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 f3cdae6..e832c2f 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,12 +20,6 @@
  */
 package jalview.datamodel;
 
-import java.util.Locale;
-
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -33,9 +27,14 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 /**
  * DOCUMENT ME!
  * 
@@ -96,6 +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
@@ -382,21 +385,24 @@ public class AlignmentAnnotation
         // annotations[i].secondaryStructure + "'");
         // TODO: 2.8.2 should this ss symbol validation check be a function in
         // RNA/ResidueProperties ?
+        // allow for DSSP extended code:
+        // https://www.wikidoc.org/index.php/Secondary_structure#The_DSSP_code
+        // GHITEBS as well as C and X (for missing?)
         if (annotations[i].secondaryStructure == '('
                 || annotations[i].secondaryStructure == '['
                 || annotations[i].secondaryStructure == '<'
                 || annotations[i].secondaryStructure == '{'
                 || annotations[i].secondaryStructure == 'A'
-                || annotations[i].secondaryStructure == 'B'
-                || annotations[i].secondaryStructure == 'C'
+                // || annotations[i].secondaryStructure == 'B'
+                // || annotations[i].secondaryStructure == 'C'
                 || annotations[i].secondaryStructure == 'D'
                 // || annotations[i].secondaryStructure == 'E' // ambiguous on
                 // its own -- already checked above
                 || annotations[i].secondaryStructure == 'F'
-                || annotations[i].secondaryStructure == 'G'
+                // || annotations[i].secondaryStructure == 'G'
                 // || annotations[i].secondaryStructure == 'H' // ambiguous on
                 // its own -- already checked above
-                || annotations[i].secondaryStructure == 'I'
+                // || annotations[i].secondaryStructure == 'I'
                 || annotations[i].secondaryStructure == 'J'
                 || annotations[i].secondaryStructure == 'K'
                 || annotations[i].secondaryStructure == 'L'
@@ -406,12 +412,12 @@ public class AlignmentAnnotation
                 || annotations[i].secondaryStructure == 'P'
                 || annotations[i].secondaryStructure == 'Q'
                 || annotations[i].secondaryStructure == 'R'
-                || annotations[i].secondaryStructure == 'S'
-                || annotations[i].secondaryStructure == 'T'
+                // || annotations[i].secondaryStructure == 'S'
+                // || annotations[i].secondaryStructure == 'T'
                 || annotations[i].secondaryStructure == 'U'
                 || annotations[i].secondaryStructure == 'V'
                 || annotations[i].secondaryStructure == 'W'
-                || annotations[i].secondaryStructure == 'X'
+                // || annotations[i].secondaryStructure == 'X'
                 || annotations[i].secondaryStructure == 'Y'
                 || annotations[i].secondaryStructure == 'Z')
         {
@@ -547,12 +553,12 @@ public class AlignmentAnnotation
                       : annotations[index + offset].displayCharacter == null
                               || annotations[index
                                       + offset].displayCharacter
-                                              .length() == 0
-                                                      ? annotations[index
-                                                              + offset].secondaryStructure
-                                                      : annotations[index
-                                                              + offset].displayCharacter
-                                                                      .charAt(0));
+                                      .length() == 0
+                                              ? annotations[index
+                                                      + offset].secondaryStructure
+                                              : annotations[index
+                                                      + offset].displayCharacter
+                                                      .charAt(0));
     }
 
     @Override
@@ -594,7 +600,7 @@ public class AlignmentAnnotation
     }
     return null;
   }
-
+  
   /**
    * Creates a new AlignmentAnnotation object.
    * 
@@ -706,7 +712,7 @@ public class AlignmentAnnotation
       }
     }
   }
-
+  
   /**
    * Copy constructor creates a new independent annotation row with the same
    * associated sequenceRef
@@ -716,6 +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)
     {
@@ -739,6 +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<>();
@@ -834,15 +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)
@@ -970,6 +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)
@@ -1171,7 +1192,7 @@ public class AlignmentAnnotation
   {
     return hasScore || !Double.isNaN(score);
   }
-
+  
   /**
    * Score only annotation
    * 
@@ -1202,6 +1223,7 @@ public class AlignmentAnnotation
     makeVisibleAnnotation(hidden);
   }
 
+
   public void setPadGaps(boolean padgaps, char gapchar)
   {
     this.padGaps = padgaps;
@@ -1559,7 +1581,7 @@ public class AlignmentAnnotation
   {
     if (annotations != null)
     {
-      makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+      makeVisibleAnnotation(0, annotations.length - 1, hiddenColumns);
     }
   }
 
@@ -1661,7 +1683,6 @@ public class AlignmentAnnotation
           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
           String label)
   {
-
     ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : list)
     {
@@ -1706,7 +1727,6 @@ public class AlignmentAnnotation
   public static Iterable<AlignmentAnnotation> findAnnotation(
           List<AlignmentAnnotation> list, String calcId)
   {
-
     List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {
@@ -1724,4 +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;
+  }
+
 }