X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=9cfdff6dbadd957baeb30925cdecc56a29523dfc;hb=3f9ed3a1f79978b51fbdd98608bc3558278d5569;hp=35297b56bce55cbf0a93f2fbd00c22d17b95d05f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 35297b5..9cfdff6 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,63 +18,121 @@
 */
 package jalview.datamodel;
 
-public class AlignmentAnnotation {
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentAnnotation
+{
+    /** DOCUMENT ME!! */
     public String label;
+
+    /** DOCUMENT ME!! */
     public String description;
+
+    /** DOCUMENT ME!! */
     public Annotation[] annotations;
+
+    /** DOCUMENT ME!! */
     public boolean isGraph = false;
+
+    /** DOCUMENT ME!! */
     public float graphMin;
+
+    /** DOCUMENT ME!! */
     public float graphMax;
+
+    /** DOCUMENT ME!! */
     public int windowLength;
 
     // Graphical hints and tips
+
+    /** DOCUMENT ME!! */
     public boolean editable = false;
+
+    /** DOCUMENT ME!! */
     public boolean hasIcons; //
+
+    /** DOCUMENT ME!! */
     public boolean hasText;
+
+    /** DOCUMENT ME!! */
     public boolean visible = true;
+
+    /** DOCUMENT ME!! */
     public int height = 0;
 
+    /**
+     * Creates a new AlignmentAnnotation object.
+     *
+     * @param label DOCUMENT ME!
+     * @param description DOCUMENT ME!
+     * @param annotations DOCUMENT ME!
+     */
     public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations) {
+        Annotation[] annotations)
+    {
         // always editable?
         editable = true;
         this.label = label;
         this.description = description;
         this.annotations = annotations;
 
-        for (int i = 0; i < annotations.length; i++) {
+        for (int i = 0; i < annotations.length; i++)
+        {
             if ((annotations[i] != null) &&
                     ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E'))) {
+                    (annotations[i].secondaryStructure == 'E')))
+            {
                 hasIcons = true;
             }
 
             if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0)) {
+                    (annotations[i].displayCharacter.length() > 0))
+            {
                 hasText = true;
             }
         }
     }
 
+    /**
+     * Creates a new AlignmentAnnotation object.
+     *
+     * @param label DOCUMENT ME!
+     * @param description DOCUMENT ME!
+     * @param annotations DOCUMENT ME!
+     * @param min DOCUMENT ME!
+     * @param max DOCUMENT ME!
+     * @param winLength DOCUMENT ME!
+     */
     public AlignmentAnnotation(String label, String description,
-        Annotation[] annotations, float min, float max, int winLength) {
+        Annotation[] annotations, float min, float max, int winLength)
+    {
         // graphs are not editable
         this.label = label;
         this.description = description;
         this.annotations = annotations;
         isGraph = true;
 
-        if (min == max) {
-            for (int i = 0; i < annotations.length; i++) {
-                if (annotations[i] == null) {
+        if (min == max)
+        {
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] == null)
+                {
                     continue;
                 }
 
-                if (annotations[i].value > max) {
+                if (annotations[i].value > max)
+                {
                     max = annotations[i].value;
                 }
 
-                if (annotations[i].value < min) {
+                if (annotations[i].value < min)
+                {
                     min = annotations[i].value;
                 }
             }
@@ -84,30 +142,46 @@ public class AlignmentAnnotation {
         graphMax = max;
         windowLength = winLength;
 
-        for (int i = 0; i < annotations.length; i++) {
+        for (int i = 0; i < annotations.length; i++)
+        {
             if ((annotations[i] != null) &&
                     ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E'))) {
+                    (annotations[i].secondaryStructure == 'E')))
+            {
                 hasIcons = true;
             }
 
             if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0)) {
+                    (annotations[i].displayCharacter.length() > 0))
+            {
                 hasText = true;
             }
         }
     }
 
-    public String toString() {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String toString()
+    {
         StringBuffer buffer = new StringBuffer();
 
-        for (int i = 0; i < annotations.length; i++) {
-            if (annotations[i] != null) {
-                if (isGraph) {
+        for (int i = 0; i < annotations.length; i++)
+        {
+            if (annotations[i] != null)
+            {
+                if (isGraph)
+                {
                     buffer.append(annotations[i].value);
-                } else if (hasIcons) {
+                }
+                else if (hasIcons)
+                {
                     buffer.append(annotations[i].secondaryStructure);
-                } else {
+                }
+                else
+                {
                     buffer.append(annotations[i].displayCharacter);
                 }
             }
@@ -115,11 +189,14 @@ public class AlignmentAnnotation {
             buffer.append(", ");
         }
 
-        if (label.equals("Consensus")) {
+        if (label.equals("Consensus"))
+        {
             buffer.append("\n");
 
-            for (int i = 0; i < annotations.length; i++) {
-                if (annotations[i] != null) {
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] != null)
+                {
                     buffer.append(annotations[i].description);
                 }