biojava · sbliven · Aug 11, 2016 · May 13, 2016 · May 13, 2016 · May 14, 2016
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -39,7 +39,7 @@ public static String formatExonStructure(GeneChromosomePosition chromosomePositi
         return formatExonStructureReverse(chromosomePosition);
 
     }
-    
+
 
     private static String formatExonStructureForward(GeneChromosomePosition chromPos) {
 

diff --git a/...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure.align.gui.jmol;
 
+import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
 import java.awt.Dimension;
@@ -40,6 +41,7 @@
 import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuBar;
+import javax.swing.JPanel;
 import javax.swing.JTextField;
 
 import org.biojava.nbio.structure.Atom;
@@ -56,6 +58,7 @@
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
 import org.biojava.nbio.structure.align.webstart.AligUIManager;
+import org.biojava.nbio.structure.gui.WrapLayout;
 import org.biojava.nbio.structure.jama.Matrix;
 import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.phylogeny.Phylogeny;
@@ -137,14 +140,13 @@ public void windowClosing(WindowEvent e) {
 		});
 
 		Container contentPane = frame.getContentPane();
-		Box vBox = Box.createVerticalBox();
 
 		jmolPanel.addMouseMotionListener(this);
 		jmolPanel.addMouseListener(this);
-		jmolPanel
-				.setPreferredSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));
+		jmolPanel.setPreferredSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));
+		contentPane.add(jmolPanel,BorderLayout.CENTER);
 
-		vBox.add(jmolPanel);
+		Box vBox = Box.createVerticalBox();
 
 		// / USER SCRIPTING COMMAND
 		JTextField field = new JTextField();
@@ -162,8 +164,10 @@ public void windowClosing(WindowEvent e) {
 		// / STRUCTURE SELECTION
 		if (multAln != null) {
 
-			Box hBox00 = Box.createHorizontalBox();
-			hBox00.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
+			JPanel modelSelection = new JPanel();
+			modelSelection.setLayout(new WrapLayout(WrapLayout.LEFT));
+			modelSelection.setSize(new Dimension(DEFAULT_WIDTH,30));
+			vBox.add(modelSelection);
 
 			JButton show = new JButton("Show Only: ");
 			show.addActionListener(new ActionListener() {
@@ -184,27 +188,16 @@ public void actionPerformed(ActionEvent e) {
 					jmolPanel.executeCmd(cmd + " restore selection;");
 				}
 			});
-			hBox00.add(show);
-			hBox00.add(Box.createGlue());
-			vBox.add(hBox00);
+			modelSelection.add(show);
 
-			// A line of structures of maximum 5
-			for (int line = 0; line < 1 + (multAln.size() / 5); line++) {
-				Box hBox0 = Box.createHorizontalBox();
-				hBox0.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
-
-				for (int str = line * 5; str < Math.min((line + 1) * 5,
-						multAln.size()); str++) {
-					JCheckBox structureSelection = new JCheckBox(multAln
-							.getEnsemble().getStructureIdentifiers().get(str)
-							.getIdentifier());
-					hBox0.add(structureSelection);
-					hBox0.add(Box.createGlue());
-					structureSelection.setSelected(true);
-					selectedStructures.add(structureSelection);
-				}
-
-				vBox.add(hBox0);
+			// Check boxes for all models
+			for(int str = 0; str < multAln.size();str++) {
+				JCheckBox structureSelection = new JCheckBox(multAln
+						.getEnsemble().getStructureIdentifiers().get(str)
+						.getIdentifier());
+				modelSelection.add(structureSelection);
+				structureSelection.setSelected(true);
+				selectedStructures.add(structureSelection);
 			}
 		}
 
@@ -214,35 +207,35 @@ public void actionPerformed(ActionEvent e) {
 
 		String[] styles = new String[] { "Cartoon", "Backbone", "CPK",
 				"Ball and Stick", "Ligands", "Ligands and Pocket" };
-		JComboBox style = new JComboBox(styles);
+		JComboBox<String> style = new JComboBox<>(styles);
 
 		hBox1.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
 
 		hBox1.add(new JLabel("Style"));
 		hBox1.add(style);
 		vBox.add(hBox1);
-		contentPane.add(vBox);
 
 		style.addActionListener(jmolPanel);
 
 		String[] colorModes = new String[] { "Secondary Structure", "By Chain",
 				"Rainbow", "By Element", "By Amino Acid", "Hydrophobicity",
 				"Suggest Domains", "Show SCOP Domains" };
-		JComboBox jcolors = new JComboBox(colorModes);
+		JComboBox<String> jcolors = new JComboBox<>(colorModes);
 		jcolors.addActionListener(jmolPanel);
 
 		hBox1.add(Box.createGlue());
 		hBox1.add(new JLabel("Color"));
 		hBox1.add(jcolors);
 
 		String[] cPalette = { "Spectral", "Set1", "Set2", "Pastel" };
-		JComboBox palette = new JComboBox(cPalette);
+		JComboBox<String> palette = new JComboBox<>(cPalette);
 
 		palette.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
 
-				JComboBox source = (JComboBox) e.getSource();
+				@SuppressWarnings("unchecked")
+				JComboBox<String> source = (JComboBox<String>) e.getSource();
 				String value = source.getSelectedItem().toString();
 				evalString("save selection; select *; color grey; "
 						+ "select ligand; color CPK;");
@@ -268,6 +261,7 @@ public void actionPerformed(ActionEvent e) {
 
 		// / CHECK BOXES
 		Box hBox2 = Box.createHorizontalBox();
+		hBox2.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
 
 		JButton resetDisplay = new JButton("Reset Display");
 		resetDisplay.addActionListener(new ActionListener() {
@@ -337,7 +331,7 @@ public void itemStateChanged(ItemEvent e) {
 
 		vBox.add(hBox);
 
-		contentPane.add(vBox);
+		contentPane.add(vBox,BorderLayout.SOUTH);
 		MyJmolStatusListener li = (MyJmolStatusListener) jmolPanel
 				.getStatusListener();
 

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java
@@ -0,0 +1,195 @@
+package org.biojava.nbio.structure.gui;
+
+import java.awt.*;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+/**
+ *  FlowLayout subclass that fully supports wrapping of components.
+ *  
+ *  Originally written by Rob Camick
+ *  https://tips4java.wordpress.com/2008/11/06/wrap-layout/
+ */
+public class WrapLayout extends FlowLayout
+{
+	private Dimension preferredLayoutSize;
+
+	/**
+	* Constructs a new <code>WrapLayout</code> with a left
+	* alignment and a default 5-unit horizontal and vertical gap.
+	*/
+	public WrapLayout()
+	{
+		super();
+	}
+
+	/**
+	* Constructs a new <code>FlowLayout</code> with the specified
+	* alignment and a default 5-unit horizontal and vertical gap.
+	* The value of the alignment argument must be one of
+	* <code>WrapLayout</code>, <code>WrapLayout</code>,
+	* or <code>WrapLayout</code>.
+	* @param align the alignment value
+	*/
+	public WrapLayout(int align)
+	{
+		super(align);
+	}
+
+	/**
+	* Creates a new flow layout manager with the indicated alignment
+	* and the indicated horizontal and vertical gaps.
+	* <p>
+	* The value of the alignment argument must be one of
+	* <code>WrapLayout</code>, <code>WrapLayout</code>,
+	* or <code>WrapLayout</code>.
+	* @param align the alignment value
+	* @param hgap the horizontal gap between components
+	* @param vgap the vertical gap between components
+	*/
+	public WrapLayout(int align, int hgap, int vgap)
+	{
+		super(align, hgap, vgap);
+	}
+
+	/**
+	* Returns the preferred dimensions for this layout given the
+	* <i>visible</i> components in the specified target container.
+	* @param target the component which needs to be laid out
+	* @return the preferred dimensions to lay out the
+	* subcomponents of the specified container
+	*/
+	@Override
+	public Dimension preferredLayoutSize(Container target)
+	{
+		return layoutSize(target, true);
+	}
+
+	/**
+	* Returns the minimum dimensions needed to layout the <i>visible</i>
+	* components contained in the specified target container.
+	* @param target the component which needs to be laid out
+	* @return the minimum dimensions to lay out the
+	* subcomponents of the specified container
+	*/
+	@Override
+	public Dimension minimumLayoutSize(Container target)
+	{
+		Dimension minimum = layoutSize(target, false);
+		minimum.width -= (getHgap() + 1);
+		return minimum;
+	}
+
+	/**
+	* Returns the minimum or preferred dimension needed to layout the target
+	* container.
+	*
+	* @param target target to get layout size for
+	* @param preferred should preferred size be calculated
+	* @return the dimension to layout the target container
+	*/
+	private Dimension layoutSize(Container target, boolean preferred)
+	{
+	synchronized (target.getTreeLock())
+	{
+		//  Each row must fit with the width allocated to the containter.
+		//  When the container width = 0, the preferred width of the container
+		//  has not yet been calculated so lets ask for the maximum.
+
+		int targetWidth = target.getSize().width;
+		Container container = target;
+
+		while (container.getSize().width == 0 && container.getParent() != null)
+		{
+			container = container.getParent();
+		}
+
+		targetWidth = container.getSize().width;
+
+		if (targetWidth == 0)
+			targetWidth = Integer.MAX_VALUE;
+
+		int hgap = getHgap();
+		int vgap = getVgap();
+		Insets insets = target.getInsets();
+		int horizontalInsetsAndGap = insets.left + insets.right + (hgap * 2);
+		int maxWidth = targetWidth - horizontalInsetsAndGap;
+
+		//  Fit components into the allowed width
+
+		Dimension dim = new Dimension(0, 0);
+		int rowWidth = 0;
+		int rowHeight = 0;
+
+		int nmembers = target.getComponentCount();
+
+		for (int i = 0; i < nmembers; i++)
+		{
+			Component m = target.getComponent(i);
+
+			if (m.isVisible())
+			{
+				Dimension d = preferred ? m.getPreferredSize() : m.getMinimumSize();
+
+				//  Can't add the component to current row. Start a new row.
+
+				if (rowWidth + d.width > maxWidth)
+				{
+					addRow(dim, rowWidth, rowHeight);
+					rowWidth = 0;
+					rowHeight = 0;
+				}
+
+				//  Add a horizontal gap for all components after the first
+
+				if (rowWidth != 0)
+				{
+					rowWidth += hgap;
+				}
+
+				rowWidth += d.width;
+				rowHeight = Math.max(rowHeight, d.height);
+			}
+		}
+
+		addRow(dim, rowWidth, rowHeight);
+
+		dim.width += horizontalInsetsAndGap;
+		dim.height += insets.top + insets.bottom + vgap * 2;
+
+		//	When using a scroll pane or the DecoratedLookAndFeel we need to
+		//  make sure the preferred size is less than the size of the
+		//  target containter so shrinking the container size works
+		//  correctly. Removing the horizontal gap is an easy way to do this.
+
+		Container scrollPane = SwingUtilities.getAncestorOfClass(JScrollPane.class, target);
+
+		if (scrollPane != null && target.isValid())
+		{
+			dim.width -= (hgap + 1);
+		}
+
+		return dim;
+	}
+	}
+
+	/*
+	 *  A new row has been completed. Use the dimensions of this row
+	 *  to update the preferred size for the container.
+	 *
+	 *  @param dim update the width and height when appropriate
+	 *  @param rowWidth the width of the row to add
+	 *  @param rowHeight the height of the row to add
+	 */
+	private void addRow(Dimension dim, int rowWidth, int rowHeight)
+	{
+		dim.width = Math.max(dim.width, rowWidth);
+
+		if (dim.height > 0)
+		{
+			dim.height += getVgap();
+		}
+
+		dim.height += rowHeight;
+	}
+}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -721,7 +721,7 @@ public void documentEnd() {
 			}
 
 			// we'll only add seqres chains that are polymeric or unknown
-			if (type==null || (type!=null && type==EntityType.POLYMER) ) {
+			if (type==null || type==EntityType.POLYMER ) {
 				seqResChains.add(seqres);	
 			}
 
@@ -1318,6 +1318,7 @@ private void setStructNcsOps() {
 		}
 	}
 
+
 	/** This method will return the parsed protein structure, once the parsing has been finished
 	 *
 	 * @return a BioJava protein structure object

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java
@@ -167,7 +167,7 @@ private ChemComp downloadAndAdd(String recordName){
 		final File [] files = new File[1];
 		Path cif = m_tempDir.resolve("chemcomp").resolve(recordName + ".cif.gz");
 		files[0] = cif.toFile();
-		if (files != null) {
+		if (files[0] != null) {
 			addToZipFileSystem(m_zipFile, files, m_zipRootDir);
 			if (m_removeCif) for (File f : files) f.delete();
 		}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -39,7 +39,7 @@ public static String formatExonStructure(GeneChromosomePosition chromosomePositi
		return formatExonStructureReverse(chromosomePosition);

		}



		private static String formatExonStructureForward(GeneChromosomePosition chromPos) {

Expand Down