+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;
-import compbio.ws.client.Services;
public class AADisorderClient extends JabawsAlignCalcWorker implements
AlignCalcWorkerI
{
+ private static final String THRESHOLD = "THRESHOLD";
+
String typeName;
String methodName;
private static Map<String, Map<String, Map<String, Object>>> annotMap;
private static String DONTCOMBINE = "DONTCOMBINE";
+
private static String INVISIBLE = "INVISIBLE";
static
{
+ // TODO: turn this into some kind of configuration file that's a bit easier
+ // to edit
featureMap = new HashMap<String, Map<String, String[]>>();
Map<String, String[]> fmap;
featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("Dydx", new HashMap<String, Object>());
amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
+ amap.get("Dydx").put(THRESHOLD, new double[]
+ { 1, 0 });
amap.put("SmoothedScore", new HashMap<String, Object>());
- amap.get("SmoothedScore").put(INVISIBLE,INVISIBLE);
+ amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
amap.put("RawScore", new HashMap<String, Object>());
- amap.get("RawScore").put(INVISIBLE,INVISIBLE);
+ amap.get("RawScore").put(INVISIBLE, INVISIBLE);
annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
-
+ amap.put("COILS", new HashMap<String, Object>());
+ amap.put("HOTLOOPS", new HashMap<String, Object>());
+ amap.put("REM465", new HashMap<String, Object>());
+ amap.get("COILS").put(THRESHOLD, new double[]
+ { 1, 0.516 });
+ amap.get("HOTLOOPS").put(THRESHOLD, new double[]
+ { 1, 0.6 });
+ amap.get("REM465").put(THRESHOLD, new double[]
+ { 1, 0.1204 });
+
+ annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+ amap = new HashMap<String, Map<String, Object>>());
+ amap.put("Long", new HashMap<String, Object>());
+ amap.put("Short", new HashMap<String, Object>());
+ amap.get("Long").put(THRESHOLD, new double[]
+ { 1, 0.5 });
+ amap.get("Short").put(THRESHOLD, new double[]
+ { 1, 0.5 });
+ 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 });
}
@Override
/**
* grouping for any annotation rows created
*/
- int graphGroup = 1, iGraphGroup = 1;
+ int graphGroup = 1;
if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
{
for (AlignmentAnnotation ala : alignViewport.getAlignment()
}
else
{
- if (scr.getScores().size()==0)
+ if (scr.getScores().size() == 0)
{
continue;
}
AlignmentAnnotation annot = createAnnotationRowsForScores(
ourAnnot, service.serviceType + " (" + scr.getMethod()
- + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
- base, scr);
+ + ")",
+ service.getServiceTypeURI() + "/" + scr.getMethod(),
+ aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
- annot.visible = (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(INVISIBLE) == null);
-
- if (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
+ annot.visible = (annotTypeMap == null
+ || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
+ .get(scr.getMethod()).get(INVISIBLE) == null);
+ double[] thrsh = (annotTypeMap == null || annotTypeMap.get(scr
+ .getMethod()) == null) ? null : (double[]) annotTypeMap
+ .get(scr.getMethod()).get(THRESHOLD);
+ if (annotTypeMap == null
+ || annotTypeMap.get(scr.getMethod()) == null
+ || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
{
{
if (!sameGroup)
annot.graphGroup = graphGroup;
}
}
-
- annot.description = service.getActionText() + " - raw scores";
+
+ annot.description = "<html>" + service.getActionText()
+ + " - raw scores";
+ if (thrsh != null)
+ {
+ String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
+ + thrsh[1] + " indicates disorder";
+ annot.threshold = new GraphLine((float) thrsh[1], threshNote,
+ Color.red);
+ annot.description += "<br/>" + threshNote;
+ }
+ annot.description += "</html>";
Color col = new UserColourScheme(typeName)
.createColourFromName(typeName + scr.getMethod());
for (int p = 0, ps = annot.annotations.length; p < ps; p++)
annot.annotations[p].colour = col;
}
}
- annot._linecolour=col;
+ annot._linecolour = col;
}
}
if (lastAnnot + 1 == ourAnnot.size())
fr.setColour(ft, ggc);
}
}
- // TODO: JAL-1150 - create sequence feature settings API for defining styles and enabling/disabling feature overlay on alignment panel
+ // TODO: JAL-1150 - create sequence feature settings API for defining
+ // styles and enabling/disabling feature overlay on alignment panel
((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
- if (af.alignPanel==ap)
+ if (af.alignPanel == ap)
{
// only do this if the alignFrame is currently showing this view.
af.setShowSeqFeatures(true);
- }
+ }
ap.paintAlignment(true);
}
if (ourAnnot.size() > 0)
git://source.jalview.org / jalview.git / blobdiff