JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 8642f5a..9e2cf72 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -33,11 +33,21 @@ public class HiddenSequences
 
   AlignmentI alignment;
 
+  /**
+   * Constructor given a reference to an alignment (with no hidden sequences)
+   * 
+   * @param al
+   */
   public HiddenSequences(AlignmentI al)
   {
     alignment = al;
   }
 
+  /**
+   * Answers the number of hidden sequences
+   * 
+   * @return
+   */
   public int getSize()
   {
     if (hiddenSequences == null)
@@ -45,9 +55,9 @@ public class HiddenSequences
       return 0;
     }
     int count = 0;
-    for (int i = 0; i < hiddenSequences.length; i++)
+    for (SequenceI seq : hiddenSequences)
     {
-      if (hiddenSequences[i] != null)
+      if (seq != null)
       {
         count++;
       }
@@ -56,15 +66,23 @@ public class HiddenSequences
     return count;
   }
 
+  /**
+   * Answers the length of the longest hidden sequence
+   * 
+   * @return
+   */
   public int getWidth()
   {
+    if (hiddenSequences == null)
+    {
+      return 0;
+    }
     int width = 0;
-    for (int i = 0; i < hiddenSequences.length; i++)
+    for (SequenceI seq : hiddenSequences)
     {
-      if (hiddenSequences[i] != null
-              && hiddenSequences[i].getLength() > width)
+      if (seq != null && seq.getLength() > width)
       {
-        width = hiddenSequences[i].getLength();
+        width = seq.getLength();
       }
     }
 
@@ -72,7 +90,7 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are removed from the main alignment
+   * Call this method after a sequence is removed from the main alignment
    */
   public void adjustHeightSequenceDeleted(int seqIndex)
   {
@@ -108,8 +126,7 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are added to or removed from the main
-   * alignment
+   * Call this method after a sequence is added to the main alignment
    */
   public void adjustHeightSequenceAdded()
   {
@@ -125,6 +142,11 @@ public class HiddenSequences
     hiddenSequences = tmp;
   }
 
+  /**
+   * Mark the specified sequence as hidden
+   * 
+   * @param sequence
+   */
   public void hideSequence(SequenceI sequence)
   {
     if (hiddenSequences == null)
@@ -163,6 +185,17 @@ public class HiddenSequences
     return revealedSeqs;
   }
 
+  /**
+   * Reveals (unhides) consecutive hidden sequences just above the given
+   * alignment index. The revealed sequences are selected (including their
+   * visible representative sequence if there was one and 'reveal' is being
+   * performed on it).
+   * 
+   * @param alignmentIndex
+   * @param hiddenRepSequences
+   *          a map of representative sequences to the sequences they represent
+   * @return
+   */
   public List<SequenceI> showSequence(int alignmentIndex,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
@@ -203,20 +236,22 @@ public class HiddenSequences
                     + " has been deleted whilst hidden");
           }
         }
-
       }
     }
-
     return revealedSeqs;
   }
 
   public SequenceI getHiddenSequence(int alignmentIndex)
   {
-    return hiddenSequences[alignmentIndex];
+    return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
   }
 
   public int findIndexWithoutHiddenSeqs(int alignmentIndex)
   {
+    if (hiddenSequences == null)
+    {
+      return alignmentIndex;
+    }
     int index = 0;
     int hiddenSeqs = 0;
     if (hiddenSequences.length <= alignmentIndex)
@@ -232,13 +267,16 @@ public class HiddenSequences
       }
       index++;
     }
-    ;
 
     return (alignmentIndex - hiddenSeqs);
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
+    if (hiddenSequences == null)
+    {
+      return alignmentIndex;
+    }
     int index = 0;
     int hSize = hiddenSequences.length;
     while (index <= alignmentIndex && index < hSize)
@@ -254,22 +292,37 @@ public class HiddenSequences
     return alignmentIndex;
   }
 
+  /**
+   * makes a copy of the alignment with hidden sequences included. Using the
+   * copy for anything other than simple output is not recommended. Note - this
+   * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+   * 
+   * @return
+   */
   public AlignmentI getFullAlignment()
   {
-    int isize = hiddenSequences.length;
-    SequenceI[] seq = new Sequence[isize];
-
-    int index = 0;
-    for (int i = 0; i < hiddenSequences.length; i++)
+    SequenceI[] seq;
+    if (hiddenSequences == null)
     {
-      if (hiddenSequences[i] != null)
-      {
-        seq[i] = hiddenSequences[i];
-      }
-      else
+      seq = alignment.getSequencesArray();
+    }
+    else
+    {
+      int isize = hiddenSequences.length;
+      seq = new Sequence[isize];
+
+      int index = 0;
+      for (int i = 0; i < hiddenSequences.length; i++)
       {
-        seq[i] = alignment.getSequenceAt(index);
-        index++;
+        if (hiddenSequences[i] != null)
+        {
+          seq[i] = hiddenSequences[i];
+        }
+        else
+        {
+          seq[i] = alignment.getSequenceAt(index);
+          index++;
+        }
       }
     }
     Alignment fAlignmt = new Alignment(seq);
@@ -277,6 +330,7 @@ public class HiddenSequences
     fAlignmt.alignmentProperties = alignment.getProperties();
     fAlignmt.groups = alignment.getGroups();
     fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+    fAlignmt.setSeqrep(alignment.getSeqrep());
 
     return fAlignmt;
   }