X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=5a2c46e0b3e2be52032af8a67f02cfbefdde6cfc;hb=521ce3c96d5977a9bd941894eda7a13dd09deea9;hp=35297b56bce55cbf0a93f2fbd00c22d17b95d05f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 35297b5..5a2c46e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,63 +18,151 @@
 */
 package jalview.datamodel;
 
-public class AlignmentAnnotation {
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignmentAnnotation
+{
+    public SequenceI sequenceRef;
+
+    /** DOCUMENT ME!! */
     public String label;
+
+    /** DOCUMENT ME!! */
     public String description;
+
+    /** DOCUMENT ME!! */
     public Annotation[] annotations;
-    public boolean isGraph = false;
+
+    public java.util.Hashtable sequenceMapping;
+
+    /** 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) {
+        boolean drawValues = true;
+
+        if (min == max)
+        {
+            min = 999999999;
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] == null)
+                {
                     continue;
                 }
 
-                if (annotations[i].value > max) {
+                if(drawValues && annotations[i].displayCharacter.length() > 1 )
+                {
+                  drawValues = false;
+                }
+
+                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 +170,58 @@ public class AlignmentAnnotation {
 
         graphMin = min;
         graphMax = max;
-        windowLength = winLength;
 
-        for (int i = 0; i < annotations.length; i++) {
-            if ((annotations[i] != null) &&
-                    ((annotations[i].secondaryStructure == 'H') ||
-                    (annotations[i].secondaryStructure == 'E'))) {
+        for (int i = 0; i < annotations.length; i++)
+        {
+            if (!hasIcons
+                && annotations[i] != null
+                && ((annotations[i].secondaryStructure == 'H') ||
+                    (annotations[i].secondaryStructure == 'E')))
+            {
                 hasIcons = true;
             }
 
-            if ((annotations[i] != null) &&
-                    (annotations[i].displayCharacter.length() > 0)) {
+            if (!hasText
+                && annotations[i]!=null
+                && annotations[i].displayCharacter.length() > 0)
+            {
                 hasText = true;
             }
         }
+
+        if(!drawValues && graphType!=NO_GRAPH)
+        {
+          for (int i = 0; i < annotations.length; i++)
+          {
+            if (annotations[i] != null)
+              annotations[i].displayCharacter = "";
+          }
+        }
     }
 
-    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 +229,14 @@ 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 +245,85 @@ public class AlignmentAnnotation {
         }
 
         return buffer.toString();
-    }
+      }
+
+      public void setThreshold(GraphLine line)
+      {
+        threshold = line;
+      }
+
+      public GraphLine getThreshold()
+      {
+          return threshold;
+      }
+
+      /**
+       * This
+       */
+      public void createSequenceMapping(SequenceI seqRef, int startRes)
+      {
+        if(seqRef == null)
+          return;
+
+        sequenceMapping = new java.util.Hashtable();
+
+        sequenceRef = seqRef;
+
+        if(startRes < sequenceRef.getStart())
+          startRes = sequenceRef.getStart();
+
+        int seqPos;
+
+        int fileOffset = 0;
+        if(startRes > sequenceRef.getStart())
+        {
+          fileOffset = startRes - sequenceRef.getStart();
+        }
+
+        for(int i = 0; i < annotations.length; i++)
+        {
+            seqPos = sequenceRef.findPosition(i + fileOffset);
+            if(seqPos<annotations.length)
+            {
+              if (annotations[i] != null)
+              {
+                  sequenceMapping.put(new Integer(seqPos),
+                                      annotations[i]);
+              }
+            }
+         }
+
+        adjustForAlignment();
+
+      }
+
+      public void adjustForAlignment()
+      {
+          int a=0, aSize = sequenceRef.getLength();
+
+          if(aSize == 0)
+          {
+            //Its been deleted
+            return;
+          }
+
+          int position;
+          Annotation[] temp = new Annotation[aSize];
+          Integer index;
+
+          for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+          {
+              index = new Integer(a);
+              if(sequenceMapping.containsKey(index))
+              {
+                position = sequenceRef.findIndex(a)-1;
+
+                temp[position] = (Annotation)sequenceMapping.get(index);
+              }
+          }
+
+          annotations = temp;
+      }
 }
+
+