X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=b60813950ae4c84a22587a8e3c769765fa0a966d;hb=a97a5c93ecd4b0ecd0c55ae2c58c6174c05190f0;hp=e0a8e6e684768af6a06ee6bec1bd4fd926b93bd0;hpb=f4c507635c079ec4cb16273b4911bc33b29afb31;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index e0a8e6e..b608139 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,17 +20,18 @@ */ package jalview.datamodel; -import jalview.analysis.Rna; -import jalview.analysis.SecStrConsensus.SimpleBP; -import jalview.analysis.WUSSParseException; - import java.util.ArrayList; -import java.util.Enumeration; +import java.util.Collection; +import java.util.Collections; import java.util.HashMap; -import java.util.Hashtable; +import java.util.Iterator; import java.util.Map; import java.util.Map.Entry; +import jalview.analysis.Rna; +import jalview.analysis.SecStrConsensus.SimpleBP; +import jalview.analysis.WUSSParseException; + /** * DOCUMENT ME! * @@ -39,6 +40,15 @@ import java.util.Map.Entry; */ public class AlignmentAnnotation { + /* + * Identifers for different types of profile data + */ + public static final int SEQUENCE_PROFILE = 0; + + public static final int STRUCTURE_PROFILE = 1; + + public static final int CDNA_PROFILE = 2; + /** * If true, this annotations is calculated every edit, eg consensus, quality * or conservation graphs @@ -73,9 +83,10 @@ public class AlignmentAnnotation public SequenceFeature[] _rnasecstr = null; /** - * position of annotation resulting in invalid WUSS parsing or -1 + * position of annotation resulting in invalid WUSS parsing or -1. -2 means + * there was no RNA structure in this annotation */ - private long invalidrnastruc = -1; + private long invalidrnastruc = -2; /** * Updates the _rnasecstr field Determines the positions that base pair and @@ -108,14 +119,51 @@ public class AlignmentAnnotation isrna = true; showAllColLabels = true; scaleColLabel = true; + _markRnaHelices(); } // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup()); + } + private void _markRnaHelices() + { + int mxval = 0; + // Figure out number of helices + // Length of rnasecstr is the number of pairs of positions that base pair + // with each other in the secondary structure + for (int x = 0; x < _rnasecstr.length; x++) + { + + /* + * System.out.println(this.annotation._rnasecstr[x] + " Begin" + + * this.annotation._rnasecstr[x].getBegin()); + */ + // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); + int val = 0; + try + { + val = Integer.valueOf(_rnasecstr[x].getFeatureGroup()); + if (mxval < val) + { + mxval = val; + } + } catch (NumberFormatException q) + { + } + ; + + annotations[_rnasecstr[x].getBegin()].value = val; + annotations[_rnasecstr[x].getEnd()].value = val; + + // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val; + // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val; + } + setScore(mxval); + } /** * map of positions in the associated annotation */ - public java.util.Hashtable sequenceMapping; + private Map sequenceMapping; /** DOCUMENT ME!! */ public float graphMin; @@ -453,13 +501,13 @@ public class AlignmentAnnotation @Override public char charAt(int index) { - String dc; return ((index + offset < 0) || (index + offset) >= max - || annotations[index + offset] == null || (dc = annotations[index - + offset].displayCharacter.trim()).length() < 1) ? '.' : dc - .charAt(0); + || annotations[index + offset] == null || (annotations[index + + offset].secondaryStructure < ' ') ? ' ' + : annotations[index + offset].secondaryStructure); } + @Override public String toString() { char[] string = new char[max - offset]; @@ -467,9 +515,8 @@ public class AlignmentAnnotation for (int i = offset; i < mx; i++) { - String dc; - string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter - .trim()).length() < 1) ? '.' : dc.charAt(0); + string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' ' + : annotations[i].secondaryStructure; } return new String(string); } @@ -650,9 +697,9 @@ public class AlignmentAnnotation { threshold = new GraphLine(annotation.threshold); } + Annotation[] ann = annotation.annotations; if (annotation.annotations != null) { - Annotation[] ann = annotation.annotations; this.annotations = new Annotation[ann.length]; for (int i = 0; i < ann.length; i++) { @@ -665,24 +712,27 @@ public class AlignmentAnnotation } } } - ; - if (annotation.sequenceRef != null) + } + if (annotation.sequenceRef != null) + { + this.sequenceRef = annotation.sequenceRef; + if (annotation.sequenceMapping != null) { - this.sequenceRef = annotation.sequenceRef; - if (annotation.sequenceMapping != null) + Integer p = null; + sequenceMapping = new HashMap(); + Iterator pos = annotation.sequenceMapping.keySet() + .iterator(); + while (pos.hasNext()) { - Integer p = null; - sequenceMapping = new Hashtable(); - Enumeration pos = annotation.sequenceMapping.keys(); - while (pos.hasMoreElements()) + // could optimise this! + p = pos.next(); + Annotation a = annotation.sequenceMapping.get(p); + if (a == null) + { + continue; + } + if (ann != null) { - // could optimise this! - p = (Integer) pos.nextElement(); - Annotation a = annotation.sequenceMapping.get(p); - if (a == null) - { - continue; - } for (int i = 0; i < ann.length; i++) { if (ann[i] == a) @@ -692,10 +742,10 @@ public class AlignmentAnnotation } } } - else - { - this.sequenceMapping = null; - } + } + else + { + this.sequenceMapping = null; } } // TODO: check if we need to do this: JAL-952 @@ -749,11 +799,11 @@ public class AlignmentAnnotation int epos = sequenceRef.findPosition(endRes); if (sequenceMapping != null) { - Hashtable newmapping = new Hashtable(); - Enumeration e = sequenceMapping.keys(); - while (e.hasMoreElements()) + Map newmapping = new HashMap(); + Iterator e = sequenceMapping.keySet().iterator(); + while (e.hasNext()) { - Integer pos = (Integer) e.nextElement(); + Integer pos = e.next(); if (pos.intValue() >= spos && pos.intValue() <= epos) { newmapping.put(pos, sequenceMapping.get(pos)); @@ -796,9 +846,10 @@ public class AlignmentAnnotation * * @return DOCUMENT ME! */ + @Override public String toString() { - StringBuffer buffer = new StringBuffer(); + StringBuilder buffer = new StringBuilder(256); for (int i = 0; i < annotations.length; i++) { @@ -871,7 +922,7 @@ public class AlignmentAnnotation { return; } - sequenceMapping = new java.util.Hashtable(); + sequenceMapping = new HashMap(); int seqPos; @@ -1183,7 +1234,7 @@ public class AlignmentAnnotation .getTo() == sq.getDatasetSequence()) : false; // TODO build a better annotation element map and get rid of annotations[] - Hashtable mapForsq = new Hashtable(); + Map mapForsq = new HashMap(); if (sequenceMapping != null) { if (sp2sq != null) @@ -1235,7 +1286,8 @@ public class AlignmentAnnotation { if (mapping != null) { - Hashtable old = sequenceMapping, remap = new Hashtable(); + Map old = sequenceMapping; + Map remap = new HashMap(); int index = -1; for (int mp[] : mapping) { @@ -1307,8 +1359,21 @@ public class AlignmentAnnotation { if (properties == null) { - return Collections.EMPTY_LIST; + return Collections.emptyList(); } return properties.keySet(); } + + /** + * Returns the Annotation for the given sequence position (base 1) if any, + * else null + * + * @param position + * @return + */ + public Annotation getAnnotationForPosition(int position) + { + return sequenceMapping == null ? null : sequenceMapping.get(position); + + } }