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Merge branch 'master' of github.com:biojava/biojava
* 'master' of github.com:biojava/biojava: (36 commits) Add some tests for negative residue ranges Minor javadoc & warnings fixes Fix compilation errors from merge Fix MultipleAlignmentJmol resizing bug Fixed bug where bonds from struct conn records were not made for multiple models. Latest ECOD now contains string quotes around some data fields. Need to remove them for junit tests to parse. update test for type of group based on comments from @josemduarte Fixing cath urls according to their final layout [maven-release-plugin]prepare for next development iteration [maven-release-plugin]prepare release biojava-4.2.4 new utility class for chromosome mappings. adding new dependency on guava new utility class for chromosome mappings. new utility class for chromosome mappings. Adding test for genome mapping Complete new CATH file names biojava#546 and biojava#544 Fixing biojava#544 and improving logging Some work towards fixing biojava#544 Back-porting cloning fix (see biojava#541) into bugfixes-4.2 biojava#542 changing default SCOP download location to Berkeley- SCOP. ...
2 parents 3e59d75 + 9c9d82c commit 7d39984

12 files changed

Lines changed: 341 additions & 105 deletions

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‎biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ public static String formatExonStructure(GeneChromosomePosition chromosomePositi
3939
return formatExonStructureReverse(chromosomePosition);
4040

4141
}
42-
42+
4343

4444
private static String formatExonStructureForward(GeneChromosomePosition chromPos) {
4545

‎biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -201,6 +201,24 @@ public void testGetSubRanges() throws StructureException {
201201
chain = substr.getChainByIndex(0);
202202
assertEquals("Did not find the expected number of residues in "+range, 1, chain.getAtomLength() );
203203

204+
205+
// negative residues
206+
range = "A:-3";
207+
substr = StructureTools.getSubRanges(structure2, range);
208+
assertEquals("Wrong number of chains in "+range, 1, substr.size());
209+
chain = substr.getChainByIndex(0);
210+
assertEquals("Did not find the expected number of residues in "+range, 1, chain.getAtomLength() );
211+
range = "A:-3--1";
212+
substr = StructureTools.getSubRanges(structure2, range);
213+
assertEquals("Wrong number of chains in "+range, 1, substr.size());
214+
chain = substr.getChainByIndex(0);
215+
assertEquals("Did not find the expected number of residues in "+range, 3, chain.getAtomLength() );
216+
range = "A:-3-1";
217+
substr = StructureTools.getSubRanges(structure2, range);
218+
assertEquals("Wrong number of chains in "+range, 1, substr.size());
219+
chain = substr.getChainByIndex(0);
220+
assertEquals("Did not find the expected number of residues in "+range, 4, chain.getAtomLength() );
221+
204222
// Special '-' case
205223
range = "-";
206224
substr = StructureTools.getSubRanges(structure2, range);

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java‎

Lines changed: 26 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@
2020
*/
2121
package org.biojava.nbio.structure.align.gui.jmol;
2222

23+
import java.awt.BorderLayout;
2324
import java.awt.Color;
2425
import java.awt.Container;
2526
import java.awt.Dimension;
@@ -40,6 +41,7 @@
4041
import javax.swing.JFrame;
4142
import javax.swing.JLabel;
4243
import javax.swing.JMenuBar;
44+
import javax.swing.JPanel;
4345
import javax.swing.JTextField;
4446

4547
import org.biojava.nbio.structure.Atom;
@@ -56,6 +58,7 @@
5658
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentTools;
5759
import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentWriter;
5860
import org.biojava.nbio.structure.align.webstart.AligUIManager;
61+
import org.biojava.nbio.structure.gui.WrapLayout;
5962
import org.biojava.nbio.structure.jama.Matrix;
6063
import org.forester.archaeopteryx.Archaeopteryx;
6164
import org.forester.phylogeny.Phylogeny;
@@ -137,14 +140,13 @@ public void windowClosing(WindowEvent e) {
137140
});
138141

139142
Container contentPane = frame.getContentPane();
140-
Box vBox = Box.createVerticalBox();
141143

142144
jmolPanel.addMouseMotionListener(this);
143145
jmolPanel.addMouseListener(this);
144-
jmolPanel
145-
.setPreferredSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));
146+
jmolPanel.setPreferredSize(new Dimension(DEFAULT_WIDTH, DEFAULT_HEIGHT));
147+
contentPane.add(jmolPanel,BorderLayout.CENTER);
146148

147-
vBox.add(jmolPanel);
149+
Box vBox = Box.createVerticalBox();
148150

149151
// / USER SCRIPTING COMMAND
150152
JTextField field = new JTextField();
@@ -162,8 +164,10 @@ public void windowClosing(WindowEvent e) {
162164
// / STRUCTURE SELECTION
163165
if (multAln != null) {
164166

165-
Box hBox00 = Box.createHorizontalBox();
166-
hBox00.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
167+
JPanel modelSelection = new JPanel();
168+
modelSelection.setLayout(new WrapLayout(WrapLayout.LEFT));
169+
modelSelection.setSize(new Dimension(DEFAULT_WIDTH,30));
170+
vBox.add(modelSelection);
167171

168172
JButton show = new JButton("Show Only: ");
169173
show.addActionListener(new ActionListener() {
@@ -184,27 +188,16 @@ public void actionPerformed(ActionEvent e) {
184188
jmolPanel.executeCmd(cmd + " restore selection;");
185189
}
186190
});
187-
hBox00.add(show);
188-
hBox00.add(Box.createGlue());
189-
vBox.add(hBox00);
191+
modelSelection.add(show);
190192

191-
// A line of structures of maximum 5
192-
for (int line = 0; line < 1 + (multAln.size() / 5); line++) {
193-
Box hBox0 = Box.createHorizontalBox();
194-
hBox0.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
195-
196-
for (int str = line * 5; str < Math.min((line + 1) * 5,
197-
multAln.size()); str++) {
198-
JCheckBox structureSelection = new JCheckBox(multAln
199-
.getEnsemble().getStructureIdentifiers().get(str)
200-
.getIdentifier());
201-
hBox0.add(structureSelection);
202-
hBox0.add(Box.createGlue());
203-
structureSelection.setSelected(true);
204-
selectedStructures.add(structureSelection);
205-
}
206-
207-
vBox.add(hBox0);
193+
// Check boxes for all models
194+
for(int str = 0; str < multAln.size();str++) {
195+
JCheckBox structureSelection = new JCheckBox(multAln
196+
.getEnsemble().getStructureIdentifiers().get(str)
197+
.getIdentifier());
198+
modelSelection.add(structureSelection);
199+
structureSelection.setSelected(true);
200+
selectedStructures.add(structureSelection);
208201
}
209202
}
210203

@@ -214,35 +207,35 @@ public void actionPerformed(ActionEvent e) {
214207

215208
String[] styles = new String[] { "Cartoon", "Backbone", "CPK",
216209
"Ball and Stick", "Ligands", "Ligands and Pocket" };
217-
JComboBox style = new JComboBox(styles);
210+
JComboBox<String> style = new JComboBox<>(styles);
218211

219212
hBox1.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
220213

221214
hBox1.add(new JLabel("Style"));
222215
hBox1.add(style);
223216
vBox.add(hBox1);
224-
contentPane.add(vBox);
225217

226218
style.addActionListener(jmolPanel);
227219

228220
String[] colorModes = new String[] { "Secondary Structure", "By Chain",
229221
"Rainbow", "By Element", "By Amino Acid", "Hydrophobicity",
230222
"Suggest Domains", "Show SCOP Domains" };
231-
JComboBox jcolors = new JComboBox(colorModes);
223+
JComboBox<String> jcolors = new JComboBox<>(colorModes);
232224
jcolors.addActionListener(jmolPanel);
233225

234226
hBox1.add(Box.createGlue());
235227
hBox1.add(new JLabel("Color"));
236228
hBox1.add(jcolors);
237229

238230
String[] cPalette = { "Spectral", "Set1", "Set2", "Pastel" };
239-
JComboBox palette = new JComboBox(cPalette);
231+
JComboBox<String> palette = new JComboBox<>(cPalette);
240232

241233
palette.addActionListener(new ActionListener() {
242234
@Override
243235
public void actionPerformed(ActionEvent e) {
244236

245-
JComboBox source = (JComboBox) e.getSource();
237+
@SuppressWarnings("unchecked")
238+
JComboBox<String> source = (JComboBox<String>) e.getSource();
246239
String value = source.getSelectedItem().toString();
247240
evalString("save selection; select *; color grey; "
248241
+ "select ligand; color CPK;");
@@ -268,6 +261,7 @@ public void actionPerformed(ActionEvent e) {
268261

269262
// / CHECK BOXES
270263
Box hBox2 = Box.createHorizontalBox();
264+
hBox2.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
271265

272266
JButton resetDisplay = new JButton("Reset Display");
273267
resetDisplay.addActionListener(new ActionListener() {
@@ -337,7 +331,7 @@ public void itemStateChanged(ItemEvent e) {
337331

338332
vBox.add(hBox);
339333

340-
contentPane.add(vBox);
334+
contentPane.add(vBox,BorderLayout.SOUTH);
341335
MyJmolStatusListener li = (MyJmolStatusListener) jmolPanel
342336
.getStatusListener();
343337

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/WrapLayout.java‎

Lines changed: 195 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,195 @@
1+
package org.biojava.nbio.structure.gui;
2+
3+
import java.awt.*;
4+
import javax.swing.JScrollPane;
5+
import javax.swing.SwingUtilities;
6+
7+
/**
8+
* FlowLayout subclass that fully supports wrapping of components.
9+
*
10+
* Originally written by Rob Camick
11+
* https://tips4java.wordpress.com/2008/11/06/wrap-layout/
12+
*/
13+
public class WrapLayout extends FlowLayout
14+
{
15+
private Dimension preferredLayoutSize;
16+
17+
/**
18+
* Constructs a new <code>WrapLayout</code> with a left
19+
* alignment and a default 5-unit horizontal and vertical gap.
20+
*/
21+
public WrapLayout()
22+
{
23+
super();
24+
}
25+
26+
/**
27+
* Constructs a new <code>FlowLayout</code> with the specified
28+
* alignment and a default 5-unit horizontal and vertical gap.
29+
* The value of the alignment argument must be one of
30+
* <code>WrapLayout</code>, <code>WrapLayout</code>,
31+
* or <code>WrapLayout</code>.
32+
* @param align the alignment value
33+
*/
34+
public WrapLayout(int align)
35+
{
36+
super(align);
37+
}
38+
39+
/**
40+
* Creates a new flow layout manager with the indicated alignment
41+
* and the indicated horizontal and vertical gaps.
42+
* <p>
43+
* The value of the alignment argument must be one of
44+
* <code>WrapLayout</code>, <code>WrapLayout</code>,
45+
* or <code>WrapLayout</code>.
46+
* @param align the alignment value
47+
* @param hgap the horizontal gap between components
48+
* @param vgap the vertical gap between components
49+
*/
50+
public WrapLayout(int align, int hgap, int vgap)
51+
{
52+
super(align, hgap, vgap);
53+
}
54+
55+
/**
56+
* Returns the preferred dimensions for this layout given the
57+
* <i>visible</i> components in the specified target container.
58+
* @param target the component which needs to be laid out
59+
* @return the preferred dimensions to lay out the
60+
* subcomponents of the specified container
61+
*/
62+
@Override
63+
public Dimension preferredLayoutSize(Container target)
64+
{
65+
return layoutSize(target, true);
66+
}
67+
68+
/**
69+
* Returns the minimum dimensions needed to layout the <i>visible</i>
70+
* components contained in the specified target container.
71+
* @param target the component which needs to be laid out
72+
* @return the minimum dimensions to lay out the
73+
* subcomponents of the specified container
74+
*/
75+
@Override
76+
public Dimension minimumLayoutSize(Container target)
77+
{
78+
Dimension minimum = layoutSize(target, false);
79+
minimum.width -= (getHgap() + 1);
80+
return minimum;
81+
}
82+
83+
/**
84+
* Returns the minimum or preferred dimension needed to layout the target
85+
* container.
86+
*
87+
* @param target target to get layout size for
88+
* @param preferred should preferred size be calculated
89+
* @return the dimension to layout the target container
90+
*/
91+
private Dimension layoutSize(Container target, boolean preferred)
92+
{
93+
synchronized (target.getTreeLock())
94+
{
95+
// Each row must fit with the width allocated to the containter.
96+
// When the container width = 0, the preferred width of the container
97+
// has not yet been calculated so lets ask for the maximum.
98+
99+
int targetWidth = target.getSize().width;
100+
Container container = target;
101+
102+
while (container.getSize().width == 0 && container.getParent() != null)
103+
{
104+
container = container.getParent();
105+
}
106+
107+
targetWidth = container.getSize().width;
108+
109+
if (targetWidth == 0)
110+
targetWidth = Integer.MAX_VALUE;
111+
112+
int hgap = getHgap();
113+
int vgap = getVgap();
114+
Insets insets = target.getInsets();
115+
int horizontalInsetsAndGap = insets.left + insets.right + (hgap * 2);
116+
int maxWidth = targetWidth - horizontalInsetsAndGap;
117+
118+
// Fit components into the allowed width
119+
120+
Dimension dim = new Dimension(0, 0);
121+
int rowWidth = 0;
122+
int rowHeight = 0;
123+
124+
int nmembers = target.getComponentCount();
125+
126+
for (int i = 0; i < nmembers; i++)
127+
{
128+
Component m = target.getComponent(i);
129+
130+
if (m.isVisible())
131+
{
132+
Dimension d = preferred ? m.getPreferredSize() : m.getMinimumSize();
133+
134+
// Can't add the component to current row. Start a new row.
135+
136+
if (rowWidth + d.width > maxWidth)
137+
{
138+
addRow(dim, rowWidth, rowHeight);
139+
rowWidth = 0;
140+
rowHeight = 0;
141+
}
142+
143+
// Add a horizontal gap for all components after the first
144+
145+
if (rowWidth != 0)
146+
{
147+
rowWidth += hgap;
148+
}
149+
150+
rowWidth += d.width;
151+
rowHeight = Math.max(rowHeight, d.height);
152+
}
153+
}
154+
155+
addRow(dim, rowWidth, rowHeight);
156+
157+
dim.width += horizontalInsetsAndGap;
158+
dim.height += insets.top + insets.bottom + vgap * 2;
159+
160+
// When using a scroll pane or the DecoratedLookAndFeel we need to
161+
// make sure the preferred size is less than the size of the
162+
// target containter so shrinking the container size works
163+
// correctly. Removing the horizontal gap is an easy way to do this.
164+
165+
Container scrollPane = SwingUtilities.getAncestorOfClass(JScrollPane.class, target);
166+
167+
if (scrollPane != null && target.isValid())
168+
{
169+
dim.width -= (hgap + 1);
170+
}
171+
172+
return dim;
173+
}
174+
}
175+
176+
/*
177+
* A new row has been completed. Use the dimensions of this row
178+
* to update the preferred size for the container.
179+
*
180+
* @param dim update the width and height when appropriate
181+
* @param rowWidth the width of the row to add
182+
* @param rowHeight the height of the row to add
183+
*/
184+
private void addRow(Dimension dim, int rowWidth, int rowHeight)
185+
{
186+
dim.width = Math.max(dim.width, rowWidth);
187+
188+
if (dim.height > 0)
189+
{
190+
dim.height += getVgap();
191+
}
192+
193+
dim.height += rowHeight;
194+
}
195+
}

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