Fix some typos

sbliven · sbliven · commit 403241f1c45b · 2024-08-30T15:27:04.000+02:00
Most are in docstrings. One misspelled public method has been deprecated.
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
@@ -76,7 +76,7 @@ public class MenuCreator {
 	 * Menus included:
 	 * <ul><li>File: open, save, export, import, exit.
 	 * <li>Align: new pairwise alignment, new multiple alignment.
-	 * <li>View: aligment panel, aligned pairs, text format,
+	 * <li>View: alignment panel, aligned pairs, text format,
 	 * FatCat format, distance matrices, dot plot.
 	 * <li>Help
 	 * </ul>
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentJmolDisplay.java
@@ -92,6 +92,15 @@ else if (pos < ca.length) {
 		return lst;
 	}
 
+	/**
+	 * @deprecated Replace with {@see showMultipleAlignmentPanel}
+	 */
+	@Deprecated
+	public static void showMultipleAligmentPanel(MultipleAlignment multAln,
+			AbstractAlignmentJmol jmol) throws StructureException {
+		showMultipleAlignmentPanel(multAln, jmol);
+	}
+
 	/**
 	 * Creates a new Frame with the MultipleAlignment Sequence Panel.
 	 * The panel can communicate with the Jmol 3D visualization by
@@ -102,7 +111,7 @@ else if (pos < ca.length) {
 
 	 * @throws StructureException
 	 */
-	public static void showMultipleAligmentPanel(MultipleAlignment multAln,
+	public static void showMultipleAlignmentPanel(MultipleAlignment multAln,
 			AbstractAlignmentJmol jmol) throws StructureException {
 
 		MultipleAligPanel me = new MultipleAligPanel(multAln, jmol);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MySaveFileListener.java
@@ -47,7 +47,7 @@
  * and from a Jmol view an XML format is saved.
  *
  * @author Aleix Lafita
- * @version 2.0 - adapted for MultipleAligments
+ * @version 2.0 - adapted for MultipleAlignments
  *
  */
 public class MySaveFileListener implements ActionListener {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -385,7 +385,7 @@ public void actionPerformed(ActionEvent ae) {
 						.showAlignmentImage(multAln, result);
 
 			} else if (cmd.equals(MenuCreator.ALIGNMENT_PANEL)) {
-				MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(multAln,
+				MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(multAln,
 						this);
 
 			} else if (cmd.equals(MenuCreator.FATCAT_TEXT)) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -684,7 +684,8 @@ private String drawSymmetryAxes() {
 		return s.toString();
 	}
 
-	private Vector3d getAligmentVector(Point3d point, Vector3d axis) {
+
+	private Vector3d getAlignmentVector(Point3d point, Vector3d axis) {
 		// for system with a single Cn axis
 		if (rotationGroup.getPointGroup().startsWith("C") || rotationGroup.getPointGroup().startsWith("D")) {
 			// if axis is orthogonal to principal axis, use principal axis as reference axis
@@ -760,14 +761,14 @@ private String getSymmetryAxis(int i, int j, String pointGroup, int n, Vector3d
 		if (drawPolygon) {
 			double polygonRadius = getMeanExtension() * 0.06;
 			if (n == 2) {
-				referenceAxis = getAligmentVector(p1, axis);
+				referenceAxis = getAlignmentVector(p1, axis);
 				s.append(getC2PolygonJmol(i, p1, referenceAxis, axis, color, polygonRadius, name));
-				referenceAxis = getAligmentVector(p2, axis);
+				referenceAxis = getAlignmentVector(p2, axis);
 				s.append(getC2PolygonJmol(j, p2,  referenceAxis, axis, color, polygonRadius, name));
 			} else if (n > 2) {
-				referenceAxis = getAligmentVector(p1, axis);
+				referenceAxis = getAlignmentVector(p1, axis);
 				s.append(getPolygonJmol(i, p1, referenceAxis, axis, n, color, polygonRadius, name));
-				referenceAxis = getAligmentVector(p2, axis);
+				referenceAxis = getAlignmentVector(p2, axis);
 				s.append(getPolygonJmol(j, p2, referenceAxis, axis, n, color, polygonRadius, name));
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -124,8 +124,8 @@ public interface Block extends ScoresCache {
 
 	/**
 	 * Calculates and returns the first position of the specified structure in
-	 * the alignment that is not null. This will return the aligment index, not
-	 * the reisude aligned in that position.
+	 * the alignment that is not null. This will return the alignment index, not
+	 * the residue aligned in that position.
 	 *
 	 * @param str
 	 *            structure index
@@ -148,8 +148,8 @@ public interface Block extends ScoresCache {
 
 	/**
 	 * Calculates and returns the last position of the specified structure in
-	 * the alignment that is not null. This will return the aligment index, not
-	 * the reisude aligned in that position.
+	 * the alignment that is not null. This will return the alignment index, not
+	 * the residue aligned in that position.
 	 *
 	 * @param str
 	 *            structure index
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -210,7 +210,7 @@ private void initialize() throws StructureException {
 			}
 		}
 
-		// Set the superposition and score for the seed aligment
+		// Set the superposition and score for the seed alignment
 		checkGaps();
 		msa.clear();
 		imposer.superimpose(msa);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -721,7 +721,7 @@ public static List<Atom[]> transformAtoms(MultipleAlignment alignment) {
 
 	/**
 	 * Calculate a List of alignment indicies that correspond to the core of a
-	 * Block, which means that all structures have a residue in that positon.
+	 * Block, which means that all structures have a residue in that position.
 	 *
 	 * @param block
 	 *            alignment Block
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
@@ -213,7 +213,7 @@ private void run() {
 		calcOriginalCenters();
 		calcCentroid();
 		calcCenters();
-		calcMomentsOfIntertia();
+		calcMomentsOfInertia();
 	}
 
 	private void calcOriginalCenters() {
@@ -272,7 +272,7 @@ public Point3d getUpperBound() {
 		return upper;
 	}
 
-	private void calcMomentsOfIntertia() {
+	private void calcMomentsOfInertia() {
 		for (Point3d[] trace : caCoords) {
 			for (Point3d p : trace) {
 				momentsOfInertia.addPoint(p, 1.0f);
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
@@ -101,7 +101,7 @@ public class SymmOptimizer {
 	private List<Double> mcScoreHistory;
 
 	/**
-	 * Constructor with a seed MultipleAligment storing a refined symmetry
+	 * Constructor with a seed MultipleAlignment storing a refined symmetry
 	 * alignment of the repeats. To perform the optimization use the call or
 	 * optimize methods after instantiation.
 	 *

Original file line number	Diff line number	Diff line change
`@@ -47,7 +47,7 @@`
`47`	`47`	`* and from a Jmol view an XML format is saved.`
`48`	`48`	`*`
`49`	`49`	`* @author Aleix Lafita`
`50`		`- * @version 2.0 - adapted for MultipleAligments`
	`50`	`+ * @version 2.0 - adapted for MultipleAlignments`
`51`	`51`	`*`
`52`	`52`	`*/`
`53`	`53`	`public class MySaveFileListener implements ActionListener {`
Original file line number	Diff line number	Diff line change
`@@ -210,7 +210,7 @@ private void initialize() throws StructureException {`
`210`	`210`	`}`
`211`	`211`	`}`
`212`	`212`
`213`		`- // Set the superposition and score for the seed aligment`
	`213`	`+ // Set the superposition and score for the seed alignment`
`214`	`214`	`checkGaps();`
`215`	`215`	`msa.clear();`
`216`	`216`	`imposer.superimpose(msa);`
Original file line number	Diff line number	Diff line change
`@@ -721,7 +721,7 @@ public static List<Atom[]> transformAtoms(MultipleAlignment alignment) {`
`721`	`721`
`722`	`722`	`/**`
`723`	`723`	`* Calculate a List of alignment indicies that correspond to the core of a`
`724`		`- * Block, which means that all structures have a residue in that positon.`
	`724`	`+ * Block, which means that all structures have a residue in that position.`
`725`	`725`	`*`
`726`	`726`	`* @param block`
`727`	`727`	`* alignment Block`
Original file line number	Diff line number	Diff line change
`@@ -101,7 +101,7 @@ public class SymmOptimizer {`
`101`	`101`	`private List<Double> mcScoreHistory;`
`102`	`102`
`103`	`103`	`/**`
`104`		`- * Constructor with a seed MultipleAligment storing a refined symmetry`
	`104`	`+ * Constructor with a seed MultipleAlignment storing a refined symmetry`
`105`	`105`	`* alignment of the repeats. To perform the optimization use the call or`
`106`	`106`	`* optimize methods after instantiation.`
`107`	`107`	`*`