JAL-4313 Test and patch annots trimming

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0f41850..e832c2f 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -95,6 +95,10 @@ public class AlignmentAnnotation
    */
   private long invalidrnastruc = -2;
 
+  private double bitScore;
+
+  private double eValue;
+
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
@@ -596,7 +600,7 @@ public class AlignmentAnnotation
     }
     return null;
   }
-
+  
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -708,7 +712,7 @@ public class AlignmentAnnotation
       }
     }
   }
-
+  
   /**
    * Copy constructor creates a new independent annotation row with the same
    * associated sequenceRef
@@ -718,6 +722,17 @@ public class AlignmentAnnotation
   public AlignmentAnnotation(AlignmentAnnotation annotation)
   {
     setAnnotationId();
+    updateAlignmentAnnotationFrom(annotation);
+  }
+
+  /**
+   * copy attributes and annotation from an existing annotation (used by copy
+   * constructor). This method does not update the unique annotationId
+   * 
+   * @param annotation
+   */
+  public void updateAlignmentAnnotationFrom(AlignmentAnnotation annotation)
+  {
     this.label = new String(annotation.label);
     if (annotation.description != null)
     {
@@ -741,6 +756,9 @@ public class AlignmentAnnotation
     this.scaleColLabel = annotation.scaleColLabel;
     this.showAllColLabels = annotation.showAllColLabels;
     this.calcId = annotation.calcId;
+    this.bitScore = annotation.bitScore;
+    this.eValue = annotation.eValue;
+
     if (annotation.properties != null)
     {
       properties = new HashMap<>();
@@ -836,15 +854,15 @@ public class AlignmentAnnotation
     }
     if (startRes >= annotations.length)
     {
-      startRes = annotations.length - 1;
+      startRes = annotations.length;
     }
-    if (endRes >= annotations.length)
+    if (endRes < 0)
     {
-      endRes = annotations.length - 1;
+      endRes = -1;
     }
-    if (annotations == null)
+    if (endRes >= annotations.length)
     {
-      return;
+      endRes = annotations.length - 1;
     }
     Annotation[] temp = new Annotation[endRes - startRes + 1];
     if (startRes < annotations.length)
@@ -972,6 +990,7 @@ public class AlignmentAnnotation
    * @param seqRef
    * @param startRes
    * @param alreadyMapped
+   *          - annotation are at aligned columns
    */
   public void createSequenceMapping(SequenceI seqRef, int startRes,
           boolean alreadyMapped)
@@ -1173,7 +1192,7 @@ public class AlignmentAnnotation
   {
     return hasScore || !Double.isNaN(score);
   }
-
+  
   /**
    * Score only annotation
    * 
@@ -1204,6 +1223,7 @@ public class AlignmentAnnotation
     makeVisibleAnnotation(hidden);
   }
 
+
   public void setPadGaps(boolean padgaps, char gapchar)
   {
     this.padGaps = padgaps;
@@ -1561,7 +1581,7 @@ public class AlignmentAnnotation
   {
     if (annotations != null)
     {
-      makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+      makeVisibleAnnotation(0, annotations.length - 1, hiddenColumns);
     }
   }
 
@@ -1663,7 +1683,6 @@ public class AlignmentAnnotation
           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
           String label)
   {
-
     ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : list)
     {
@@ -1708,7 +1727,6 @@ public class AlignmentAnnotation
   public static Iterable<AlignmentAnnotation> findAnnotation(
           List<AlignmentAnnotation> list, String calcId)
   {
-
     List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {
@@ -1726,4 +1744,42 @@ public class AlignmentAnnotation
     return aa;
   }
 
+  public double getBitScore()
+  {
+    return bitScore;
+  }
+
+  public void setBitScore(double bitScore)
+  {
+    this.bitScore = bitScore;
+  }
+
+  public double getEValue()
+  {
+    return eValue;
+  }
+
+  public void setEValue(double eValue)
+  {
+    this.eValue = eValue;
+  }
+
+  public static AlignmentAnnotation findFirstAnnotation(
+          Iterable<AlignmentAnnotation> alignmentAnnotation, String name,
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
+  {
+
+    for (AlignmentAnnotation annot : alignmentAnnotation)
+    {
+      if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+              && (calcId == null || annot.getCalcId().equals(calcId))
+              && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+      {
+        return annot;
+      }
+    }
+    return null;
+  }
+
 }