Introduce CE-Symm parameter to control optimization steps

lafita · lafita · commit 821b410dfc36 · 2016-02-03T11:12:51.000+01:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CESymmParameters.java
@@ -48,6 +48,7 @@ public class CESymmParameters extends CeParameters {
 	private int minCoreLength;
 	private double distanceCutoff;
 	private boolean gaps;
+	private int optimizationSteps;
 
 	public static enum OrderDetectorMethod {
 		SEQUENCE_FUNCTION, GRAPH_COMPONENT, ANGLE, USER_INPUT;
@@ -101,6 +102,7 @@ public CESymmParameters clone() {
 		p.minCoreLength = minCoreLength;
 		p.distanceCutoff = distanceCutoff;
 		p.gaps = gaps;
+		p.optimizationSteps = optimizationSteps;
 
 		p.winSize = winSize;
 		p.rmsdThr = rmsdThr;
@@ -135,6 +137,7 @@ public void reset() {
 		minCoreLength = 15;
 		distanceCutoff = 7.0;
 		gaps = true;
+		optimizationSteps = 0;
 	}
 
 	@Override
@@ -220,6 +223,10 @@ public List<String> getUserConfigHelp() {
 
 		// gaps
 		params.add("MStA Gaps: allow gaps in the multiple alignment if true.");
+		
+		// optimization steps
+		params.add("Optimization Steps: maximum number of optimization steps:"
+				+ " 0 means calculated automatically with the alignment length.");
 
 		return params;
 	}
@@ -240,6 +247,7 @@ public List<String> getUserConfigParameters() {
 		params.add("MinCoreLength");
 		params.add("DistanceCutoff");
 		params.add("Gaps");
+		params.add("OptimizationSteps");
 		return params;
 	}
 
@@ -259,6 +267,7 @@ public List<String> getUserConfigParameterNames() {
 		params.add("Minimum Core Length");
 		params.add("Distance Cutoff");
 		params.add("MStA Gaps");
+		params.add("Optimization Steps");
 		return params;
 	}
 
@@ -279,6 +288,7 @@ public List<Class> getUserConfigTypes() {
 		params.add(Integer.class);
 		params.add(Double.class);
 		params.add(Boolean.class);
+		params.add(Integer.class);
 		return params;
 	}
 
@@ -395,4 +405,12 @@ public void setGaps(Boolean gaps) {
 		this.gaps = gaps;
 	}
 
+	public int getOptimizationSteps() {
+		return optimizationSteps;
+	}
+
+	public void setOptimizationSteps(Integer optimizationSteps) {
+		this.optimizationSteps = optimizationSteps;
+	}
+
 }
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
@@ -69,7 +69,7 @@ public class SymmOptimizer {
 	// Optimization parameters
 	private int Rmin = 2; // min aligned subunits per column
 	private int Lmin; // min subunit length
-	private int maxIterFactor = 100; // max iterations constant
+	private int maxIter; // max iterations
 	private double C = 20; // probability of accept bad moves constant
 
 	// Score function parameters
@@ -127,6 +127,10 @@ public SymmOptimizer(CeSymmResult symmResult) {
 			Rmin = Math.max(order / 2, 2);
 		else
 			Rmin = order;
+		
+		maxIter = symmResult.getParams().getOptimizationSteps();
+		if (maxIter < 1)
+			maxIter = 100 * atoms.length;
 	}
 
 	private void initialize() throws StructureException, RefinerFailedException {
@@ -192,8 +196,7 @@ public MultipleAlignment optimize() throws StructureException,
 
 		int conv = 0; // Number of steps without an alignment improvement
 		int i = 1;
-		int maxIter = maxIterFactor * atoms.length;
-		int stepsToConverge = Math.max(maxIter / 50, 1000);
+		int stepsToConverge = Math.max(maxIter / 20, 1000);
 
 		while (i < maxIter && conv < stepsToConverge) {
 
