From 1e31232ca2c48ae852b506fc637a2610c99b4c22 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 1 Apr 2005 16:44:57 +0000
Subject: [PATCH] parses jpredfile into new alignment annotation

---
 src/jalview/io/JPredClient.java |   99 ++++++++++++++++++++++++++++++++++-----
 1 file changed, 88 insertions(+), 11 deletions(-)

diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
index c3415ee..7c2675d 100755
--- a/src/jalview/io/JPredClient.java
+++ b/src/jalview/io/JPredClient.java
@@ -154,30 +154,107 @@ public class JPredClient
     {
       output.setText(OutputHeader + result.getOutput());
       try {
+        // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
         JPredFile prediction=new JPredFile(result.getOutput(), "Paste");
         SequenceI[] preds = prediction.getSeqsAsArray();
-        int i=0;
+        Alignment al = new Alignment(preds);
+
+        AlignmentAnnotation annot;
+        Annotation [] annotations = null;
+        int i = 0;
         // Rename the query sequence
-        while (i<preds.length && !preds[i].getName().equals("QUERY")) {
+        while (i < preds.length)
+        {
+          String id = preds[i].getName().toUpperCase();
+          if(id.startsWith("LUPAS") || id.startsWith("JNET"))
+          {
+            annotations = new Annotation[al.getWidth()];
+
+            if(id.equals("JNETPRED")
+               || id.equals("JNETPSSM")
+               || id.equals("JNETFREQ")
+               || id.equals("JNETHMM")
+               || id.equals("JNETALIGN"))
+            {
+              for (int j = 0; j < al.getWidth(); j++)
+                annotations[j] = new Annotation("", "", preds[i].getCharAt(j), 0);
+            }
+            else if(id.equals("JNETCONF"))
+            {
+              for (int j = 0; j < al.getWidth(); j++)
+              {
+                float value = Float.parseFloat(preds[i].getCharAt(j)+"");
+                annotations[j] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);
+              }
+            }
+            else
+            {
+              for (int j = 0; j < al.getWidth(); j++)
+                annotations[j] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);
+            }
+
+            if(id.equals("JNETCONF"))
+              annot = new AlignmentAnnotation(preds[i].getName(),
+                                           "Jpred Output",
+                                           annotations,0f,10f,1);
+
+            else   annot = new AlignmentAnnotation(preds[i].getName(),
+                                            "Jpred Output",
+                                            annotations);
+            al.addAnnotation(annot);
+            al.deleteSequence(preds[i]);
+          }
           i++;
         }
-        if (i<preds.length) {
-          preds[i].setName(sequence.getId());
+
+        Hashtable scores = prediction.Scores;
+
+        Vector values = (Vector)scores.get("JNETPROPH");
+        annotations = new Annotation[al.getWidth()];
+        for (int j = 0; j < al.getWidth(); j++)
+        {
+          float value = Float.parseFloat(values.get(j).toString());
+          annotations[j] = new Annotation("", value+"",' ',value);
         }
-        AlignFrame af = new AlignFrame(new Alignment(preds));
+        annot = new AlignmentAnnotation("Jnetproph", "Jpred Output", annotations, 0f,1f,1);
+        al.addAnnotation(annot);
+
+        values = (Vector)scores.get("JNETPROPB");
+             annotations = new Annotation[al.getWidth()];
+             for (int j = 0; j < al.getWidth(); j++)
+             {
+               float value = Float.parseFloat(values.get(j).toString());
+               annotations[j] = new Annotation("", value+"",' ',value);
+             }
+             annot = new AlignmentAnnotation("JnetpropB", "Jpred Output", annotations, 0f,1f,1);
+             al.addAnnotation(annot);
+
+             values = (Vector)scores.get("JNETPROPC");
+                  annotations = new Annotation[al.getWidth()];
+                  for (int j = 0; j < al.getWidth(); j++)
+                  {
+                    float value = Float.parseFloat(values.get(j).toString());
+                    annotations[j] = new Annotation("", value+"",' ',value);
+                  }
+                  annot = new AlignmentAnnotation("JnetpropC", "Jpred Output", annotations, 0f,1f,1);
+                  al.addAnnotation(annot);
+
+
+
+        AlignFrame af = new AlignFrame(al);
+
+
         /*  JBPNote - need to set correct style of display for the secstrpred alignment object.
             af.clustalColour.setSelected(true);
             af.clustalColour_actionPerformed(null);
          */
-        Desktop.addInternalFrame(af, "JNet Prediction for sequence "+sequence.getId(),
+        Desktop.addInternalFrame(af,
+                                 "JNet Prediction for sequence ",
                                  700, 500);
-      }
-      catch (Exception e) {
-        output.setText(output.getText()+"\nError! File did not parse correctly\n"+e.getMessage()+"\n");
-        e.printStackTrace();
-      }
+      }catch(Exception ex){ex.printStackTrace();}
 
     }
 
   }
 }
+
-- 
1.7.10.2