--- /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);
+ 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