Bundle plots font, to eliminate external font dependencies

uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel.java

@@ -41,6 +41,7 @@
 import javax.swing.JTextField;
 
 import uk.ac.babraham.FastQC.FastQCApplication;
+import uk.ac.babraham.FastQC.Utilities.FontManager;
 
 /**
  * The Class SeqMonkTitlePanel.
@@ -132,48 +133,48 @@ public void mouseClicked(MouseEvent e) {
 		constraints.fill = GridBagConstraints.NONE;
 
 		JLabel program = new SmoothJLabel("FastQC High Throughput Sequence QC Report",JLabel.CENTER);
-		program.setFont(new Font("Dialog",Font.BOLD,18));
+		program.setFont(FontManager.getFont(Font.BOLD, 18f));
 		program.setForeground(new Color(200,0,0));
 		c.add(program,constraints);
 
 		constraints.gridy++;
 		JLabel version = new SmoothJLabel("Version: "+FastQCApplication.VERSION, JLabel.CENTER);
-		version.setFont(new Font("Dialog",Font.BOLD,15));
+		version.setFont(FontManager.getFont(Font.BOLD, 15f));
 		version.setForeground(new Color(0,0,200));
 		c.add(version,constraints);
 
 		constraints.gridy++;
 		// Use a text field so they can copy this
 		JLabel website = new JLabel(" www.bioinformatics.babraham.ac.uk/projects/ ");
-		website.setFont(new Font("Dialog",Font.PLAIN,14));
+		website.setFont(FontManager.getFont(Font.PLAIN, 14f));
 		website.setBorder(null);
 		website.setOpaque(false);
 		website.setHorizontalAlignment(JTextField.CENTER);
 		c.add(website,constraints);
 		constraints.gridy++;
 
 		JLabel copyright = new JLabel("\u00a9 Simon Andrews, Pierre Lindenbaum, Brian Howard, Phil Ewels 2011-26,", JLabel.CENTER);
-		copyright.setFont(new Font("Dialog",Font.PLAIN,14));
+		copyright.setFont(FontManager.getFont(Font.PLAIN, 14f));
 		c.add(copyright,constraints);
 		constraints.gridy++;
 
 		JLabel copyright2 = new JLabel("HTSJDK BAM/SAM reader v2.24.1 from Samtools 2022", JLabel.CENTER);
-		copyright2.setFont(new Font("Dialog",Font.PLAIN,10));
+		copyright2.setFont(FontManager.getFont(Font.PLAIN, 10f));
 		c.add(copyright2,constraints);
 		constraints.gridy++;
 
 		JLabel copyright3 = new JLabel("BZip decompression \u00a9Matthew J. Francis, 2011", JLabel.CENTER);
-		copyright3.setFont(new Font("Dialog",Font.PLAIN,10));
+		copyright3.setFont(FontManager.getFont(Font.PLAIN, 10f));
 		c.add(copyright3,constraints);
 		constraints.gridy++;
 
 		JLabel copyright4 = new JLabel("Base64 encoding \u00a9Robert Harder, 2012", JLabel.CENTER);
-		copyright4.setFont(new Font("Dialog",Font.PLAIN,10));
+		copyright4.setFont(FontManager.getFont(Font.PLAIN, 10f));
 		c.add(copyright4,constraints);
 		constraints.gridy++;
 
 		JLabel copyright5 = new JLabel("Java HDF5 reader \u00a9ETH, CISD and SIS, 2007-14", JLabel.CENTER);
-		copyright5.setFont(new Font("Dialog",Font.PLAIN,10));
+		copyright5.setFont(FontManager.getFont(Font.PLAIN, 10f));
 		c.add(copyright5,constraints);
 
 		add(c,BorderLayout.CENTER);

uk/ac/babraham/FastQC/Graphs/LineGraph.java

@@ -29,6 +29,8 @@
 
 import javax.swing.JPanel;
 
+import uk.ac.babraham.FastQC.Utilities.FontManager;
+
 public class LineGraph extends JPanel {
 
 	private String [] xTitles;
@@ -105,7 +107,8 @@ public Dimension getMinimumSize () {
 
 	public void paint (Graphics g) {
 		super.paint(g);
-
+
+		g.setFont(FontManager.defaultFont());
 		g.setColor(Color.WHITE);
 		g.fillRect(0, 0, getWidth(), getHeight());
 		g.setColor(Color.BLACK);
@@ -138,8 +141,10 @@ public void paint (Graphics g) {
 		xOffset += 5;
 
 		// Draw the graph title
+		g.setFont(FontManager.defaultBoldFont());
 		int titleWidth = g.getFontMetrics().stringWidth(graphTitle);
 		g.drawString(graphTitle, (xOffset + ((getWidth()-(xOffset+10))/2)) - (titleWidth/2), 30);
+		g.setFont(FontManager.defaultFont());
 
 
 		// Now draw the axes
@@ -174,7 +179,7 @@ public void paint (Graphics g) {
 
 			if (baseNumberPosition > lastXLabelEnd) {
 				g.drawString(baseNumber,baseNumberPosition, getHeight()-25);
-				lastXLabelEnd = baseNumberPosition+baseNumberWidth+5;
+				lastXLabelEnd = baseNumberPosition+baseNumberWidth+g.getFontMetrics().getHeight()-2;
 			}
 		}
 
@@ -209,7 +214,7 @@ public void paint (Graphics g) {
 		// Now draw the data legend
 
 		// Make the letters thicker for this so we can see the colours better
-		g.setFont(g.getFont().deriveFont(Font.BOLD));
+		g.setFont(FontManager.defaultBoldFont());
 
 		if (g instanceof Graphics2D) {
 			((Graphics2D)g).setStroke(new BasicStroke(1));
@@ -241,7 +246,7 @@ public void paint (Graphics g) {
 
 
 		// Put the font back how we found it
-		g.setFont(g.getFont().deriveFont(Font.PLAIN));
+		g.setFont(FontManager.defaultFont());
 
 
 	}

uk/ac/babraham/FastQC/Graphs/QualityBoxPlot.java

@@ -24,6 +24,8 @@
 
 import javax.swing.JPanel;
 
+import uk.ac.babraham.FastQC.Utilities.FontManager;
+
 public class QualityBoxPlot extends JPanel {
 
 	private double [] means;
@@ -64,7 +66,8 @@ public QualityBoxPlot (double [] means, double [] medians, double [] lowest, dou
 
 	public void paint (Graphics g) {
 		super.paint(g);
-
+
+		g.setFont(FontManager.defaultFont());
 		g.setColor(Color.WHITE);
 		g.fillRect(0, 0, getWidth(), getHeight());
 		g.setColor(Color.BLACK);
@@ -102,8 +105,10 @@ public void paint (Graphics g) {
 
 
 		// Draw the graph title
+		g.setFont(FontManager.defaultBoldFont());
 		int titleWidth = g.getFontMetrics().stringWidth(graphTitle);
 		g.drawString(graphTitle, (xOffset + ((getWidth()-(xOffset+10))/2)) - (titleWidth/2), 30);
+		g.setFont(FontManager.defaultFont());
 
 
 
@@ -149,7 +154,7 @@ public void paint (Graphics g) {
 
 			if (labelStart > lastXLabelEnd) {
 				g.drawString(xLabels[i], labelStart, getHeight()-25);
-				lastXLabelEnd = labelStart+g.getFontMetrics().stringWidth(xLabels[i])+5;
+				lastXLabelEnd = labelStart+baseNumberWidth+g.getFontMetrics().getHeight()-2;
 			}
 		}
 

uk/ac/babraham/FastQC/Graphs/TileGraph.java

@@ -29,6 +29,7 @@
 import javax.swing.JPanel;
 
 import uk.ac.babraham.FastQC.Modules.ModuleConfig;
+import uk.ac.babraham.FastQC.Utilities.FontManager;
 import uk.ac.babraham.FastQC.Utilities.HotColdColourGradient;
 
 public class TileGraph extends JPanel {
@@ -54,6 +55,7 @@ private int getY(double y) {
 	public void paint (Graphics g) {
 		super.paint(g);
 
+		g.setFont(FontManager.defaultFont());
 		g.setColor(Color.WHITE);
 		g.fillRect(0, 0, getWidth(), getHeight());
 		g.setColor(Color.BLACK);
@@ -81,8 +83,10 @@ public void paint (Graphics g) {
 
 		// Draw the graph title
 		String graphTitle = "Quality per tile";
+		g.setFont(FontManager.defaultBoldFont());
 		int titleWidth = g.getFontMetrics().stringWidth(graphTitle);
 		g.drawString(graphTitle, (xOffset + ((getWidth()-(xOffset+10))/2)) - (titleWidth/2), 30);
+		g.setFont(FontManager.defaultFont());
 
 
 		// Now draw the axes
@@ -115,7 +119,7 @@ public void paint (Graphics g) {
 
 			if (baseNumberPosition > lastXLabelEnd) {
 				g.drawString(baseNumber,baseNumberPosition, getHeight()-25);
-				lastXLabelEnd = baseNumberPosition+baseNumberWidth+5;
+				lastXLabelEnd = baseNumberPosition+baseNumberWidth+g.getFontMetrics().getHeight()-2;
 			}
 		}
 

uk/ac/babraham/FastQC/Resources/Fonts/LICENSE

@@ -0,0 +1,102 @@
+Digitized data copyright (c) 2010 Google Corporation
+	with Reserved Font Arimo, Tinos and Cousine.
+Copyright (c) 2012 Red Hat, Inc.
+	with Reserved Font Name Liberation.
+
+This Font Software is licensed under the SIL Open Font License,
+Version 1.1.
+
+This license is copied below, and is also available with a FAQ at:
+http://scripts.sil.org/OFL
+
+SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+
+PREAMBLE The goals of the Open Font License (OFL) are to stimulate
+worldwide development of collaborative font projects, to support the font
+creation efforts of academic and linguistic communities, and to provide
+a free and open framework in which fonts may be shared and improved in
+partnership with others.
+
+The OFL allows the licensed fonts to be used, studied, modified and
+redistributed freely as long as they are not sold by themselves.
+The fonts, including any derivative works, can be bundled, embedded,
+redistributed and/or sold with any software provided that any reserved
+names are not used by derivative works.  The fonts and derivatives,
+however, cannot be released under any other type of license.  The
+requirement for fonts to remain under this license does not apply to
+any document created using the fonts or their derivatives.
+
+
+
+DEFINITIONS
+"Font Software" refers to the set of files released by the Copyright
+Holder(s) under this license and clearly marked as such.
+This may include source files, build scripts and documentation.
+
+"Reserved Font Name" refers to any names specified as such after the
+copyright statement(s).
+
+"Original Version" refers to the collection of Font Software components
+as distributed by the Copyright Holder(s).
+
+"Modified Version" refers to any derivative made by adding to, deleting,
+or substituting ? in part or in whole ?
+any of the components of the Original Version, by changing formats or
+by porting the Font Software to a new environment.
+
+"Author" refers to any designer, engineer, programmer, technical writer
+or other person who contributed to the Font Software.
+
+
+PERMISSION & CONDITIONS
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of the Font Software, to use, study, copy, merge, embed, modify,
+redistribute, and sell modified and unmodified copies of the Font
+Software, subject to the following conditions:
+
+1) Neither the Font Software nor any of its individual components,in
+   Original or Modified Versions, may be sold by itself.
+
+2) Original or Modified Versions of the Font Software may be bundled,
+   redistributed and/or sold with any software, provided that each copy
+   contains the above copyright notice and this license. These can be
+   included either as stand-alone text files, human-readable headers or
+   in the appropriate machine-readable metadata fields within text or
+   binary files as long as those fields can be easily viewed by the user.
+
+3) No Modified Version of the Font Software may use the Reserved Font
+   Name(s) unless explicit written permission is granted by the
+   corresponding Copyright Holder. This restriction only applies to the
+   primary font name as presented to the users.
+
+4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+   Software shall not be used to promote, endorse or advertise any
+   Modified Version, except to acknowledge the contribution(s) of the
+   Copyright Holder(s) and the Author(s) or with their explicit written
+   permission.
+
+5) The Font Software, modified or unmodified, in part or in whole, must
+   be distributed entirely under this license, and must not be distributed
+   under any other license. The requirement for fonts to remain under
+   this license does not apply to any document created using the Font
+   Software.
+
+
+
+TERMINATION
+This license becomes null and void if any of the above conditions are not met.
+
+
+
+DISCLAIMER
+THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT.  IN NO EVENT SHALL THE
+COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER
+DEALINGS IN THE FONT SOFTWARE.
+