/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
+ * 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/>.
+ * 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 java.util.List;
import java.util.Map;
+import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
{
private static final String THRESHOLD = "THRESHOLD";
+
private static final String RANGE = "RANGE";
String typeName;
return "Submitting amino acid sequences for disorder prediction.";
}
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 0);
+ }
+
private static Map<String, Map<String, String[]>> featureMap;
private static Map<String, Map<String, Map<String, Object>>> annotMap;
amap.get("Dydx").put(THRESHOLD, new double[]
{ 1, 0 });
amap.get("Dydx").put(RANGE, new float[]
- { -1, +1 });
+ { -1, +1 });
amap.put("SmoothedScore", new HashMap<String, Object>());
amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
amap.get("COILS").put(THRESHOLD, new double[]
{ 1, 0.516 });
amap.get("COILS").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
amap.get("HOTLOOPS").put(THRESHOLD, new double[]
{ 1, 0.6 });
amap.get("HOTLOOPS").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
amap.get("REM465").put(THRESHOLD, new double[]
{ 1, 0.1204 });
amap.get("REM465").put(RANGE, new float[]
- { 0, 1 });
-
+ { 0, 1 });
annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.get("Long").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Long").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
amap.get("Short").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Short").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("JRonn", new HashMap<String, Object>());
amap.get("JRonn").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("JRonn").put(RANGE, new float[]
- { 0, 1 });
+ { 0, 1 });
}
@Override
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
- int base = seq.findPosition(start)-1;
+ int base = seq.findPosition(start) - 1;
aseq = seq;
while ((dseq = seq).getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
}
ScoreHolder scores = null;
- try {
+ try
+ {
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
.info("Couldn't recover disorder prediction for sequence "
+ seq.getName()
+ "(Prediction name was "
- + seqId+")"
+ + seqId
+ + ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
}
float last = Float.NaN, val = Float.NaN;
int lastAnnot = ourAnnot.size();
- if (scores!=null && scores.scores!=null) {
+ if (scores != null && scores.scores != null)
+ {
for (Score scr : scores.scores)
{
{
continue;
}
+ String typename, calcName;
AlignmentAnnotation annot = createAnnotationRowsForScores(
ourAnnot,
- service.serviceType + " (" + scr.getMethod() + ")",
- service.getServiceTypeURI() + "/" + scr.getMethod(),
+ typename = service.serviceType + " ("
+ + scr.getMethod() + ")",
+ calcName = service.getServiceTypeURI() + "/"
+ + scr.getMethod(),
aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
-
- Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
-
+
+ Map<String, Object> styleMap = (annotTypeMap == null) ? null
+ : annotTypeMap.get(scr.getMethod());
+
annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
- double[] thrsh = (styleMap==null) ? null
- : (double[]) styleMap.get(
- THRESHOLD);
- float[] range = (styleMap==null) ? null : (float[]) styleMap.get(
- RANGE);
- if (range!=null)
+ double[] thrsh = (styleMap == null) ? null
+ : (double[]) styleMap.get(THRESHOLD);
+ float[] range = (styleMap == null) ? null
+ : (float[]) styleMap.get(RANGE);
+ if (range != null)
{
annot.graphMin = range[0];
annot.graphMax = range[1];
}
- if (styleMap==null || styleMap.get(DONTCOMBINE) == null)
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
{
if (!sameGroup)
}
}
annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
}
}
}
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff