X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=001f6a88ca2aa2765c3b7d754d9defba80e01a6a;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=e158da789498035c8accfaff35e912e9aee57ee5;hpb=d2defd0ed16a1d013296854a3030e54e838b7a0c;p=jalview.git
diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index e158da7..001f6a8 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,32 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.api.FeatureColourI;
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 jalview.schemes.GraduatedColor;
-import jalview.schemes.UserColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
@@ -38,16 +41,17 @@ 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 JabawsCalcWorker implements
- AlignCalcWorkerI
+public class AADisorderClient extends JabawsCalcWorker
{
private static final String THRESHOLD = "THRESHOLD";
+
private static final String RANGE = "RANGE";
String typeName;
@@ -79,6 +83,12 @@ public class AADisorderClient extends JabawsCalcWorker 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;
@@ -94,34 +104,29 @@ public class AADisorderClient extends JabawsCalcWorker implements
Map fmap;
featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
fmap = new HashMap());
- fmap.put("Glob", new String[]
- { "Globular Domain", "Predicted globular domain" });
+ fmap.put("Glob", new String[] { "Globular Domain",
+ "Predicted globular domain" });
featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
fmap = new HashMap());
featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
fmap = new HashMap());
- fmap.put("REM465", new String[]
- { "REM465", "Missing density" });
- fmap.put("HOTLOOPS", new String[]
- { "HOTLOOPS", "Flexible loops" });
- fmap.put("COILS", new String[]
- { "COILS", "Random coil" });
+ fmap.put("REM465", new String[] { "REM465", "Missing density" });
+ fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
+ fmap.put("COILS", new String[] { "COILS", "Random coil" });
featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
fmap = new HashMap());
- fmap.put("GlobDoms", new String[]
- { "Globular Domain", "Predicted globular domain" });
- fmap.put("Disorder", new String[]
- { "Protein Disorder", "Probable unstructured peptide region" });
+ fmap.put("GlobDoms", new String[] { "Globular Domain",
+ "Predicted globular domain" });
+ fmap.put("Disorder", new String[] { "Protein Disorder",
+ "Probable unstructured peptide region" });
Map> amap;
annotMap = new HashMap>>();
annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
amap = new HashMap>());
amap.put("Dydx", new HashMap());
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.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);
@@ -132,40 +137,27 @@ public class AADisorderClient extends JabawsCalcWorker implements
amap.put("COILS", new HashMap());
amap.put("HOTLOOPS", new HashMap());
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 });
+ 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>());
amap.put("Long", new HashMap());
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 });
+ 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 });
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
}
@Override
@@ -201,14 +193,15 @@ public class AADisorderClient extends JabawsCalcWorker 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 = null;
- try {
+ try
+ {
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
@@ -216,12 +209,14 @@ public class AADisorderClient extends JabawsCalcWorker implements
.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)
{
@@ -237,8 +232,8 @@ public class AADisorderClient extends JabawsCalcWorker implements
if (type == null)
{
// create a default type for this feature
- type = new String[]
- { typeName + " (" + scr.getMethod() + ")",
+ type = new String[] {
+ typeName + " (" + scr.getMethod() + ")",
service.getActionText() };
}
if (vals.hasNext())
@@ -253,7 +248,7 @@ public class AADisorderClient extends JabawsCalcWorker implements
+ rn.from, base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
- if (last != val && last != Float.NaN)
+ if (last != val && !Float.isNaN(last))
{
fc.put(sf.getType(), sf);
}
@@ -267,27 +262,29 @@ public class AADisorderClient extends JabawsCalcWorker implements
{
continue;
}
+ String typename, calcName;
AlignmentAnnotation annot = createAnnotationRowsForScores(
ourAnnot,
- service.serviceType + " (" + scr.getMethod() + ")",
- service.getServiceTypeURI() + "/" + scr.getMethod(),
- aseq, base + 1, scr);
+ 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());
-
+
+ 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)
+ 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)
@@ -311,8 +308,8 @@ public class AADisorderClient extends JabawsCalcWorker implements
annot.description += "
" + threshNote;
}
annot.description += "