X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=09859c9aff81aaae02736c58a449cbd7ba4166ef;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=b669ee50903dff5d89c44c1d65a1224b71937310;hpb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index b669ee5..09859c9 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -20,6 +20,18 @@ */ package jalview.io; +import java.awt.Color; +import java.io.BufferedReader; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; + import jalview.analysis.Conservation; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; @@ -35,51 +47,32 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.util.ColorUtils; -import java.awt.Color; -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 { - public AnnotationFile() - { - init(); - } + private static final String GRAPHLINE = "GRAPHLINE"; + + private static final String COMBINE = "COMBINE"; - /** - * character used to write newlines - */ protected String newline = System.getProperty("line.separator"); + private StringBuffer text; + + private SequenceI refSeq = null; + + private String refSeqId = null; + + private long nlinesread = 0; + + private String lastread = ""; + /** - * set new line string and reset the output buffer - * - * @param nl + * Constructor */ - public void setNewlineString(String nl) + public AnnotationFile() { - newline = nl; init(); } - public String getNewlineString() - { - return newline; - } - - StringBuffer text; - private void init() { text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: " @@ -100,7 +93,8 @@ 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 +113,8 @@ 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 +134,7 @@ 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) @@ -199,10 +192,8 @@ 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; } @@ -217,7 +208,8 @@ 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 @@ -226,14 +218,15 @@ 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); } } @@ -266,15 +259,15 @@ 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); @@ -362,11 +355,8 @@ 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 = ","; } } @@ -418,8 +408,8 @@ 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]; @@ -570,8 +560,8 @@ 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) { @@ -645,12 +635,8 @@ public class AnnotationFile } } - SequenceI refSeq = null; - - 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(); @@ -662,8 +648,8 @@ 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); @@ -680,57 +666,30 @@ 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)); - } - else if (sourceType == DataSourceType.URL) - { - URL url = new URL(file); - in = new BufferedReader(new InputStreamReader(url.openStream())); - } - else if (sourceType == DataSourceType.PASTE) - { - in = new BufferedReader(new StringReader(file)); - } - else if (sourceType == DataSourceType.CLASSLOADER) - { - java.io.InputStream is = getClass().getResourceAsStream("/" + file); - if (is != null) - { - in = new BufferedReader(new java.io.InputStreamReader(is)); - } - } + in = new FileParse().getBufferedReader(file, sourceType); if (in != null) { return parseAnnotationFrom(al, hidden, in); } - } catch (Exception ex) { ex.printStackTrace(); 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; } return false; } - long nlinesread = 0; - - String lastread = ""; - - private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; - public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden, BufferedReader in) throws Exception { @@ -765,7 +724,7 @@ public class AnnotationFile autoAnnotsKey(aa[aai], aa[aai].sequenceRef, (aa[aai].groupRef == null ? null : aa[aai].groupRef.getName())), - new Integer(1)); + Integer.valueOf(1)); } } } @@ -826,7 +785,8 @@ 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; } @@ -839,8 +799,9 @@ 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; } @@ -860,8 +821,8 @@ 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) { @@ -962,14 +923,14 @@ 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; @@ -1046,9 +1007,8 @@ 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; @@ -1066,14 +1026,14 @@ 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); @@ -1081,8 +1041,8 @@ 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 { @@ -1115,8 +1075,8 @@ 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 @@ -1127,7 +1087,8 @@ 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; @@ -1143,12 +1104,13 @@ 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 ); } } @@ -1162,13 +1124,13 @@ 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 ); } } @@ -1232,8 +1194,7 @@ 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 @@ -1272,7 +1233,7 @@ public class AnnotationFile { displayChar = token; // foo - value = new Float(token).floatValue(); + value = Float.valueOf(token).floatValue(); parsedValue = true; continue; } catch (NumberFormatException ex) @@ -1286,8 +1247,8 @@ 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 @@ -1407,8 +1368,8 @@ 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!"); } } @@ -1474,8 +1435,8 @@ 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); @@ -1521,7 +1482,8 @@ public class AnnotationFile } else { - sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false); + sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), + false); } } } @@ -1588,108 +1550,120 @@ public class AnnotationFile } String name = st.nextToken(); - SequenceGroup sg = null; - for (SequenceGroup _sg : al.getGroups()) + + Map properties = new HashMap<>(); + while (st.hasMoreTokens()) { - if ((sg = _sg).getName().equals(name)) - { - break; - } - else + String keyValue = st.nextToken(); + String key = keyValue.substring(0, keyValue.indexOf("=")); + String value = keyValue.substring(keyValue.indexOf("=") + 1); + properties.put(key, value); + } + + for (SequenceGroup sg : al.getGroups()) + { + if (sg.getName().equals(name)) { - sg = null; + addProperties(sg, properties, al); } } + } - if (sg != null) + /** + * Helper method that applies any specified properties to a SequenceGroup + * + * @param sg + * @param properties + * @param al + */ + private void addProperties(SequenceGroup sg, + Map properties, AlignmentI al) + { + ColourSchemeI def = sg.getColourScheme(); + for (String key : properties.keySet()) { - String keyValue, key, value; - ColourSchemeI def = sg.getColourScheme(); - while (st.hasMoreTokens()) + String value = properties.get(key); + if (key.equalsIgnoreCase("description")) { - keyValue = st.nextToken(); - key = keyValue.substring(0, keyValue.indexOf("=")); - value = keyValue.substring(keyValue.indexOf("=") + 1); - - if (key.equalsIgnoreCase("description")) - { - sg.setDescription(value); - } - else if (key.equalsIgnoreCase("colour")) - { - sg.cs.setColourScheme(ColourSchemeProperty - .getColourScheme(al, value)); - } - else if (key.equalsIgnoreCase("pidThreshold")) - { - sg.cs.setThreshold(Integer.parseInt(value), true); + sg.setDescription(value); + } + else if (key.equalsIgnoreCase("colour")) + { + // 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")) + { + sg.cs.setThreshold(Integer.parseInt(value), true); - } - else if (key.equalsIgnoreCase("consThreshold")) - { - sg.cs.setConservationInc(Integer.parseInt(value)); - Conservation c = new Conservation("Group", sg.getSequences(null), - sg.getStartRes(), sg.getEndRes() + 1); + } + else if (key.equalsIgnoreCase("consThreshold")) + { + sg.cs.setConservationInc(Integer.parseInt(value)); + Conservation c = new Conservation("Group", sg.getSequences(null), + sg.getStartRes(), sg.getEndRes() + 1); - c.calculate(); - c.verdict(false, 25); // TODO: refer to conservation percent threshold + c.calculate(); + c.verdict(false, 25); // TODO: refer to conservation percent threshold - sg.cs.setConservation(c); + sg.cs.setConservation(c); - } - else if (key.equalsIgnoreCase("outlineColour")) - { - sg.setOutlineColour(ColorUtils.parseColourString(value)); - } - else if (key.equalsIgnoreCase("displayBoxes")) - { - sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue()); - } - else if (key.equalsIgnoreCase("showUnconserved")) - { - sg.setShowNonconserved(Boolean.valueOf(value).booleanValue()); - } - else if (key.equalsIgnoreCase("displayText")) - { - sg.setDisplayText(Boolean.valueOf(value).booleanValue()); - } - else if (key.equalsIgnoreCase("colourText")) - { - sg.setColourText(Boolean.valueOf(value).booleanValue()); - } - else if (key.equalsIgnoreCase("textCol1")) - { - sg.textColour = ColorUtils.parseColourString(value); - } - else if (key.equalsIgnoreCase("textCol2")) - { - sg.textColour2 = ColorUtils.parseColourString(value); - } - else if (key.equalsIgnoreCase("textColThreshold")) - { - sg.thresholdTextColour = Integer.parseInt(value); - } - else if (key.equalsIgnoreCase("idColour")) - { - Color idColour = ColorUtils.parseColourString(value); - sg.setIdColour(idColour == null ? Color.black : idColour); - } - else if (key.equalsIgnoreCase("hide")) - { - // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847 - sg.setHidereps(true); - } - else if (key.equalsIgnoreCase("hidecols")) - { - // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847 - sg.setHideCols(true); - } - sg.recalcConservation(); } - if (sg.getColourScheme() == null) + else if (key.equalsIgnoreCase("outlineColour")) + { + sg.setOutlineColour(ColorUtils.parseColourString(value)); + } + else if (key.equalsIgnoreCase("displayBoxes")) + { + sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue()); + } + else if (key.equalsIgnoreCase("showUnconserved")) + { + sg.setShowNonconserved(Boolean.valueOf(value).booleanValue()); + } + else if (key.equalsIgnoreCase("displayText")) + { + sg.setDisplayText(Boolean.valueOf(value).booleanValue()); + } + else if (key.equalsIgnoreCase("colourText")) + { + sg.setColourText(Boolean.valueOf(value).booleanValue()); + } + else if (key.equalsIgnoreCase("textCol1")) + { + sg.textColour = ColorUtils.parseColourString(value); + } + else if (key.equalsIgnoreCase("textCol2")) + { + sg.textColour2 = ColorUtils.parseColourString(value); + } + else if (key.equalsIgnoreCase("textColThreshold")) + { + sg.thresholdTextColour = Integer.parseInt(value); + } + else if (key.equalsIgnoreCase("idColour")) + { + Color idColour = ColorUtils.parseColourString(value); + sg.setIdColour(idColour == null ? Color.black : idColour); + } + else if (key.equalsIgnoreCase("hide")) + { + // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847 + sg.setHidereps(true); + } + else if (key.equalsIgnoreCase("hidecols")) { - sg.setColourScheme(def); + // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847 + sg.setHideCols(true); } + sg.recalcConservation(); + } + + if (sg.getColourScheme() == null) + { + sg.setColourScheme(def); } } @@ -1699,8 +1673,8 @@ 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()) { @@ -1779,10 +1753,13 @@ 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); }