Superimpose freely at the end in case more than one symmetry level

lafita · lafita · commit e15234852680 · 2016-02-03T12:04:36.000+01:00
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java
@@ -180,6 +180,12 @@ public static JMenuBar initJmolMenu(JFrame frame,
 				dotplot.addActionListener(new DotPlotListener(afpChain));
 				view.add(dotplot);
 			}
+			//Phylogenetics - only if it is a MultipleAlignment
+			if (afpChain == null){
+				JMenuItem tree = new JMenuItem(PHYLOGENETIC_TREE);
+				tree.setMnemonic(KeyEvent.VK_T);
+				view.add(tree);
+			}
 		}
 		menu.add(view);
 
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
@@ -408,12 +408,17 @@ public static CeSymmResult analyze(Atom[] atoms, CESymmParameters params)
 		CeSymmResult result = iter.execute(atoms);
 
 		if (result.isSignificant()) {
-			// Optimize the global alignment once more (final step)
+			// Optimize the global alignment freely once more (final step)
 			if (params.getOptimization() && result.getSymmLevels() > 1) {
 				try {
+					//Remove the axes to do free superposition optimization
+					SymmetryAxes axes = result.getAxes();
+					result.setAxes(null);
 					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());
 					// Return the un-optimized result instead
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -196,7 +196,7 @@ public MultipleAlignment optimize() throws StructureException,
 
 		int conv = 0; // Number of steps without an alignment improvement
 		int i = 1;
-		int stepsToConverge = Math.max(maxIter / 20, 1000);
+		int stepsToConverge = Math.max(maxIter / 50, 1000);
 
 		while (i < maxIter && conv < stepsToConverge) {
 

Original file line number	Diff line number	Diff line change
`@@ -180,6 +180,12 @@ public static JMenuBar initJmolMenu(JFrame frame,`
`180`	`180`	`dotplot.addActionListener(new DotPlotListener(afpChain));`
`181`	`181`	`view.add(dotplot);`
`182`	`182`	`}`
	`183`	`+ //Phylogenetics - only if it is a MultipleAlignment`
	`184`	`+ if (afpChain == null){`
	`185`	`+ JMenuItem tree = new JMenuItem(PHYLOGENETIC_TREE);`
	`186`	`+ tree.setMnemonic(KeyEvent.VK_T);`
	`187`	`+ view.add(tree);`
	`188`	`+ }`
`183`	`189`	`}`
`184`	`190`	`menu.add(view);`
`185`	`191`