JAL-1894 update year/version in copyright

[jalview.git] / src / jalview / analysis / Grouping.java

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 7b6dda1..b01c815 100644 (file)
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -91,8 +91,90 @@ public class Grouping
     i = 0;
     for (String key : gps.keySet())
     {
-      SequenceGroup group = new SequenceGroup(gps.get(key),
-              "Subseq: " + key, null, true, true, false, 0, width - 1);
+      SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
+              + key, null, true, true, false, 0, width - 1);
+
+      groups[i++] = group;
+    }
+    gps.clear();
+    pgroup.clear();
+    return groups;
+  }
+
+  /**
+   * Divide the given sequences based on the equivalence of characters at
+   * selected columns If exgroups is provided, existing groups will be
+   * subdivided.
+   * 
+   * @param sequences
+   * @param columnSelection
+   * @param list
+   * @return
+   */
+  public static SequenceGroup[] makeGroupsFromCols(SequenceI[] sequences,
+          ColumnSelection cs, List<SequenceGroup> list)
+  {
+    // TODO: determine how to get/recover input data for group generation
+    Map<String, List<SequenceI>> gps = new HashMap<String, List<SequenceI>>();
+    Map<String, SequenceGroup> pgroup = new HashMap<String, SequenceGroup>();
+    if (list != null)
+    {
+      for (SequenceGroup sg : list)
+      {
+        for (SequenceI sq : sg.getSequences(null))
+        {
+          pgroup.put(sq.toString(), sg);
+        }
+      }
+    }
+    int[] spos = new int[cs.getSelected().size()];
+    int width = -1;
+    int i = 0;
+    for (Integer pos : cs.getSelected())
+    {
+      spos[i++] = pos.intValue();
+    }
+    ;
+    for (i = 0; i < sequences.length; i++)
+    {
+      int slen = sequences[i].getLength();
+      if (width < slen)
+      {
+        width = slen;
+      }
+
+      SequenceGroup pgp = pgroup.get(((Object) sequences[i]).toString());
+      StringBuilder schar = new StringBuilder();
+      if (pgp != null)
+      {
+        schar.append(pgp.getName() + ":");
+      }
+      for (int p : spos)
+      {
+        if (p >= slen)
+        {
+          schar.append("~");
+        }
+        else
+        {
+          schar.append(sequences[i].getCharAt(p));
+        }
+      }
+      List<SequenceI> svec = gps.get(schar.toString());
+      if (svec == null)
+      {
+        svec = new ArrayList<SequenceI>();
+        gps.put(schar.toString(), svec);
+      }
+      svec.add(sequences[i]);
+    }
+    // make some groups
+    SequenceGroup[] groups = new SequenceGroup[gps.size()];
+    i = 0;
+    for (String key : gps.keySet())
+    {
+      SequenceGroup group = new SequenceGroup(gps.get(key), "Subseq: "
+              + key, null, true, true, false, 0, width - 1);
 
       groups[i++] = group;
     }