X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=773633238ace37a835129e194cc4593d3fefc9cd;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=b3a22df894f169bc408c3bef653c8eb86d691723;hpb=59c3078b53669a38f4e1c1158675691fe60349b3;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index b3a22df..7736332 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -1,19 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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. + * 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 . + * 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; @@ -131,8 +134,8 @@ public class AnnotationFile StringBuffer colours = new StringBuffer(); StringBuffer graphLine = new StringBuffer(); StringBuffer rowprops = new StringBuffer(); - Hashtable graphGroup = new Hashtable(); - Hashtable graphGroup_refs = new Hashtable(); + Hashtable graphGroup = new Hashtable(); + Hashtable graphGroup_refs = new Hashtable(); BitSet graphGroupSeen = new BitSet(); java.awt.Color color; @@ -141,16 +144,19 @@ public class AnnotationFile { row = annotations[i]; - if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup))) + if (!row.visible + && !row.hasScore() + && !(row.graphGroup > -1 && graphGroupSeen + .get(row.graphGroup))) { continue; } color = null; oneColour = true; - + // mark any sequence references for the row - writeSequence_Ref(refSeq ,row.sequenceRef); + writeSequence_Ref(refSeq, row.sequenceRef); refSeq = row.sequenceRef; // mark any group references for the row writeGroup_Ref(refGroup, row.groupRef); @@ -217,11 +223,12 @@ public class AnnotationFile if (graphGroup.containsKey(key)) { graphGroup.put(key, graphGroup.get(key) + "\t" + row.label); - + } else { - graphGroup_refs.put(key, new Object[] { refSeq, refGroup}); + graphGroup_refs.put(key, new Object[] + { refSeq, refGroup }); graphGroup.put(key, row.label); } } @@ -338,32 +345,38 @@ public class AnnotationFile rowprops.append(row.centreColLabels); rowprops.append(newline); } + if (graphLine.length() > 0) + { + text.append(graphLine.toString()); + graphLine.setLength(0); + } } text.append(newline); text.append(colours.toString()); - text.append(graphLine.toString()); if (graphGroup.size() > 0) { SequenceI oldRefSeq = refSeq; SequenceGroup oldRefGroup = refGroup; - for (Map.Entry combine_statement:graphGroup.entrySet()) - { - Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey()); - - writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]); - refSeq = (SequenceI)seqRefAndGroup[0]; - - writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]); - refGroup = (SequenceGroup)seqRefAndGroup[1]; + for (Map.Entry combine_statement : graphGroup + .entrySet()) + { + Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement + .getKey()); + + writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]); + refSeq = (SequenceI) seqRefAndGroup[0]; + + writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]); + refGroup = (SequenceGroup) seqRefAndGroup[1]; text.append("COMBINE\t"); text.append(combine_statement.getValue()); text.append(newline); } writeSequence_Ref(refSeq, oldRefSeq); refSeq = oldRefSeq; - + writeGroup_Ref(refGroup, oldRefGroup); refGroup = oldRefGroup; } @@ -396,7 +409,8 @@ public class AnnotationFile return text.toString(); } - private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup) + private Object writeGroup_Ref(SequenceGroup refGroup, + SequenceGroup next_refGroup) { if (next_refGroup == null) { @@ -421,13 +435,13 @@ public class AnnotationFile return true; } } - return false; + return false; } - + private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq) { - if (next_refSeq==null) + if (next_refSeq == null) { if (refSeq != null) { @@ -612,20 +626,28 @@ public class AnnotationFile { ex.printStackTrace(); System.out.println("Problem reading annotation file: " + ex); - if (nlinesread>0) { - System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ..."); + if (nlinesread > 0) + { + System.out.println("Last read line " + nlinesread + ": '" + + lastread + "' (first 80 chars) ..."); } return false; } return false; } - long nlinesread=0; - String lastread=""; + + long nlinesread = 0; + + String lastread = ""; + + private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; + public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in) throws Exception { nlinesread = 0; ArrayList combineAnnotation_calls = new ArrayList(); + ArrayList deferredAnnotation_calls = new ArrayList(); boolean modified = false; String groupRef = null; Hashtable groupRefRows = new Hashtable(); @@ -670,7 +692,8 @@ public class AnnotationFile boolean jvAnnotationFile = false; while ((line = in.readLine()) != null) { - nlinesread++;lastread = new String(line); + nlinesread++; + lastread = new String(line); if (line.indexOf("#") == 0) { continue; @@ -691,7 +714,8 @@ public class AnnotationFile while ((line = in.readLine()) != null) { - nlinesread++;lastread = new String(line); + nlinesread++; + lastread = new String(line); if (line.indexOf("#") == 0 || line.indexOf("JALVIEW_ANNOTATION") > -1 || line.length() == 0) @@ -709,10 +733,11 @@ public class AnnotationFile continue; } - else if (token.equalsIgnoreCase("COMBINE")) + 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; } @@ -722,9 +747,11 @@ public class AnnotationFile modified = true; continue; } - else if (token.equalsIgnoreCase("GRAPHLINE")) + else if (token.equalsIgnoreCase(GRAPHLINE)) { - addLine(al, st); + // resolve at end + deferredAnnotation_calls.add(new Object[] + { GRAPHLINE, st, refSeq, groupRef }); modified = true; continue; } @@ -784,6 +811,7 @@ public class AnnotationFile else if (token.equalsIgnoreCase("SEQUENCE_GROUP")) { addGroup(al, st); + modified = true; continue; } @@ -928,7 +956,7 @@ public class AnnotationFile modified = true; } // Resolve the groupRefs - Hashtable groupRefLookup=new Hashtable(); + Hashtable groupRefLookup = new Hashtable(); Enumeration en = groupRefRows.keys(); while (en.hasMoreElements()) @@ -952,7 +980,7 @@ public class AnnotationFile { matched = true; Vector rowset = (Vector) groupRefRows.get(groupRef); - groupRefLookup.put(groupRef, theGroup); + groupRefLookup.put(groupRef, theGroup); if (rowset != null && rowset.size() > 0) { AlignmentAnnotation alan = null; @@ -967,20 +995,39 @@ public class AnnotationFile } ((Vector) groupRefRows.get(groupRef)).removeAllElements(); } + // process any deferred attribute settings for each context + for (Object[] _deferred_args : deferredAnnotation_calls) + { + if (_deferred_args[0] == GRAPHLINE) + { + addLine(al, + (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 + ); + } + } + // finally, combine all the annotation rows within each context. /** - * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones + * number of combine statements in this annotation file. Used to create + * new groups for combined annotation graphs without disturbing existing + * ones */ int combinecount = 0; - for (Object[] _combine_args:combineAnnotation_calls) { - combineAnnotations(al, + for (Object[] _combine_args : combineAnnotation_calls) + { + combineAnnotations(al, ++combinecount, (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 - ); + (_combine_args[2] == null) ? null : groupRefLookup + .get((String) _combine_args[2]) // the reference group, + // or null + ); } - } return modified; } @@ -1137,31 +1184,35 @@ public class AnnotationFile } } - void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef) + void combineAnnotations(AlignmentI al, int combineCount, + StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef) { String group = st.nextToken(); // First make sure we are not overwriting the graphIndex - int graphGroup=0; + int graphGroup = 0; if (al.getAlignmentAnnotation() != null) { for (int i = 0; i < al.getAlignmentAnnotation().length; i++) { AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; - - if (aa.graphGroup>graphGroup) + + if (aa.graphGroup > graphGroup) { // try to number graphGroups in order of occurence. - graphGroup=aa.graphGroup+1; + graphGroup = aa.graphGroup + 1; } - if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group)) + if (aa.sequenceRef == seqRef && aa.groupRef == groupRef + && aa.label.equalsIgnoreCase(group)) { - if (aa.graphGroup>-1) + if (aa.graphGroup > -1) { graphGroup = aa.graphGroup; - } else { + } + else + { if (graphGroup <= combineCount) { - graphGroup=combineCount+1; + graphGroup = combineCount + 1; } aa.graphGroup = graphGroup; } @@ -1176,7 +1227,8 @@ public class AnnotationFile for (int i = 0; i < al.getAlignmentAnnotation().length; i++) { AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; - if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group)) + if (aa.sequenceRef == seqRef && aa.groupRef == groupRef + && aa.label.equalsIgnoreCase(group)) { aa.graphGroup = graphGroup; break; @@ -1191,19 +1243,29 @@ public class AnnotationFile } } - void addLine(AlignmentI al, StringTokenizer st) + void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, + SequenceGroup groupRef) { String group = st.nextToken(); AlignmentAnnotation annotation = null, alannot[] = al .getAlignmentAnnotation(); + float value = new Float(st.nextToken()).floatValue(); + String label = st.hasMoreTokens() ? st.nextToken() : null; + java.awt.Color colour = null; + if (st.hasMoreTokens()) + { + UserColourScheme ucs = new UserColourScheme(st.nextToken()); + colour = ucs.findColour('A'); + } if (alannot != null) { for (int i = 0; i < alannot.length; i++) { - if (alannot[i].label.equalsIgnoreCase(group)) + if (alannot[i].label.equalsIgnoreCase(group) + && (seqRef == null || alannot[i].sequenceRef == seqRef) + && (groupRef == null || alannot[i].groupRef == groupRef)) { - annotation = alannot[i]; - break; + alannot[i].setThreshold(new GraphLine(value, label, colour)); } } } @@ -1211,16 +1273,6 @@ public class AnnotationFile { return; } - float value = new Float(st.nextToken()).floatValue(); - String label = st.hasMoreTokens() ? st.nextToken() : null; - java.awt.Color colour = null; - if (st.hasMoreTokens()) - { - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - colour = ucs.findColour('A'); - } - - annotation.setThreshold(new GraphLine(value, label, colour)); } void addGroup(AlignmentI al, StringTokenizer st)