Logging and documentation

sbliven · sbliven · commit 402c1773208c · 2016-03-25T10:54:15.000+01:00
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
@@ -41,6 +41,8 @@
 import org.biojava.nbio.structure.jama.Matrix;
 import org.jcolorbrewer.ColorBrewer;
 import org.jmol.api.JmolViewer;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * An Abstract Class to generalize the visualization of AFP and
@@ -52,6 +54,7 @@
 public abstract class AbstractAlignmentJmol
 implements MouseMotionListener, MouseListener, WindowListener, ActionListener {
 
+	private static final Logger logger = LoggerFactory.getLogger(AbstractAlignmentJmol.class);
 	protected Structure structure;
 	protected ColorBrewer colorPalette = ColorBrewer.Spectral;
 
@@ -81,7 +84,7 @@ public abstract class AbstractAlignmentJmol
 	 * Set all the member variables to null.
 	 */
 	public void destroy(){
-		System.err.println("cleaning up AlignmentJmol window");
+		logger.debug("cleaning up AlignmentJmol window");
 		jmolPanel.removeMouseListener(this);
 		jmolPanel.removeMouseMotionListener(this);
 		jmolPanel.destroy();
@@ -135,7 +138,7 @@ public void setJmolPanel(JmolPanel jmolPanel) {
 	 */
 	public void evalString(String rasmolScript){
 		if ( jmolPanel == null ){
-			System.err.println("please install Jmol first");
+			logger.error("please install Jmol first");
 			return;
 		}
 		jmolPanel.evalString(rasmolScript);
@@ -148,7 +151,7 @@ public void evalString(String rasmolScript){
 	public void setStructure(Structure s) {
 
 		if (jmolPanel == null){
-			System.err.println("please install Jmol first");
+			logger.error("please install Jmol first");
 			return;
 		}
 		setTitle(s.getPDBCode());
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
@@ -222,7 +222,9 @@ public List<String> getUserConfigHelp() {
 				+ "between two aligned residues.");
 
 		// gaps
-		params.add("MStA Gaps: allow gaps in the multiple alignment if true.");
+		params.add("Internal Gaps: allow up to 50% of repeats to have gaps in "
+				+ "the multiple alignment if true, "
+				+ "otherwise all repeats must be aligned at each position.");
 
 		// optimization steps
 		params.add("Optimization Steps: maximum number of optimization steps:"
@@ -266,7 +268,7 @@ public List<String> getUserConfigParameterNames() {
 		params.add("SSE Threshold");
 		params.add("Minimum Core Length");
 		params.add("Distance Cutoff");
-		params.add("MStA Gaps");
+		params.add("Internal Gaps");
 		params.add("Optimization Steps");
 		return params;
 	}
