Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 23c1d00..a9334ff 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2843,6 +2843,30 @@ public abstract class AlignmentViewport
     viewStyle.setProteinFontAsCdna(b);
   }
 
+  @Override
+  public void setShowComplementFeatures(boolean b)
+  {
+    viewStyle.setShowComplementFeatures(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeatures()
+  {
+    return viewStyle.isShowComplementFeatures();
+  }
+
+  @Override
+  public void setShowComplementFeaturesOnTop(boolean b)
+  {
+    viewStyle.setShowComplementFeaturesOnTop(b);
+  }
+
+  @Override
+  public boolean isShowComplementFeaturesOnTop()
+  {
+    return viewStyle.isShowComplementFeaturesOnTop();
+  }
+
   /**
    * @return true if view should scroll to show the highlighted region of a
    *         sequence
@@ -3182,4 +3206,46 @@ public abstract class AlignmentViewport
       codingComplement.setUpdateStructures(needToUpdateStructureViews);
     }
   }
+
+  /**
+   * Filters out sequences with an eValue higher than the specified value. The
+   * filtered sequences are hidden or deleted. Sequences with no eValues are also
+   * filtered out.
+   * 
+   * @param eValue
+   * @param delete
+   */
+  public void filterByEvalue(double eValue)
+  {
+    for (SequenceI seq : alignment.getSequencesArray())
+    {
+      if ((seq.getAnnotation("Search Scores") == null
+              || seq.getAnnotation("Search Scores")[0].getEValue() > eValue)
+              && seq.getHMM() == null)
+      {
+        hideSequence(new SequenceI[] { seq });
+      }
+    }
+  }
+
+  /**
+   * Filters out sequences with an score lower than the specified value. The
+   * filtered sequences are hidden or deleted.
+   * 
+   * @param score
+   * @param delete
+   */
+  public void filterByScore(double score)
+  {
+    for (SequenceI seq : alignment.getSequencesArray())
+    {
+      if ((seq.getAnnotation("Search Scores") == null
+              || seq.getAnnotation("Search Scores")[0]
+                      .getBitScore() < score)
+              && seq.getHMM() == null)
+      {
+        hideSequence(new SequenceI[] { seq });
+      }
+    }
+  }
 }