From 9ca6b95ab67df6eaeea56765cc293133da436e76 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 25 Apr 2007 14:05:45 +0000
Subject: [PATCH] alignmentProperties added

---
 src/jalview/datamodel/Alignment.java           |   19 +++++++++++++++++++
 src/jalview/datamodel/AlignmentAnnotation.java |   13 +++++++++----
 src/jalview/datamodel/AlignmentI.java          |    8 ++++++--
 3 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 83d2499..34cc78f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -40,6 +40,8 @@ public class Alignment
 
   HiddenSequences hiddenSequences = new HiddenSequences(this);
 
+  public Hashtable alignmentProperties;
+
   private void initAlignment(SequenceI[] seqs)
   {
     int i = 0;
@@ -702,4 +704,21 @@ public class Alignment
     return cal;
   }
 
+  public void setProperty(Object key, Object value)
+  {
+    if(alignmentProperties==null)
+      alignmentProperties = new Hashtable();
+
+    alignmentProperties.put(key,value);
+  }
+
+  public Object getProperty(Object key)
+  {
+    if(alignmentProperties!=null)
+      return alignmentProperties.get(key);
+    else
+      return null;
+  }
+
+
 }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 3ad05ea..04eab48 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -57,12 +57,12 @@ public class AlignmentAnnotation
   /**
    * Score associated with label and description.
    */
-  public float score;
+  public float score= Float.NaN;
   /**
    * flag indicating if annotation has a score.
    */
   public boolean hasScore=false;
-  
+
   public GraphLine threshold;
 
   // Graphical hints and tips
@@ -96,6 +96,8 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
+  public boolean belowAlignment = true;
+
 
   public static int getGraphValueFromString(String string)
   {
@@ -118,7 +120,8 @@ public class AlignmentAnnotation
    *
    * @param label DOCUMENT ME!
    * @param description DOCUMENT ME!
-   * @param annotations DOCUMENT ME!
+   * @param annotations DOCUMENT ME!about:blank
+Loading...
    */
   public AlignmentAnnotation(String label, String description,
                              Annotation[] annotations)
@@ -223,11 +226,13 @@ public class AlignmentAnnotation
    * if appropriate.
    */
   private void validateRangeAndDisplay() {
+
     if (annotations==null)
     {
       visible=false; // try to prevent renderer from displaying.
       return; // this is a non-annotation row annotation - ie a sequence score.
     }
+
     int graphType = graph;
     float min = graphMin;
     float max = graphMax;
@@ -617,7 +622,7 @@ public class AlignmentAnnotation
     this.score = score;
   }
   /**
-   * 
+   *
    * @return true if annotation has an associated score
    */
   public boolean hasScore()
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index a43b259..96b1972 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -165,7 +165,7 @@ public interface AlignmentI
 
   /**
    * Adds a new AlignmentAnnotation to this alignment
-   * @note Care should be taken to ensure that annotation is at 
+   * @note Care should be taken to ensure that annotation is at
    * least as wide as the longest sequence in the alignment
    * for rendering purposes.
    */
@@ -226,7 +226,7 @@ public interface AlignmentI
 
   /**
    * Set the associated dataset for the alignment, or create one.
-   * @param dataset The dataset alignment or null to construct one. 
+   * @param dataset The dataset alignment or null to construct one.
    */
   public void setDataset(Alignment dataset);
 
@@ -243,4 +243,8 @@ public interface AlignmentI
    * @return CigarArray
    */
   public CigarArray getCompactAlignment();
+
+  public void setProperty(Object key, Object value);
+
+  public Object getProperty(Object key);
 }
-- 
1.7.10.2