X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentView.java;h=9db9f3820242a3aaf427a67b846f45f93b7c8ed7;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=273a6851f2a557fa39739edd5e70cb8ade4e3d64;hpb=27b77d2219147d3741d4af7377e13918a8ae972a;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 273a685..9db9f38 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1,29 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.util.MessageManager;
 import jalview.util.ShiftList;
 
 import java.io.PrintStream;
-import java.util.Enumeration;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Vector;
 
 /**
  * Transient object compactly representing a 'view' of an alignment - with
@@ -44,11 +46,13 @@ public class AlignmentView
    * one or more ScGroup objects, which are referenced by each seqCigar's group
    * membership
    */
-  private Vector scGroups;
+  private List<ScGroup> scGroups = null;
+
+  private boolean isNa = false;
 
-  private boolean isNa=false;
   /**
    * false if the view concerns peptides
+   * 
    * @return
    */
   public boolean isNa()
@@ -64,13 +68,51 @@ public class AlignmentView
    */
   private class ScGroup
   {
-    public Vector seqs;
+    public List<SeqCigar> seqs;
 
     public SequenceGroup sg;
 
     ScGroup()
     {
-      seqs = new Vector();
+      seqs = new ArrayList<SeqCigar>();
+    }
+
+    /**
+     * @param seq
+     * @return true if seq was not a member before and was added to group
+     */
+    public boolean add(SeqCigar seq)
+    {
+      if (!seq.isMemberOf(this))
+      {
+        seqs.add(seq);
+        seq.setGroupMembership(this);
+        return true;
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    /**
+     * 
+     * @param seq
+     * @return true if seq was a member and was removed from group
+     */
+    public boolean remove(SeqCigar seq)
+    {
+      if (seq.removeGroupMembership(this))
+      {
+        seqs.remove(seq);
+        return true;
+      }
+      return false;
+    }
+
+    public int size()
+    {
+      return seqs.size();
     }
   }
 
@@ -78,7 +120,7 @@ public class AlignmentView
    * vector of selected seqCigars. This vector is also referenced by each
    * seqCigar contained in it.
    */
-  private Vector selected;
+  private ScGroup selected;
 
   /**
    * Construct an alignmentView from a live jalview alignment view. Note -
@@ -119,7 +161,7 @@ public class AlignmentView
     if (selection != null && selection.getSize() > 0)
     {
       List<SequenceI> sel = selection.getSequences(null);
-      this.selected = new Vector();
+      this.selected = new ScGroup();
       selseqs = selection
               .getSequencesInOrder(alignment, selectedRegionOnly);
     }
@@ -128,27 +170,24 @@ public class AlignmentView
       selseqs = alignment.getSequencesArray();
     }
 
+    List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
     // get the alignment's group list and make a copy
-    Vector grps = new Vector();
+    List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
     List<SequenceGroup> gg = alignment.getGroups();
     grps.addAll(gg);
     ScGroup[] sgrps = null;
     boolean addedgps[] = null;
     if (grps != null)
     {
-      SequenceGroup sg;
       if (selection != null && selectedRegionOnly)
       {
         // trim annotation to the region being stored.
         // strip out any groups that do not actually intersect with the
         // visible and selected region
         int ssel = selection.getStartRes(), esel = selection.getEndRes();
-        Vector isg = new Vector();
-        Enumeration en = grps.elements();
-        while (en.hasMoreElements())
+        List<SequenceGroup> isg = new ArrayList<SequenceGroup>();
+        for (SequenceGroup sg : grps)
         {
-          sg = (SequenceGroup) en.nextElement();
-
           if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
           {
             // adjust bounds of new group, if necessary.
@@ -163,7 +202,7 @@ public class AlignmentView
             sg.setStartRes(sg.getStartRes() - ssel + 1);
             sg.setEndRes(sg.getEndRes() - ssel + 1);
 
-            isg.addElement(sg);
+            isg.add(sg);
           }
         }
         grps = isg;
@@ -173,13 +212,15 @@ public class AlignmentView
       addedgps = new boolean[grps.size()];
       for (int g = 0; g < sgrps.length; g++)
       {
-        sg = (SequenceGroup) grps.elementAt(g);
+        SequenceGroup sg = grps.get(g);
         sgrps[g] = new ScGroup();
         sgrps[g].sg = new SequenceGroup(sg);
         addedgps[g] = false;
-        grps.setElementAt(sg.getSequences(null), g);
+        // can't set entry 0 in an empty list
+        // seqsets.set(g, sg.getSequences(null));
+        seqsets.add(sg.getSequences());
       }
-      // grps now contains vectors (should be sets) for each group, so we can
+      // seqsets now contains vectors (should be sets) for each group, so we can
       // track when we've done with the group
     }
     int csi = 0;
@@ -190,26 +231,24 @@ public class AlignmentView
         if (selection != null && selection.getSize() > 0
                 && !selectedRegionOnly)
         {
-          sequences[csi].setGroupMembership(selected);
-          selected.addElement(sequences[csi]);
+          selected.add(sequences[csi]);
         }
-        if (grps != null)
+        if (seqsets != null)
         {
           for (int sg = 0; sg < sgrps.length; sg++)
           {
-            if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
+            if ((seqsets.get(sg)).contains(selseqs[i]))
             {
-              sequences[csi].setGroupMembership(sgrps[sg]);
               sgrps[sg].sg.deleteSequence(selseqs[i], false);
-              sgrps[sg].seqs.addElement(sequences[csi]);
+              sgrps[sg].add(sequences[csi]);
               if (!addedgps[sg])
               {
                 if (scGroups == null)
                 {
-                  scGroups = new Vector();
+                  scGroups = new ArrayList<ScGroup>();
                 }
                 addedgps[sg] = true;
-                scGroups.addElement(sgrps[sg]);
+                scGroups.add(sgrps[sg]);
               }
             }
           }
@@ -295,8 +334,7 @@ public class AlignmentView
   {
     ColumnSelection colsel = new ColumnSelection();
 
-    return new Object[]
-    {
+    return new Object[] {
         SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
                 contigs), colsel };
   }
@@ -352,7 +390,7 @@ public class AlignmentView
           SequenceGroup[] nsg = new SequenceGroup[nvg];
           for (int g = 0; g < nvg; g++)
           {
-            SequenceGroup sg = ((ScGroup) scGroups.elementAt(g)).sg;
+            SequenceGroup sg = scGroups.get(g).sg;
             if (r)
             {
               if (sg.getStartRes() > gend || sg.getEndRes() < gstart)
@@ -438,7 +476,7 @@ public class AlignmentView
             for (int g = 0; g < nvg; g++)
             {
               if (nsg[g] != null
-                      && sequences[nsq].isMemberOf(scGroups.elementAt(g)))
+                      && sequences[nsq].isMemberOf(scGroups.get(g)))
               {
                 nsg[g].addSequence(aln[nsq], false);
               }
@@ -462,6 +500,7 @@ public class AlignmentView
    * alignment.
    * 
    * @param c
+   *          gap character to use to recreate the alignment
    * @return
    */
   private SequenceI[] getVisibleSeqs(char c)
@@ -469,13 +508,9 @@ public class AlignmentView
     SequenceI[] aln = new SequenceI[sequences.length];
     for (int i = 0, j = sequences.length; i < j; i++)
     {
-      aln[i] = sequences[i].getSeq('-');
-    }
-    // Remove hidden regions from sequence objects.
-    String seqs[] = getSequenceStrings('-');
-    for (int i = 0, j = aln.length; i < j; i++)
-    {
-      aln[i].setSequence(seqs[i]);
+      aln[i] = sequences[i].getSeq(c);
+      // Remove hidden regions from sequence
+      aln[i].setSequence(getASequenceString(c, i));
     }
     return aln;
   }
@@ -511,8 +546,38 @@ public class AlignmentView
   }
 
   /**
+   * build a string excluding hidden regions from a particular sequence in the
+   * view
+   * 
+   * @param c
+   * @param n
+   * @return
+   */
+  private String getASequenceString(char c, int n)
+  {
+    String sqn;
+    String fullseq = sequences[n].getSequenceString(c);
+    if (contigs != null)
+    {
+      sqn = "";
+      int p = 0;
+      for (int h = 0; h < contigs.length; h += 3)
+      {
+        sqn += fullseq.substring(p, contigs[h + 1]);
+        p = contigs[h + 1] + contigs[h + 2];
+      }
+      sqn += fullseq.substring(p);
+    }
+    else
+    {
+      sqn = fullseq;
+    }
+    return sqn;
+  }
+
+  /**
    * get an array of visible sequence strings for a view on an alignment using
-   * the given gap character
+   * the given gap character uses getASequenceString
    * 
    * @param c
    *          char
@@ -523,22 +588,7 @@ public class AlignmentView
     String[] seqs = new String[sequences.length];
     for (int n = 0; n < sequences.length; n++)
     {
-      String fullseq = sequences[n].getSequenceString(c);
-      if (contigs != null)
-      {
-        seqs[n] = "";
-        int p = 0;
-        for (int h = 0; h < contigs.length; h += 3)
-        {
-          seqs[n] += fullseq.substring(p, contigs[h + 1]);
-          p = contigs[h + 1] + contigs[h + 2];
-        }
-        seqs[n] += fullseq.substring(p);
-      }
-      else
-      {
-        seqs[n] = fullseq;
-      }
+      seqs[n] = getASequenceString(c, n);
     }
     return seqs;
   }
@@ -648,7 +698,9 @@ public class AlignmentView
   {
     if (sequences == null || width <= 0)
     {
-      throw new Error("empty view cannot be updated.");
+      throw new Error(
+              MessageManager
+                      .getString("error.empty_view_cannot_be_updated"));
     }
     if (nvismsa == null)
     {
@@ -679,10 +731,16 @@ public class AlignmentView
               if (mseq.length != sequences.length)
               {
                 throw new Error(
-                        "Mismatch between number of sequences in block "
-                                + j + " (" + mseq.length
-                                + ") and the original view ("
-                                + sequences.length + ")");
+                        MessageManager
+                                .formatMessage(
+                                        "error.mismatch_between_number_of_sequences_in_block",
+                                        new String[] {
+                                            Integer.valueOf(j).toString(),
+                                            Integer.valueOf(mseq.length)
+                                                    .toString(),
+                                            Integer.valueOf(
+                                                    sequences.length)
+                                                    .toString() }));
               }
               swidth = mseq[0].getLength(); // JBPNote: could ensure padded
               // here.
@@ -835,27 +893,30 @@ public class AlignmentView
               else
               {
                 // place gaps.
-                throw new Error("Padding not yet implemented.");
+                throw new Error(
+                        MessageManager
+                                .getString("error.padding_not_yet_implemented"));
               }
             }
           }
         }
       }
-      return new Object[]
-      { alignment, columnselection };
+      return new Object[] { alignment, columnselection };
     }
     else
     {
       if (nvismsa.length != 1)
       {
         throw new Error(
-                "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
-                        + nvismsa.length);
+                MessageManager
+                        .formatMessage(
+                                "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",
+                                new String[] { Integer.valueOf(
+                                        nvismsa.length).toString() }));
       }
       if (nvismsa[0] != null)
       {
-        return new Object[]
-        { nvismsa[0], new ColumnSelection() };
+        return new Object[] { nvismsa[0], new ColumnSelection() };
       }
       else
       {
@@ -916,8 +977,7 @@ public class AlignmentView
     }
     else
     {
-      return new int[]
-      { 0, width };
+      return new int[] { 0, width };
     }
   }
 
@@ -1040,17 +1100,17 @@ public class AlignmentView
               + " groups defined on the view.");
       for (int g = 0; g < view.scGroups.size(); g++)
       {
-        ScGroup sgr = (ScGroup) view.scGroups.elementAt(g);
+        ScGroup sgr = view.scGroups.get(g);
         os.println("Group " + g + ": Name = " + sgr.sg.getName()
                 + " Contains " + sgr.seqs.size() + " Seqs.");
         os.println("This group runs from " + sgr.sg.getStartRes() + " to "
                 + sgr.sg.getEndRes());
         for (int s = 0; s < sgr.seqs.size(); s++)
         {
-          if (!((SeqCigar) sgr.seqs.elementAt(s)).isMemberOf(sgr))
+          // JBPnote this should be a unit test for ScGroup
+          if (!sgr.seqs.get(s).isMemberOf(sgr))
           {
-            os.println("** WARNING: sequence "
-                    + ((SeqCigar) sgr.seqs.elementAt(s)).toString()
+            os.println("** WARNING: sequence " + sgr.seqs.get(s).toString()
                     + " is not marked as member of group.");
           }
         }