Merge branch 'develop' into bug/JAL-2510amendFeatures

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

diff --git a/src/jalview/datamodel/AllRowsCollection.java b/src/jalview/datamodel/AllRowsCollection.java
new file mode 100644 (file)
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+++ b/src/jalview/datamodel/AllRowsCollection.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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 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 Public License for more details.
+ * 
+ * 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.
+ */
+package jalview.datamodel;
+
+import jalview.api.AlignmentRowsCollectionI;
+
+import java.util.Iterator;
+
+public class AllRowsCollection implements AlignmentRowsCollectionI
+{
+  int start;
+
+  int end;
+
+  AlignmentI alignment;
+
+  HiddenSequences hidden;
+
+  public AllRowsCollection(int s, int e, AlignmentI al)
+  {
+    start = s;
+    end = e;
+    alignment = al;
+    hidden = al.getHiddenSequences();
+  }
+
+  @Override
+  public Iterator<Integer> iterator()
+  {
+    return new AllRowsIterator(start, end, alignment);
+  }
+
+  @Override
+  public boolean isHidden(int seq)
+  {
+    return hidden.isHidden(seq);
+  }
+
+  @Override
+  public SequenceI getSequence(int seq)
+  {
+    return alignment.getSequenceAtAbsoluteIndex(seq);
+  }
+}
+