X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=82e71b546fc42c5e991a2e902a86802ad5f49419;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=773633238ace37a835129e194cc4593d3fefc9cd;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 7736332..82e71b5 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.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. * @@ -20,13 +20,33 @@ */ package jalview.io; -import java.io.*; -import java.net.*; -import java.util.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.analysis.Conservation; +import jalview.api.AlignViewportI; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.GraphLine; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.InputStreamReader; +import java.io.StringReader; +import java.net.URL; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; public class AnnotationFile { @@ -67,18 +87,18 @@ public class AnnotationFile } /** - * convenience method for pre-2.4 feature files which have no view, hidden + * convenience method for pre-2.9 annotation files which have no view, hidden * columns or hidden row keywords. * * @param annotations * @param list * @param properties - * @return feature file as a string. + * @return annotation file as a string. */ public String printAnnotations(AlignmentAnnotation[] annotations, List list, Hashtable properties) { - return printAnnotations(annotations, list, properties, null); + return printAnnotations(annotations, list, properties, null, null, null); } @@ -119,10 +139,56 @@ public class AnnotationFile * @return annotation file */ public String printAnnotations(AlignmentAnnotation[] annotations, - List list, Hashtable properties, ViewDef[] views) + List list, Hashtable properties, + ColumnSelection cs, AlignmentI al, ViewDef view) { - // TODO: resolve views issue : annotationFile could contain visible region, - // or full data + hidden region specifications for a view. + if (view != null) + { + if (view.viewname != null) + { + text.append("VIEW_DEF\t" + view.viewname + "\n"); + } + if (list == null) + { + list = view.visibleGroups; + } + if (cs == null) + { + cs = view.hiddencols; + } + if (al == null) + { + // add hidden rep sequences. + } + } + // first target - store and restore all settings for a view. + if (al != null && al.hasSeqrep()) + { + text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n"); + } + if (cs != null && cs.hasHiddenColumns()) + { + text.append("VIEW_HIDECOLS\t"); + List hc = cs.getHiddenColumns(); + boolean comma = false; + for (int[] r : hc) + { + if (!comma) + { + comma = true; + } + else + { + text.append(","); + } + text.append(r[0]); + text.append("-"); + text.append(r[1]); + } + text.append("\n"); + } + // TODO: allow efficient recovery of annotation data shown in several + // different views if (annotations != null) { boolean oneColour = true; @@ -174,7 +240,7 @@ public class AnnotationFile && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter .equals(" ")); hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' '); - hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't + hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't // be // rendered.. hasText |= (row.annotations[j].description != null && row.annotations[j].description @@ -227,8 +293,7 @@ public class AnnotationFile } else { - graphGroup_refs.put(key, new Object[] - { refSeq, refGroup }); + graphGroup_refs.put(key, new Object[] { refSeq, refGroup }); graphGroup.put(key, row.label); } } @@ -264,13 +329,13 @@ public class AnnotationFile } if (hasValues) { - if (row.annotations[j].value != Float.NaN) + if (!Float.isNaN(row.annotations[j].value)) { text.append(comma + row.annotations[j].value); } else { - System.err.println("Skipping NaN - not valid value."); + // System.err.println("Skipping NaN - not valid value."); text.append(comma + 0f);// row.annotations[j].value); } comma = ","; @@ -320,7 +385,9 @@ public class AnnotationFile } if (row.hasScore()) + { text.append("\t" + row.score); + } text.append(newline); @@ -403,7 +470,9 @@ public class AnnotationFile text.append(properties.get(key)); } // TODO: output alignment visualization settings here if required - + // iterate through one or more views, defining, marking columns and rows + // as visible/hidden, and emmitting view properties. + // View specific annotation is } return text.toString(); @@ -590,26 +659,50 @@ public class AnnotationFile String refSeqId = null; + public boolean annotateAlignmentView(AlignViewportI viewport, + String file, DataSourceType protocol) + { + ColumnSelection colSel = viewport.getColumnSelection(); + if (colSel == null) + { + colSel = new ColumnSelection(); + } + boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel, + file, protocol); + if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns())) + { + viewport.setColumnSelection(colSel); + } + + return rslt; + } + public boolean readAnnotationFile(AlignmentI al, String file, - String protocol) + DataSourceType sourceType) + { + return readAnnotationFile(al, null, file, sourceType); + } + + public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel, + String file, DataSourceType sourceType) { BufferedReader in = null; try { - if (protocol.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { in = new BufferedReader(new FileReader(file)); } - else if (protocol.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { URL url = new URL(file); in = new BufferedReader(new InputStreamReader(url.openStream())); } - else if (protocol.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { in = new BufferedReader(new StringReader(file)); } - else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { java.io.InputStream is = getClass().getResourceAsStream("/" + file); if (is != null) @@ -619,7 +712,7 @@ public class AnnotationFile } if (in != null) { - return parseAnnotationFrom(al, in); + return parseAnnotationFrom(al, colSel, in); } } catch (Exception ex) @@ -642,8 +735,8 @@ public class AnnotationFile private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; - public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in) - throws Exception + public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel, + BufferedReader in) throws Exception { nlinesread = 0; ArrayList combineAnnotation_calls = new ArrayList(); @@ -736,8 +829,8 @@ public class AnnotationFile else if (token.equalsIgnoreCase(COMBINE)) { // keep a record of current state and resolve groupRef at end - combineAnnotation_calls.add(new Object[] - { st, refSeq, groupRef }); + combineAnnotation_calls + .add(new Object[] { st, refSeq, groupRef }); modified = true; continue; } @@ -750,8 +843,8 @@ public class AnnotationFile else if (token.equalsIgnoreCase(GRAPHLINE)) { // resolve at end - deferredAnnotation_calls.add(new Object[] - { GRAPHLINE, st, refSeq, groupRef }); + deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, + refSeq, groupRef }); modified = true; continue; } @@ -834,6 +927,58 @@ public class AnnotationFile modified = true; continue; } + // else if (token.equalsIgnoreCase("VIEW_DEF")) + // { + // addOrSetView(al,st); + // modified = true; + // continue; + // } + else if (token.equalsIgnoreCase("VIEW_SETREF")) + { + if (refSeq != null) + { + al.setSeqrep(refSeq); + } + modified = true; + continue; + } + else if (token.equalsIgnoreCase("VIEW_HIDECOLS")) + { + if (st.hasMoreTokens()) + { + if (colSel == null) + { + colSel = new ColumnSelection(); + } + parseHideCols(colSel, st.nextToken()); + } + modified = true; + continue; + } + else if (token.equalsIgnoreCase("HIDE_INSERTIONS")) + { + SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq; + if (sr == null) + { + sr = al.getSequenceAt(0); + } + if (sr != null) + { + if (colSel == null) + { + System.err + .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: " + + line); + } + else + { + // consider deferring this till after the file has been parsed ? + colSel.hideInsertionsFor(sr); + } + } + modified = true; + continue; + } // Parse out the annotation row graphStyle = AlignmentAnnotation.getGraphValueFromString(token); @@ -852,7 +997,9 @@ public class AnnotationFile { description = line; if (st.hasMoreTokens()) + { line = st.nextToken(); + } } if (st.hasMoreTokens()) @@ -1004,8 +1151,8 @@ public class AnnotationFile (StringTokenizer) _deferred_args[1], // st (SequenceI) _deferred_args[2], // refSeq (_deferred_args[3] == null) ? null : groupRefLookup - .get((String) _deferred_args[3]) // the reference - // group, or null + .get(_deferred_args[3]) // the reference + // group, or null ); } } @@ -1024,14 +1171,48 @@ public class AnnotationFile (StringTokenizer) _combine_args[0], // st (SequenceI) _combine_args[1], // refSeq (_combine_args[2] == null) ? null : groupRefLookup - .get((String) _combine_args[2]) // the reference group, - // or null + .get(_combine_args[2]) // the reference group, + // or null ); } } return modified; } + private void parseHideCols(ColumnSelection colSel, String nextToken) + { + StringTokenizer inval = new StringTokenizer(nextToken, ","); + while (inval.hasMoreTokens()) + { + String range = inval.nextToken().trim(); + int from, to = range.indexOf("-"); + if (to == -1) + { + from = to = Integer.parseInt(range); + if (from >= 0) + { + colSel.hideColumns(from, to); + } + } + else + { + from = Integer.parseInt(range.substring(0, to)); + if (to < range.length() - 1) + { + to = Integer.parseInt(range.substring(to + 1)); + } + else + { + to = from; + } + if (from > 0 && to >= from) + { + colSel.hideColumns(from, to); + } + } + } + } + private Object autoAnnotsKey(AlignmentAnnotation annotation, SequenceI refSeq, String groupRef) { @@ -1118,8 +1299,8 @@ public class AnnotationFile } } if (hasSymbols - && (token.equals("H") || token.equals("E") - || token.equals("S") || token.equals(" "))) + && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz" + .contains(token))) { // Either this character represents a helix or sheet // or an integer which can be displayed @@ -1456,8 +1637,7 @@ public class AnnotationFile else if (key.equalsIgnoreCase("consThreshold")) { sg.cs.setConservationInc(Integer.parseInt(value)); - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), + Conservation c = new Conservation("Group", sg.getSequences(null), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -1578,6 +1758,10 @@ public class AnnotationFile */ public String printCSVAnnotations(AlignmentAnnotation[] annotations) { + if (annotations == null) + { + return ""; + } StringBuffer sp = new StringBuffer(); for (int i = 0; i < annotations.length; i++) { @@ -1602,4 +1786,19 @@ public class AnnotationFile } return sp.toString(); } + + public String printAnnotationsForView(AlignViewportI viewport) + { + return printAnnotations(viewport.isShowAnnotation() ? viewport + .getAlignment().getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), viewport.getAlignment() + .getProperties(), viewport.getColumnSelection(), + viewport.getAlignment(), null); + } + + public String printAnnotationsForAlignment(AlignmentI al) + { + return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), + al.getProperties(), null, al, null); + } }