+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
import jalview.ws.jws2.dm.AAConSettings;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.regex.Pattern;
import compbio.data.sequence.RNAStructReader.AlifoldResult;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructScoreManager;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.metadata.Argument;
-public class RNAalifoldClient extends JabawsAlignCalcWorker implements
+/**
+ * Client for the JABA RNA Alifold Service
+ *
+ * @author daluke - Daniel Barton
+ *
+ */
+
+public class RNAalifoldClient extends JabawsCalcWorker implements
AlignCalcWorkerI
{
WsParamSetI preset, List<Argument> paramset)
{
super(sh, alignFrame, preset, paramset);
-
- if (arguments == null)
- arguments = new ArrayList<Argument>();
-
af = alignFrame;
methodName = sh.serviceType;
-
+ alignedSeqs = true;
+ submitGaps = true;
nucleotidesAllowed = true;
proteinAllowed = false;
initViewportParams();
}
- protected void initViewportParams()
+ public String getCalcId()
+ {
+ return CALC_ID;
+ }
+
+ private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
+
+ public static AlignAnalysisUIText getAlignAnalysisUITest()
{
- ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
- getCalcId(),
- new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
+ return new AlignAnalysisUIText(
+ compbio.ws.client.Services.RNAalifoldWS.toString(),
+ jalview.ws.jws2.RNAalifoldClient.class,
+ CALC_ID,
+ true,
+ false,
+ true,
+ "RNAAliFold Prediction",
+ "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.",
+ "Change RNAAliFold settings...",
+ "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters");
+
}
@Override
}
@Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 1);
+ }
+
+ @Override
public void updateResultAnnotation(boolean immediate)
{
private AlignmentAnnotation constructAnnotationFromScoreHolder(
AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
{
- Annotation[] anns = new Annotation[struct.length()];
+ Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
+ : struct.length()];
if (data != null
&& data.size() > 1
basePairs.put(score.getRanges().first(), new Float(score
.getScores().get(0)));
}
- for (int i = 0; i < struct.length(); i++)
- {
+ for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
+ {
+ if (gapMap != null)
+ {
+ // skip any gapped columns in the input data
+ while (!gapMap[ri])
+ {
+ ri++;
+ }
+ }
// Return all the contacts associated with position i
LinkedHashMap<Range, Float> contacts = isContact(basePairs, i + 1);
}
}
- anns[i] = new Annotation(struct.substring(i, i + 1), description,
+ anns[ri] = new Annotation(struct.substring(i, i + 1), description,
isSS(struct.charAt(i)), prob);
}
}
else if (data == null || data.size() == 1)
{
- for (int i = 0; i < struct.length(); i++)
+ for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
{
-
- anns[i] = new Annotation(struct.substring(i, i + 1), "",
+ if (gapMap != null)
+ {
+ // skip any gapped columns in the input data
+ while (!gapMap[ri] && ri < gapMap.length)
+ {
+ ri++;
+ }
+ if (ri == gapMap.length)
+ {
+ break;
+ }
+ }
+ anns[ri] = new Annotation(struct.substring(i, i + 1), "",
isSS(struct.charAt(i)), Float.NaN);
}
char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
return ss;
}
-
- public String getCalcId()
- {
- return SequenceAnnotationWSClient.AAConCalcId;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff