X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=91be2e62969e0256a484d57f9de73bed104e6769;hb=27f5f6fdfea52770ebd513c4607a6dde87821d48;hp=d64a9564034aec46c92b87048fa638194d2c729a;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index d64a956..91be2e6 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,25 +1,28 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
@@ -36,17 +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;
@@ -76,6 +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;
@@ -117,6 +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());
@@ -128,10 +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>());
@@ -139,13 +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
@@ -181,109 +210,136 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
{
boolean sameGroup = false;
SequenceI dseq, aseq, seq = seqNames.get(seqId);
- int base = seq.getStart() - 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();
- for (Score scr : scores.scores)
+ if (scores != null && scores.scores != null)
{
-
- if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ for (Score scr : scores.scores)
{
- Iterator vals = scr.getScores().iterator();
- // make features on sequence
- for (Range rn : scr.getRanges())
- {
- SequenceFeature sf;
- String[] type = featureTypeMap.get(scr.getMethod());
- if (type == null)
- {
- // create a default type for this feature
- type = new String[]
- { typeName + " (" + scr.getMethod() + ")",
- service.getActionText() };
- }
- if (vals.hasNext())
+ if (scr.getRanges() != null && scr.getRanges().size() > 0)
+ {
+ Iterator vals = scr.getScores().iterator();
+ // make features on sequence
+ for (Range rn : scr.getRanges())
{
- sf = new SequenceFeature(type[0], type[1], base + rn.from,
- base + rn.to, val = vals.next().floatValue(),
- methodName);
+
+ SequenceFeature sf;
+ String[] type = featureTypeMap.get(scr.getMethod());
+ if (type == null)
+ {
+ // create a default type for this feature
+ type = new String[]
+ { typeName + " (" + scr.getMethod() + ")",
+ service.getActionText() };
+ }
+ if (vals.hasNext())
+ {
+ sf = new SequenceFeature(type[0], type[1],
+ base + rn.from, base + rn.to, val = vals.next()
+ .floatValue(), methodName);
+ }
+ else
+ {
+ sf = new SequenceFeature(type[0], type[1], null, base
+ + rn.from, base + rn.to, methodName);
+ }
+ dseq.addSequenceFeature(sf);
+ if (last != val && !Float.isNaN(last))
+ {
+ fc.put(sf.getType(), sf);
+ }
+ last = val;
+ dispFeatures = true;
}
- else
+ }
+ else
+ {
+ if (scr.getScores().size() == 0)
{
- sf = new SequenceFeature(type[0], type[1], null, base
- + rn.from, base + rn.to, methodName);
+ continue;
}
- dseq.addSequenceFeature(sf);
- if (last != val && last != Float.NaN)
+ String typename, calcName;
+ AlignmentAnnotation annot = createAnnotationRowsForScores(
+ ourAnnot,
+ typename = service.serviceType + " ("
+ + scr.getMethod() + ")",
+ calcName = service.getServiceTypeURI() + "/"
+ + scr.getMethod(),
+ aseq, base + 1, scr);
+ annot.graph = AlignmentAnnotation.LINE_GRAPH;
+
+ 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)
{
- fc.put(sf.getType(), sf);
+ annot.graphMin = range[0];
+ annot.graphMax = range[1];
}
- last = val;
- dispFeatures = true;
- }
- }
- else
- {
- if (scr.getScores().size() == 0)
- {
- continue;
- }
- AlignmentAnnotation annot = createAnnotationRowsForScores(
- ourAnnot, service.serviceType + " (" + scr.getMethod()
- + ")",
- 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)
- {
+ if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
{
- if (!sameGroup)
{
- graphGroup++;
- sameGroup = true;
- }
+ if (!sameGroup)
+ {
+ graphGroup++;
+ sameGroup = true;
+ }
- annot.graphGroup = graphGroup;
+ annot.graphGroup = graphGroup;
+ }
}
- }
- annot.description = "" + 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 += "
" + threshNote;
- }
- annot.description += "";
- Color col = new UserColourScheme(typeName)
- .createColourFromName(typeName + scr.getMethod());
- for (int p = 0, ps = annot.annotations.length; p < ps; p++)
- {
- if (annot.annotations[p] != null)
+ annot.description = "" + 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 += "
" + threshNote;
+ }
+ annot.description += "";
+ 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;
+ if (annot.annotations[p] != null)
+ {
+ annot.annotations[p].colour = col;
+ }
}
+ annot._linecolour = col;
+ // finally, update any dataset annotation
+ replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+ aseq);
}
- annot._linecolour = col;
}
}
if (lastAnnot + 1 == ourAnnot.size())
@@ -295,7 +351,7 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
{
if (dispFeatures)
{
- jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+ jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
.cloneFeatureRenderer();
for (String ft : fc.keySet())
{
@@ -331,4 +387,11 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
}
}
+ @Override
+ public String getCalcId()
+ {
+ // Disorder predictions are not dynamically updated so we return null
+ return null;
+ }
+
}