X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=2c4b71a474b23b141c32249e74c89c6d9ed07e7e;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=1a7c63f28b5d9334089fea511cb67d648b08a0d4;hpb=21559d1d8350538846655bfa6ccfc7320dd9e2e5;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 1a7c63f..2c4b71a 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,41 +1,76 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.ws.rest.params;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.Option;
 import jalview.ws.rest.AlignmentProcessor;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
-import java.util.Vector;
+import java.util.Arrays;
+import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
 
 /**
- * Represents the partitions defined on the alignment as indices
- * e.g. for a partition (A,B,C),(D,E),(F)
- * The indices would be 3,2,1. Note, the alignment must be ordered so groups are contiguous before this input type can be used.
+ * Represents the partitions defined on the alignment as indices e.g. for a
+ * partition (A,B,C),(D,E),(F) The indices would be 3,2,1. Note, the alignment
+ * must be ordered so groups are contiguous before this input type can be used.
+ * 
  * @author JimP
- *
+ * 
  */
-public class SeqGroupIndexVector extends InputType implements AlignmentProcessor{
+public class SeqGroupIndexVector extends InputType implements
+        AlignmentProcessor
+{
   public SeqGroupIndexVector()
   {
-    super(new Class[] { AlignmentI.class} );
+    super(new Class[]
+    { AlignmentI.class });
   }
+
   /**
    * separator for list of sequence Indices - default is ','
    */
-  public String sep=",";
+  public String sep = ",";
+
+  /**
+   * min size of each partition
+   */
+  public int minsize = 1;
+
   molType type;
+
   /**
    * prepare the context alignment for this input
-   * @param al - alignment to be processed
+   * 
+   * @param al
+   *          - alignment to be processed
    * @return al or a new alignment with appropriate attributes/order for input
    */
   public AlignmentI prepareAlignment(AlignmentI al)
@@ -43,57 +78,212 @@ public class SeqGroupIndexVector extends InputType implements AlignmentProcessor
     jalview.analysis.AlignmentSorter.sortByGroup(al);
     return al;
   }
+
   @Override
-  public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+  public ContentBody formatForInput(RestJob rj)
+          throws UnsupportedEncodingException, NoValidInputDataException
   {
     StringBuffer idvector = new StringBuffer();
-    boolean list=false;
+    boolean list = false;
     AlignmentI al = rj.getAlignmentForInput(token, type);
-    // assume that alignment is properly ordered so groups form consecutive blocks
+    // assume that alignment is properly ordered so groups form consecutive
+    // blocks
     ArrayList<int[]> gl = new ArrayList<int[]>();
-    for (SequenceGroup sg : (Vector<SequenceGroup>)al.getGroups())
+    int p = 0,lowest=al.getHeight(), highest=0;
+    List<SequenceGroup> sgs;
+    synchronized (sgs = al.getGroups())
     {
-      // TODO: refactor to sequenceGroup for efficiency - getAlignmentRowInterval(AlignmentI al)
-      int[] se=null;
-      for (SequenceI sq: sg.getSequencesInOrder(al))
+      for (SequenceGroup sg : sgs)
       {
-        int p = al.findIndex(sq);
-        if (se==null)
+        if (sg.getSize() < minsize)
         {
-          se=new int[] { p, p};
+          throw new NoValidInputDataException("Group contains less than "
+                  + minsize + " sequences.");
         }
-        else {
-          if (p<se[0])
-            se[0]=p;
-          if (p>se[1])
-            se[1]=p;
+        // TODO: refactor to sequenceGroup for efficiency -
+        // getAlignmentRowInterval(AlignmentI al)
+        int[] se = null;
+        for (SequenceI sq : sg.getSequencesInOrder(al))
+        {
+          p = al.findIndex(sq);
+          if (lowest>p)
+          {
+            lowest=p;
+          }
+          if (highest<p)
+          {
+            highest=p;
+          }
+          if (se == null)
+          {
+            se = new int[]
+            { p, p };
+          }
+          else
+          {
+            if (p < se[0])
+              se[0] = p;
+            if (p > se[1])
+              se[1] = p;
+          }
         }
+        if (se != null)
+        {
+          gl.add(se);
+        }
+      }
+    }
+    // are there any more sequences ungrouped that should be added as a single
+    // remaining group ? - these might be at the start or the end
+    if (gl.size() > 0)
+    {
+      if (lowest-1>minsize)
+      {
+        gl.add(0, new int[]
+          { 0, lowest-2});
       }
-      if (se!=null)
+      if ((al.getHeight()-1-highest)>minsize)
       {
-        gl.add(se);
+        gl.add(new int[] { highest+1, al.getHeight()-1});
       }
     }
+    else
+    {
+      gl.add(new int[]
+      { 0, al.getHeight() - 1 });
+    }
+    if (min >= 0 && gl.size() < min)
+    {
+      throw new NoValidInputDataException(
+              "Not enough sequence groups for input. Need at least " + min
+                      + " groups (including ungrouped regions).");
+    }
+    if (max > 0 && gl.size() > max)
+    {
+      throw new NoValidInputDataException(
+              "Too many sequence groups for input. Need at most " + max
+                      + " groups (including ungrouped regions).");
+    }
     int[][] vals = gl.toArray(new int[gl.size()][]);
     int[] srt = new int[gl.size()];
-    for (int i=0;i<vals.length;i++)
-      srt[i]=vals[i][0];
+    for (int i = 0; i < vals.length; i++)
+      srt[i] = vals[i][0];
     jalview.util.QuickSort.sort(srt, vals);
-    list=false;
-    int last=vals[0][0];
-    for (int[] range:vals)
+    list = false;
+    int last = vals[0][0] - 1;
+    for (int[] range : vals)
     {
-      if (range[1]>last) {
+      if (range[1] > last)
+      {
         if (list)
+        {
+          idvector.append(sep);
+        }
+        idvector.append(range[1] - last);
+        last = range[1];
+        list = true;
+      }
+    }
+    return new StringBody(idvector.toString());
+  }
+
+  /**
+   * set minimum number of sequences allowed in a partition. Default is 1
+   * sequence.
+   * 
+   * @param i
+   *          (number greater than 1)
+   */
+  public void setMinsize(int i)
+  {
+    if (minsize >= 1)
+    {
+      minsize = i;
+    }
+    else
+    {
+      minsize = 1;
+    }
+  }
+
+  @Override
+  public List<String> getURLEncodedParameter()
+  {
+    ArrayList<String> prms = new ArrayList<String>();
+    super.addBaseParams(prms);
+    prms.add("minsize='" + minsize + "'");
+    prms.add("sep='" + sep + "'");
+    if (type != null)
+    {
+      prms.add("type='" + type + "'");
+    }
+    return prms;
+  }
+
+  @Override
+  public String getURLtokenPrefix()
+  {
+    return "PARTITION";
+  }
+
+  @Override
+  public boolean configureProperty(String tok, String val,
+          StringBuffer warnings)
+  {
+
+    if (tok.startsWith("sep"))
+    {
+      sep = val;
+      return true;
+    }
+    if (tok.startsWith("minsize"))
+    {
+      try
       {
-        idvector.append(sep);
+        minsize = Integer.valueOf(val);
+        if (minsize >= 0)
+          return true;
+      } catch (Exception x)
+      {
+
       }
-      idvector.append(range[1]-last+1);
-      last=range[1];
-      list=true;
+      warnings.append("Invalid minsize value '" + val
+              + "'. Must be a positive integer.\n");
+    }
+    if (tok.startsWith("type"))
+    {
+      try
+      {
+        type = molType.valueOf(val);
+        return true;
+      } catch (Exception x)
+      {
+        warnings.append("Invalid molecule type '" + val
+                + "'. Must be one of (");
+        for (molType v : molType.values())
+        {
+          warnings.append(" " + v);
+        }
+        warnings.append(")\n");
       }
     }
-    return new StringBody(idvector.toString());
+    return false;
+  }
+
+  @Override
+  public List<OptionI> getOptions()
+  {
+    List<OptionI> lst = getBaseOptions();
+    lst.add(new Option("sep",
+            "Separator character between elements of vector", true, ",",
+            sep, Arrays.asList(new String[]
+            { " ", ",", ";", "\t", "|" }), null));
+    lst.add(new IntegerParameter("minsize",
+            "Minimum size of partition allowed by service", true, 1,
+            minsize, 1, 0));
+    lst.add(createMolTypeOption("type", "Sequence type", false, type,
+            molType.MIX));
+    return lst;
   }
-  
-}
\ No newline at end of file
+
+}