Skip to content

Commit 0756453

Browse files
lafitalafita
committed
A couple of SymmetryGUI improvements
1 parent 11d7162 commit 0756453

File tree

2 files changed

+33
-26
lines changed

2 files changed

+33
-26
lines changed

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

Lines changed: 32 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -48,8 +48,8 @@
4848
import org.biojava.nbio.structure.StructureException;
4949
import org.biojava.nbio.structure.StructureIdentifier;
5050
import org.biojava.nbio.structure.align.gui.MenuCreator;
51-
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
5251
import org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI;
52+
import org.biojava.nbio.structure.align.gui.MultipleAlignmentJmolDisplay;
5353
import org.biojava.nbio.structure.align.multiple.Block;
5454
import org.biojava.nbio.structure.align.multiple.BlockSet;
5555
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
@@ -78,8 +78,7 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
7878
private JCheckBox colorByBlocks;
7979
private List<JCheckBox> selectedStructures;
8080

81-
private static final String LIGAND_DISPLAY_SCRIPT =
82-
"select ligand; wireframe 40; spacefill 120; color CPK;";
81+
private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
8382

8483
private static final Logger logger = LoggerFactory
8584
.getLogger(MultipleAlignmentJmol.class);
@@ -162,17 +161,19 @@ public void windowClosing(WindowEvent e) {
162161

163162
// / STRUCTURE SELECTION
164163
if (multAln != null) {
165-
Box hBox0 = Box.createHorizontalBox();
166-
hBox0.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
167164

165+
Box hBox00 = Box.createHorizontalBox();
166+
hBox00.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
167+
168168
JButton show = new JButton("Show Only: ");
169169
show.addActionListener(new ActionListener() {
170170

171171
@Override
172172
public void actionPerformed(ActionEvent e) {
173173
jmolPanel.evalString("save selection;");
174-
String cmd = getJmolString(multAln, transformedAtoms,
175-
colorPalette, colorByBlocks.isSelected());
174+
String cmd = getJmolString(multAln,
175+
transformedAtoms, colorPalette,
176+
colorByBlocks.isSelected());
176177
cmd += "; restrict ";
177178
for (int st = 0; st < multAln.size(); st++) {
178179
if (selectedStructures.get(st).isSelected()) {
@@ -183,21 +184,28 @@ public void actionPerformed(ActionEvent e) {
183184
jmolPanel.executeCmd(cmd + " restore selection;");
184185
}
185186
});
187+
hBox00.add(show);
188+
hBox00.add(Box.createGlue());
189+
vBox.add(hBox00);
190+
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+
}
186206

187-
hBox0.add(show);
188-
hBox0.add(Box.createGlue());
189-
190-
for (int str = 0; str < multAln.size(); str++) {
191-
JCheckBox structureSelection = new JCheckBox(multAln
192-
.getEnsemble().getStructureIdentifiers().get(str)
193-
.getIdentifier());
194-
hBox0.add(structureSelection);
195-
hBox0.add(Box.createGlue());
196-
structureSelection.setSelected(true);
197-
selectedStructures.add(structureSelection);
207+
vBox.add(hBox0);
198208
}
199-
200-
vBox.add(hBox0);
201209
}
202210

203211
// / COMBO BOXES
@@ -260,7 +268,6 @@ public void actionPerformed(ActionEvent e) {
260268

261269
// / CHECK BOXES
262270
Box hBox2 = Box.createHorizontalBox();
263-
hBox2.setMaximumSize(new Dimension(Short.MAX_VALUE, 30));
264271

265272
JButton resetDisplay = new JButton("Reset Display");
266273
resetDisplay.addActionListener(new ActionListener() {
@@ -414,12 +421,12 @@ public void actionPerformed(ActionEvent ae) {
414421
// Kimura, Structural and Fractional Dissimilarity Score
415422
Phylogeny kimura = MultipleAlignmentTools
416423
.getKimuraTree(multAln);
417-
Phylogeny sdm = MultipleAlignmentTools
418-
.getHSDMTree(multAln);
424+
Phylogeny sdm = MultipleAlignmentTools.getHSDMTree(multAln);
419425
// Phylogeny structural = MultipleAlignmentTools
420-
// .getStructuralTree(multAln);
426+
// .getStructuralTree(multAln);
421427

422-
Archaeopteryx.createApplication(new Phylogeny[] { kimura, sdm });
428+
Archaeopteryx
429+
.createApplication(new Phylogeny[] { kimura, sdm });
423430
}
424431
} catch (Exception e) {
425432
logger.error("Could not complete display option.", e);

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ public void actionPerformed(ActionEvent ae) {
6666
try {
6767
if (cmd.equals("Repeats Superposition")) {
6868
MultipleAlignmentJmol j = SymmetryDisplay.displayRepeats(symm);
69-
String s = SymmetryDisplay.printSymmetryAxes(symm);
69+
String s = SymmetryDisplay.printSymmetryAxes(symm, false);
7070
j.evalString(s);
7171

7272
} else if (cmd.equals("Multiple Structure Alignment")) {

0 commit comments

Comments
 (0)