/*
* 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;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.gui.AlignFrame;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.OptionI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.JpredAlignment;
import compbio.metadata.Argument;
public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
{
/**
*
* @return default args for this service when run as dynamic web service
*/
public List selectDefaultArgs()
{
List rgs = new ArrayList();
for (ArgumentI argi : service.getParamStore().getServiceParameters())
{
if (argi instanceof OptionI)
{
List o = ((OptionI) argi).getPossibleValues();
if (o.contains("-pred-nohits"))
{
OptionI cpy = ((OptionI) argi).copy();
cpy.setValue("-pred-nohits");
rgs.add(cpy);
}
}
}
return JabaParamStore.getJabafromJwsArgs(rgs);
}
public JPred301Client(Jws2Instance service, AlignFrame alignFrame,
WsParamSetI preset, List paramset)
{
super(service, alignFrame, preset, paramset);
submitGaps = true;
alignedSeqs = true;
nucleotidesAllowed = false;
proteinAllowed = true;
gapMap = new boolean[0];
updateParameters(null, selectDefaultArgs());
}
@Override
boolean checkValidInputSeqs(boolean dynamic, List seqs)
{
return (seqs.size() > 1);
}
@Override
public String getServiceActionText()
{
return "calculating consensus secondary structure prediction using JPred service";
}
private static Map jpredRowLabels = new HashMap();
private static final Set jpredRes_graph;
private static final Set jpredRes_ssonly;
static
{
jpredRes_ssonly = new HashSet();
jpredRes_ssonly.add("jnetpred".toLowerCase());
jpredRes_ssonly.add("jnetpssm".toLowerCase());
jpredRes_ssonly.add("jnethmm".toLowerCase());
jpredRes_graph = new HashSet();
jpredRes_graph.add("jnetconf".toLowerCase());
jpredRes_graph.add("jnet burial".toLowerCase());
}
/**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
@Override
public void updateResultAnnotation(boolean immediate)
{
if (immediate || !calcMan.isWorking(this) && msascoreset != null)
{
if (msascoreset instanceof compbio.data.sequence.JpredAlignment)
{
JpredAlignment jpres = (JpredAlignment) msascoreset;
int alWidth = alignViewport.getAlignment().getWidth();
ArrayList ourAnnot = new ArrayList();
char[] sol = new char[jpres.getJpredSequences().get(0).getLength()];
boolean firstsol = true;
for (FastaSequence fsq : jpres.getJpredSequences())
{
String[] k = jpredRowLabels.get(fsq.getId());
if (k == null)
{
k = new String[] { fsq.getId(), "JNet Output" };
}
if (fsq.getId().startsWith("JNETSOL"))
{
char amnt = (fsq.getId().endsWith("25") ? "3" : fsq.getId()
.endsWith("5") ? "6" : "9").charAt(0);
char[] vseq = fsq.getSequence().toCharArray();
for (int spos = 0, sposL = fsq.getLength(); spos < sposL; spos++)
{
if (firstsol)
{
sol[spos] = '0';
}
if (vseq[spos] == 'B'
&& (sol[spos] == '0' || sol[spos] < amnt))
{
sol[spos] = amnt;
}
}
firstsol = false;
}
else
{
createAnnotationRowFromString(
ourAnnot,
getCalcId(),
alWidth,
k[0],
k[1],
jpredRes_graph.contains(fsq.getId()) ? AlignmentAnnotation.BAR_GRAPH
: AlignmentAnnotation.NO_GRAPH, 0f, 9f,
fsq.getSequence());
}
}
createAnnotationRowFromString(
ourAnnot,
getCalcId(),
alWidth,
"Jnet Burial",
"Prediction of Solvent Accessibility
levels are- 0 - Exposed
- 3 - 25% or more S.A. accessible
- 6 - 5% or more S.A. accessible
- 9 - Buried (<5% exposed)
",
AlignmentAnnotation.BAR_GRAPH, 0f, 9f, new String(sol));
for (FastaSequence fsq : jpres.getSequences())
{
if (fsq.getId().equalsIgnoreCase("QUERY"))
{
createAnnotationRowFromString(ourAnnot, getCalcId(), alWidth,
"Query", "JPred Reference Sequence",
AlignmentAnnotation.NO_GRAPH, 0f, 0f, fsq.getSequence());
}
}
if (ourAnnot.size() > 0)
{
updateOurAnnots(ourAnnot);
}
}
}
}
private void createAnnotationRowFromString(
ArrayList ourAnnot, String calcId,
int alWidth, String label, String descr, int rowType, float min,
float max, String jpredPrediction)
{
// simple annotation row
AlignmentAnnotation annotation = alignViewport.getAlignment()
.findOrCreateAnnotation(label, calcId, true, null, null);
if (alWidth == gapMap.length) // scr.getScores().size())
{
annotation.label = new String(label);
annotation.description = new String(descr);
annotation.graph = rowType;
annotation.graphMin = min;
annotation.graphMax = max;
if (constructAnnotationFromString(annotation, jpredPrediction,
alWidth, rowType))
{
// created a valid annotation from the data
ourAnnot.add(annotation);
// annotation.validateRangeAndDisplay();
}
}
}
private boolean constructAnnotationFromString(
AlignmentAnnotation annotation, String sourceData, int alWidth,
int rowType)
{
if (sourceData.length() == 0 && alWidth > 0)
{
return false;
}
Annotation[] elm = new Annotation[alWidth];
boolean ssOnly = jpredRes_ssonly.contains(annotation.label
.toLowerCase());
boolean graphOnly = rowType != AlignmentAnnotation.NO_GRAPH;
if (!ssOnly && !graphOnly)
{
// for burial 'B'
annotation.showAllColLabels = true;
}
for (int i = 0, iSize = sourceData.length(); i < iSize; i++)
{
char annot = sourceData.charAt(i);
// if we're at a gapped column then skip to next ungapped position
if (gapMap != null && gapMap.length > 0)
{
while (!gapMap[i])
{
elm[i++] = new Annotation("", "", ' ', Float.NaN);
}
}
switch (rowType)
{
case AlignmentAnnotation.NO_GRAPH:
elm[i] = ssOnly ? new Annotation("", "", annot, Float.NaN,
colourSS(annot)) : new Annotation("" + annot, "" + annot,
'\0', Float.NaN);
break;
default:
try
{
elm[i] = new Annotation("" + annot, "" + annot, annot,
Integer.valueOf("" + annot));
} catch (Exception x)
{
System.err.println("Expected numeric value in character '"
+ annot + "'");
}
}
}
annotation.annotations = elm;
annotation.belowAlignment = true;
annotation.validateRangeAndDisplay();
return true;
}
private Color colourSS(char annot)
{
switch (annot)
{
case 'H':
return jalview.renderer.AnnotationRenderer.HELIX_COLOUR;
case 'E':
return jalview.renderer.AnnotationRenderer.SHEET_COLOUR;
}
return jalview.renderer.AnnotationRenderer.GLYPHLINE_COLOR;
}
@Override
public String getCalcId()
{
return CALC_ID;
}
private static String CALC_ID = "jabaws21.JPred3Cons";
public static AlignAnalysisUIText getAlignAnalysisUITest()
{
return new AlignAnalysisUIText(
compbio.ws.client.Services.JpredWS.toString(),
jalview.ws.jws2.JPred301Client.class, CALC_ID, false, true,
true, "JPred Consensus",
"When checked, JPred consensus is updated automatically.",
"Change JPred Settings...",
"Modify settings for JPred calculations.");
}
}