+++ /dev/null
-/*
- VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
- Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
- electronic mail : Yann.Ponty@lri.fr
- paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
-
- This file is part of VARNA version 3.1.
- VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
- VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
- without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- See the GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along with VARNA version 3.1.
- If not, see http://www.gnu.org/licenses.
- */
-package fr.orsay.lri.varna.applications;
-
-
-import java.awt.Graphics2D;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Rectangle2D;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.imageio.IIOImage;
-import javax.imageio.ImageIO;
-import javax.imageio.ImageWriteParam;
-import javax.imageio.ImageWriter;
-import javax.imageio.stream.FileImageOutputStream;
-import javax.swing.JFrame;
-
-import fr.orsay.lri.varna.VARNAPanel;
-import fr.orsay.lri.varna.exceptions.ExceptionExportFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
-import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
-import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-import fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden;
-import fr.orsay.lri.varna.factories.RNAFactory;
-import fr.orsay.lri.varna.interfaces.InterfaceParameterLoader;
-import fr.orsay.lri.varna.models.FullBackup;
-import fr.orsay.lri.varna.models.VARNAConfig;
-import fr.orsay.lri.varna.models.VARNAConfigLoader;
-import fr.orsay.lri.varna.models.rna.RNA;
-
-public class VARNAcmd implements InterfaceParameterLoader {
-
- public class ExitCode extends Exception{
- /**
- *
- */
- private static final long serialVersionUID = -3011196062868355584L;
- private int _c;
- private String _msg;
- public ExitCode(int c,String msg){
- _c = c;
- _msg = msg;
- }
- public int getExitCode(){
- return _c;
- }
- public String getExitMessage(){
- return _msg;
- }
- }
-
-
- private Hashtable<String, String> _optsValues = new Hashtable<String, String>();
- private Hashtable<String, String> _basicOptsInv = new Hashtable<String, String>();
- private String _inFile = "";
- private String _outFile = "";
- int _baseWidth = 400;
- double _scale = 1.0;
- float _quality = 0.9f;
-
- private String[] _basicOptions = { VARNAConfigLoader.algoOpt,
- VARNAConfigLoader.bpStyleOpt, VARNAConfigLoader.bondColorOpt,
- VARNAConfigLoader.backboneColorOpt, VARNAConfigLoader.periodNumOpt,
- VARNAConfigLoader.baseInnerColorOpt,
- VARNAConfigLoader.baseOutlineColorOpt,
-
- };
-
- public VARNAcmd(Vector<String> args) throws ExitCode {
- for (int j = 0; j < _basicOptions.length; j++) {
- _basicOptsInv.put(_basicOptions[j], _basicOptions[j]);
- }
- int i = 0;
- while (i < args.size()) {
- String opt = args.elementAt(i);
- if (opt.charAt(0) != '-') {
- errorExit("Missing or unknown option \"" + opt + "\"");
- }
- if (opt.equals("-h")) {
- displayLightHelpExit();
- }
- if (opt.equals("-x")) {
- displayDetailledHelpExit();
- } else {
- if (i + 1 >= args.size()) {
- errorExit("Missing argument for option \"" + opt + "\"");
- }
- String val = args.get(i + 1);
- if (opt.equals("-i")) {
- _inFile = val;
- } else if (opt.equals("-o")) {
- _outFile = val;
- } else if (opt.equals("-quality")) {
- _quality = Float.parseFloat(val);
- } else if (opt.equals("-resolution")) {
- _scale = Float.parseFloat(val);
- } else {
- addOption(opt, val);
- }
- }
- i += 2;
- }
- }
-
- public void addOption(String key, String value) {
- if (key.equals("-i")) {
- _inFile = value;
- } else if (key.equals("-o")) {
- _outFile = value;
- } else {
- _optsValues.put(key.substring(1), value);
- }
- }
-
- private String getDescription() {
- return "VARNA v"
- + VARNAConfig.MAJOR_VERSION
- + "."
- + VARNAConfig.MINOR_VERSION
- + " Assisted drawing of RNA secondary structure (Command Line version)";
- }
-
- private String indent(int k) {
- String result = "";
- for (int i = 0; i < k; i++) {
- result += " ";
- }
- return result;
- }
-
- private String complete(String s, int k) {
- String result = s;
- while (result.length() < k) {
- result += " ";
- }
- return result;
- }
-
- Vector<String[]> matrix = new Vector<String[]>();
-
- private void addLine(String opt, String val) {
- String[] line = { opt, val };
- matrix.add(line);
- }
-
- private static int MAX_WIDTH = 100;
-
- @SuppressWarnings("unchecked")
- private void printMatrix(int ind) {
- String[][] values = new String[matrix.size()][];
- matrix.toArray(values);
- Arrays.sort(values, new Comparator() {
- public int compare(Object o1, Object o2) {
- String[] tab1 = (String[]) o1;
- String[] tab2 = (String[]) o2;
- return tab1[0].compareTo(tab2[0]);
- }
- });
-
- int maxSize = 0;
- for (int i = 0; i < values.length; i++) {
- String[] elem = values[i];
- maxSize = Math.max(maxSize, elem[0].length());
- }
- maxSize += ind + 2;
- for (int i = 0; i < values.length; i++) {
- String[] elem = values[i];
- String opt = elem[0];
- String msg = elem[1];
- opt = complete("", ind) + "-" + complete(opt, maxSize - ind);
- System.out.println(opt + msg.substring(0, Math.min(MAX_WIDTH - opt.length(), msg.length())));
- if (opt.length() + msg.length() >= MAX_WIDTH) {
- int off = MAX_WIDTH - opt.length();
- while (off < msg.length()) {
- String nmsg = msg.substring(off, Math.min(off + MAX_WIDTH
- - opt.length(), msg.length()));
- System.out.println(complete("", opt.length())+nmsg);
- off += MAX_WIDTH - opt.length();
- }
- }
- }
- matrix = new Vector<String[]>();
- }
-
- private void printUsage() {
- System.out
- .println("Usage: java -cp . [-i InFile|-sequenceDBN XXX -structureDBN YYY] -o OutFile [Options]");
- System.out.println("Where:");
- System.out.println(indent(1)
- + "OutFile\tSupported formats: {JPEG,PNG,EPS,XFIG,SVG}");
- System.out
- .println(indent(1)
- + "InFile\tSecondary structure file: Supported formats: {BPSEQ,CT,RNAML,DBN}");
-
- }
-
- private void printHelpOptions() {
- System.out.println("\nMain options:");
- addLine("h", "Displays a short description of main options and exits");
- addLine("x", "Displays a detailled description of all options");
- printMatrix(2);
- }
-
- private void printMainOptions(String[][] info) {
- System.out.println("\nMain options:");
- addLine("h", "Displays a short description of main options and exits");
- addLine("x", "Displays a detailled description of all options");
- for (int i = 0; i < info.length; i++) {
- String key = info[i][0];
- if (_basicOptsInv.containsKey(key)) {
- addLine(key, info[i][2]);
- }
- }
- printMatrix(2);
- }
-
- private void printAdvancedOptions(String[][] info) {
- System.out.println("\nAdvanced options:");
- for (int i = 0; i < info.length; i++) {
- String key = info[i][0];
- if (!_basicOptsInv.containsKey(key)) {
- addLine(key, info[i][2]);
- }
- }
- addLine("quality", "Sets quality (non-vector file formats only)");
- addLine("resolution", "Sets resolution (non-vector file formats only)");
- printMatrix(2);
- }
-
- private void displayLightHelpExit() throws ExitCode {
- String[][] info = VARNAConfigLoader.getParameterInfo();
- System.out.println(getDescription());
- printUsage();
- printMainOptions(info);
- throw(new ExitCode(1,""));
- }
-
- private void displayDetailledHelpExit() throws ExitCode {
- String[][] info = VARNAConfigLoader.getParameterInfo();
- System.out.println(getDescription());
- printUsage();
- printMainOptions(info);
- printAdvancedOptions(info);
- throw(new ExitCode(1,""));
- }
-
- private void errorExit(String msg) throws ExitCode {
- System.out.println(getDescription());
- System.out.println("Error: " + msg + "\n");
- printUsage();
- printHelpOptions();
- throw(new ExitCode(1,""));
- }
-
- public String getParameterValue(String key, String def) {
- if (_optsValues.containsKey(key)) {
- return _optsValues.get(key);
- }
- return def;
- }
-
- public String formatOutputPath(String base,int index, int total)
- {
- String result = base;
-
- if (total>1)
- {
- int indexDot = base.lastIndexOf('.');
- String pref;
- String ext;
- if (indexDot!=-1)
- {
- pref = base.substring(0,indexDot);
- ext = base.substring(indexDot);
- }
- else{
- pref=base;
- ext="";
- }
- result = pref+"-"+index+ext;
- }
- System.err.println("Output file: "+result);
- return result;
- }
-
- public void run() throws IOException, ExitCode {
- VARNAConfigLoader VARNAcfg = new VARNAConfigLoader(this);
- ArrayList<VARNAPanel> vpl;
- ArrayList<FullBackup> confs = new ArrayList<FullBackup>();
- try {
- if (!_inFile.equals("")) {
- if (!_inFile.toLowerCase().endsWith(".varna")) {
- Collection<RNA> rnas = RNAFactory.loadSecStr(_inFile);
- if (rnas.isEmpty())
- {
- FullBackup f = null;
- try{
- f = VARNAPanel.importSession(new FileInputStream(_inFile), _inFile);
- confs.add(f);
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- if (f==null)
- {
- throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from file '"+_inFile+"'.");
- }
- }
- else{
- for (RNA r: rnas)
- {
- confs.add(new FullBackup(r,_inFile));
- }
- }
- }
- else{
- confs.add(VARNAPanel.importSession(_inFile));
- }
- } else {
- RNA r = new RNA();
- r.setRNA(this.getParameterValue("sequenceDBN",
- ""), this.getParameterValue(
- "structureDBN", ""));
- confs.add(new FullBackup(r,"From Params"));
- }
- if (!_outFile.equals(""))
- {
- int index = 1;
- for (FullBackup r: confs)
- {
- VARNAcfg.setRNA(r.rna);
- vpl = VARNAcfg.createVARNAPanels();
- if (vpl.size() > 0) {
- VARNAPanel _vp = vpl.get(0);
- if (r.hasConfig())
- {
- _vp.setConfig(r.config);
- }
- RNA _rna = _vp.getRNA();
- Rectangle2D.Double bbox = _vp.getRNA().getBBox();
- //System.out.println(_vp.getRNA().getBBox());
-
- if (_outFile.toLowerCase().endsWith(".jpeg")
- || _outFile.toLowerCase().endsWith(".jpg")
- || _outFile.toLowerCase().endsWith(".png"))
- {
- _vp.setTitleFontSize((int)(_scale*_vp.getTitleFont().getSize()));
- _vp.setSize((int)(_baseWidth*_scale), (int)((_scale*_baseWidth*bbox.height)/((double)bbox.width)));
- }
-
- if (_outFile.toLowerCase().endsWith(".eps")) {
- _rna.saveRNAEPS(formatOutputPath(_outFile,index, confs.size()), _vp.getConfig());
- } else if (_outFile.toLowerCase().endsWith(".xfig")
- || _outFile.toLowerCase().endsWith(".fig")) {
- _rna.saveRNAXFIG(formatOutputPath(_outFile,index, confs.size()), _vp.getConfig());
- } else if (_outFile.toLowerCase().endsWith(".svg")) {
- _rna.saveRNASVG(formatOutputPath(_outFile,index, confs.size()), _vp.getConfig());
- } else if (_outFile.toLowerCase().endsWith(".jpeg")
- || _outFile.toLowerCase().endsWith(".jpg")) {
- this.saveToJPEG(formatOutputPath(_outFile,index, confs.size()), _vp);
- } else if (_outFile.toLowerCase().endsWith(".png")) {
- this.saveToPNG(formatOutputPath(_outFile,index, confs.size()), _vp);
- } else if (_outFile.toLowerCase().endsWith(".varna")) {
- _vp.saveSession(formatOutputPath(_outFile,index, confs.size()));
- } else {
- errorExit("Unknown extension for output file \"" + _outFile
- + "\"");
- }
- }
- index++;
- }
- }
- // No output file => Open GUI
- else
- {
- VARNAGUI d = new VARNAGUI();
- d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- d.pack();
- d.setVisible(true);
- for (FullBackup b: confs)
- {
- RNA r = b.rna;
- VARNAcfg.setRNA(r);
- vpl = VARNAcfg.createVARNAPanels();
- if (vpl.size() > 0) {
- VARNAPanel _vp = vpl.get(0);
- VARNAConfig cfg = _vp.getConfig();
- if (b.hasConfig())
- {
- cfg = b.config;
- }
- RNA rna = _vp.getRNA();
- d.addRNA(rna, cfg);
-
- }
- }
- }
- } catch (ExceptionWritingForbidden e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionJPEGEncoding e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionParameterError e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionModeleStyleBaseSyntaxError e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionNonEqualLength e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionUnmatchedClosingParentheses e) {
- e.printStackTrace();
- System.exit(1);
- } catch (ExceptionExportFailed e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionPermissionDenied e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionLoadingFailed e) {
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (ExceptionFileFormatOrSyntax e) {
- e.setPath(_inFile);
- e.printStackTrace();
- throw(new ExitCode(1,""));
- } catch (FileNotFoundException e) {
- throw(new ExitCode(1,"Error: Missing input file \""+_inFile+"\"."));
- }
-
- if (!_outFile.equals(""))
- throw(new ExitCode(0,""));
-
-
-
- }
-
- public void saveToJPEG(String filename, VARNAPanel vp)
- throws ExceptionJPEGEncoding, ExceptionExportFailed {
-
- BufferedImage myImage = new BufferedImage((int) Math.round(vp
- .getWidth()
- ), (int) Math.round(vp.getHeight() ),
- BufferedImage.TYPE_INT_RGB);
- Graphics2D g2 = myImage.createGraphics();
- vp.paintComponent(g2);
- g2.dispose();
- try {
- FileImageOutputStream out = new FileImageOutputStream(new File(filename));
- ImageWriter writer = ImageIO.getImageWritersByFormatName("jpeg").next();
- ImageWriteParam params = writer.getDefaultWriteParam();
- params.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
- params.setCompressionQuality(_quality);
- writer.setOutput(out);
- IIOImage myIIOImage = new IIOImage(myImage, null, null);
- writer.write(null, myIIOImage, params);
- out.close();
- } catch (IOException e) {
- throw new ExceptionExportFailed(e.getMessage(), filename);
- }
- }
-
- public void saveToPNG(String filename, VARNAPanel vp)
- throws ExceptionExportFailed {
- BufferedImage myImage = new BufferedImage((int) Math.round(vp
- .getWidth()), (int) Math.round(vp.getHeight() ),
- BufferedImage.TYPE_INT_RGB);
- Graphics2D g2 = myImage.createGraphics();
- vp.paintComponent(g2);
- g2.dispose();
- try {
- ImageIO.write(myImage, "PNG", new File(filename));
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- public static void main(String[] argv) {
- Vector<String> opts = new Vector<String>();
- for (int i = 0; i < argv.length; i++) {
- opts.add(argv[i]);
- }
- try {
- VARNAcmd app = new VARNAcmd(opts);
- app.run();
- } catch (IOException e) {
- e.printStackTrace();
- } catch (ExitCode e) {
- System.err.println(e.getExitMessage());
- System.exit(e.getExitCode());
- }
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff