X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=6c438be41c3aaeedc40a1e4022dbaeb3c93b3c97;hb=35bef7106ec457c8240eb0656b0901c77cf362da;hp=512c40d48fc285ba034578d59d0459bf17ee3e69;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 512c40d..6c438be 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,26 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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 .
+ * 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.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
-
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@@ -37,17 +39,21 @@ import java.util.Hashtable;
import java.util.Iterator;
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;
import compbio.metadata.Argument;
-public class AADisorderClient extends JabawsAlignCalcWorker implements
+public class AADisorderClient extends JabawsCalcWorker implements
AlignCalcWorkerI
{
private static final String THRESHOLD = "THRESHOLD";
+ private static final String RANGE = "RANGE";
+
String typeName;
String methodName;
@@ -77,6 +83,12 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
return "Submitting amino acid sequences for disorder prediction.";
}
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List seqs)
+ {
+ return (seqs.size() > 0);
+ }
+
private static Map> featureMap;
private static Map>> annotMap;
@@ -118,6 +130,9 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
amap.get("Dydx").put(THRESHOLD, new double[]
{ 1, 0 });
+ amap.get("Dydx").put(RANGE, new float[]
+ { -1, +1 });
+
amap.put("SmoothedScore", new HashMap());
amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
amap.put("RawScore", new HashMap());
@@ -129,10 +144,17 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
amap.put("REM465", new HashMap());
amap.get("COILS").put(THRESHOLD, new double[]
{ 1, 0.516 });
+ amap.get("COILS").put(RANGE, new float[]
+ { 0, 1 });
+
amap.get("HOTLOOPS").put(THRESHOLD, new double[]
{ 1, 0.6 });
+ amap.get("HOTLOOPS").put(RANGE, new float[]
+ { 0, 1 });
amap.get("REM465").put(THRESHOLD, new double[]
{ 1, 0.1204 });
+ amap.get("REM465").put(RANGE, new float[]
+ { 0, 1 });
annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap>());
@@ -140,13 +162,19 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
amap.put("Short", new HashMap());
amap.get("Long").put(THRESHOLD, new double[]
{ 1, 0.5 });
+ amap.get("Long").put(RANGE, new float[]
+ { 0, 1 });
amap.get("Short").put(THRESHOLD, new double[]
{ 1, 0.5 });
+ amap.get("Short").put(RANGE, new float[]
+ { 0, 1 });
annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
amap = new HashMap>());
amap.put("JRonn", new HashMap());
amap.get("JRonn").put(THRESHOLD, new double[]
{ 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[]
+ { 0, 1 });
}
@Override
@@ -182,17 +210,30 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
{
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 = 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();
- if (scores!=null && scores.scores!=null) {
+ if (scores != null && scores.scores != null)
+ {
for (Score scr : scores.scores)
{
@@ -238,22 +279,30 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
{
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;
- 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)
+
+ Map 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)
+ {
+ annot.graphMin = range[0];
+ annot.graphMax = range[1];
+ }
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
{
if (!sameGroup)
@@ -287,6 +336,9 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
}
}
annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
}
}
}
@@ -335,4 +387,11 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}