X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FVARNAcmd.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fapplications%2FVARNAcmd.java;h=7b16c6183361c9c0b0a1443a75f89fec8dc6b8c4;hb=8a43b8353b89a47002ef17c959ed61281fc4d826;hp=0000000000000000000000000000000000000000;hpb=55bfdb07355198ae1a1a8b5e14933b4669113ca6;p=jalview.git

diff --git a/srcjar/fr/orsay/lri/varna/applications/VARNAcmd.java b/srcjar/fr/orsay/lri/varna/applications/VARNAcmd.java
new file mode 100644
index 0000000..7b16c61
--- /dev/null
+++ b/srcjar/fr/orsay/lri/varna/applications/VARNAcmd.java
@@ -0,0 +1,529 @@
+/*
+ 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());
+		}
+	}
+
+}