/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2.jabaws2;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.util.MessageManager;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
import compbio.data.sequence.Score;
public class AAConClient extends JabawsAnnotationInstance
{
// configuration for factory
public static String getServiceActionText()
{
return "calculating Amino acid consensus using AACon service";
}
private static String CALC_ID = "jabaws2.AACon";
public static AlignAnalysisUIText getAlignAnalysisUIText()
{
return new AlignAnalysisUIText(
compbio.ws.client.Services.AAConWS.toString(),
AAConClient.class, CALC_ID, false, true, true, true,
true, 2, MessageManager.getString("label.aacon_calculations"),
MessageManager.getString("tooltip.aacon_calculations"),
MessageManager.getString("label.aacon_settings"),
MessageManager.getString("tooltip.aacon_settings"));
}
// instance
public AAConClient(Jws2Instance handle)
{
super(handle);
}
@Override
List annotationFromScoreManager(AlignmentI seqs,
Map featureColours,
Map featureFilters)
{
return aacons_annotation(seqs.getWidth(), seqs, null);
}
private List aacons_annotation(int alWidth,
AlignmentI alignViewport, boolean[] gapMap)
{
Map> scoremap = scoremanager.asMap();
ArrayList ourAnnot = new ArrayList<>();
for (String score : scoremap.keySet())
{
Set scores = scoremap.get(score);
for (Score scr : scores)
{
if (scr.getRanges() != null && scr.getRanges().size() > 0)
{
/**
* annotation in range annotation = findOrCreate(scr.getMethod(),
* true, null, null); Annotation[] elm = new Annotation[alWidth];
* Iterator vals = scr.getScores().iterator(); for (Range rng :
* scr.getRanges()) { float val = vals.next().floatValue(); for (int i
* = rng.from; i <= rng.to; i++) { elm[i] = new Annotation("", "", '
* ', val); } } annotation.annotations = elm;
* annotation.validateRangeAndDisplay();
*/
}
else
{
createAnnotationRowsForScores(alignViewport, null, ourAnnot,
getCalcId(),
scr.getScores().size(), scr);
}
}
}
return ourAnnot;
}
}