* 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
* 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.
*
*
* 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/>.
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
private static Map<String, Map<String, String[]>> featureMap;
private static Map<String, Map<String, Map<String, Object>>> annotMap;
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[]
amap.get("Dydx").put(THRESHOLD, new double[]
{ 1, 0 });
amap.get("Dydx").put(RANGE, new float[]
amap.put("SmoothedScore", new HashMap<String, Object>());
amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
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[]
amap.get("COILS").put(THRESHOLD, new double[]
{ 1, 0.516 });
amap.get("COILS").put(RANGE, new float[]
amap.get("HOTLOOPS").put(THRESHOLD, new double[]
{ 1, 0.6 });
amap.get("HOTLOOPS").put(RANGE, new float[]
amap.get("HOTLOOPS").put(THRESHOLD, new double[]
{ 1, 0.6 });
amap.get("HOTLOOPS").put(RANGE, new float[]
amap.get("REM465").put(THRESHOLD, new double[]
{ 1, 0.1204 });
amap.get("REM465").put(RANGE, new float[]
amap.get("REM465").put(THRESHOLD, new double[]
{ 1, 0.1204 });
amap.get("REM465").put(RANGE, new float[]
annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
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[]
amap.get("Long").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Long").put(RANGE, new float[]
amap.get("Short").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Short").put(RANGE, new float[]
amap.get("Short").put(THRESHOLD, new double[]
{ 1, 0.5 });
amap.get("Short").put(RANGE, new float[]
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[]
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[]
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
- ;
- ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
+ ScoreHolder scores = null;
+ try
+ {
+ scores = scoremanager.getAnnotationForSequence(seqId);
+ } catch (Exception q)
+ {
+ Cache.log
+ .info("Couldn't recover disorder prediction for sequence "
+ + seq.getName()
+ + "(Prediction name was "
+ + 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();
float last = Float.NaN, val = Float.NaN;
int lastAnnot = ourAnnot.size();
service.getServiceTypeURI() + "/" + scr.getMethod(),
aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
service.getServiceTypeURI() + "/" + scr.getMethod(),
aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
- 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)