X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=f02c26229494279788116ddafaee2b63625c2981;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=4e7026e3fdf7df23f0ad4aa5d365de82b0c61b0f;hpb=a9570778f83fa5a2138205488da1d20049acdecf;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 4e7026e..f02c262 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,16 +1,39 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ *******************************************************************************/
 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.RestServiceDescription;
 import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 import java.util.Vector;
 
 import org.apache.http.entity.mime.content.ContentBody;
@@ -68,18 +91,20 @@ public class SeqGroupIndexVector extends InputType implements
     // assume that alignment is properly ordered so groups form consecutive
     // blocks
     ArrayList<int[]> gl = new ArrayList<int[]>();
+    int p = 0;
     for (SequenceGroup sg : (Vector<SequenceGroup>) al.getGroups())
     {
-      if (sg.getSize()<minsize)
+      if (sg.getSize() < minsize)
       {
-        throw new NoValidInputDataException("Group contains less than "+minsize+" sequences.");
+        throw new NoValidInputDataException("Group contains less than "
+                + minsize + " sequences.");
       }
       // TODO: refactor to sequenceGroup for efficiency -
       // getAlignmentRowInterval(AlignmentI al)
       int[] se = null;
       for (SequenceI sq : sg.getSequencesInOrder(al))
       {
-        int p = al.findIndex(sq);
+        p = al.findIndex(sq);
         if (se == null)
         {
           se = new int[]
@@ -98,6 +123,63 @@ public class SeqGroupIndexVector extends InputType implements
         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)
+    {
+      int[] tail = gl.get(0);
+      if (tail[0] > 0)
+      {
+        if (1 + tail[0] > minsize)
+        {
+          gl.add(0, new int[]
+          { 0, tail[0] - 1 });
+        }
+        else
+        {
+          // lets be intelligent here - if the remaining sequences aren't enough
+          // to make a final group, then don't make one.
+          // throw new
+          // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
+        }
+      }
+      else
+      {
+        tail = gl.get(gl.size() - 1);
+        if (1 + tail[1] < al.getHeight())
+        {
+          if (al.getHeight() - (1 + tail[1]) > minsize)
+          {
+            gl.add(new int[]
+            { tail[1] + 1, al.getHeight() - 1 });
+          }
+          else
+          {
+            // lets be intelligent here - if the remaining sequences aren't
+            // enough to make a final group, then don't make one.
+            // throw new
+            // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
+          }
+        }
+      }
+    }
+    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++)
@@ -121,4 +203,100 @@ public class SeqGroupIndexVector extends InputType implements
     return new StringBody(idvector.toString());
   }
 
-}
\ No newline at end of file
+  /**
+   * 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
+      {
+        minsize = Integer.valueOf(val);
+        if (minsize >= 0)
+          return true;
+      } catch (Exception x)
+      {
+
+      }
+      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 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;
+  }
+
+}