X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2Fparams%2FSeqGroupIndexVector.java;h=9210414bc55099d40b668cc465347f748dc2b13c;hb=7f09e6ac5717bc78373c5d77f309831403e6ebf8;hp=4b21229f39dbb4483836245d773cd7bbe3935283;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 4b21229..9210414 100644
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -1,25 +1,29 @@
/*
- * 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
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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.util.MessageManager;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
@@ -27,14 +31,11 @@ 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;
import org.apache.http.entity.mime.content.StringBody;
@@ -47,13 +48,12 @@ import org.apache.http.entity.mime.content.StringBody;
* @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 });
}
/**
@@ -75,6 +75,7 @@ public class SeqGroupIndexVector extends InputType implements
* - alignment to be processed
* @return al or a new alignment with appropriate attributes/order for input
*/
+ @Override
public AlignmentI prepareAlignment(AlignmentI al)
{
jalview.analysis.AlignmentSorter.sortByGroup(al);
@@ -90,17 +91,19 @@ public class SeqGroupIndexVector extends InputType implements
AlignmentI al = rj.getAlignmentForInput(token, type);
// assume that alignment is properly ordered so groups form consecutive
// blocks
- ArrayList gl = new ArrayList();
- int p = 0;
- List sgs;
- synchronized (sgs = al.getGroups())
+ ArrayList gl = new ArrayList<>();
+ int p = 0, lowest = al.getHeight(), highest = 0;
+ List sgs = al.getGroups();
+ synchronized (sgs)
{
for (SequenceGroup sg : sgs)
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException("Group contains less than "
- + minsize + " sequences.");
+ throw new NoValidInputDataException(MessageManager.formatMessage(
+ "exception.notvaliddata_group_contains_less_than_min_seqs",
+ new String[]
+ { Integer.valueOf(minsize).toString() }));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
@@ -108,17 +111,28 @@ public class SeqGroupIndexVector extends InputType implements
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 };
+ se = new int[] { p, p };
}
else
{
if (p < se[0])
+ {
se[0] = p;
+ }
if (p > se[1])
+ {
se[1] = p;
+ }
}
}
if (se != null)
@@ -131,46 +145,18 @@ public class SeqGroupIndexVector extends InputType implements
// 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 (lowest - 1 > minsize)
{
- 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.");
- }
+ gl.add(0, new int[] { 0, lowest - 2 });
}
- else
+ if ((al.getHeight() - 1 - highest) > minsize)
{
- 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.");
- }
- }
+ gl.add(new int[] { highest + 1, al.getHeight() - 1 });
}
}
else
{
- gl.add(new int[]
- { 0, al.getHeight() - 1 });
+ gl.add(new int[] { 0, al.getHeight() - 1 });
}
if (min >= 0 && gl.size() < min)
{
@@ -187,7 +173,9 @@ public class SeqGroupIndexVector extends InputType implements
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];
+ }
jalview.util.QuickSort.sort(srt, vals);
list = false;
int last = vals[0][0] - 1;
@@ -229,7 +217,7 @@ public class SeqGroupIndexVector extends InputType implements
@Override
public List getURLEncodedParameter()
{
- ArrayList prms = new ArrayList();
+ ArrayList prms = new ArrayList<>();
super.addBaseParams(prms);
prms.add("minsize='" + minsize + "'");
prms.add("sep='" + sep + "'");
@@ -262,7 +250,9 @@ public class SeqGroupIndexVector extends InputType implements
{
minsize = Integer.valueOf(val);
if (minsize >= 0)
+ {
return true;
+ }
} catch (Exception x)
{
@@ -278,8 +268,8 @@ public class SeqGroupIndexVector extends InputType implements
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);