height - abounds.height) / 2); 32 | super.setVisible(true); 33 | requestFocus(); 34 | } 35 | 36 | private void initUi() { 37 | // ComboBox 38 | final JComboBox cbSpecies = new JComboBox(); 39 | final JButton btDel = new JButton("Delete"); 40 | 41 | cbSpecies.setPreferredSize(new Dimension(160, 28)); 42 | for (String speciesName : MainData.getSpeciesNames()) { 43 | cbSpecies.addItem(speciesName); 44 | } 45 | 46 | getContentPane().add(cbSpecies); 47 | getContentPane().add(btDel); 48 | 49 | // Button 50 | btDel.addActionListener(new ActionListener() { 51 | public void actionPerformed(ActionEvent e) { 52 | if (null == cbSpecies.getSelectedItem()) { 53 | return; 54 | } 55 | String delSpecies = cbSpecies.getSelectedItem().toString(); 56 | // Delete Species and its File 57 | if (null != MainData.getSpeciesFile().get(delSpecies)) { 58 | MainData.getSpeciesFile().remove(delSpecies); 59 | } 60 | for(int i = MainData.getSpeciesNames().size() - 1; i>=0; i--) { 61 | if(MainData.getSpeciesNames().get(i).equalsIgnoreCase(delSpecies)) { 62 | MainData.getSpeciesNames().remove(i); 63 | } 64 | } 65 | CircView.log.error(delSpecies + " is DELETED"); 66 | SpeciesDelDialog.this.dispose(); 67 | } 68 | 69 | }); 70 | } 71 | } 72 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/CloneUtils.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | import java.io.ByteArrayInputStream; 4 | import java.io.ByteArrayOutputStream; 5 | import java.io.ObjectInputStream; 6 | import java.io.ObjectOutputStream; 7 | import java.io.Serializable; 8 | 9 | public class CloneUtils { 10 | @SuppressWarnings("unchecked") 11 | public static T clone(T obj) { 12 | T cloneObj = null; 13 | try { 14 | // 写入字节流 15 | ByteArrayOutputStream out = new ByteArrayOutputStream(); 16 | ObjectOutputStream obs = new ObjectOutputStream(out); 17 | obs.writeObject(obj); 18 | obs.close(); 19 | 20 | // 分配内存，写入原始对象，生成新对象 21 | ByteArrayInputStream ios = new ByteArrayInputStream(out.toByteArray()); 22 | ObjectInputStream ois = new ObjectInputStream(ios); 23 | // 返回生成的新对象 24 | cloneObj = (T) ois.readObject(); 25 | ois.close(); 26 | } catch (Exception e) { 27 | e.printStackTrace(); 28 | } 29 | return cloneObj; 30 | } 31 | } 32 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/Constant.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | import java.io.File; 4 | import java.util.TreeMap; 5 | import java.util.Vector; 6 | 7 | public class Constant { 8 | public final static String TOOL_CIRCEXPLORER = "CIRCexplorer"; 9 | public final static String TOOL_CIRCRNAFINDER = "circRNA_finder"; 10 | public final static String TOOL_CIRI = "CIRI"; 11 | public final static String TOOL_FIND_CIRC = "find_circ"; 12 | public final static String TOOL_MAPSPLICE = "Mapsplice"; 13 | public final static String TOOL_UROBORUS = "UROBORUS"; 14 | public final static Vector CIRCRNA_TOOLS = new Vector() { 15 | private static final long serialVersionUID = 1L; 16 | 17 | { 18 | add(TOOL_CIRCEXPLORER); 19 | add(TOOL_CIRCRNAFINDER); 20 | add(TOOL_CIRI); 21 | add(TOOL_FIND_CIRC); 22 | add(TOOL_MAPSPLICE); 23 | add(TOOL_UROBORUS); 24 | } 25 | }; 26 | 27 | public final static String HUMAN_HG38 = "human (hg38)"; 28 | public final static String HUMAN_HG19 = "human (hg19)"; 29 | public final static String MOUSE_MM10 = "mouse (mm10)"; 30 | public final static String MOUSE_MM9 = "mouse (mm9)"; 31 | public final static String ZEBRAFISH = "zebrafish (zv9)"; 32 | public final static String FLY = "fly (dm6)"; 33 | public final static String C_ELEGANS = "c.elegans (ce10)"; 34 | public final static Vector SPECIES = new Vector() { 35 | private static final long serialVersionUID = 1L; 36 | { 37 | add(HUMAN_HG38); 38 | add(HUMAN_HG19); 39 | add(MOUSE_MM10); 40 | add(MOUSE_MM9); 41 | add(ZEBRAFISH); 42 | add(FLY); 43 | add(C_ELEGANS); 44 | } 45 | }; 46 | 47 | public final static String HUMAN_HG38_FILE = "annotation" + File.separator + "Human_hg38.txt"; 48 | public final static String HUMAN_HG19_FILE = "annotation" + File.separator + "Human_hg19.txt"; 49 | public final static String MOUSE_MM10_FILE = "annotation" + File.separator + "Mouse_mm10.txt"; 50 | public final static String MOUSE_MM9_FILE = "annotation" + File.separator + "Mouse_mm9.txt"; 51 | public final static String ZEBRAFISH_FILE = "annotation" + File.separator + "Zebrafish_zv9.txt"; 52 | public final static String FLY_FILE = "annotation" + File.separator + "Fly_dm6.txt"; 53 | public final static String C_ELEGANS_FILE = "annotation" + File.separator + "C_elegans_ce10.txt"; 54 | public final static TreeMap SPECIES_FILE = new TreeMap() { 55 | private static final long serialVersionUID = 1L; 56 | { 57 | put(HUMAN_HG38, HUMAN_HG38_FILE); 58 | put(HUMAN_HG19, HUMAN_HG19_FILE); 59 | put(MOUSE_MM10, MOUSE_MM10_FILE); 60 | put(MOUSE_MM9, MOUSE_MM9_FILE); 61 | put(ZEBRAFISH, ZEBRAFISH_FILE); 62 | put(FLY, FLY_FILE); 63 | put(C_ELEGANS, C_ELEGANS_FILE); 64 | } 65 | }; 66 | 67 | public final static String SEPERATER = "==>"; 68 | public final static int ASSIGN_TOLERATION = 2; 69 | public final static int BP_MATCH_TOLERATE = 10; 70 | // RBP tables; 71 | public final static String RBP_TABLE_STRUCTS = "(chr varchar(10), start int, end int, rbp varchar(512), detail varchar(1024))"; 72 | 73 | // MRE tables; 74 | public static final String MRE_TABLE_STRUCTS = "(chr varchar(10), start int, end int, mre varchar(512), detail varchar(1024))"; 75 | 76 | // Default Database Configure 77 | public final static String DEFAULT_DB_SERVER = "127.0.0.1"; 78 | public final static String DEFAULT_DB_PORT = "3306"; 79 | public final static String DEFAULT_DB_USER = "root"; 80 | public final static String DEFAULT_DB_PASSWD = "12345"; 81 | public final static String DEFAULT_DB_NAME = "mre_rbp"; 82 | 83 | // Data Configure 84 | public final static String CONFIG_FILE = "config.properties"; 85 | public final static String CONFIG_DB_SERVER = "dbserver"; 86 | public final static String CONFIG_DB_PORT = "dbport"; 87 | public final static String CONFIG_DB_USER = "dbuser"; 88 | public final static String CONFIG_DB_PASSWD = "dbpasswd"; 89 | public final static String CONFIG_DB_NAME = "dbname"; 90 | public final static String CONFIG_SPECIES = "species"; 91 | public final static String CONFIG_CIRCRNA_TOOLS = "circrnatools"; 92 | 93 | // Logfile Configure 94 | public final static String LOG_FILE = "log4j.properties"; 95 | public final static String LOG4J_ROOTLOGGER = "log4j.rootLogger"; 96 | public final static String LOG4J_APPENDER_CONSOLE = "log4j.appender.Console"; 97 | public final static String LOG4J_APPENDER_CONSOLE_TARGET = "log4j.appender.Console.Target"; 98 | public final static String LOG4J_APPENDER_CONSOLE_LAYOUT = "log4j.appender.Console.layout"; 99 | public final static String LOG4J_APPENDER_CONSOLE_LAYOUT_CONV_PATT = "log4j.appender.Console.layout.ConversionPattern"; 100 | public final static String LOG4J_APPENDER_FILE = "log4j.appender.File"; 101 | public final static String LOG4J_APPENDER_FILE_FILE = "log4j.appender.File.File"; 102 | public final static String LOG4J_APPENDER_FILE_MAXFILESIZE = "log4j.appender.File.MaxFileSize"; 103 | public final static String LOG4J_APPENDER_FILE_THRESHOLD = "log4j.appender.File.Threshold"; 104 | public final static String LOG4J_APPENDER_FILE_LAYOUT = "log4j.appender.File.layout"; 105 | public final static String LOG4J_APPENDER_FILE_LAYOUT_CONV_PATT = "log4j.appender.File.layout.ConversionPattern"; 106 | 107 | public final static String LOG4J_ROOTLOGGER_VALUE = "INFO,Console,File"; 108 | public final static String LOG4J_APPENDER_CONSOLE_VALUE = "org.apache.log4j.ConsoleAppender"; 109 | public final static String LOG4J_APPENDER_CONSOLE_TARGET_VALUE = "System.out"; 110 | public final static String LOG4J_APPENDER_CONSOLE_LAYOUT_VALUE = "org.apache.log4j.PatternLayout"; 111 | public final static String LOG4J_APPENDER_CONSOLE_LAYOUT_CONV_PATT_VALUE = "[%c] - %m%n"; 112 | public final static String LOG4J_APPENDER_FILE_VALUE = "org.apache.log4j.RollingFileAppender"; 113 | public final static String LOG4J_APPENDER_FILE_FILE_VALUE = "logs/circview.log"; 114 | public final static String LOG4J_APPENDER_FILE_MAXFILESIZE_VALUE = "10MB"; 115 | public final static String LOG4J_APPENDER_FILE_THRESHOLD_VALUE = "ALL"; 116 | public final static String LOG4J_APPENDER_FILE_LAYOUT_VALUE = "org.apache.log4j.PatternLayout"; 117 | public final static String LOG4J_APPENDER_FILE_LAYOUT_CONV_PATT_VALUE = "[%p] [%d{yyyy-MM-dd HH:mm:ss}][%c]%m%n"; 118 | 119 | // About Content 120 | public static final String ABOUT = "Circular RNAs Viewer"; 121 | public static final String VERSION = "version 1.0.0"; 122 | public static final String AUTHOR = "Report bug to: gfeng@whu.edu.cn"; 123 | } 124 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/DbConfig.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | public class DbConfig { 4 | public String dbServer; 5 | public String dbPort; 6 | public String dbUser; 7 | public String dbPasswd; 8 | public String dbName; 9 | 10 | public String getDbServer() { 11 | return dbServer; 12 | } 13 | 14 | public void setDbServer(String dbServer) { 15 | this.dbServer = dbServer; 16 | } 17 | 18 | public String getDbPort() { 19 | return dbPort; 20 | } 21 | 22 | public void setDbPort(String dbPort) { 23 | this.dbPort = dbPort; 24 | } 25 | 26 | public String getDbUser() { 27 | return dbUser; 28 | } 29 | 30 | public void setDbUser(String dbUser) { 31 | this.dbUser = dbUser; 32 | } 33 | 34 | public String getDbPasswd() { 35 | return dbPasswd; 36 | } 37 | 38 | public void setDbPasswd(String dbPasswd) { 39 | this.dbPasswd = dbPasswd; 40 | } 41 | 42 | public String getDbName() { 43 | return dbName; 44 | } 45 | 46 | public void setDbName(String dbName) { 47 | this.dbName = dbName; 48 | } 49 | } 50 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/DbUtil.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | import java.sql.Connection; 4 | import java.sql.DriverManager; 5 | import java.sql.ResultSet; 6 | import java.sql.SQLException; 7 | import java.sql.Statement; 8 | import java.util.Vector; 9 | import java.util.regex.Matcher; 10 | import java.util.regex.Pattern; 11 | 12 | import cn.edu.whu.MainData; 13 | import cn.edu.whu.CircView; 14 | 15 | public class DbUtil { 16 | public static Connection connectDb() throws ClassNotFoundException, SQLException { 17 | String server = MainData.getDbConfig().getDbServer(); 18 | String port = MainData.getDbConfig().getDbPort(); 19 | String user = MainData.getDbConfig().getDbUser(); 20 | String passwd = MainData.getDbConfig().getDbPasswd(); 21 | 22 | String url = "jdbc:mysql://" + server + ":" + port + "?" + "user=" + user + "&password=" + passwd; 23 | CircView.log.info(url); 24 | Class.forName("com.mysql.jdbc.Driver"); 25 | return (DriverManager.getConnection(url)); 26 | } 27 | 28 | public static void createDb(Connection conn) throws SQLException, ClassNotFoundException { 29 | if (null == conn || conn.isClosed()) { 30 | conn = connectDb(); 31 | } 32 | String sql = "create database if not exists " + MainData.getDbConfig().getDbName(); 33 | CircView.log.info(sql); 34 | Statement st = conn.createStatement(); 35 | st.executeUpdate(sql); 36 | } 37 | 38 | public static void useDb(Connection conn) throws ClassNotFoundException, SQLException { 39 | if (null == conn || conn.isClosed()) { 40 | conn = connectDb(); 41 | } 42 | String sql = "use " + MainData.getDbConfig().getDbName(); 43 | CircView.log.info(sql); 44 | Statement st = conn.createStatement(); 45 | st.executeUpdate(sql); 46 | } 47 | 48 | public static void createRbpTable(Connection conn, String table) throws SQLException, ClassNotFoundException { 49 | if (null == conn || conn.isClosed()) { 50 | conn = connectDb(); 51 | } 52 | String sql = "create table " + table + " " + Constant.RBP_TABLE_STRUCTS; 53 | CircView.log.info(sql); 54 | Statement st = conn.createStatement(); 55 | st.executeUpdate(sql); 56 | } 57 | 58 | public static void createMreTable(Connection conn, String table) throws SQLException, ClassNotFoundException { 59 | if (null == conn || conn.isClosed()) { 60 | conn = connectDb(); 61 | } 62 | String sql = "create table " + table + " " + Constant.MRE_TABLE_STRUCTS; 63 | CircView.log.info(sql); 64 | Statement st = conn.createStatement(); 65 | st.executeUpdate(sql); 66 | } 67 | 68 | public static Vector selectRbp(Connection conn, String table, String chrom, Vector starts, 69 | Vector ends) throws SQLException { 70 | if (0 == starts.size()) { 71 | CircView.log.info("There is no results from " + table); 72 | return null; 73 | } 74 | Vector result = new Vector(); 75 | // Sql Statement 76 | String sql = "select chr, start, end, rbp, detail from " + table + " where "; 77 | for (int i = 0; i < starts.size(); i++) { 78 | sql += "chr='" + chrom + "' and " + starts.get(i) + "<=start and end<=" + ends.get(i) + " or "; 79 | } 80 | sql = sql.substring(0, sql.length() - 3); 81 | CircView.log.info(sql); 82 | Statement stmt = conn.createStatement(); 83 | ResultSet rs = stmt.executeQuery(sql); 84 | while (rs.next()) { 85 | String chr = rs.getString(1); 86 | long start = rs.getInt(2); 87 | long end = rs.getInt(3); 88 | String rbp = rs.getString(4); 89 | String detail = rs.getString(5); 90 | result.addElement(chr + "\t" + start + "\t" + end + "\t" + rbp + "\t" + detail); 91 | CircView.log.info(chr + "\t" + start + "\t" + end + "\t" + rbp + "\t" + detail); 92 | } 93 | return result; 94 | } 95 | 96 | public static Vector selectMre(Connection conn, String table, String chrom, Vector starts, 97 | Vector ends) throws SQLException { 98 | if (0 == starts.size()) { 99 | CircView.log.info("There is no results from " + table); 100 | return null; 101 | } 102 | Vector result = new Vector(); 103 | // Sql Statement 104 | String sql = "select chr, start, end, mre, detail from " + table + " where "; 105 | for (int i = 0; i < starts.size(); i++) { 106 | sql += "chr='" + chrom + "' and " + starts.get(i) + "<=start and end<=" + ends.get(i) + " or "; 107 | } 108 | sql = sql.substring(0, sql.length() - 3); 109 | CircView.log.info(sql); 110 | Statement stmt = conn.createStatement(); 111 | ResultSet rs = stmt.executeQuery(sql); 112 | while (rs.next()) { 113 | String chr = rs.getString(1); 114 | long start = rs.getInt(2); 115 | long end = rs.getInt(3); 116 | String rbp = rs.getString(4); 117 | String detail = rs.getString(5); 118 | result.addElement(chr + "\t" + start + "\t" + end + "\t" + rbp + "\t" + detail); 119 | CircView.log.info(chr + "\t" + start + "\t" + end + "\t" + rbp + "\t" + detail); 120 | } 121 | return result; 122 | } 123 | 124 | public static void file2Db(Connection conn, String fileName, String table) throws SQLException { 125 | if (System.getProperty("os.name").toLowerCase().indexOf("win") >= 0) { 126 | CircView.log.info("Running under Windows Operating System."); 127 | fileName = fileName.replaceAll("\\\\", "\\\\\\\\"); 128 | } 129 | Statement st = conn.createStatement(); 130 | String sql = "load data local infile '" + fileName + "' into table " + table 131 | + " fields terminated by '\t' lines terminated by '\n'"; 132 | CircView.log.info(sql); 133 | st.execute(sql); 134 | 135 | // Statement st = conn.createStatement(); 136 | // File file = new File(fileName); 137 | // if (file.isFile() && file.exists()) { 138 | // try { 139 | // InputStreamReader rd = new InputStreamReader(new 140 | // FileInputStream(file)); 141 | // BufferedReader reader = new BufferedReader(rd); 142 | // String lineTxt = null; 143 | // while ((lineTxt = reader.readLine()) != null) { 144 | // String[] item = lineTxt.split("\t"); 145 | // String chr = item[0]; 146 | // long start = Long.parseLong(item[1]); 147 | // long end = Long.parseLong(item[2]); 148 | // String miRna = item[3]; 149 | // String others = item[4]; 150 | // String sql = "insert into " + table + " values ('" + chr + "'," + 151 | // start + "," + end + ",'" + miRna 152 | // + "','" + others + "')"; 153 | // CircView.log.info(sql); 154 | // st.execute(sql); 155 | // } 156 | // } catch (IOException e) { 157 | // CircView.log.warn(e.getMessage()); 158 | // } 159 | // } else { 160 | // CircView.log.info("Can not find the file"); 161 | // } 162 | } 163 | 164 | public static void dropTable(Connection conn, String table) throws ClassNotFoundException, SQLException { 165 | if (null == conn || conn.isClosed()) { 166 | conn = connectDb(); 167 | } 168 | String sql = "drop table " + table; 169 | CircView.log.info(sql); 170 | Statement st = conn.createStatement(); 171 | st.execute(sql); 172 | } 173 | 174 | public static void closeDb(Connection conn) throws SQLException { 175 | CircView.log.info("Database Closed"); 176 | conn.close(); 177 | } 178 | 179 | public static String species2TableName(String species) { 180 | String regex = "[\\W]+"; 181 | Pattern pattern = Pattern.compile(regex); 182 | Matcher matcher = pattern.matcher(species); 183 | return matcher.replaceAll("_").trim(); 184 | } 185 | 186 | public static boolean existTable(Connection conn, String tableName) throws ClassNotFoundException, SQLException { 187 | boolean ret = false; 188 | if (null == conn || conn.isClosed()) { 189 | conn = connectDb(); 190 | } 191 | String sql = "show tables like '" + tableName + "'"; 192 | // CircView.log.info(sql); 193 | Statement stmt = conn.createStatement(); 194 | ResultSet rs = stmt.executeQuery(sql); 195 | while (rs.next()) { 196 | ret = true; 197 | } 198 | return ret; 199 | } 200 | } 201 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/EvenOddRenderer.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | import java.awt.Color; 4 | import java.awt.Component; 5 | 6 | import javax.swing.JTable; 7 | import javax.swing.table.DefaultTableCellRenderer; 8 | import javax.swing.table.TableCellRenderer; 9 | 10 | public class EvenOddRenderer implements TableCellRenderer { 11 | 12 | public static final DefaultTableCellRenderer DEFAULT_RENDERER = new DefaultTableCellRenderer(); 13 | 14 | public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, 15 | int row, int column) { 16 | Component renderer = DEFAULT_RENDERER.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, 17 | column); 18 | Color foreground, background; 19 | if (isSelected) { 20 | foreground = Color.YELLOW; 21 | background = Color.GREEN; 22 | } else { 23 | if (row % 2 == 0) { 24 | foreground = Color.GRAY; 25 | background = Color.WHITE; 26 | } else { 27 | foreground = Color.WHITE; 28 | background = Color.GRAY; 29 | } 30 | } 31 | renderer.setForeground(foreground); 32 | renderer.setBackground(background); 33 | return renderer; 34 | } 35 | } -------------------------------------------------------------------------------- /src/cn/edu/whu/util/MyMath.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | import java.util.Vector; 4 | 5 | public class MyMath { 6 | public static void main(String[] args) { 7 | String[] a = { "A", "B", "C", "D", "E" }; 8 | String[] res = new String[10]; 9 | combine(a, 0, res, 0, 2); 10 | // for (int i = 1; i <= a.length; i++) { 11 | // System.out.println(a.length + "选" + i); 12 | // String[] res = new String[i]; 13 | // combine(a, 0, res, 0, 1); 14 | // } 15 | } 16 | 17 | final static public void combine(final Object src[], final int srcIndex, final Object des[], final int desIndex, 18 | final int num) { 19 | if (desIndex >= num) { 20 | for (int i = 0; i < num; i++) 21 | System.out.print(des[i] + " "); 22 | System.out.println(); 23 | } else 24 | for (int ap = srcIndex; ap < src.length; ap++) { 25 | des[desIndex] = src[ap]; 26 | combine(src, ap + 1, des, desIndex + 1, num); 27 | } 28 | } 29 | 30 | final static public void getNfromM(final Vector src, final int srcIndex, final Vector des, 31 | final int desIndex, final int num) { 32 | 33 | } 34 | 35 | } 36 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/RuntimeUtils.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | public class RuntimeUtils { 4 | public static long getAvailableMemory() { 5 | Runtime runtime = Runtime.getRuntime(); 6 | long maxMemory = runtime.maxMemory(); 7 | long allocatedMemory = runtime.totalMemory(); 8 | long freeMemory = runtime.freeMemory(); 9 | return freeMemory + (maxMemory - allocatedMemory); 10 | } 11 | } 12 | -------------------------------------------------------------------------------- /src/cn/edu/whu/util/TextAreaCellRenderer.java: -------------------------------------------------------------------------------- 1 | package cn.edu.whu.util; 2 | 3 | import java.awt.Color; 4 | import java.awt.Component; 5 | import javax.swing.JTable; 6 | import javax.swing.JTextArea; 7 | import javax.swing.table.DefaultTableCellRenderer; 8 | import javax.swing.table.TableCellRenderer; 9 | 10 | public class TextAreaCellRenderer extends JTextArea implements TableCellRenderer { 11 | 12 | private static final long serialVersionUID = 1L; 13 | public static final DefaultTableCellRenderer DEFAULT_RENDERER = new DefaultTableCellRenderer(); 14 | 15 | public TextAreaCellRenderer() { 16 | setLineWrap(true); 17 | setWrapStyleWord(true); 18 | } 19 | 20 | public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, 21 | int row, int column) { 22 | 23 | // Component renderer = 24 | // DEFAULT_RENDERER.getTableCellRendererComponent(table, value, 25 | // isSelected, hasFocus, row, 26 | // column); 27 | // Color foreground, background; 28 | // if (isSelected) { 29 | // foreground = Color.YELLOW; 30 | // background = Color.GREEN; 31 | // } else { 32 | // if (row % 2 == 0) { 33 | // foreground = Color.GRAY; 34 | // background = Color.WHITE; 35 | // } else { 36 | // foreground = Color.WHITE; 37 | // background = Color.GRAY; 38 | // } 39 | // } 40 | // renderer.setForeground(foreground); 41 | // renderer.setBackground(background); 42 | 43 | // 计算当下行的最佳高度 44 | int maxPreferredHeight = 0; 45 | for (int i = 0; i < table.getColumnCount(); i++) { 46 | setText("" + table.getValueAt(row, i)); 47 | setSize(table.getColumnModel().getColumn(column).getWidth(), 0); 48 | maxPreferredHeight = Math.max(maxPreferredHeight, getPreferredSize().height); 49 | } 50 | 51 | if (table.getRowHeight(row) != maxPreferredHeight)// 少了这行则处理器瞎忙 52 | table.setRowHeight(row, maxPreferredHeight); 53 | setText(value == null ? "" : value.toString()); 54 | 55 | return this; 56 | // return renderer; 57 | } 58 | } -------------------------------------------------------------------------------- /testdata/human.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/GeneFeng/CircView/299fde303bdde161bcf9f0cb0248d5c5faec9812/testdata/human.tar.gz --------------------------------------------------------------------------------