X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=08d72719b984107b9c22ee7842cd8f912f84bfda;hb=43c02ae950e2d1a068bf2455f33c8756951b82ed;hp=8f94e97a6d6946f4a1e9c08d9aade46da18f7d66;hpb=093795d37cb42b73f7620e1d3a6d70b4d16fa692;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 8f94e97..08d7271 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -27,6 +27,7 @@ import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
 import jalview.io.FormatAdapter;
+import jalview.io.*;
 
 public class JPredClient
     extends WSClient
@@ -57,6 +58,7 @@ public class JPredClient
       wsInfo = setWebService();
 
     SequenceI seq = msf[0];
+
     altitle = "JNet prediction on " + seq.getName() +
         " using alignment from " + title;
 
@@ -65,8 +67,10 @@ public class JPredClient
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
                            "\n");
     SequenceI aln[] = new SequenceI[msf.length];
-    for (int i=0,j=msf.length; i<j;i++)
-      aln[i] = new jalview.datamodel.Sequence(msf[i]);
+    for (int i=0,j=msf.length; i<j;i++) {
+        aln[i] = new jalview.datamodel.Sequence(msf[i]);
+    }
+
     SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
     if (!locateWebService())
@@ -105,7 +109,7 @@ public class JPredClient
     WebServiceName = "JNetWS";
     WebServiceJobTitle = "JNet secondary structure prediction";
     WebServiceReference =
-        "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +
+        "\"Cuff J. A and Barton G.J (2000) Application of " +
         "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
         "Proteins 40:502-511\".";
     WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
@@ -124,6 +128,8 @@ public class JPredClient
     {
       this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
       ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
+      //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
+
     }
     catch (Exception ex)
     {
@@ -137,7 +143,7 @@ public class JPredClient
                              " Service location failed\nfor URL :" + WsURL +
                              "\n" +
                              ex.getMessage());
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
       return false;
     }
@@ -172,9 +178,9 @@ public class JPredClient
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",
                                                 msf[0].getSequence()));
 
-      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
       this.msa = new vamsas.objects.simple.Msfalignment();
-      msa.setMsf(mwrite.print(msf));
+      jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+      msa.setMsf(pileup.print(msf));
     }
 
     public void run()
@@ -235,6 +241,7 @@ public class JPredClient
         catch (Exception ex)
         {
           allowedServerExceptions--;
+
           wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
                                     ex.getMessage());
 
@@ -334,7 +341,7 @@ public class JPredClient
 
 
 
-    private void addFloatAnnotations(Alignment al, int[] gapmap,
+  /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
                                      Vector values, String Symname,
                                      String Visname, float min,
                                      float max, int winLength)
@@ -350,7 +357,7 @@ public class JPredClient
 
       al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
                                                annotations, min, max, winLength));
-    }
+    }*/
 
     void parseResult()
     {
@@ -396,23 +403,24 @@ public class JPredClient
         {
           jalview.bin.Cache.log.debug("Getting associated alignment.");
           // we ignore the returned alignment if we only predicted on a single sequence
-          String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
+          String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(),
               "Paste");
 
           if (jalview.io.FormatAdapter.formats.contains(format))
           {
             al = new Alignment(new FormatAdapter().readFile(
                 result.getAligfile(), "Paste", format));
+            SequenceI sqs[] = new SequenceI[al.getHeight()];
             for (int i=0, j=al.getHeight(); i<j; i++) {
-              SequenceI sq = al.getSequenceAt(i);
-              if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-                  sq, (Hashtable) SequenceInfo.get(sq.getName())))
+              sqs[i] = al.getSequenceAt(i);
+            }
+            if (!jalview.analysis.SeqsetUtils.deuniquify(
+                  (Hashtable) SequenceInfo,sqs))
               {
                 throw (new Exception(
-                    "Couldn't recover sequence properties for JNet "
-                    +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
+                    "Couldn't recover sequence properties for alignment."));
               }
-            }
+
             noMsa = false;
             FirstSeq = 0;
           }
@@ -435,101 +443,15 @@ public class JPredClient
           }
         }
 
+        al.setDataset(null);
 
-        AlignmentAnnotation annot;
-        Annotation[] annotations = null;
-        int i = 0;
-        int width = preds[0].getSequence().length();
-
-        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
-
-        if (gapmap.length != width)
-        {
-          throw (new Exception(
-              "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +
-              al.getSequenceAt(FirstSeq).getName() + "\n" +
-              al.getSequenceAt(FirstSeq).getSequence() +
-              "\nDiffer from number of prediction sites in \n" +
-              result.getPredfile() + "\n"));
+        try {
+          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+              noMsa);
         }
-
-        // JBPNote Should also rename the query sequence sometime...
-        i = 0;
-
-        while (i < preds.length)
-        {
-          String id = preds[i].getName().toUpperCase();
-
-          if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
-              id.startsWith("JPRED"))
-          {
-            annotations = new Annotation[al.getWidth()];
-
-            if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
-                id.equals("JNETFREQ") || id.equals("JNETHMM") ||
-                id.equals("JNETALIGN") || id.equals("JPRED"))
-            {
-              for (int j = 0; j < width; j++)
-              {
-                annotations[gapmap[j]] = new Annotation("", "",
-                    preds[i].getCharAt(j), 0);
-              }
-            }
-            else if (id.equals("JNETCONF"))
-            {
-              for (int j = 0; j < width; j++)
-              {
-                float value = Float.parseFloat(preds[i].getCharAt(
-                    j) + "");
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                    j) + "", "", preds[i].getCharAt(j),
-                    value);
-              }
-            }
-            else
-            {
-              for (int j = 0; j < width; j++)
-              {
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                    j) + "", "", ' ', 0);
-              }
-            }
-
-            if (id.equals("JNETCONF"))
-            {
-              annot = new AlignmentAnnotation(preds[i].getName(),
-                                              "JNet Output", annotations, 0f,
-                                              10f, 1);
-            }
-            else
-            {
-              annot = new AlignmentAnnotation(preds[i].getName(),
-                                              "JNet Output", annotations);
-            }
-
-            al.addAnnotation(annot);
-
-            if (noMsa)
-            {
-              al.deleteSequence(preds[i]);
-            }
-          }
-
-          i++;
+        catch (Exception e) {
+          jalview.bin.Cache.log.error("JNet Client: JPred Annotation Parse Error", e);
         }
-
-        Hashtable scores = prediction.getScores();
-
-        /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                              "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
-
-          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-         "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
-
-          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                              "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-         */
-
         wsInfo.setProgressText(OutputHeader);
         jalview.bin.Cache.log.debug("Finished parsing output.");
         AlignFrame af = new AlignFrame(al);
@@ -540,8 +462,7 @@ public class JPredClient
       }
       catch (Exception ex)
       {
-        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
-        jalview.bin.Cache.log.debug("Exception: ",ex);
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);
       }
     }
   }