X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=f0f1ca3dfb07cc17c106d784b425818e93cbe16a;hb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;hp=c3e71da29700169891ca9cbe4d4f6f42027c1d4e;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index c3e71da..f0f1ca3 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -100,7 +100,8 @@ public class AnnotationFile public String printAnnotations(AlignmentAnnotation[] annotations, List list, Hashtable properties) { - return printAnnotations(annotations, list, properties, null, null, null); + return printAnnotations(annotations, list, properties, null, null, + null); } @@ -119,8 +120,8 @@ public class AnnotationFile public final Hashtable hiddenRepSeqs; - public ViewDef(String vname, HiddenSequences hseqs, - HiddenColumns hcols, Hashtable hRepSeqs) + public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns hcols, + Hashtable hRepSeqs) { this.viewname = vname; this.hidseqs = hseqs; @@ -140,8 +141,7 @@ public class AnnotationFile * @return annotation file */ public String printAnnotations(AlignmentAnnotation[] annotations, - List list, Hashtable properties, - HiddenColumns cs, + List list, Hashtable properties, HiddenColumns cs, AlignmentI al, ViewDef view) { if (view != null) @@ -171,22 +171,9 @@ public class AnnotationFile if (cs != null && cs.hasHiddenColumns()) { text.append("VIEW_HIDECOLS\t"); - List hc = cs.getHiddenRegions(); - boolean comma = false; - for (int[] r : hc) - { - if (!comma) - { - comma = true; - } - else - { - text.append(","); - } - text.append(r[0]); - text.append("-"); - text.append(r[1]); - } + + String regions = cs.regionsToString(",", "-"); + text.append(regions); text.append("\n"); } // TODO: allow efficient recovery of annotation data shown in several @@ -202,8 +189,8 @@ 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; @@ -212,10 +199,8 @@ 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; } @@ -230,7 +215,8 @@ public class AnnotationFile writeGroup_Ref(refGroup, row.groupRef); refGroup = row.groupRef; - boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false; + boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, + hasValues = row.hasScore, hasText = false; // lookahead to check what the annotation row object actually contains. for (int j = 0; row.annotations != null && j < row.annotations.length @@ -239,14 +225,15 @@ public class AnnotationFile if (row.annotations[j] != null) { hasLabels |= (row.annotations[j].displayCharacter != null - && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter - .equals(" ")); - hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' '); + && row.annotations[j].displayCharacter.length() > 0 + && !row.annotations[j].displayCharacter.equals(" ")); + hasGlyphs |= (row.annotations[j].secondaryStructure != 0 + && row.annotations[j].secondaryStructure != ' '); hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't // be // rendered.. - hasText |= (row.annotations[j].description != null && row.annotations[j].description - .length() > 0); + hasText |= (row.annotations[j].description != null + && row.annotations[j].description.length() > 0); } } @@ -279,15 +266,15 @@ public class AnnotationFile graphLine.append("\t"); graphLine.append(row.getThreshold().label); graphLine.append("\t"); - graphLine.append(jalview.util.Format.getHexString(row - .getThreshold().colour)); + graphLine.append(jalview.util.Format + .getHexString(row.getThreshold().colour)); graphLine.append(newline); } if (row.graphGroup > -1) { graphGroupSeen.set(row.graphGroup); - Integer key = new Integer(row.graphGroup); + Integer key = Integer.valueOf(row.graphGroup); if (graphGroup.containsKey(key)) { graphGroup.put(key, graphGroup.get(key) + "\t" + row.label); @@ -375,11 +362,8 @@ public class AnnotationFile if (row.annotations[j].colour != null && row.annotations[j].colour != java.awt.Color.black) { - text.append(comma - + "[" - + jalview.util.Format - .getHexString(row.annotations[j].colour) - + "]"); + text.append(comma + "[" + jalview.util.Format + .getHexString(row.annotations[j].colour) + "]"); comma = ","; } } @@ -431,8 +415,8 @@ public class AnnotationFile for (Map.Entry combine_statement : graphGroup .entrySet()) { - Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement - .getKey()); + Object[] seqRefAndGroup = graphGroup_refs + .get(combine_statement.getKey()); writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]); refSeq = (SequenceI) seqRefAndGroup[0]; @@ -583,8 +567,8 @@ public class AnnotationFile if (sg.cs != null) { text.append("colour="); - text.append(ColourSchemeProperty.getColourName(sg.cs - .getColourScheme())); + text.append(ColourSchemeProperty + .getColourName(sg.cs.getColourScheme())); text.append("\t"); if (sg.cs.getThreshold() != 0) { @@ -662,8 +646,8 @@ public class AnnotationFile String refSeqId = null; - public boolean annotateAlignmentView(AlignViewportI viewport, - String file, DataSourceType protocol) + public boolean annotateAlignmentView(AlignViewportI viewport, Object file, + DataSourceType protocol) { ColumnSelection colSel = viewport.getColumnSelection(); HiddenColumns hidden = viewport.getAlignment().getHiddenColumns(); @@ -675,8 +659,8 @@ public class AnnotationFile { hidden = new HiddenColumns(); } - boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, - file, protocol); + boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file, + protocol); if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns())) { viewport.setColumnSelection(colSel); @@ -693,23 +677,23 @@ public class AnnotationFile } public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden, - String file, DataSourceType sourceType) + Object file, DataSourceType sourceType) { BufferedReader in = null; try { if (sourceType == DataSourceType.FILE) { - in = new BufferedReader(new FileReader(file)); + in = FileLoader.getBufferedReader(file); } else if (sourceType == DataSourceType.URL) { - URL url = new URL(file); + URL url = new URL(file.toString()); in = new BufferedReader(new InputStreamReader(url.openStream())); } else if (sourceType == DataSourceType.PASTE) { - in = new BufferedReader(new StringReader(file)); + in = new BufferedReader(new StringReader(file.toString())); } else if (sourceType == DataSourceType.CLASSLOADER) { @@ -730,8 +714,8 @@ public class AnnotationFile System.out.println("Problem reading annotation file: " + ex); if (nlinesread > 0) { - System.out.println("Last read line " + nlinesread + ": '" - + lastread + "' (first 80 chars) ..."); + System.out.println("Last read line " + nlinesread + ": '" + lastread + + "' (first 80 chars) ..."); } return false; } @@ -748,8 +732,8 @@ public class AnnotationFile BufferedReader in) throws Exception { nlinesread = 0; - ArrayList combineAnnotation_calls = new ArrayList(); - ArrayList deferredAnnotation_calls = new ArrayList(); + ArrayList combineAnnotation_calls = new ArrayList<>(); + ArrayList deferredAnnotation_calls = new ArrayList<>(); boolean modified = false; String groupRef = null; Hashtable groupRefRows = new Hashtable(); @@ -778,7 +762,7 @@ public class AnnotationFile autoAnnotsKey(aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef == null ? null : aa[aai].groupRef.getName())), - new Integer(1)); + Integer.valueOf(1)); } } } @@ -839,7 +823,8 @@ public class AnnotationFile { // keep a record of current state and resolve groupRef at end combineAnnotation_calls - .add(new Object[] { st, refSeq, groupRef }); + .add(new Object[] + { st, refSeq, groupRef }); modified = true; continue; } @@ -852,8 +837,9 @@ 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; } @@ -873,8 +859,8 @@ public class AnnotationFile if (refSeqIndex < 1) { refSeqIndex = 1; - System.out - .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile"); + System.out.println( + "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile"); } } catch (Exception ex) { @@ -975,14 +961,14 @@ public class AnnotationFile { if (hidden == null) { - System.err - .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: " + 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 ? - hidden.hideInsertionsFor(sr); + hidden.hideList(sr.getInsertions()); } } modified = true; @@ -1059,9 +1045,8 @@ public class AnnotationFile (index == 0) ? null : annotations, 0, 0, graphStyle); annotation.score = score; - if (!overrideAutoAnnot - && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq, - groupRef))) + if (!overrideAutoAnnot && autoAnnots + .containsKey(autoAnnotsKey(annotation, refSeq, groupRef))) { // skip - we've already got an automatic annotation of this type. continue; @@ -1079,14 +1064,14 @@ public class AnnotationFile // TODO: verify that undo/redo with 1:many sequence associated // annotations can be undone correctly AlignmentAnnotation ann = new AlignmentAnnotation(annotation); - annotation - .createSequenceMapping(referedSeq, refSeqIndex, false); + annotation.createSequenceMapping(referedSeq, refSeqIndex, + false); annotation.adjustForAlignment(); referedSeq.addAlignmentAnnotation(annotation); al.addAnnotation(annotation); al.setAnnotationIndex(annotation, - al.getAlignmentAnnotation().length - - existingAnnotations - 1); + al.getAlignmentAnnotation().length - existingAnnotations + - 1); if (groupRef != null) { ((Vector) groupRefRows.get(groupRef)).addElement(annotation); @@ -1094,8 +1079,8 @@ public class AnnotationFile // and recover our virgin copy to use again if necessary. annotation = ann; - } while (refSeqId != null - && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null); + } while (refSeqId != null && (referedSeq = al.findName(referedSeq, + refSeqId, true)) != null); } else { @@ -1112,7 +1097,7 @@ public class AnnotationFile modified = true; } // Resolve the groupRefs - Hashtable groupRefLookup = new Hashtable(); + Hashtable groupRefLookup = new Hashtable<>(); Enumeration en = groupRefRows.keys(); while (en.hasMoreElements()) @@ -1128,8 +1113,8 @@ public class AnnotationFile { // TODO: specify and implement duplication of alignment annotation // for multiple group references. - System.err - .println("Ignoring 1:many group reference mappings for group name '" + System.err.println( + "Ignoring 1:many group reference mappings for group name '" + groupRef + "'"); } else @@ -1140,7 +1125,8 @@ public class AnnotationFile if (rowset != null && rowset.size() > 0) { AlignmentAnnotation alan = null; - for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++) + for (int elm = 0, elmSize = rowset + .size(); elm < elmSize; elm++) { alan = (AlignmentAnnotation) rowset.elementAt(elm); alan.groupRef = theGroup; @@ -1156,12 +1142,13 @@ public class AnnotationFile { if (_deferred_args[0] == GRAPHLINE) { - addLine(al, - (StringTokenizer) _deferred_args[1], // st + addLine(al, (StringTokenizer) _deferred_args[1], // st (SequenceI) _deferred_args[2], // refSeq - (_deferred_args[3] == null) ? null : groupRefLookup - .get(_deferred_args[3]) // the reference - // group, or null + (_deferred_args[3] == null) ? null + : groupRefLookup.get(_deferred_args[3]) // the + // reference + // group, or + // null ); } } @@ -1175,13 +1162,13 @@ public class AnnotationFile int combinecount = 0; for (Object[] _combine_args : combineAnnotation_calls) { - combineAnnotations(al, - ++combinecount, + combineAnnotations(al, ++combinecount, (StringTokenizer) _combine_args[0], // st (SequenceI) _combine_args[1], // refSeq - (_combine_args[2] == null) ? null : groupRefLookup - .get(_combine_args[2]) // the reference group, - // or null + (_combine_args[2] == null) ? null + : groupRefLookup.get(_combine_args[2]) // the reference + // group, + // or null ); } } @@ -1245,8 +1232,7 @@ public class AnnotationFile int j = string.indexOf("]"); if (i > -1 && j > -1) { - colour = ColorUtils.parseColourString(string.substring(i + 1, - j)); + colour = ColorUtils.parseColourString(string.substring(i + 1, j)); if (i > 0 && string.charAt(i - 1) == ',') { // clip the preceding comma as well @@ -1285,7 +1271,7 @@ public class AnnotationFile { displayChar = token; // foo - value = new Float(token).floatValue(); + value = Float.valueOf(token).floatValue(); parsedValue = true; continue; } catch (NumberFormatException ex) @@ -1299,8 +1285,8 @@ public class AnnotationFile displayChar = token; } } - if (hasSymbols - && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz" + if (hasSymbols && (token.length() == 1 + && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz" .contains(token))) { // Either this character represents a helix or sheet @@ -1420,8 +1406,8 @@ public class AnnotationFile } else { - System.err - .println("Couldn't combine annotations. None are added to alignment yet!"); + System.err.println( + "Couldn't combine annotations. None are added to alignment yet!"); } } @@ -1487,8 +1473,8 @@ public class AnnotationFile } } catch (Exception e) { - System.err - .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '" + System.err.println( + "Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '" + rng + "' - assuming alignment width for group."); // assume group is full width sg.setStartRes(0); @@ -1534,7 +1520,8 @@ public class AnnotationFile } else { - sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false); + sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), + false); } } } @@ -1630,8 +1617,10 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("colour")) { - sg.cs.setColourScheme(ColourSchemeProperty - .getColourScheme(al, value)); + // TODO need to notify colourscheme of view reference once it is + // available + sg.cs.setColourScheme( + ColourSchemeProperty.getColourScheme(null, al, value)); } else if (key.equalsIgnoreCase("pidThreshold")) { @@ -1712,8 +1701,8 @@ public class AnnotationFile AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation(); if (ala == null) { - System.err - .print("Warning - no annotation to set below for sequence associated annotation:"); + System.err.print( + "Warning - no annotation to set below for sequence associated annotation:"); } while (st.hasMoreTokens()) { @@ -1792,10 +1781,13 @@ public class AnnotationFile public String printAnnotationsForView(AlignViewportI viewport) { - return printAnnotations(viewport.isShowAnnotation() ? viewport - .getAlignment().getAlignmentAnnotation() : null, viewport - .getAlignment().getGroups(), viewport.getAlignment() - .getProperties(), viewport.getAlignment().getHiddenColumns(), + return printAnnotations( + viewport.isShowAnnotation() + ? viewport.getAlignment().getAlignmentAnnotation() + : null, + viewport.getAlignment().getGroups(), + viewport.getAlignment().getProperties(), + viewport.getAlignment().getHiddenColumns(), viewport.getAlignment(), null); }