X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=0532035809c53a2a0383c4b84f614d24755ff9e6;hb=0ad16a9baa3247d1b2b61c21bbe869ad3feaf34e;hp=91b1fff5a05a4915e4da668d33fc59b1be20c9ca;hpb=4a3c64c3d8e65cc34ce36dd2cf8a575eea6d5493;p=jalview.git

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 91b1fff..0532035 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,17 +1,37 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.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;
@@ -68,71 +88,80 @@ 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())
+    int p = 0,lowest=al.getHeight(), highest=0;
+    List<SequenceGroup> sgs;
+    synchronized (sgs = al.getGroups())
     {
-      if (sg.getSize()<minsize)
+      for (SequenceGroup sg : sgs)
       {
-        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))
-      {
-        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
+        // TODO: refactor to sequenceGroup for efficiency -
+        // getAlignmentRowInterval(AlignmentI al)
+        int[] se = null;
+        for (SequenceI sq : sg.getSequencesInOrder(al))
         {
-          if (p < se[0])
-            se[0] = p;
-          if (p > se[1])
-            se[1] = p;
+          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);
         }
-      }
-      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)
+    // 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)
+      if (lowest-1>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.");       
+        gl.add(0, new int[]
+          { 0, lowest-2});
       }
-      } 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.");       
-          }
-        }
+      if ((al.getHeight()-1-highest)>minsize)
+      {
+        gl.add(new int[] { highest+1, al.getHeight()-1});
       }
-    } else {
-      gl.add(new int[] { 0, al.getHeight()-1});
     }
-    if (min>=0 && gl.size()<min)
+    else
     {
-      throw new NoValidInputDataException("Not enough sequence groups for input. Need at least "+min+" groups (including ungrouped regions).");
+      gl.add(new int[]
+      { 0, al.getHeight() - 1 });
     }
-    if (max>0 && gl.size()>max)
+    if (min >= 0 && gl.size() < min)
     {
-      throw new NoValidInputDataException("Too many sequence groups for input. Need at most "+max+" groups (including ungrouped regions).");
+      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()];
@@ -158,16 +187,102 @@ public class SeqGroupIndexVector extends InputType implements
   }
 
   /**
-   * set minimum number of sequences allowed in a partition. Default is 1 sequence.
-   * @param i (number greater than 1)
+   * 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)
+    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)
       {
-      minsize=i;
-      } else {
-        minsize=1;
+
+      }
+      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;
   }
-}
\ No newline at end of file
+
+  @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;
+  }
+
+}