Final CeSymm display options before release

lafita · lafita · commit 065624ccbed6 · 2016-03-07T10:53:01.000+01:00
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -102,7 +102,8 @@ public static MultipleAlignmentJmol displayFull(CeSymmResult symm)
 	public static AbstractAlignmentJmol display(CeSymmResult symmResult)
 			throws StructureException {
 
-		if (symmResult.isRefined()) {
+		if (symmResult.isSignificant() && symmResult.isRefined()) {
+			// Show the structure colored by repeat
 			MultipleAlignment msa = symmResult.getMultipleAlignment();
 			List<Atom[]> atoms = msa.getAtomArrays();
 			MultipleAlignmentJmol jmol = new MultipleAlignmentJmol(msa, atoms);
@@ -113,14 +114,16 @@ public static AbstractAlignmentJmol display(CeSymmResult symmResult)
 			jmol.setTitle(getSymmTitle(symmResult));
 			return jmol;
 		} else {
-			// Show the optimal alignment only if it was not refined
+			// Show the optimal self-alignment
 			Logger.info("Showing optimal self-alignment");
 			Atom[] cloned = StructureTools
 					.cloneAtomArray(symmResult.getAtoms());
 			AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
 					symmResult.getSelfAlignment(), symmResult.getAtoms(),
 					cloned);
-			jmol.setTitle(jmol.getTitle() + " Optimal Self-Alignment");
+			RotationAxis axis = new RotationAxis(symmResult.getSelfAlignment());
+			jmol.evalString(axis.getJmolScript(symmResult.getAtoms()));
+			jmol.setTitle(getSymmTitle(symmResult));
 			return jmol;
 		}
 	}
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryListener.java
@@ -28,6 +28,7 @@
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
 import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
 import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
+import org.biojava.nbio.structure.align.util.RotationAxis;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -77,7 +78,9 @@ public void actionPerformed(ActionEvent ae) {
 				Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
 				AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
 						symm.getSelfAlignment(), symm.getAtoms(), cloned);
-				jmol.setTitle(jmol.getTitle() + " Optimal Self-Alignment");
+				RotationAxis axis = new RotationAxis(symm.getSelfAlignment());
+				jmol.evalString(axis.getJmolScript(symm.getAtoms()));
+				jmol.setTitle(SymmetryDisplay.getSymmTitle(symm));
 
 			} else if (cmd.equals("Show Symmetry Group")) {
 				String script = SymmetryDisplay.printSymmetryGroup(symm);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -248,12 +248,6 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params)
 		// Store the optimal self-alignment
 		result.setSelfAlignment(optimalAFP);
 		result.setStructureId(id);
-		
-		// Do not try the refinement if the self-alignment is not significant
-		if (optimalAFP.getTMScore() < params.getScoreThreshold()){
-			result.setSymmOrder(1);
-			return result;
-		}
 
 		// Determine the symmetry Type or get the one in params
 		if (params.getSymmType() == SymmetryType.AUTO) {
@@ -266,6 +260,12 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params)
 			}
 		} else
 			result.setType(params.getSymmType());
+		
+		// Do not try the refinement if the self-alignment is not significant
+		if (optimalAFP.getTMScore() < params.getScoreThreshold()){
+			result.setSymmOrder(1);
+			return result;
+		}
 
 		// STEP 3: order detection & symmetry refinement, apply consistency
 		try {
@@ -416,19 +416,14 @@ public static CeSymmResult analyze(Atom[] atoms, CESymmParameters params)
 		if (result.isRefined()) {
 			// Optimize the global alignment freely once more (final step)
 			if (params.getOptimization() && result.getSymmLevels() > 1) {
-				// Remove the axes to do free superposition optimization TODO
-				SymmetryAxes axes = result.getAxes();
-				result.setAxes(null);
 				try {
 					SymmOptimizer optimizer = new SymmOptimizer(result);
 					MultipleAlignment optimized = optimizer.optimize();
 					// Set the optimized MultipleAlignment and the axes
 					result.setMultipleAlignment(optimized);
-					result.setAxes(axes);
 				} catch (RefinerFailedException e) {
 					logger.info("Final optimization failed:" + e.getMessage());
 				}
-				result.setAxes(axes);
 			}
 			result.getMultipleAlignment().getEnsemble()
 					.setStructureIdentifiers(result.getRepeatsID());
