X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=5a2c46e0b3e2be52032af8a67f02cfbefdde6cfc;hb=d6e1bbede5adc04f34c969213ac6a4c6d9e5d34a;hp=337d8797a398d125178535ac8f74f01f1dab3673;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 337d879..5a2c46e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -16,107 +16,314 @@
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
-
 package jalview.datamodel;
 
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class AlignmentAnnotation
 {
-  public String label;
-  public String description;
-  public Annotation  [] annotations;
-  public boolean isGraph = false;
-  public float graphMin, graphMax;
-  public int windowLength;
-
-  // Graphical hints and tips
-  public boolean editable = false;
-  public boolean hasIcons; //
-  public boolean hasText;
-  public boolean visible = true;
-  public int height=0;
-
-  public AlignmentAnnotation(String label, String description, Annotation [] annotations)
-  {
-    // always editable?
-    editable = true;
-    this.label = label;
-    this.description = description;
-    this.annotations = annotations;
-    for(int i=0; i<annotations.length; i++)
-    {
-      if (annotations[i]!=null &&(
-          annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E'))
-        hasIcons = true;
+    public SequenceI sequenceRef;
+
+    /** DOCUMENT ME!! */
+    public String label;
+
+    /** DOCUMENT ME!! */
+    public String description;
+
+    /** DOCUMENT ME!! */
+    public Annotation[] annotations;
+
+    public java.util.Hashtable sequenceMapping;
+
+    /** DOCUMENT ME!! */
+    public float graphMin;
+
+    /** DOCUMENT ME!! */
+    public float graphMax;
+
+    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;
 
-      if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)
-        hasText = true;
+    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;
     }
-  }
-
-  public AlignmentAnnotation(String label, String description, 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)
+
+    /**
+     * 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)
     {
-      for(int i=0; i<annotations.length; i++)
-      {
-        if(annotations[i]==null)
-          continue;
-        if(annotations[i].value>max)
-          max = annotations[i].value;
-        if(annotations[i].value<min)
-          min = annotations[i].value;
-      }
+        // always editable?
+        editable = true;
+        this.label = label;
+        this.description = description;
+        this.annotations = annotations;
+
+        for (int i = 0; i < annotations.length; i++)
+        {
+            if ((annotations[i] != null) &&
+                    ((annotations[i].secondaryStructure == 'H') ||
+                    (annotations[i].secondaryStructure == 'E')))
+            {
+                hasIcons = true;
+            }
+
+            if ((annotations[i] != null) &&
+                    (annotations[i].displayCharacter.length() > 0))
+            {
+                hasText = true;
+            }
+        }
     }
 
-    graphMin = min;
-    graphMax = max;
-    windowLength = winLength;
-    for(int i=0; i<annotations.length; i++)
+    /**
+     * 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 graphType)
     {
-      if (annotations[i]!=null &&(
-          annotations[i].secondaryStructure == 'H' ||
-          annotations[i].secondaryStructure == 'E'))
-        hasIcons = true;
+        // graphs are not editable
+        this.label = label;
+        this.description = description;
+        this.annotations = annotations;
+        graph = graphType;
+
+        boolean drawValues = true;
+
+        if (min == max)
+        {
+            min = 999999999;
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] == null)
+                {
+                    continue;
+                }
+
+                if(drawValues && annotations[i].displayCharacter.length() > 1 )
+                {
+                  drawValues = false;
+                }
+
+                if (annotations[i].value > max)
+                {
+                    max = annotations[i].value;
+                }
+
+                if (annotations[i].value < min)
+                {
+                    min = annotations[i].value;
+                }
+            }
+        }
+
+        graphMin = min;
+        graphMax = max;
+
+        for (int i = 0; i < annotations.length; i++)
+        {
+            if (!hasIcons
+                && annotations[i] != null
+                && ((annotations[i].secondaryStructure == 'H') ||
+                    (annotations[i].secondaryStructure == 'E')))
+            {
+                hasIcons = true;
+            }
+
+            if (!hasText
+                && annotations[i]!=null
+                && annotations[i].displayCharacter.length() > 0)
+            {
+                hasText = true;
+            }
+        }
 
-      if (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()
-  {
-    StringBuffer buffer = new StringBuffer();
-    for(int i=0; i<annotations.length; i++)
-   {
-     if(annotations[i]!=null)
-     {
-       if(isGraph)
-         buffer.append(annotations[i].value);
-       else if(hasIcons)
-         buffer.append(annotations[i].secondaryStructure);
-       else
-         buffer.append(annotations[i].displayCharacter);
-
-     }
-     buffer.append(", ");
-   }
-   if(label.equals("Consensus"))
-   {
-     buffer.append("\n");
-     for (int i = 0; i < annotations.length; i++)
-     {
-       if (annotations[i] != null)
-           buffer.append(annotations[i].description);
-       buffer.append(", ");
-     }
-   }
-   return buffer.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 (graph!=0)
+                {
+                    buffer.append(annotations[i].value);
+                }
+                else if (hasIcons)
+                {
+                    buffer.append(annotations[i].secondaryStructure);
+                }
+                else
+                {
+                    buffer.append(annotations[i].displayCharacter);
+                }
+            }
+
+            buffer.append(", ");
+        }
+
+        if (label.equals("Consensus"))
+        {
+            buffer.append("\n");
+
+            for (int i = 0; i < annotations.length; i++)
+            {
+                if (annotations[i] != null)
+                {
+                    buffer.append(annotations[i].description);
+                }
+
+                buffer.append(", ");
+            }
+        }
+
+        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;
+      }
 }
+
+