Fix small bug in QuatSymmetryResults

lafita · lafita · commit 97f26351350d · 2016-07-25T12:55:33.000+02:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoQuatSymmetryJmol.java b/biojava-structure-gui/src/main/java/demo/DemoQuatSymmetryJmol.java
@@ -61,7 +61,7 @@ public class DemoQuatSymmetryJmol {
 	public static void main(String[] args) throws IOException,
 			StructureException {
 
-		String name = "4hhb";
+		String name = "1VYM";
 
 		// Download the biological assembly
 		AtomCache cache = new AtomCache();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
@@ -24,6 +24,7 @@
 
 import java.util.Collections;
 import java.util.List;
+
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.cluster.SubunitCluster;
 import org.biojava.nbio.structure.cluster.SubunitClusterUtils;
@@ -47,6 +48,7 @@ public class QuatSymmetryResults {
 
 	// Cached properties
 	private String stoichiometry;
+	int subunitCount;
 
 	// Information about the symmetry
 	private SymmetryPerceptionMethod method;
@@ -70,7 +72,11 @@ public QuatSymmetryResults(List<SubunitCluster> clusters,
 		this.clusters = clusters;
 		this.stoichiometry = SubunitClusterUtils
 				.getStoichiometryString(clusters);
-
+		
+		subunitCount = 0;
+		for (SubunitCluster c : clusters)
+			subunitCount += c.size();
+			
 		this.rotationGroup = rotationGroup;
 		this.method = method;
 	}
@@ -102,7 +108,16 @@ public QuatSymmetryResults(List<SubunitCluster> clusters,
 	public List<SubunitCluster> getSubunitClusters() {
 		return Collections.unmodifiableList(clusters);
 	}
-
+	
+	/**
+	 * Return the number of Subunits involved in the symmetry.
+	 * 
+	 * @return the number of Subunits
+	 */
+	public int getSubunitCount() {
+		return subunitCount;
+	}
+	
 	/**
 	 * @return rotation group (point group) information representing rotational
 	 *         quaternary symmetry.
@@ -211,7 +226,7 @@ public void setStructure(Structure structure) {
 	@Override
 	public String toString() {
 		return "QuatSymmetryResults [stoichiometry: " + getStoichiometry()
-				+ ", symmetry: " + getSymmetry() + ", pseudoStoichiometric: "
+				+ ", symmetry: " + getSymmetry() + ", pseudo-stoichiometric: "
 				+ isPseudoStoichiometric() + ", local: " + local + ", method: "
 				+ method + "]";
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetrySubunits.java
@@ -106,10 +106,16 @@ public List<Integer> getClusterIds() {
 	 * @return A List of the Chain Ids of each Subunit
 	 */
 	public List<String> getChainIds() {
-		return clusters
-				.stream()
-				.map(c -> c.getSubunits().get(0).getRepresentativeAtoms()[0]
-						.getGroup().getChainId()).collect(Collectors.toList());
+		
+		List<String> chains = new ArrayList<String>(getSubunitCount());
+
+		// Loop through all subunits in the clusters and fill Lists
+		for (int c = 0; c < clusters.size(); c++) {
+			for (int s = 0; s < clusters.get(c).size(); s++)
+				chains.add(clusters.get(c).getSubunits().get(s).getName());
+		}
+		
+		return chains;
 	}
 
 	/**
@@ -120,7 +126,8 @@ public List<String> getChainIds() {
 	 * @return A List of the Model number of each Subunit
 	 */
 	public List<Integer> getModelNumbers() {
-		List<Integer> models = new ArrayList<Integer>(clusterIds.size());
+		
+		List<Integer> models = new ArrayList<Integer>(getSubunitCount());
 
 		// Loop through all subunits in the clusters and fill Lists
 		for (int c = 0; c < clusters.size(); c++) {
