X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=c3ccb0ba99b0eba2867bdc5ec17bf02a2e84eb07;hb=14bad6b2390493bb6ad030c6f3ea7cde4cba1b53;hp=35297b56bce55cbf0a93f2fbd00c22d17b95d05f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 35297b5..c3ccb0b 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,63 +18,148 @@
 */
 package jalview.datamodel;
 
-public class AlignmentAnnotation {
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentAnnotation
+{
+    public SequenceI sequenceRef;
+
+    /** This annotation is the original loaded annotation
+     *  without any gaps. It is necessary to adjust the annotation
+     *  if sequences are updated */
+    public AlignmentAnnotation datasetAnnotation;
+
+    /** DOCUMENT ME!! */
     public String label;
+
+    /** DOCUMENT ME!! */
     public String description;
+
+    /** DOCUMENT ME!! */
     public Annotation[] annotations;
-    public boolean isGraph = false;
+
+
+    /** DOCUMENT ME!! */
     public float graphMin;
+
+    /** DOCUMENT ME!! */
     public float graphMax;
-    public int windowLength;
+
+    public GraphLine threshold;
 
     // 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;
+
+    public int graphGroup = -1;
+
+    /** DOCUMENT ME!! */
     public int height = 0;
 
+    public int graph = 0;
+
+    public int graphHeight = 40;
+
+    public static final int NO_GRAPH = 0;
+
+    public static final int BAR_GRAPH = 1;
+
+    public static final int LINE_GRAPH = 2;
+
+    public static int getGraphValueFromString(String string)
+    {
+      if(string.equalsIgnoreCase("BAR_GRAPH"))
+        return BAR_GRAPH;
+      else if(string.equalsIgnoreCase("LINE_GRAPH"))
+        return LINE_GRAPH;
+      else
+        return NO_GRAPH;
+    }
+
+    /**
+     * 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 graphType)
+    {
         // graphs are not editable
         this.label = label;
         this.description = description;
         this.annotations = annotations;
-        isGraph = true;
+        graph = graphType;
 
-        if (min == max) {
-            for (int i = 0; i < annotations.length; i++) {
-                if (annotations[i] == null) {
+        if (min == max)
+        {
+            min = 999999999;
+            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;
                 }
             }
@@ -82,32 +167,47 @@ public class AlignmentAnnotation {
 
         graphMin = min;
         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 (graph!=0)
+                {
                     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 +215,14 @@ 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);
                 }
 
@@ -128,5 +231,37 @@ public class AlignmentAnnotation {
         }
 
         return buffer.toString();
-    }
+      }
+
+      public void setThreshold(GraphLine line)
+      {
+        threshold = line;
+      }
+
+      public GraphLine getThreshold()
+      {
+          return threshold;
+      }
+
+      public void adjustForAlignment()
+      {
+          int a=0, aSize = sequenceRef.getLength();
+
+          int index = 0;
+          Annotation[] temp = new Annotation[aSize];
+
+          for (a = 0; a < aSize; a++)
+          {
+            if (!jalview.util.Comparison.isGap(sequenceRef.getCharAt(a)))
+            {
+              index = sequenceRef.findPosition(a);
+              if(datasetAnnotation.annotations.length>index)
+                temp[a] = datasetAnnotation.annotations[index];
+            }
+          }
+
+          annotations = temp;
+      }
 }
+
+