org.pathvisio.libgpml.util.Utils Maven / Gradle / Ivy
/*******************************************************************************
* PathVisio, a tool for data visualization and analysis using biological pathways
* Copyright 2006-2022 BiGCaT Bioinformatics, WikiPathways
*
* Licensed under the Apache License, Version 2.0 (the "License"); you may not
* use this file except in compliance with the License. You may obtain a copy
* of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
* License for the specific language governing permissions and limitations under
* the License.
******************************************************************************/
package org.pathvisio.libgpml.util;
import java.awt.Font;
import java.awt.geom.Point2D;
import java.io.InputStream;
import java.io.PrintStream;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.pathvisio.libgpml.model.LineElement;
import org.pathvisio.libgpml.model.PathwayObject;
import org.pathvisio.libgpml.model.ShapedElement;
import org.pathvisio.libgpml.model.type.ObjectType;
import org.pathvisio.libgpml.prop.StaticProperty;
/**
* Various utility functions.
*
* @author unknown
*/
public class Utils {
// ================================================================================
// String Manipulation Methods
// ================================================================================
/**
* Case insensitive contains method for List.
*
* @param str the string.
* @param strList the string list.
* @return true if string list contains given string regardless of case.
*/
public static boolean containsCaseInsensitive(String str, List strList) {
return strList.stream().anyMatch(x -> x.equalsIgnoreCase(str));
}
/**
* Compares two Strings, returning true if they are equal.
*
* @see java.lang.String#equals(Object)
* @param str1 the first String, may be null
* @param str2 the second String, may be null
* @return true if the Strings are equal, case sensitive, or both
* null
*/
public static boolean stringEquals(String str1, String str2) {
return str1 == null ? str2 == null : str1.equals(str2);
}
/**
* Compares two Strings, returning true if they are equal. In this
* case, null is considered equal to Empty.
*
* @see java.lang.String#equals(Object)
* @param str1 the first String, may be null or empty
* @param str2 the second String, may be null or empty
* @return true if the Strings are equal, case sensitive, or both
* null or empty
*/
public static boolean stringNullEqualsEmpty(String str1, String str2) {
if (str1 == null && stringEquals(str2, "")) {
return true; // str1 is null and str2 is empty
} else if (str2 == null && stringEquals(str1, "")) {
return true;// str2 is null and str1 is empty
} else {
return stringEquals(str1, str2); // check
}
}
/**
* Returns true if string is empty or null.
*
* @param str the string.
* @return true if string is empty or null.
*/
public static boolean isEmpty(String str) {
return str == null || str.length() == 0;
}
// ================================================================================
// Direction Methods (LineElement)
// ================================================================================
/**
* Get the direction of the line on the x axis
*
* @param start The start point of the line
* @param end The end point of the line
* @return 1 if the direction is positive (from left to right), -1 if the
* direction is negative (from right to left)
*/
public static int getDirectionX(Point2D start, Point2D end) {
return (int) Math.signum(end.getX() - start.getX());
}
/**
* Get the direction of the line on the y axis
*
* @param start The start point of the line
* @param end The end point of the line
* @return 1 if the direction is positive (from top to bottom), -1 if the
* direction is negative (from bottom to top)
*/
public static int getDirectionY(Point2D start, Point2D end) {
return (int) Math.signum(end.getY() - start.getY());
}
// ================================================================================
// Core Methods
// ================================================================================
public static final int OS_UNSUPPORTED = -1;
public static final int OS_WINDOWS = 0;
public static final int OS_LINUX = 1;
public static final int OS_MAC = 2;
/**
* Returns the OS.
*
* @return the OS.
*/
public static int getOS() {
String os = System.getProperty("os.name");
if (os.startsWith("Win")) {
return OS_WINDOWS;
} else if (os.startsWith("Lin")) {
return OS_LINUX;
} else if (os.startsWith("Mac")) {
return OS_MAC;
} else {
return OS_UNSUPPORTED;
}
}
/**
* Useful if you want to use one item from a set, and you don't care which one.
*
* @param set a set that you want one element out of
* @return null if the set is empty or null, or an element from the set
* otherwise.
*/
static public T oneOf(Set set) {
if (set == null || set.size() == 0) {
return null;
} else {
return set.iterator().next();
}
}
/**
* Creates a new Set of the given value(s)
*/
static public Set setOf(T val) {
Set result = new HashSet();
result.add(val);
return result;
}
/**
* For safely adding a value to a multimap (i.e. a map of sets).
*/
static public void multimapPut(Map> map, U key, V val) {
Set x;
if (map.containsKey(key))
x = map.get(key);
else {
x = new HashSet();
map.put(key, x);
}
x.add(val);
}
/**
* Returns a set of all unique values of a multimap (i.e. a map of sets).
*/
public static Set multimapValues(Map> map) {
Set result = new HashSet();
for (Set set : map.values())
result.addAll(set);
return result;
}
/**
* Formats a message that will be displayed in a dialog, so it's not longer than
* 80 symbols in each line
*
* @param msg the message to format.
*/
public static String formatExceptionMsg(String msg) {
msg = msg.replace("\n", "");
if (msg.length() > 80) {
String result = "";
for (int i = 0; i < msg.length(); i = i + 80) {
int end = i + 80;
if (msg.length() < i + 80)
end = msg.length();
String s = msg.substring(i, end);
int index = s.lastIndexOf(" ");
if (index == -1) {
result = result + s + "\n";
} else {
result = result + msg.substring(i, i + index) + "\n";
i = i - (s.length() - index);
}
}
return result;
} else
return msg;
}
// ================================================================================
// Currently Unused Methods TODO
// ================================================================================
/** append a property to the summary */
private static void summaryHelper(PathwayObject elt, StringBuilder result, StaticProperty p, String shortHand) {
if (!elt.getStaticPropertyKeys().contains(p))
return;
result.append(',');
result.append(shortHand);
result.append('=');
result.append(elt.getStaticProperty(p));
}
/**
* Returns string summary information for a pathway object. TODO
*
* @param elt
* @return
*/
public static String summary(PathwayObject elt) {
if (elt == null) {
return "null";
}
StringBuilder result = new StringBuilder("[" + elt.getObjectType().getTag());
summaryHelper(elt, result, StaticProperty.ELEMENTID, "id");
if (elt instanceof ShapedElement) {
summaryHelper(elt, result, StaticProperty.TEXTLABEL, "lbl");
summaryHelper(elt, result, StaticProperty.WIDTH, "w");
summaryHelper(elt, result, StaticProperty.HEIGHT, "h");
summaryHelper(elt, result, StaticProperty.CENTERX, "cx");
summaryHelper(elt, result, StaticProperty.CENTERY, "cy");
}
if (elt instanceof LineElement) {
summaryHelper(elt, result, StaticProperty.STARTX, "x1");
summaryHelper(elt, result, StaticProperty.STARTY, "y1");
summaryHelper(elt, result, StaticProperty.ENDX, "x2");
summaryHelper(elt, result, StaticProperty.ENDY, "y2");
summaryHelper(elt, result, StaticProperty.STARTELEMENTREF, "startref");
summaryHelper(elt, result, StaticProperty.ENDELEMENTREF, "endref");
}
if (elt.getObjectType() == ObjectType.PATHWAY) {
summaryHelper(elt, result, StaticProperty.TITLE, "title");
summaryHelper(elt, result, StaticProperty.AUTHOR, "author");
}
result.append("]");
return result.toString();
}
/**
* Joins collection into a single string, with a separator between.
*
* @param sep
* @param values
* @return
*/
public static String join(String sep, Collection values) {
StringBuilder builder = new StringBuilder();
boolean first = true;
for (Object o : values) {
if (first)
first = false;
else
builder.append(sep);
builder.append("" + o);
}
return builder.toString();
}
/**
* Converts a list to a string.
*
* @param list the list to convert to a string
* @param quote a quote character to use
* @param sep the separator to use
* @return a String representing the list with given seperator and quote (no
* parentheses)
*/
public static String collection2String(Collection list, String quote, String sep) {
StringBuilder strb = new StringBuilder();
for (Object o : list) {
strb.append(quote + o.toString() + quote + sep);
}
int last = strb.lastIndexOf(String.valueOf(sep));
if (last >= 0)
strb.delete(last, strb.length());
return strb.toString();
}
/**
* Converts a string to input stream.
*
* @param str the string.
* @return
*/
public static InputStream stringToInputStream(String str) {
if (str == null)
return null;
InputStream in = null;
try {
in = new java.io.ByteArrayInputStream(str.getBytes("UTF-8"));
} catch (Exception ex) {
}
return in;
}
/**
* Encodes a font to a string that can be converted back into a font object
* using Font.decode(String)
*
* @param f the font.
*/
public static String encodeFont(Font f) {
String style = "PLAIN";
if (f.isBold() && f.isItalic())
style = "BOLDITALIC";
else if (f.isBold())
style = "BOLD";
else if (f.isItalic())
style = "ITALIC";
String fs = f.getName() + "-" + style + "-" + f.getSize();
return fs;
}
/**
* Helper function to print the contents of maps or collections, or maps of
* maps, collections of maps, collections of collections etc. Useful for
* debugging. Similar in idea to the perl Data::Dumper module
*
* @param indent is for recursive use, e.g. to prefix each line with "\t"
*/
public static void printx(PrintStream out, String indent, Object o) {
if (o instanceof Map) {
Map map = (Map) o;
for (Object key : map.keySet()) {
printx(out, indent, key);
out.println(indent + "=>");
Object value = map.get(key);
printx(out, indent + "\t", value);
}
} else if (o instanceof Collection) {
Collection col = (Collection) o;
out.println(indent + "(");
for (Object item : col) {
printx(out, indent + "\t", item);
}
out.println(indent + ")");
} else {
out.println(indent + o.toString());
}
}
}
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