From a665055e234b20c818820bddedf203b7fd138252 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 17 May 2006 16:48:49 +0000
Subject: [PATCH] Refactored code for creating annotation objects from a
 jnetfile object.

---
 src/jalview/io/JnetAnnotationMaker.java |  123 +++++++++++++++++++++++++++++++
 1 file changed, 123 insertions(+)
 create mode 100755 src/jalview/io/JnetAnnotationMaker.java

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
new file mode 100755
index 0000000..9a397d7
--- /dev/null
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -0,0 +1,123 @@
+package jalview.io;
+
+import jalview.datamodel.*;
+import java.net.URL;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.io.FileReader;
+
+
+public class JnetAnnotationMaker
+{
+  /**
+   * adds the annotation parsed by prediction to al.
+   * @param prediction JPredFile
+   * @param al AlignmentI
+   * @param FirstSeq int -
+   * @param noMsa boolean
+   */
+  public static void add_annotation(JPredFile prediction, AlignmentI al,
+                                    int FirstSeq, boolean noMsa)
+      throws Exception
+  {
+    int i = 0;
+    SequenceI[] preds = prediction.getSeqsAsArray();
+    SequenceI seqRef = al.getSequenceAt(FirstSeq);
+    int width = preds[0].getSequence().length();
+    int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+    if (gapmap.length != width)
+    {
+      throw (new Exception(
+          "Number of residues in supposed query sequence ('" +
+          al.getSequenceAt(FirstSeq).getName() + "'\n" +
+          al.getSequenceAt(FirstSeq).getSequence() +
+          ")\ndiffer from number of prediction sites in prediction (" + width +
+          ")"));
+    }
+
+    AlignmentAnnotation annot;
+    Annotation[] annotations = null;
+
+    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,
+                                          AlignmentAnnotation.BAR_GRAPH);
+        }
+        else
+        {
+          annot = new AlignmentAnnotation(preds[i].getName(),
+                                          "JNet Output", annotations);
+        }
+
+        if (seqRef != null)
+        {
+          annot.createSequenceMapping(seqRef, 0);
+          seqRef.addAlignmentAnnotation(annot);
+        }
+
+        al.addAnnotation(annot);
+
+        if (noMsa)
+        {
+          al.deleteSequence(preds[i]);
+        }
+      }
+
+      i++;
+    }
+
+    //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);
+     */
+
+  }
+}
-- 
1.7.10.2