X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=084b80e4212dc2f22fa8324b452e472c9bd44977;hb=9e926ac4305fd9dff38b6e079e55b4f50664d544;hp=a0b3ff1a0696fdac5c26d9f107e725b03642de9d;hpb=a6875ff6ca7894443c98b1d068f78ea25c5bfc87;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index a0b3ff1..084b80e 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -5,16 +5,16 @@
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General License 
+ * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General License for more details.
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General License
+ * You should have received a copy of the GNU General Public License
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
@@ -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
@@ -118,7 +147,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
-   * Deletes a sequence from the alignment
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param s
    *          Sequence to be deleted.
@@ -126,7 +157,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   void deleteSequence(SequenceI s);
 
   /**
-   * Deletes a sequence from the alignment.
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param i
    *          Index of sequence to be deleted.
@@ -134,6 +167,14 @@ public interface AlignmentI extends AnnotatedCollectionI
   void deleteSequence(int i);
 
   /**
+   * Deletes a sequence in the alignment which has been hidden.
+   * 
+   * @param i
+   *          Index of sequence to be deleted
+   */
+  void deleteHiddenSequence(int i);
+
+  /**
    * Finds sequence in alignment using sequence name as query.
    * 
    * @param name
@@ -157,10 +198,11 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * Returns the first group (in the order in which groups were added) that
-   * includes the given sequence and aligned position (base 0), or null if none
-   * found
+   * includes the given sequence instance and aligned position (base 0), or null
+   * if none found
    * 
    * @param seq
+   *          - must be contained in the alignment (not a dataset sequence)
    * @param position
    * 
    * @return
@@ -285,13 +327,6 @@ public interface AlignmentI extends AnnotatedCollectionI
   char getGapCharacter();
 
   /**
-   * Test for all nucleotide alignment
-   * 
-   * @return true if alignment is nucleotide sequence
-   */
-  boolean isNucleotide();
-
-  /**
    * Test if alignment contains RNA structure
    * 
    * @return true if RNA structure AligmnentAnnotation was added to alignment
@@ -323,6 +358,8 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   HiddenSequences getHiddenSequences();
 
+  HiddenColumns getHiddenColumns();
+
   /**
    * Compact representation of alignment
    * 
@@ -543,12 +580,6 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
-  /**
-   * Calculate the visible start and end index of an alignment. The result is
-   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
-   * 
-   * @param hiddenCols
-   * @return
-   */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+  public void setHiddenColumns(HiddenColumns cols);
+
 }