Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure...

[jalview.git] / src / jalview / commands / JustifyLeftOrRightCommand.java

diff --git a/src/jalview/commands/JustifyLeftOrRightCommand.java b/src/jalview/commands/JustifyLeftOrRightCommand.java
new file mode 100644 (file)
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+++ b/src/jalview/commands/JustifyLeftOrRightCommand.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.commands;
+
+import java.util.List;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+public class JustifyLeftOrRightCommand extends EditCommand
+{
+  /**
+   * Constructs and performs a trim alignment command
+   * 
+   * @param description
+   *          (to show in Undo/Redo menu)
+   * @param justifyLeft
+   *          if true left justify, otherwise right
+   * @param seqs
+   *          the sequences to justify
+   * @param start
+   *          - leftmost column (base 0) to justify
+   * 
+   * @param end
+   *          - rightmost column (base 0) to justify
+   * 
+   * @param al
+   */
+  public JustifyLeftOrRightCommand(String description, boolean left,
+          List<SequenceI> seqs, int from, int to, AlignmentI al)
+  {
+    this.description = description;
+
+    for (SequenceI seq : seqs)
+    {
+      ContiguousI cont = seq.findPositions(from + 1, to + 1);
+      if (cont == null)
+      {
+        continue;
+      }
+      char[] range = seq.getSequence(from, to+1);
+      if (range==null || range.length==0)
+      {
+        continue;
+      }
+      int dsstart = seq.getDatasetSequence().getStart();
+      char[] sqchar = seq.getDatasetSequence().getSequence(
+              -dsstart + cont.getBegin(), -dsstart + cont.getEnd() + 1);
+      // debug
+      // println sqchar;
+      char[] alseq = new char[to - from + 1];
+      int sqstart = left ? 0 : alseq.length - sqchar.length;
+      int gaps = alseq.length - sqchar.length;
+      int gapstart = left ? sqchar.length : 0;
+      char gc = al.getGapCharacter();
+      for (int gp = 0; gp < gaps; gp++)
+      {
+        alseq[gapstart + gp] = gc;
+      }
+
+      for (int sqp = 0,insp=0; sqp<alseq.length; sqp++)
+      {
+        if (sqp < range.length && !Comparison.isGap(range[sqp]))
+        {
+          alseq[insp++ + sqstart] = range[sqp];
+        }
+      }
+      SequenceI[] sqa = new SequenceI[1];
+      sqa[0] = seq;
+
+      addEdit(new jalview.commands.EditCommand.Edit(
+              jalview.commands.EditCommand.Action.REPLACE, sqa, from,
+              to + 1, al, new String(alseq)));
+    }
+
+    performEdit(0, null);
+  }
+}