Java tutorial
/* Copyright (c) 2013 Daniel Marbach We release this software open source under an MIT license (see below). If this software was useful for your scientific work, please cite our paper available at: http://networkinference.org Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package edu.mit.genecircuits; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStreamReader; import java.text.DecimalFormat; import java.util.ArrayList; import org.apache.commons.math3.linear.MatrixUtils; import org.apache.commons.math3.linear.RealMatrix; import cern.colt.matrix.tdouble.DoubleMatrix2D; import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix2D; /** * Some static utility functions */ public class GcUtils { /** Scientific format with plenty of digits (no loss in precision) */ private static DecimalFormat scientific_ = new DecimalFormat("0.###############E0#####"); /** Scientific format with around 10 digits (good for writing doubles to file) */ private static DecimalFormat scientific10_ = new DecimalFormat("0.#######E0#"); // ---------------------------------------------------------------------------- /** * Take a time in [ms] and convert it into [h min s ms]. * @param dt [ms] * @return Time [h m s ms] */ public static String chronometer(long dt) { int numHours = 0; int numMinutes = 0; int numSeconds = 0; //System.out.println(dt); numHours = (int) Math.floor(dt / 3600000.0); dt -= numHours * 3600000.0; numMinutes = (int) Math.floor(dt / 60000.0); dt -= numMinutes * 60000.0; numSeconds = (int) Math.floor(dt / 1000.0); dt -= numSeconds * 1000.0; String time = Integer.toString(numHours) + "h "; time += Integer.toString(numMinutes) + "min "; time += Integer.toString(numSeconds) + "s "; time += Integer.toString((int) dt) + "ms"; return time; } // ---------------------------------------------------------------------------- public static void printArray(double[] v) { int size = v.length; for (int i = 0; i < size; i++) System.out.print(v[i] + "\t"); System.out.println(""); } // ---------------------------------------------------------------------------- /** Return true if the given array is an ordered list of positive integers, given in increasing order */ public static boolean posIntIncreasing(ArrayList<Integer> x) { if (x == null || x.size() == 0) return true; for (int i = 0; i < x.size(); i++) { if (x.get(i) < 1) return false; if (i > 0 && x.get(i) <= x.get(i - 1)) return false; } return true; } // ---------------------------------------------------------------------------- /** Return true if the given array is an ordered list of positive doubles, given in increasing order */ public static boolean posDoubleIncreasing(ArrayList<Double> x) { if (x == null || x.size() == 0) return true; for (int i = 0; i < x.size(); i++) { if (x.get(i) <= 0) return false; if (i > 0 && x.get(i) <= x.get(i - 1)) return false; } return true; } // ---------------------------------------------------------------------------- // /** Extract the basic file name without path and without extension */ // static public String extractBasicFilename(String filename) { // // return extractBasicFilename(filename, true); // } // ---------------------------------------------------------------------------- /** Extract the basic file name without path and without extension */ static public String extractBasicFilename(String filename, boolean includePath) { // The beginning of the filename (without the path) int start = filename.lastIndexOf("/") + 1; if (start == -1) start = filename.lastIndexOf("\\") + 1; // windows if (start == -1) start = 0; // Remove .gz if (filename.endsWith(".gz")) filename = filename.substring(0, filename.length() - 3); // The end of the filename (without file extension) int end = filename.lastIndexOf("."); if (end == -1 || end <= start) // not found or part of the path end = filename.length(); // The output filename String basicFilename = filename.substring((includePath ? 0 : start), end); // Add custom suffix if (Settings.outputSuffix_ != null && Settings.outputSuffix_.compareTo("") != 0) basicFilename += Settings.outputSuffix_; return basicFilename; } // ---------------------------------------------------------------------------- /** Scientific format */ static public String toStringScientific(double x) { return scientific_.format(x); } // ---------------------------------------------------------------------------- /** Scientific format with limited precision (around 10 digits, good for writing doubles to file) */ static public String toStringScientific10(double x) { return scientific10_.format(x); } // ---------------------------------------------------------------------------- /** Convert dense Colt to Apache Commons matrix */ static public RealMatrix colt2apache(DoubleMatrix2D colt) { RealMatrix apache = MatrixUtils.createRealMatrix(colt.rows(), colt.columns()); for (int i = 0; i < colt.rows(); i++) for (int j = 0; j < colt.columns(); j++) apache.setEntry(i, j, colt.get(i, j)); return apache; } // ---------------------------------------------------------------------------- /** Convert dense Apache Commons to Colt matrix */ static public DoubleMatrix2D apache2colt(RealMatrix apache) { // Convert apache commons matrix to colt DoubleMatrix2D colt = new DenseDoubleMatrix2D(apache.getRowDimension(), apache.getColumnDimension()); for (int i = 0; i < apache.getRowDimension(); i++) for (int j = 0; j < apache.getColumnDimension(); j++) colt.set(i, j, apache.getEntry(i, j)); return colt; } static public void exec(String command) { try { // Execute command System.out.println(command); Process p; p = Runtime.getRuntime().exec(command); BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream())); BufferedReader stdError = new BufferedReader(new InputStreamReader(p.getErrorStream())); // read the output from the command String s; while ((s = stdInput.readLine()) != null) { System.out.println(s); } // read any errors from the attempted command System.out.println("Here is the standard error of the command (if any):\n"); while ((s = stdError.readLine()) != null) { System.out.println(s); } } catch (IOException e) { GcMain.error(e); } } // // ---------------------------------------------------------------------------- // // /** Get a URL from a relative path */ // public URL getURL(String path) // { // try // { // return new File(path).toURI().toURL(); // } // catch (MalformedURLException e) // { // log_.log(Level.WARNING, "NgseaSettings::getURL(): Bad URL", e); // } // return null; // } }