X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=d5593e38ba1c92de0b224433949d3effa987c042;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=9a397d7597c3c02c1c799c89362d79825b12cf20;hpb=a665055e234b20c818820bddedf203b7fd138252;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 9a397d7..d5593e3 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,123 +1,254 @@
-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);
- */
-
- }
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+public class JnetAnnotationMaker
+{
+ public static void add_annotation(JPredFile prediction, AlignmentI al,
+ int firstSeq, boolean noMsa) throws Exception
+ {
+ JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa,
+ (int[]) null);
+ }
+
+ /**
+ * adds the annotation parsed by prediction to al.
+ *
+ * @param prediction
+ * JPredFile
+ * @param al
+ * AlignmentI
+ * @param firstSeq
+ * int the index of the sequence to attach the annotation to (usually
+ * zero)
+ * @param noMsa
+ * boolean
+ * @param delMap
+ * mapping from columns in JPredFile prediction to residue number in
+ * al.getSequence(firstSeq)
+ */
+ public static void add_annotation(JPredFile prediction, AlignmentI al,
+ int firstSeq, boolean noMsa, int[] delMap) throws Exception
+ {
+ int i = 0;
+ SequenceI[] preds = prediction.getSeqsAsArray();
+ // in the future we could search for the query
+ // sequence in the alignment before calling this function.
+ SequenceI seqRef = al.getSequenceAt(firstSeq);
+ int width = preds[0].getSequence().length;
+ int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
+ if ((delMap != null && delMap.length > width)
+ || (delMap == null && gapmap.length != width))
+ {
+ throw (new Exception(
+ MessageManager
+ .formatMessage(
+ "exception.number_of_residues_in_query_sequence_differ_from_prediction",
+ new String[] {
+ (delMap == null ? "" : MessageManager
+ .getString("label.mapped")),
+ al.getSequenceAt(firstSeq).getName(),
+ al.getSequenceAt(firstSeq)
+ .getSequenceAsString(),
+ Integer.valueOf(width).toString() })));
+ }
+
+ AlignmentAnnotation annot;
+ Annotation[] annotations = null;
+
+ int existingAnnotations = 0;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ existingAnnotations = al.getAlignmentAnnotation().length;
+ }
+
+ Annotation[] sol = new Annotation[al.getWidth()];
+ boolean firstsol = true;
+
+ while (i < preds.length)
+ {
+ String id = preds[i].getName().toUpperCase();
+
+ if (id.startsWith("LUPAS") || id.startsWith("JNET")
+ || id.startsWith("JPRED"))
+ {
+ if (id.startsWith("JNETSOL"))
+ {
+ float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f);
+ for (int spos = 0; spos < width; spos++)
+ {
+ int sposw = (delMap == null) ? gapmap[spos]
+ : gapmap[delMap[spos]];
+ if (firstsol)
+ {
+ sol[sposw] = new Annotation(0f);
+ }
+ if (preds[i].getCharAt(spos) == 'B'
+ && (sol[sposw].value == 0f || sol[sposw].value < amnt))
+ {
+ sol[sposw].value = amnt;
+ }
+ }
+ firstsol = false;
+ }
+ else
+ {
+ // some other kind of annotation
+ annotations = new Annotation[al.getWidth()];
+ /*
+ * if (delMap!=null) { for (int j=0; jPrediction of Solvent Accessibility
levels are- 0 - Exposed
- 3 - 25% or more S.A. accessible
- 6 - 5% or more S.A. accessible
- 9 - Buried (<5% exposed)
",
+ sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
+
+ annot.validateRangeAndDisplay();
+ if (seqRef != null)
+ {
+ annot.createSequenceMapping(seqRef, 1, true);
+ seqRef.addAlignmentAnnotation(annot);
+ }
+ al.addAnnotation(annot);
+ al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
+ - existingAnnotations - 1);
+ }
+ // 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);
+ */
+
+ }
+}