JAL-2388 Initial removal of hidden cols/seqs out of overview

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5d185cd..1ecff9a 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -31,13 +31,22 @@ import java.util.Set;
 public interface AlignmentI extends AnnotatedCollectionI
 {
   /**
-   * Calculates the number of sequences in an alignment
+   * Calculates the number of sequences in an alignment, excluding hidden
+   * sequences
    * 
    * @return Number of sequences in alignment
    */
   int getHeight();
 
   /**
+   * Calculates the number of sequences in an alignment, including hidden
+   * sequences
+   * 
+   * @return Number of sequences in alignment
+   */
+  int getAbsoluteHeight();
+
+  /**
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
@@ -65,6 +74,15 @@ public interface AlignmentI extends AnnotatedCollectionI
   boolean isAligned(boolean includeHidden);
 
   /**
+   * Answers if the sequence at alignmentIndex is hidden
+   * 
+   * @param alignmentIndex
+   *          the index to check
+   * @return true if the sequence is hidden
+   */
+  boolean isHidden(int alignmentIndex);
+
+  /**
    * Gets sequences as a Synchronized collection
    * 
    * @return All sequences in alignment.
@@ -90,6 +108,17 @@ public interface AlignmentI extends AnnotatedCollectionI
   SequenceI getSequenceAt(int i);
 
   /**
+   * Find a specific sequence in this alignment.
+   * 
+   * @param i
+   *          Index of required sequence in full alignment, i.e. if all columns
+   *          were visible
+   * 
+   * @return SequenceI at given index.
+   */
+  SequenceI getSequenceAtAbsoluteIndex(int i);
+
+  /**
    * Returns a map of lists of sequences keyed by sequence name.
    * 
    * @return