Port the getReasons method from symmetry project

lafita · lafita · commit 3037f707e013 · 2016-03-29T12:37:39.000+02:00
Now included into CeSymmResults.
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
@@ -43,7 +43,9 @@
 import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;
 import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGeneratorPointGroup;
 import org.biojava.nbio.structure.symmetry.utils.SymmetryTools;
-import org.jmol.util.Logger;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Class that provides visualizations methods for symmetry alignments. Call the
@@ -54,6 +56,9 @@
  *
  */
 public class SymmetryDisplay {
+	
+	private static final Logger logger = LoggerFactory
+			.getLogger(SymmetryDisplay.class);
 
 	/**
 	 * Displays a multiple alignment of the symmetry repeats.
@@ -115,7 +120,7 @@ public static AbstractAlignmentJmol display(CeSymmResult symmResult)
 			return jmol;
 		} else {
 			// Show the optimal self-alignment
-			Logger.info("Showing optimal self-alignment");
+			logger.info("Showing optimal self-alignment");
 			Atom[] cloned = StructureTools
 					.cloneAtomArray(symmResult.getAtoms());
 			AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
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
@@ -300,11 +300,12 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params)
 						atoms);
 				break;
 			}
+			result.setSymmOrder(order);
+			
 			// REFINEMENT
 			SymmetryRefiner refiner = null;
 			switch (params.getRefineMethod()) {
 			case NOT_REFINED:
-				result.setSymmOrder(order);
 				return result;
 			case SEQUENCE_FUNCTION:
 				// Does not work for OPEN alignments
@@ -330,7 +331,7 @@ protected static CeSymmResult align(Atom[] atoms, CESymmParameters params)
 			return result;
 		}
 
-		// STEP4: determine the symmetry axis and its repeat dependencies
+		// STEP 4: determine the symmetry axis and its repeat dependencies
 		SymmetryAxes axes = new SymmetryAxes();
 		int order = result.getMultipleAlignment().size();
 		Matrix4d axis = result.getMultipleAlignment().getBlockSet(0)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java
@@ -213,7 +213,8 @@ public String getSymmGroup() {
 					else
 						symmGroup = "R";
 				}
-			} else // case asymmetric
+			} else
+				// case asymmetric
 				symmGroup = "C1";
 		}
 		return symmGroup;
@@ -255,4 +256,60 @@ public void setStructureId(StructureIdentifier structureId) {
 		this.structureId = structureId;
 	}
 
+	/**
+	 * Return a String describing the reasons for the CE-Symm final decision
+	 * in this particular result.
+	 * 
+	 * @return String decision reason
+	 */
+	public String getReason() {
+		// Cases:
+		// 1. Asymmetric because insignificant self-alignment (1itb.A_1-100)
+		double tm = selfAlignment.getTMScore();
+		if (tm < params.getUnrefinedScoreThreshold()) {
+			return String.format("Insignificant self-alignment (TM=%.2f)", tm);
+		}
+		// 2. Asymmetric because order detector returned 1
+		if (symmOrder == 1) {
+			return String.format("Order detector found asymmetric alignment (TM=%.2f)", tm);
+		}
+
+		// Check that the user requested refinement
+		if (params.getRefineMethod() != RefineMethod.NOT_REFINED) {
+			// 3. Asymmetric because refinement failed
+			if (!refined) {
+				return "Refinement failed";
+			}
+			tm = multipleAlignment.getScore(
+					MultipleAlignmentScorer.AVGTM_SCORE);
+			// 4. Asymmetric because refinement & optimization were not
+			// significant
+			if (!isSignificant()) {
+				return String.format(
+						"Refinement was not significant (TM=%.2f)", tm);
+			}
+		} else {
+			// 4. Not refined, but result was not significant
+			if (!isSignificant()) {
+				return String
+						.format("Result was not significant (TM=%.2f)", tm);
+			}
+		}
+
+		String hierarchical = "";
+		if (symmLevels > 1) {
+			hierarchical = String.format("; Contains %d levels of symmetry",
+					symmLevels);
+		}
+		// 5. Symmetric.
+		// a. Open. Give # repeats (1n0r.A)
+		if (type == SymmetryType.OPEN) {
+			return String.format("Contains %d open repeats (TM=%.2f)%s",
+					getSymmOrder(), tm, hierarchical);
+		}
+		// b. Closed, non-hierarchical (1itb.A)
+		// c. Closed, heirarchical (4gcr)
+		return String.format("Significant (TM=%.2f)%s", tm, hierarchical);
+	}
+
 }
