-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class JnetAnnotationMaker\r
-{\r
- /**\r
- * adds the annotation parsed by prediction to al.\r
- * @param prediction JPredFile\r
- * @param al AlignmentI\r
- * @param FirstSeq int -\r
- * @param noMsa boolean\r
- */\r
- public static void add_annotation(JPredFile prediction, AlignmentI al,\r
- int FirstSeq, boolean noMsa)\r
- throws Exception\r
- {\r
- int i = 0;\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- // in the future we could search for the query\r
- // sequence in the alignment before calling this function.\r
- SequenceI seqRef = al.getSequenceAt(FirstSeq);\r
- int width = preds[0].getSequence().length();\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
- if (gapmap.length != width)\r
- {\r
- throw (new Exception(\r
- "Number of residues in supposed query sequence ('" +\r
- al.getSequenceAt(FirstSeq).getName() + "'\n" +\r
- al.getSequenceAt(FirstSeq).getSequence() +\r
- ")\ndiffer from number of prediction sites in prediction (" + width +\r
- ")"));\r
- }\r
-\r
- AlignmentAnnotation annot;\r
- Annotation[] annotations = null;\r
-\r
- int existingAnnotations = 0;\r
- if(al.getAlignmentAnnotation()!=null)\r
- existingAnnotations = al.getAlignmentAnnotation().length;\r
-\r
-\r
- while (i < preds.length)\r
- {\r
- String id = preds[i].getName().toUpperCase();\r
-\r
- if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
- id.startsWith("JPRED"))\r
- {\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
- id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
- id.equals("JNETALIGN") || id.equals("JPRED"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation("", "",\r
- preds[i].getCharAt(j), 0);\r
- }\r
- }\r
- else if (id.equals("JNETCONF"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- float value = new Float(preds[i].getCharAt(\r
- j) + "").floatValue();\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", preds[i].getCharAt(j),\r
- value);\r
- }\r
- }\r
- else\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", ' ', 0);\r
- }\r
- }\r
-\r
- if (id.equals("JNETCONF"))\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations, 0f,\r
- 10f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
- }\r
- else\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations);\r
- }\r
-\r
- if (seqRef != null)\r
- {\r
- annot.createSequenceMapping(seqRef, 1, false);\r
- seqRef.addAlignmentAnnotation(annot);\r
- }\r
-\r
- al.addAnnotation(annot);\r
- al.setAnnotationIndex(annot,\r
- al.getAlignmentAnnotation().\r
- length - existingAnnotations - 1);\r
-\r
- if (noMsa)\r
- {\r
- al.deleteSequence(preds[i]);\r
- }\r
- }\r
-\r
- i++;\r
- }\r
-\r
- //Hashtable scores = prediction.getScores();\r
-\r
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
- */\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * 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; j<annotations.length; j++)
+ * annotations[j] = new Annotation("","",'',0); }
+ */
+ if (id.equals("JNETPRED") || id.equals("JNETPSSM")
+ || id.equals("JNETFREQ") || id.equals("JNETHMM")
+ || id.equals("JNETALIGN") || id.equals("JPRED"))
+ {
+ if (delMap == null)
+ {
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[j]] = new Annotation("", "",
+ preds[i].getCharAt(j), 0);
+ }
+ }
+ else
+ {
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[delMap[j]]] = new Annotation("", "",
+ preds[i].getCharAt(j), 0);
+ }
+ }
+ }
+ else if (id.equals("JNETCONF"))
+ {
+ if (delMap == null)
+ {
+ for (int j = 0; j < width; j++)
+ {
+ float value = new Float(preds[i].getCharAt(j) + "")
+ .floatValue();
+ annotations[gapmap[j]] = new Annotation(
+ preds[i].getCharAt(j) + "", "",
+ preds[i].getCharAt(j), value);
+ }
+ }
+ else
+ {
+ for (int j = 0; j < width; j++)
+ {
+ float value = new Float(preds[i].getCharAt(j) + "")
+ .floatValue();
+ annotations[gapmap[delMap[j]]] = new Annotation(
+ preds[i].getCharAt(j) + "", "",
+ preds[i].getCharAt(j), value);
+ }
+ }
+ }
+ else
+ {
+ if (delMap == null)
+ {
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[j]] = new Annotation(
+ preds[i].getCharAt(j) + "", "", ' ', 0);
+ }
+ }
+ else
+ {
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[delMap[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, 1, true);
+ seqRef.addAlignmentAnnotation(annot);
+ }
+
+ al.addAnnotation(annot);
+ al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
+ - existingAnnotations - 1);
+ }
+ if (noMsa)
+ {
+ al.deleteSequence(preds[i]);
+ }
+ }
+
+ i++;
+ }
+ if (!firstsol)
+ {
+ // add the solvent accessibility
+ annot = new AlignmentAnnotation(
+ "Jnet Burial",
+ "<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>",
+ 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);
+ */
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff