X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=028b14f83440fc4876ac3b9f97c26eaa3066d459;hb=3f62ab98313f836c9e0cdec277e2ec9a0c194801;hp=372d905d6d9415a3b27f1a14f8a9c88db0f8c6ec;hpb=ecb334f98fca8ed9f27b6a7d027dea3bd4213023;p=jalview.git diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index 372d905..028b14f 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -23,6 +23,7 @@ package jalview.io; import jalview.analysis.AlignmentUtils; import jalview.analysis.SequenceIdMatcher; import jalview.api.AlignViewportI; +import jalview.api.FeatureColourI; import jalview.api.FeaturesSourceI; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; @@ -33,10 +34,8 @@ import jalview.datamodel.SequenceI; import jalview.io.gff.GffHelperBase; import jalview.io.gff.GffHelperFactory; import jalview.io.gff.GffHelperI; -import jalview.schemes.AnnotationColourGradient; -import jalview.schemes.GraduatedColor; -import jalview.schemes.UserColourScheme; -import jalview.util.Format; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; import jalview.util.MapList; import jalview.util.ParseHtmlBodyAndLinks; import jalview.util.StringUtils; @@ -45,12 +44,14 @@ import java.awt.Color; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; +import java.util.Comparator; import java.util.HashMap; -import java.util.Iterator; +import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Map.Entry; -import java.util.StringTokenizer; +import java.util.Set; /** * Parses and writes features files, which may be in Jalview, GFF2 or GFF3 @@ -78,6 +79,19 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI protected static final String GFF_VERSION = "##gff-version"; + private static final Comparator SORT_NULL_LAST = new Comparator() + { + @Override + public int compare(String o1, String o2) + { + if (o1 == null) + { + return o2 == null ? 0 : 1; + } + return (o2 == null ? -1 : o1.compareTo(o2)); + } + }; + private AlignmentI lastmatchedAl = null; private SequenceIdMatcher matcher = null; @@ -97,12 +111,13 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * Constructor which does not parse the file immediately * * @param inFile - * @param type + * @param paste * @throws IOException */ - public FeaturesFile(String inFile, String type) throws IOException + public FeaturesFile(String inFile, DataSourceType paste) + throws IOException { - super(false, inFile, type); + super(false, inFile, paste); } /** @@ -122,7 +137,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param type * @throws IOException */ - public FeaturesFile(boolean parseImmediately, String inFile, String type) + public FeaturesFile(boolean parseImmediately, String inFile, + DataSourceType type) throws IOException { super(parseImmediately, inFile, type); @@ -140,8 +156,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * - process html strings into plain text * @return true if features were added */ - public boolean parse(AlignmentI align, Map colours, - boolean removeHTML) + public boolean parse(AlignmentI align, + Map colours, boolean removeHTML) { return parse(align, colours, removeHTML, false); } @@ -177,8 +193,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * - when true, ID matches to compound sequence IDs are allowed * @return true if features were added */ - public boolean parse(AlignmentI align, Map colours, - boolean removeHTML, boolean relaxedIdmatching) + public boolean parse(AlignmentI align, + Map colours, boolean removeHTML, + boolean relaxedIdmatching) { Map gffProps = new HashMap(); /* @@ -232,12 +249,18 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI else if (ft.equalsIgnoreCase("endgroup")) { // We should check whether this is the current group, - // but at present theres no way of showing more than 1 group + // but at present there's no way of showing more than 1 group featureGroup = null; } else { - parseFeatureColour(line, ft, gffColumns, colours); + String colscheme = gffColumns[1]; + FeatureColourI colour = FeatureColour + .parseJalviewFeatureColour(colscheme); + if (colour != null) + { + colours.put(ft, colour); + } } continue; } @@ -275,7 +298,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI */ for (SequenceI newseq : newseqs) { - if (newseq.getSequenceFeatures() != null) + if (newseq.getFeatures().hasFeatures()) { align.addSequence(newseq); } @@ -297,7 +320,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @param featureGroup */ protected boolean parseJalviewFeature(String line, String[] gffColumns, - AlignmentI alignment, Map featureColours, + AlignmentI alignment, Map featureColours, boolean removeHTML, boolean relaxedIdMatching, String featureGroup) { /* @@ -349,8 +372,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * Perhaps an old style groups file with no colours - * synthesize a colour from the feature type */ - UserColourScheme ucs = new UserColourScheme(ft); - featureColours.put(ft, ucs.findColour('A')); + Color colour = ColorUtils.createColourFromName(ft); + featureColours.put(ft, new FeatureColour(colour)); } SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos, endPos, featureGroup); @@ -381,225 +404,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI } /** - * Process a feature type colour specification - * - * @param line - * the current input line (for error messages only) - * @param featureType - * the first token on the line - * @param gffColumns - * holds tokens on the line - * @param colours - * map to which to add derived colour specification - */ - protected void parseFeatureColour(String line, String featureType, - String[] gffColumns, Map colours) - { - Object colour = null; - String colscheme = gffColumns[1]; - if (colscheme.indexOf("|") > -1 - || colscheme.trim().equalsIgnoreCase("label")) - { - colour = parseGraduatedColourScheme(line, colscheme); - } - else - { - UserColourScheme ucs = new UserColourScheme(colscheme); - colour = ucs.findColour('A'); - } - if (colour != null) - { - colours.put(featureType, colour); - } - } - - /** - * Parse a Jalview graduated colour descriptor - * - * @param line - * @param colourDescriptor - * @return - */ - protected GraduatedColor parseGraduatedColourScheme(String line, - String colourDescriptor) - { - // Parse '|' separated graduated colourscheme fields: - // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue] - // can either provide 'label' only, first is optional, next two - // colors are required (but may be - // left blank), next is optional, nxt two min/max are required. - // first is either 'label' - // first/second and third are both hexadecimal or word equivalent - // colour. - // next two are values parsed as floats. - // fifth is either 'above','below', or 'none'. - // sixth is a float value and only required when fifth is either - // 'above' or 'below'. - StringTokenizer gcol = new StringTokenizer(colourDescriptor, "|", true); - // set defaults - float min = Float.MIN_VALUE, max = Float.MAX_VALUE; - boolean labelCol = false; - // Parse spec line - String mincol = gcol.nextToken(); - if (mincol == "|") - { - System.err - .println("Expected either 'label' or a colour specification in the line: " - + line); - return null; - } - String maxcol = null; - if (mincol.toLowerCase().indexOf("label") == 0) - { - labelCol = true; - mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip '|' - mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); - } - String abso = null, minval, maxval; - if (mincol != null) - { - // at least four more tokens - if (mincol.equals("|")) - { - mincol = ""; - } - else - { - gcol.nextToken(); // skip next '|' - } - // continue parsing rest of line - maxcol = gcol.nextToken(); - if (maxcol.equals("|")) - { - maxcol = ""; - } - else - { - gcol.nextToken(); // skip next '|' - } - abso = gcol.nextToken(); - gcol.nextToken(); // skip next '|' - if (abso.toLowerCase().indexOf("abso") != 0) - { - minval = abso; - abso = null; - } - else - { - minval = gcol.nextToken(); - gcol.nextToken(); // skip next '|' - } - maxval = gcol.nextToken(); - if (gcol.hasMoreTokens()) - { - gcol.nextToken(); // skip next '|' - } - try - { - if (minval.length() > 0) - { - min = Float.valueOf(minval); - } - } catch (Exception e) - { - System.err - .println("Couldn't parse the minimum value for graduated colour for type (" - + colourDescriptor - + ") - did you misspell 'auto' for the optional automatic colour switch ?"); - e.printStackTrace(); - } - try - { - if (maxval.length() > 0) - { - max = Float.valueOf(maxval); - } - } catch (Exception e) - { - System.err - .println("Couldn't parse the maximum value for graduated colour for type (" - + colourDescriptor + ")"); - e.printStackTrace(); - } - } - else - { - // add in some dummy min/max colours for the label-only - // colourscheme. - mincol = "FFFFFF"; - maxcol = "000000"; - } - - GraduatedColor colour = null; - try - { - colour = new GraduatedColor( - new UserColourScheme(mincol).findColour('A'), - new UserColourScheme(maxcol).findColour('A'), min, max); - } catch (Exception e) - { - System.err.println("Couldn't parse the graduated colour scheme (" - + colourDescriptor + ")"); - e.printStackTrace(); - } - if (colour != null) - { - colour.setColourByLabel(labelCol); - colour.setAutoScaled(abso == null); - // add in any additional parameters - String ttype = null, tval = null; - if (gcol.hasMoreTokens()) - { - // threshold type and possibly a threshold value - ttype = gcol.nextToken(); - if (ttype.toLowerCase().startsWith("below")) - { - colour.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); - } - else if (ttype.toLowerCase().startsWith("above")) - { - colour.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); - } - else - { - colour.setThreshType(AnnotationColourGradient.NO_THRESHOLD); - if (!ttype.toLowerCase().startsWith("no")) - { - System.err.println("Ignoring unrecognised threshold type : " - + ttype); - } - } - } - if (colour.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) - { - try - { - gcol.nextToken(); - tval = gcol.nextToken(); - colour.setThresh(new Float(tval).floatValue()); - } catch (Exception e) - { - System.err.println("Couldn't parse threshold value as a float: (" - + tval + ")"); - e.printStackTrace(); - } - } - // parse the thresh-is-min token ? - if (gcol.hasMoreTokens()) - { - System.err - .println("Ignoring additional tokens in parameters in graduated colour specification\n"); - while (gcol.hasMoreTokens()) - { - System.err.println("|" + gcol.nextToken()); - } - System.err.println("\n"); - } - } - return colour; - } - - /** * clear any temporary handles used to speed up ID matching */ protected void resetMatcher() @@ -684,8 +488,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks( sf.getDescription(), removeHTML, newline); - sf.description = (removeHTML) ? parsed.getNonHtmlContent() - : sf.description; + if (removeHTML) + { + sf.setDescription(parsed.getNonHtmlContent()); + } + for (String link : parsed.getLinks()) { sf.addLink(link); @@ -703,7 +510,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return features file contents */ public String printJalviewFormat(SequenceI[] sequences, - Map visible) + Map visible) { return printJalviewFormat(sequences, visible, true, true); } @@ -723,201 +530,131 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return features file contents */ public String printJalviewFormat(SequenceI[] sequences, - Map visible, boolean visOnly, boolean nonpos) + Map visible, boolean visOnly, + boolean nonpos) { - StringBuilder out = new StringBuilder(256); - boolean featuresGen = false; - if (visOnly && !nonpos && (visible == null || visible.size() < 1)) + if (visOnly && !nonpos && (visible == null || visible.isEmpty())) { // no point continuing. return "No Features Visible"; } - if (visible != null && visOnly) + /* + * write out feature colours (if we know them) + */ + // TODO: decide if feature links should also be written here ? + StringBuilder out = new StringBuilder(256); + if (visible != null && visOnly) // todo why visOnly test? { - // write feature colours only if we're given them and we are generating - // viewed features - // TODO: decide if feature links should also be written here ? - Iterator en = visible.keySet().iterator(); - String featureType, color; - while (en.hasNext()) + for (Entry featureColour : visible.entrySet()) { - featureType = en.next().toString(); - - if (visible.get(featureType) instanceof GraduatedColor) - { - GraduatedColor gc = (GraduatedColor) visible.get(featureType); - color = (gc.isColourByLabel() ? "label|" : "") - + Format.getHexString(gc.getMinColor()) + "|" - + Format.getHexString(gc.getMaxColor()) - + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|" - + gc.getMax() + "|"; - if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD) - { - if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD) - { - color += "below"; - } - else - { - if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD) - { - System.err.println("WARNING: Unsupported threshold type (" - + gc.getThreshType() + ") : Assuming 'above'"); - } - color += "above"; - } - // add the value - color += "|" + gc.getThresh(); - } - else - { - color += "none"; - } - } - else if (visible.get(featureType) instanceof Color) - { - color = Format.getHexString((Color) visible.get(featureType)); - } - else - { - // legacy support for integer objects containing colour triplet values - color = Format.getHexString(new Color(Integer.parseInt(visible - .get(featureType).toString()))); - } - out.append(featureType); - out.append(TAB); - out.append(color); - out.append(newline); + FeatureColourI colour = featureColour.getValue(); + out.append(colour.toJalviewFormat(featureColour.getKey())).append( + newline); } } + // Work out which groups are both present and visible - List groups = new ArrayList(); - int groupIndex = 0; - boolean isnonpos = false; + Set groups = new HashSet(); + String[] types = visible == null ? null : visible.keySet().toArray( + new String[visible.keySet().size()]); - SequenceFeature[] features; for (int i = 0; i < sequences.length; i++) { - features = sequences[i].getSequenceFeatures(); - if (features != null) + groups.addAll(sequences[i].getFeatures() + .getFeatureGroups(true, types)); + if (nonpos) { - for (int j = 0; j < features.length; j++) - { - isnonpos = features[j].begin == 0 && features[j].end == 0; - if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible - .containsKey(features[j].type))) - { - continue; - } - - if (features[j].featureGroup != null - && !groups.contains(features[j].featureGroup)) - { - groups.add(features[j].featureGroup); - } - } + groups.addAll(sequences[i].getFeatures().getFeatureGroups(false, + types)); } } - String group = null; - do + /* + * sort distinct groups so null group is output last + */ + List sortedGroups = new ArrayList(groups); + Collections.sort(sortedGroups, SORT_NULL_LAST); + + // TODO check where null group should be output + boolean foundSome = false; + for (String group : sortedGroups) { - if (groups.size() > 0 && groupIndex < groups.size()) + if (group != null) { - group = groups.get(groupIndex); out.append(newline); out.append("STARTGROUP").append(TAB); out.append(group); out.append(newline); } - else - { - group = null; - } + /* + * output features within groups (non-positional first if wanted) + */ for (int i = 0; i < sequences.length; i++) { - features = sequences[i].getSequenceFeatures(); - if (features != null) + List features = new ArrayList(); + if (nonpos) { - for (SequenceFeature sequenceFeature : features) - { - isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0; - if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible - .containsKey(sequenceFeature.type))) - { - // skip if feature is nonpos and we ignore them or if we only - // output visible and it isn't non-pos and it's not visible - continue; - } + features.addAll(sequences[i].getFeatures().getFeaturesForGroup( + false, group, types)); + } + features.addAll(sequences[i].getFeatures().getFeaturesForGroup( + true, group, types)); - if (group != null - && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup - .equals(group))) + for (SequenceFeature sequenceFeature : features) + { + // we have features to output + foundSome = true; + if (sequenceFeature.description == null + || sequenceFeature.description.equals("")) + { + out.append(sequenceFeature.type).append(TAB); + } + else + { + if (sequenceFeature.links != null + && sequenceFeature.getDescription().indexOf("") == -1) { - continue; + out.append(""); } - if (group == null && sequenceFeature.featureGroup != null) - { - continue; - } - // we have features to output - featuresGen = true; - if (sequenceFeature.description == null - || sequenceFeature.description.equals("")) - { - out.append(sequenceFeature.type).append(TAB); - } - else + out.append(sequenceFeature.description); + if (sequenceFeature.links != null) { - if (sequenceFeature.links != null - && sequenceFeature.getDescription().indexOf("") == -1) + for (int l = 0; l < sequenceFeature.links.size(); l++) { - out.append(""); - } - - out.append(sequenceFeature.description); - if (sequenceFeature.links != null) - { - for (int l = 0; l < sequenceFeature.links.size(); l++) - { - String label = sequenceFeature.links.elementAt(l); - String href = label.substring(label.indexOf("|") + 1); - label = label.substring(0, label.indexOf("|")); - - if (sequenceFeature.description.indexOf(href) == -1) - { - out.append(" " + label - + ""); - } - } + String label = sequenceFeature.links.elementAt(l); + String href = label.substring(label.indexOf("|") + 1); + label = label.substring(0, label.indexOf("|")); - if (sequenceFeature.getDescription().indexOf("") == -1) + if (sequenceFeature.description.indexOf(href) == -1) { - out.append(""); + out.append(" " + label + ""); } } - out.append(TAB); + if (sequenceFeature.getDescription().indexOf("") == -1) + { + out.append(""); + } } - out.append(sequences[i].getName()); - out.append("\t-1\t"); - out.append(sequenceFeature.begin); + out.append(TAB); - out.append(sequenceFeature.end); + } + out.append(sequences[i].getName()); + out.append("\t-1\t"); + out.append(sequenceFeature.begin); + out.append(TAB); + out.append(sequenceFeature.end); + out.append(TAB); + out.append(sequenceFeature.type); + if (!Float.isNaN(sequenceFeature.score)) + { out.append(TAB); - out.append(sequenceFeature.type); - if (!Float.isNaN(sequenceFeature.score)) - { - out.append(TAB); - out.append(sequenceFeature.score); - } - out.append(newline); + out.append(sequenceFeature.score); } + out.append(newline); } } @@ -926,21 +663,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI out.append("ENDGROUP").append(TAB); out.append(group); out.append(newline); - groupIndex++; - } - else - { - break; } - - } while (groupIndex < groups.size() + 1); - - if (!featuresGen) - { - return "No Features Visible"; } - return out.toString(); + return foundSome ? out.toString() : "No Features Visible"; } /** @@ -967,7 +693,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI dataset = new Alignment(new SequenceI[] {}); } - boolean parseResult = parse(dataset, null, false, true); + Map featureColours = new HashMap(); + boolean parseResult = parse(dataset, featureColours, false, true); if (!parseResult) { // pass error up somehow @@ -988,9 +715,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return error message */ @Override - public String print() + public String print(SequenceI[] sqs, boolean jvsuffix) { - return "Use printGffFormat() or printJalviewFormat()"; + System.out.println("Use printGffFormat() or printJalviewFormat()"); + return null; } /** @@ -1004,7 +732,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return */ public String printGffFormat(SequenceI[] sequences, - Map visible) + Map visible) { return printGffFormat(sequences, visible, true, true); } @@ -1021,7 +749,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI * @return */ public String printGffFormat(SequenceI[] sequences, - Map visible, boolean outputVisibleOnly, + Map visible, boolean outputVisibleOnly, boolean includeNonPositionalFeatures) { StringBuilder out = new StringBuilder(256);