JAL-2418 source formatting

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index d3aa01a..c9dce08 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -157,9 +157,10 @@ public class HiddenSequences
     int absAlignmentIndex = alignment.findIndex(sequence);
     int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
-    if (hiddenSequences[alignmentIndex] != null)
+    if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
     {
       System.out.println("ERROR!!!!!!!!!!!");
+      return;
     }
 
     hiddenSequences[alignmentIndex] = sequence;
@@ -170,7 +171,13 @@ public class HiddenSequences
   public List<SequenceI> showAll(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> revealedSeqs = new ArrayList<>();
+
+    if (hiddenSequences == null)
+    {
+      return revealedSeqs;
+    }
+
     for (int i = 0; i < hiddenSequences.length; i++)
     {
       if (hiddenSequences[i] != null)
@@ -199,7 +206,7 @@ public class HiddenSequences
   public List<SequenceI> showSequence(int alignmentIndex,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> revealedSeqs = new ArrayList<>();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if (repSequence != null && hiddenRepSequences != null
             && hiddenRepSequences.containsKey(repSequence))
@@ -232,8 +239,8 @@ public class HiddenSequences
           }
           else
           {
-            System.out.println(seq.getName()
-                    + " has been deleted whilst hidden");
+            System.out.println(
+                    seq.getName() + " has been deleted whilst hidden");
           }
         }
       }
@@ -247,7 +254,8 @@ public class HiddenSequences
   }
 
   /**
-   * Convert absolute alignment index to visible alignment index
+   * Convert absolute alignment index to visible alignment index (or -1 if
+   * before the first visible sequence)
    * 
    * @param alignmentIndex
    * @return
@@ -294,7 +302,7 @@ public class HiddenSequences
    *          the row to start from
    * @return the position of the row in the visible alignment
    */
-  public int findIndexNAboveRow(int visibleDistance, int startRow)
+  public int subtractVisibleRows(int visibleDistance, int startRow)
   {
     // walk upwards through the alignment
     // count all the non-null sequences until we have visibleDistance counted
@@ -304,7 +312,7 @@ public class HiddenSequences
       return startRow - visibleDistance;
     }
 
-    int index = startRow;
+    int index = Math.min(startRow, hiddenSequences.length - 1);
     int count = 0;
     while ((index > -1) && (count < visibleDistance))
     {
@@ -403,4 +411,20 @@ public class HiddenSequences
 
     return false;
   }
+
+  /**
+   * Answers if a sequence is hidden
+   * 
+   * @param seq
+   *          (absolute) index to test
+   * @return true if sequence at index seq is hidden
+   */
+  public boolean isHidden(int seq)
+  {
+    if (hiddenSequences != null)
+    {
+      return (hiddenSequences[seq] != null);
+    }
+    return false;
+  }
 }