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lafitalafita
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Make display verbose using logger
1 parent ed5616c commit a062cfe

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3 files changed

+32
-21
lines changed

3 files changed

+32
-21
lines changed

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

Lines changed: 17 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,8 @@
3636
import org.biojava.nbio.structure.align.webstart.AligUIManager;
3737
import org.biojava.nbio.structure.jama.Matrix;
3838
import org.jcolorbrewer.ColorBrewer;
39+
import org.slf4j.Logger;
40+
import org.slf4j.LoggerFactory;
3941

4042
/**
4143
* A class that provides a 3D visualization Frame in Jmol for
@@ -54,6 +56,9 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
5456

5557
private static final String LIGAND_DISPLAY_SCRIPT =
5658
"select ligand; wireframe 40; spacefill 120; color CPK;";
59+
60+
private static final Logger logger =
61+
LoggerFactory.getLogger(MultipleAlignmentJmol.class);
5762

5863
/**
5964
* Default constructor creates an empty JmolPanel window,
@@ -235,7 +240,7 @@ public void actionPerformed(ActionEvent e) {
235240

236241
@Override
237242
public void actionPerformed(ActionEvent e) {
238-
System.out.println("reset!!");
243+
logger.info("reset!!");
239244
jmolPanel.executeCmd("restore STATE state_1");
240245

241246
}
@@ -315,25 +320,24 @@ protected void initCoords(){
315320
if ( structure != null)
316321
setStructure(structure);
317322
else {
318-
System.err.println("could not find anything to display!");
323+
logger.error("Could not find anything to display!");
319324
return;
320325
}
321326
}
322-
Structure artificial = MultipleAlignmentDisplay.
323-
getAlignedStructure(transformedAtoms);
324-
325327
PDBHeader header = new PDBHeader();
326328
String title = multAln.getEnsemble().getAlgorithmName() +
327329
" V." +multAln.getEnsemble().getVersion() + " : ";
328330

329331
for (String name:multAln.getEnsemble().getStructureNames()){
330332
title += name + " ";
331333
}
334+
Structure artificial = MultipleAlignmentDisplay.
335+
getAlignedStructure(transformedAtoms);
332336

333-
System.out.println(title);
334-
header.setTitle(title);
335337
artificial.setPDBHeader(header);
336338
setStructure(artificial);
339+
header.setTitle(title);
340+
logger.info(title);
337341

338342
} catch (StructureException e){
339343
e.printStackTrace();
@@ -352,23 +356,22 @@ public void actionPerformed(ActionEvent e) {
352356
String cmd = e.getActionCommand();
353357
if ( cmd.equals(MenuCreator.TEXT_ONLY)) {
354358
if ( multAln == null) {
355-
System.err.println("Currently not viewing an alignment!");
359+
logger.error("Currently not viewing an alignment!");
356360
return;
357361
}
358-
System.out.println(
359-
"Option currently not available for Multiple Alignments");
362+
logger.warn("Option not available for MultipleAlignments");
360363

361364
} else if ( cmd.equals(MenuCreator.PAIRS_ONLY)) {
362365
if ( multAln == null) {
363-
System.err.println("Currently not viewing an alignment!");
366+
logger.error("Currently not viewing an alignment!");
364367
return;
365368
}
366369
String result = MultipleAlignmentWriter.toAlignedResidues(multAln);
367370
MultipleAlignmentDisplay.showAlignmentImage(multAln, result);
368371

369372
} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)){
370373
if ( multAln == null) {
371-
System.err.println("Currently not viewing an alignment!");
374+
logger.error("Currently not viewing an alignment!");
372375
return;
373376
}
374377
try {
@@ -380,7 +383,7 @@ public void actionPerformed(ActionEvent e) {
380383

381384
} else if (cmd.equals(MenuCreator.FATCAT_TEXT)){
382385
if ( multAln == null) {
383-
System.err.println("Currently not viewing an alignment!");
386+
logger.error("Currently not viewing an alignment!");
384387
return;
385388
}
386389
String result = MultipleAlignmentWriter.toFatCat(multAln)+"\n";
@@ -516,7 +519,7 @@ public void resetDisplay() {
516519
if (multAln != null && transformedAtoms != null) {
517520
String script = getJmolString(multAln, transformedAtoms,
518521
colorPalette, colorByBlocks.isSelected());
519-
//System.out.println(script);
522+
logger.debug(script);
520523
evalString(script);
521524
jmolPanel.evalString("save STATE state_1");
522525
}

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

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -82,6 +82,7 @@ public static MultipleAlignmentJmol display(MultipleAlignment msa,
8282
} else {
8383
//Show the optimal alignment if it was not refined
8484
jmol = MultipleAlignmentDisplay.display(msa);
85+
addSymmetryMenu(null, null);
8586
jmol.setColorByBlocks(true);
8687
}
8788

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

Lines changed: 14 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,8 @@
77
import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
88
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
99
import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes;
10+
import org.slf4j.Logger;
11+
import org.slf4j.LoggerFactory;
1012

1113
/**
1214
* Action Listener for the symmetry menu.
@@ -21,10 +23,13 @@ public class SymmetryListener implements ActionListener{
2123
private MultipleAlignmentJmol jmol;
2224
private MultipleAlignment msa;
2325
private SymmetryAxes axes;
26+
27+
private static final Logger logger =
28+
LoggerFactory.getLogger(SymmetryListener.class);
2429

2530
public SymmetryListener(MultipleAlignmentJmol jmol, SymmetryAxes axes) {
2631
this.jmol = jmol;
27-
this.msa = jmol.getMultipleAlignment();
32+
if (jmol != null) this.msa = jmol.getMultipleAlignment();
2833
this.axes = axes;
2934
}
3035

@@ -34,7 +39,7 @@ public void actionPerformed(ActionEvent ae) {
3439
String cmd = ae.getActionCommand();
3540
if (cmd.equals("Subunit Superposition")){
3641
if (msa == null) {
37-
System.err.println("Currently not displaying a symmetry!");
42+
logger.error("Currently not displaying a symmetry!");
3843
return;
3944
}
4045
try {
@@ -47,7 +52,7 @@ public void actionPerformed(ActionEvent ae) {
4752

4853
} else if (cmd.equals("Multiple Structure Alignment")){
4954
if (msa == null) {
50-
System.err.println("Currently not displaying a symmetry!");
55+
logger.error("Currently not displaying a symmetry!");
5156
return;
5257
}
5358
try {
@@ -59,18 +64,20 @@ public void actionPerformed(ActionEvent ae) {
5964
}
6065

6166
} else if (cmd.equals("Point Group Symmetry")){
62-
if (msa != null) {
63-
String script = SymmetryDisplay.printPointGroupAxes(msa);
64-
jmol.evalString(script);
67+
if (msa == null) {
68+
logger.error("Currently not displaying a symmetry!");
6569
return;
6670
}
71+
String script = SymmetryDisplay.printPointGroupAxes(msa);
72+
jmol.evalString(script);
73+
return;
6774

6875
} else if (cmd.equals("Show Symmetry Axes")){
6976
if (axes != null) {
7077
String s = SymmetryDisplay.printSymmetryAxes(msa, axes, false);
7178
jmol.evalString(s);
7279
return;
73-
} else System.err.println("No axes for this symmetry");
80+
} else logger.error("No axes found for this symmetry result");
7481

7582
} else if (cmd.equals("New Symmetry Analysis")){
7683
SymmetryGui.getInstance();

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