From 3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 15 Nov 2012 15:18:29 +0000 Subject: [PATCH] source formatting --- src/jalview/analysis/StructureFrequency.java | 1 - src/jalview/io/FeaturesFile.java | 2032 ++++++++++---------- src/jalview/io/IdentifyFile.java | 1 - src/jalview/io/JalviewFileChooser.java | 2 +- src/jalview/renderer/AnnotationRenderer.java | 1 - .../schemes/RNAInteractionColourScheme.java | 19 +- src/jalview/workers/StrucConsensusThread.java | 1 - src/jalview/ws/HttpClientUtils.java | 17 + src/jalview/ws/jws1/Annotate3D.java | 19 +- 9 files changed, 1085 insertions(+), 1008 deletions(-) diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index d57e1c5..32a4e29 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -254,7 +254,6 @@ public class StructureFrequency residueHash.put(PID_GAPS, new Float(percentage)); result[bpEnd] = residueHash; - } } } diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java index abf89d5..afbd223 100755 --- a/src/jalview/io/FeaturesFile.java +++ b/src/jalview/io/FeaturesFile.java @@ -15,1004 +15,1034 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ -package jalview.io; - -import java.io.*; -import java.util.*; - -import javax.xml.parsers.ParserConfigurationException; - -import org.xml.sax.SAXException; - -import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; -import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; -import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; -import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; - -import jalview.analysis.SequenceIdMatcher; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.Format; - -/** - * Parse and create Jalview Features files Detects GFF format features files and - * parses. Does not implement standard print() - call specific printFeatures or - * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object - * for the features annotation - this normally works on an exact match. - * - * @author AMW - * @version $Revision$ - */ -public class FeaturesFile extends AlignFile -{ - /** - * work around for GFF interpretation bug where source string becomes - * description rather than a group - */ - private boolean doGffSource = true; - - /** - * Creates a new FeaturesFile object. - */ - public FeaturesFile() - { - } - - /** - * Creates a new FeaturesFile object. - * - * @param inFile - * DOCUMENT ME! - * @param type - * DOCUMENT ME! - * - * @throws IOException - * DOCUMENT ME! - * @throws SAXException - * @throws ParserConfigurationException - * @throws ExceptionFileFormatOrSyntax - * @throws ExceptionLoadingFailed - * @throws ExceptionPermissionDenied - * @throws InterruptedException - * @throws ExceptionUnmatchedClosingParentheses - */ - public FeaturesFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses - { - super(inFile, type); - } - - public FeaturesFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses - { - super(source); - } - - /** - * Parse GFF or sequence features file using case-independent matching, discarding URLs - * @param align - alignment/dataset containing sequences that are to be annotated - * @param colours - hashtable to store feature colour definitions - * @param removeHTML - process html strings into plain text - * @return true if features were added - */ - public boolean parse(AlignmentI align, Hashtable colours, - boolean removeHTML) - { - return parse(align, colours, null, removeHTML, false); - } - - /** - * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs - * @param align - alignment/dataset containing sequences that are to be annotated - * @param colours - hashtable to store feature colour definitions - * @param removeHTML - process html strings into plain text - * @param relaxedIdmatching - 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) - { - return parse(align, colours, null, removeHTML, relaxedIdMatching); - } - - /** - * Parse GFF or sequence features file optionally using case-independent matching - * @param align - alignment/dataset containing sequences that are to be annotated - * @param colours - hashtable to store feature colour definitions - * @param featureLink - hashtable to store associated URLs - * @param removeHTML - process html strings into plain text - * @return true if features were added - */ - public boolean parse(AlignmentI align, Map colours, - Map featureLink, boolean removeHTML) - { - return parse(align, colours, featureLink, removeHTML, false); - } - - /** - /** - * Parse GFF or sequence features file - * @param align - alignment/dataset containing sequences that are to be annotated - * @param colours - hashtable to store feature colour definitions - * @param featureLink - hashtable to store associated URLs - * @param removeHTML - process html strings into plain text - * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed - * @return true if features were added - */ - public boolean parse(AlignmentI align, - Map colours, Map featureLink, boolean removeHTML, boolean relaxedIdmatching) - { - - String line = null; - try - { - SequenceI seq = null; - String type, desc, token = null; - - int index, start, end; - float score; - StringTokenizer st; - SequenceFeature sf; - String featureGroup = null, groupLink = null; - Map typeLink = new Hashtable(); - /** - * when true, assume GFF style features rather than Jalview style. - */ - boolean GFFFile = true; - while ((line = nextLine()) != null) - { - if (line.startsWith("#")) - { - continue; - } - - st = new StringTokenizer(line, "\t"); - if (st.countTokens() == 1) - { - if (line.trim().equalsIgnoreCase("GFF")) - { - // Start parsing file as if it might be GFF again. - GFFFile = true; - continue; - } - } - if (st.countTokens() > 1 && st.countTokens() < 4) - { - GFFFile = false; - type = st.nextToken(); - if (type.equalsIgnoreCase("startgroup")) - { - featureGroup = st.nextToken(); - if (st.hasMoreElements()) - { - groupLink = st.nextToken(); - featureLink.put(featureGroup, groupLink); - } - } - else if (type.equalsIgnoreCase("endgroup")) - { - // We should check whether this is the current group, - // but at present theres no way of showing more than 1 group - st.nextToken(); - featureGroup = null; - groupLink = null; - } - else - { - Object colour = null; - String colscheme = st.nextToken(); - if (colscheme.indexOf("|") > -1 - || colscheme.trim().equalsIgnoreCase("label")) - { - // 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(colscheme, "|", - true); - // set defaults - int threshtype = AnnotationColourGradient.NO_THRESHOLD; - float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN; - 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); - continue; - } - 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 = new Float(minval).floatValue(); - } - } catch (Exception e) - { - System.err - .println("Couldn't parse the minimum value for graduated colour for type (" - + colscheme - + ") - did you misspell 'auto' for the optional automatic colour switch ?"); - e.printStackTrace(); - } - try - { - if (maxval.length() > 0) - { - max = new Float(maxval).floatValue(); - } - } catch (Exception e) - { - System.err - .println("Couldn't parse the maximum value for graduated colour for type (" - + colscheme + ")"); - e.printStackTrace(); - } - } - else - { - // add in some dummy min/max colours for the label-only - // colourscheme. - mincol = "FFFFFF"; - maxcol = "000000"; - } - try - { - colour = new jalview.schemes.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 (" - + colscheme + ")"); - e.printStackTrace(); - } - if (colour != null) - { - ((jalview.schemes.GraduatedColor) colour) - .setColourByLabel(labelCol); - ((jalview.schemes.GraduatedColor) 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")) - { - ((jalview.schemes.GraduatedColor) colour) - .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); - } - else if (ttype.toLowerCase().startsWith("above")) - { - ((jalview.schemes.GraduatedColor) colour) - .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); - } - else - { - ((jalview.schemes.GraduatedColor) colour) - .setThreshType(AnnotationColourGradient.NO_THRESHOLD); - if (!ttype.toLowerCase().startsWith("no")) - { - System.err - .println("Ignoring unrecognised threshold type : " - + ttype); - } - } - } - if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD) - { - try - { - gcol.nextToken(); - tval = gcol.nextToken(); - ((jalview.schemes.GraduatedColor) 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"); - } - } - } - else - { - UserColourScheme ucs = new UserColourScheme(colscheme); - colour = ucs.findColour('A'); - } - if (colour != null) - { - colours.put(type, colour); - } - if (st.hasMoreElements()) - { - String link = st.nextToken(); - typeLink.put(type, link); - if (featureLink == null) - { - featureLink = new Hashtable(); - } - featureLink.put(type, link); - } - } - continue; - } - String seqId = ""; - while (st.hasMoreElements()) - { - - if (GFFFile) - { - // Still possible this is an old Jalview file, - // which does not have type colours at the beginning - seqId = token = st.nextToken(); - seq = findName(align, seqId, relaxedIdmatching); - if (seq != null) - { - desc = st.nextToken(); - String group = null; - if (doGffSource && desc.indexOf(' ') == -1) - { - // could also be a source term rather than description line - group = new String(desc); - } - type = st.nextToken(); - try - { - String stt = st.nextToken(); - if (stt.length() == 0 || stt.equals("-")) - { - start = 0; - } - else - { - start = Integer.parseInt(stt); - } - } catch (NumberFormatException ex) - { - start = 0; - } - try - { - String stt = st.nextToken(); - if (stt.length() == 0 || stt.equals("-")) - { - end = 0; - } - else - { - end = Integer.parseInt(stt); - } - } catch (NumberFormatException ex) - { - end = 0; - } - // TODO: decide if non positional feature assertion for input data - // where end==0 is generally valid - if (end == 0) - { - // treat as non-positional feature, regardless. - start = 0; - } - try - { - score = new Float(st.nextToken()).floatValue(); - } catch (NumberFormatException ex) - { - score = 0; - } - - sf = new SequenceFeature(type, desc, start, end, score, group); - - try - { - sf.setValue("STRAND", st.nextToken()); - sf.setValue("FRAME", st.nextToken()); - } catch (Exception ex) - { - } - - if (st.hasMoreTokens()) - { - StringBuffer attributes = new StringBuffer(); - while (st.hasMoreTokens()) - { - attributes.append("\t" + st.nextElement()); - } - // TODO validate and split GFF2 attributes field ? parse out - // ([A-Za-z][A-Za-z0-9_]*) ; and add as - // sf.setValue(attrib, val); - sf.setValue("ATTRIBUTES", attributes.toString()); - } - - seq.addSequenceFeature(sf); - while ((seq = align.findName(seq, seqId, true)) != null) - { - seq.addSequenceFeature(new SequenceFeature(sf)); - } - break; - } - } - - if (GFFFile && seq == null) - { - desc = token; - } - else - { - desc = st.nextToken(); - } - if (!st.hasMoreTokens()) - { - System.err - .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up."); - // in all probability, this isn't a file we understand, so bail - // quietly. - return false; - } - - token = st.nextToken(); - - if (!token.equals("ID_NOT_SPECIFIED")) - { - seq = findName(align, seqId = token, relaxedIdmatching); - st.nextToken(); - } - else - { - seqId = null; - try - { - index = Integer.parseInt(st.nextToken()); - seq = align.getSequenceAt(index); - } catch (NumberFormatException ex) - { - seq = null; - } - } - - if (seq == null) - { - System.out.println("Sequence not found: " + line); - break; - } - - start = Integer.parseInt(st.nextToken()); - end = Integer.parseInt(st.nextToken()); - - type = st.nextToken(); - - if (!colours.containsKey(type)) - { - // Probably the old style groups file - UserColourScheme ucs = new UserColourScheme(type); - colours.put(type, ucs.findColour('A')); - } - sf = new SequenceFeature(type, desc, "", start, end, featureGroup); - if (st.hasMoreTokens()) - { - try - { - score = new Float(st.nextToken()).floatValue(); - // update colourgradient bounds if allowed to - } catch (NumberFormatException ex) - { - score = 0; - } - sf.setScore(score); - } - if (groupLink != null && removeHTML) - { - sf.addLink(groupLink); - sf.description += "%LINK%"; - } - if (typeLink.containsKey(type) && removeHTML) - { - sf.addLink(typeLink.get(type).toString()); - sf.description += "%LINK%"; - } - - parseDescriptionHTML(sf, removeHTML); - - seq.addSequenceFeature(sf); - - while (seqId != null - && (seq = align.findName(seq, seqId, false)) != null) - { - seq.addSequenceFeature(new SequenceFeature(sf)); - } - // If we got here, its not a GFFFile - GFFFile = false; - } - } - resetMatcher(); - } catch (Exception ex) - { - System.out.println(line); - System.out.println("Error parsing feature file: " + ex + "\n" + line); - ex.printStackTrace(System.err); - resetMatcher(); - return false; - } - - return true; - } - - private AlignmentI lastmatchedAl = null; - - private SequenceIdMatcher matcher = null; - - /** - * clear any temporary handles used to speed up ID matching - */ - private void resetMatcher() - { - lastmatchedAl = null; - matcher = null; - } - - private SequenceI findName(AlignmentI align, String seqId, - boolean relaxedIdMatching) - { - SequenceI match = null; - if (relaxedIdMatching) - { - if (lastmatchedAl != align) - { - matcher = new SequenceIdMatcher( - (lastmatchedAl = align).getSequencesArray()); - } - match = matcher.findIdMatch(seqId); - } - else - { - match = align.findName(seqId, true); - } - return match; - } - - public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML) - { - if (sf.getDescription() == null) - { - return; - } - jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(sf.getDescription(), removeHTML, newline); - - sf.description = (removeHTML) ? parsed.getNonHtmlContent() : sf.description; - for (String link:parsed.getLinks()) - { - sf.addLink(link); - } - - } - - /** - * generate a features file for seqs includes non-pos features by default. - * - * @param seqs - * source of sequence features - * @param visible - * hash of feature types and colours - * @return features file contents - */ - public String printJalviewFormat(SequenceI[] seqs, Hashtable visible) - { - return printJalviewFormat(seqs, visible, true, true); - } - - /** - * generate a features file for seqs with colours from visible (if any) - * - * @param seqs - * source of features - * @param visible - * hash of Colours for each feature type - * @param visOnly - * when true only feature types in 'visible' will be output - * @param nonpos - * indicates if non-positional features should be output (regardless - * of group or type) - * @return features file contents - */ - public String printJalviewFormat(SequenceI[] seqs, Hashtable visible, - boolean visOnly, boolean nonpos) - { - StringBuffer out = new StringBuffer(); - SequenceFeature[] next; - boolean featuresGen = false; - if (visOnly && !nonpos && (visible == null || visible.size() < 1)) - { - // no point continuing. - return "No Features Visible"; - } - - if (visible != null && visOnly) - { - // 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 ? - Enumeration en = visible.keys(); - String type, color; - while (en.hasMoreElements()) - { - type = en.nextElement().toString(); - - if (visible.get(type) instanceof GraduatedColor) - { - GraduatedColor gc = (GraduatedColor) visible.get(type); - 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(type) instanceof java.awt.Color) - { - color = Format.getHexString((java.awt.Color) visible.get(type)); - } - else - { - // legacy support for integer objects containing colour triplet values - color = Format.getHexString(new java.awt.Color(Integer - .parseInt(visible.get(type).toString()))); - } - out.append(type); - out.append("\t"); - out.append(color); - out.append(newline); - } - } - // Work out which groups are both present and visible - Vector groups = new Vector(); - int groupIndex = 0; - boolean isnonpos = false; - - for (int i = 0; i < seqs.length; i++) - { - next = seqs[i].getSequenceFeatures(); - if (next != null) - { - for (int j = 0; j < next.length; j++) - { - isnonpos = next[j].begin == 0 && next[j].end == 0; - if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible - .containsKey(next[j].type))) - { - continue; - } - - if (next[j].featureGroup != null - && !groups.contains(next[j].featureGroup)) - { - groups.addElement(next[j].featureGroup); - } - } - } - } - - String group = null; - do - { - - if (groups.size() > 0 && groupIndex < groups.size()) - { - group = groups.elementAt(groupIndex).toString(); - out.append(newline); - out.append("STARTGROUP\t"); - out.append(group); - out.append(newline); - } - else - { - group = null; - } - - for (int i = 0; i < seqs.length; i++) - { - next = seqs[i].getSequenceFeatures(); - if (next != null) - { - for (int j = 0; j < next.length; j++) - { - isnonpos = next[j].begin == 0 && next[j].end == 0; - if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible - .containsKey(next[j].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; - } - - if (group != null - && (next[j].featureGroup == null || !next[j].featureGroup - .equals(group))) - { - continue; - } - - if (group == null && next[j].featureGroup != null) - { - continue; - } - // we have features to output - featuresGen = true; - if (next[j].description == null - || next[j].description.equals("")) - { - out.append(next[j].type + "\t"); - } - else - { - if (next[j].links != null - && next[j].getDescription().indexOf("") == -1) - { - out.append(""); - } - - out.append(next[j].description + " "); - if (next[j].links != null) - { - for (int l = 0; l < next[j].links.size(); l++) - { - String label = next[j].links.elementAt(l).toString(); - String href = label.substring(label.indexOf("|") + 1); - label = label.substring(0, label.indexOf("|")); - - if (next[j].description.indexOf(href) == -1) - { - out.append("" + label + ""); - } - } - - if (next[j].getDescription().indexOf("") == -1) - { - out.append(""); - } - } - - out.append("\t"); - } - out.append(seqs[i].getName()); - out.append("\t-1\t"); - out.append(next[j].begin); - out.append("\t"); - out.append(next[j].end); - out.append("\t"); - out.append(next[j].type); - if (next[j].score != Float.NaN) - { - out.append("\t"); - out.append(next[j].score); - } - out.append(newline); - } - } - } - - if (group != null) - { - out.append("ENDGROUP\t"); - out.append(group); - out.append(newline); - groupIndex++; - } - else - { - break; - } - - } while (groupIndex < groups.size() + 1); - - if (!featuresGen) - { - return "No Features Visible"; - } - - return out.toString(); - } - - /** - * generate a gff file for sequence features includes non-pos features by - * default. - * - * @param seqs - * @param visible - * @return - */ - public String printGFFFormat(SequenceI[] seqs, Hashtable visible) - { - return printGFFFormat(seqs, visible, true, true); - } - - public String printGFFFormat(SequenceI[] seqs, Hashtable visible, - boolean visOnly, boolean nonpos) - { - StringBuffer out = new StringBuffer(); - SequenceFeature[] next; - String source; - boolean isnonpos; - for (int i = 0; i < seqs.length; i++) - { - if (seqs[i].getSequenceFeatures() != null) - { - next = seqs[i].getSequenceFeatures(); - for (int j = 0; j < next.length; j++) - { - isnonpos = next[j].begin == 0 && next[j].end == 0; - if ((!nonpos && isnonpos) - || (!isnonpos && visOnly && !visible - .containsKey(next[j].type))) - { - continue; - } - - source = next[j].featureGroup; - if (source == null) - { - source = next[j].getDescription(); - } - - out.append(seqs[i].getName()); - out.append("\t"); - out.append(source); - out.append("\t"); - out.append(next[j].type); - out.append("\t"); - out.append(next[j].begin); - out.append("\t"); - out.append(next[j].end); - out.append("\t"); - out.append(next[j].score); - out.append("\t"); - - if (next[j].getValue("STRAND") != null) - { - out.append(next[j].getValue("STRAND")); - out.append("\t"); - } - else - { - out.append(".\t"); - } - - if (next[j].getValue("FRAME") != null) - { - out.append(next[j].getValue("FRAME")); - } - else - { - out.append("."); - } - // TODO: verify/check GFF - should there be a /t here before attribute - // output ? - - if (next[j].getValue("ATTRIBUTES") != null) - { - out.append(next[j].getValue("ATTRIBUTES")); - } - - out.append(newline); - - } - } - } - - return out.toString(); - } - - /** - * this is only for the benefit of object polymorphism - method does nothing. - */ - public void parse() - { - // IGNORED - } - - /** - * this is only for the benefit of object polymorphism - method does nothing. - * - * @return error message - */ - public String print() - { - return "USE printGFFFormat() or printJalviewFormat()"; - } - -} +package jalview.io; + +import java.io.*; +import java.util.*; + +import javax.xml.parsers.ParserConfigurationException; + +import org.xml.sax.SAXException; + +import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax; +import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed; +import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied; +import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses; + +import jalview.analysis.SequenceIdMatcher; +import jalview.datamodel.*; +import jalview.schemes.*; +import jalview.util.Format; + +/** + * Parse and create Jalview Features files Detects GFF format features files and + * parses. Does not implement standard print() - call specific printFeatures or + * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object + * for the features annotation - this normally works on an exact match. + * + * @author AMW + * @version $Revision$ + */ +public class FeaturesFile extends AlignFile +{ + /** + * work around for GFF interpretation bug where source string becomes + * description rather than a group + */ + private boolean doGffSource = true; + + /** + * Creates a new FeaturesFile object. + */ + public FeaturesFile() + { + } + + /** + * Creates a new FeaturesFile object. + * + * @param inFile + * DOCUMENT ME! + * @param type + * DOCUMENT ME! + * + * @throws IOException + * DOCUMENT ME! + * @throws SAXException + * @throws ParserConfigurationException + * @throws ExceptionFileFormatOrSyntax + * @throws ExceptionLoadingFailed + * @throws ExceptionPermissionDenied + * @throws InterruptedException + * @throws ExceptionUnmatchedClosingParentheses + */ + public FeaturesFile(String inFile, String type) throws IOException, + ExceptionFileFormatOrSyntax, ParserConfigurationException, + SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, + InterruptedException, ExceptionUnmatchedClosingParentheses + { + super(inFile, type); + } + + public FeaturesFile(FileParse source) throws IOException, + ExceptionFileFormatOrSyntax, ParserConfigurationException, + SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, + InterruptedException, ExceptionUnmatchedClosingParentheses + { + super(source); + } + + /** + * Parse GFF or sequence features file using case-independent matching, + * discarding URLs + * + * @param align + * - alignment/dataset containing sequences that are to be annotated + * @param colours + * - hashtable to store feature colour definitions + * @param removeHTML + * - process html strings into plain text + * @return true if features were added + */ + public boolean parse(AlignmentI align, Hashtable colours, + boolean removeHTML) + { + return parse(align, colours, null, removeHTML, false); + } + + /** + * Parse GFF or sequence features file optionally using case-independent + * matching, discarding URLs + * + * @param align + * - alignment/dataset containing sequences that are to be annotated + * @param colours + * - hashtable to store feature colour definitions + * @param removeHTML + * - process html strings into plain text + * @param relaxedIdmatching + * - 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) + { + return parse(align, colours, null, removeHTML, relaxedIdMatching); + } + + /** + * Parse GFF or sequence features file optionally using case-independent + * matching + * + * @param align + * - alignment/dataset containing sequences that are to be annotated + * @param colours + * - hashtable to store feature colour definitions + * @param featureLink + * - hashtable to store associated URLs + * @param removeHTML + * - process html strings into plain text + * @return true if features were added + */ + public boolean parse(AlignmentI align, Map colours, Map featureLink, + boolean removeHTML) + { + return parse(align, colours, featureLink, removeHTML, false); + } + + /** + * /** Parse GFF or sequence features file + * + * @param align + * - alignment/dataset containing sequences that are to be annotated + * @param colours + * - hashtable to store feature colour definitions + * @param featureLink + * - hashtable to store associated URLs + * @param removeHTML + * - process html strings into plain text + * @param relaxedIdmatching + * - when true, ID matches to compound sequence IDs are allowed + * @return true if features were added + */ + public boolean parse(AlignmentI align, Map colours, Map featureLink, + boolean removeHTML, boolean relaxedIdmatching) + { + + String line = null; + try + { + SequenceI seq = null; + String type, desc, token = null; + + int index, start, end; + float score; + StringTokenizer st; + SequenceFeature sf; + String featureGroup = null, groupLink = null; + Map typeLink = new Hashtable(); + /** + * when true, assume GFF style features rather than Jalview style. + */ + boolean GFFFile = true; + while ((line = nextLine()) != null) + { + if (line.startsWith("#")) + { + continue; + } + + st = new StringTokenizer(line, "\t"); + if (st.countTokens() == 1) + { + if (line.trim().equalsIgnoreCase("GFF")) + { + // Start parsing file as if it might be GFF again. + GFFFile = true; + continue; + } + } + if (st.countTokens() > 1 && st.countTokens() < 4) + { + GFFFile = false; + type = st.nextToken(); + if (type.equalsIgnoreCase("startgroup")) + { + featureGroup = st.nextToken(); + if (st.hasMoreElements()) + { + groupLink = st.nextToken(); + featureLink.put(featureGroup, groupLink); + } + } + else if (type.equalsIgnoreCase("endgroup")) + { + // We should check whether this is the current group, + // but at present theres no way of showing more than 1 group + st.nextToken(); + featureGroup = null; + groupLink = null; + } + else + { + Object colour = null; + String colscheme = st.nextToken(); + if (colscheme.indexOf("|") > -1 + || colscheme.trim().equalsIgnoreCase("label")) + { + // 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(colscheme, "|", + true); + // set defaults + int threshtype = AnnotationColourGradient.NO_THRESHOLD; + float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN; + 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); + continue; + } + 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 = new Float(minval).floatValue(); + } + } catch (Exception e) + { + System.err + .println("Couldn't parse the minimum value for graduated colour for type (" + + colscheme + + ") - did you misspell 'auto' for the optional automatic colour switch ?"); + e.printStackTrace(); + } + try + { + if (maxval.length() > 0) + { + max = new Float(maxval).floatValue(); + } + } catch (Exception e) + { + System.err + .println("Couldn't parse the maximum value for graduated colour for type (" + + colscheme + ")"); + e.printStackTrace(); + } + } + else + { + // add in some dummy min/max colours for the label-only + // colourscheme. + mincol = "FFFFFF"; + maxcol = "000000"; + } + try + { + colour = new jalview.schemes.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 (" + + colscheme + ")"); + e.printStackTrace(); + } + if (colour != null) + { + ((jalview.schemes.GraduatedColor) colour) + .setColourByLabel(labelCol); + ((jalview.schemes.GraduatedColor) 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")) + { + ((jalview.schemes.GraduatedColor) colour) + .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD); + } + else if (ttype.toLowerCase().startsWith("above")) + { + ((jalview.schemes.GraduatedColor) colour) + .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD); + } + else + { + ((jalview.schemes.GraduatedColor) colour) + .setThreshType(AnnotationColourGradient.NO_THRESHOLD); + if (!ttype.toLowerCase().startsWith("no")) + { + System.err + .println("Ignoring unrecognised threshold type : " + + ttype); + } + } + } + if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD) + { + try + { + gcol.nextToken(); + tval = gcol.nextToken(); + ((jalview.schemes.GraduatedColor) 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"); + } + } + } + else + { + UserColourScheme ucs = new UserColourScheme(colscheme); + colour = ucs.findColour('A'); + } + if (colour != null) + { + colours.put(type, colour); + } + if (st.hasMoreElements()) + { + String link = st.nextToken(); + typeLink.put(type, link); + if (featureLink == null) + { + featureLink = new Hashtable(); + } + featureLink.put(type, link); + } + } + continue; + } + String seqId = ""; + while (st.hasMoreElements()) + { + + if (GFFFile) + { + // Still possible this is an old Jalview file, + // which does not have type colours at the beginning + seqId = token = st.nextToken(); + seq = findName(align, seqId, relaxedIdmatching); + if (seq != null) + { + desc = st.nextToken(); + String group = null; + if (doGffSource && desc.indexOf(' ') == -1) + { + // could also be a source term rather than description line + group = new String(desc); + } + type = st.nextToken(); + try + { + String stt = st.nextToken(); + if (stt.length() == 0 || stt.equals("-")) + { + start = 0; + } + else + { + start = Integer.parseInt(stt); + } + } catch (NumberFormatException ex) + { + start = 0; + } + try + { + String stt = st.nextToken(); + if (stt.length() == 0 || stt.equals("-")) + { + end = 0; + } + else + { + end = Integer.parseInt(stt); + } + } catch (NumberFormatException ex) + { + end = 0; + } + // TODO: decide if non positional feature assertion for input data + // where end==0 is generally valid + if (end == 0) + { + // treat as non-positional feature, regardless. + start = 0; + } + try + { + score = new Float(st.nextToken()).floatValue(); + } catch (NumberFormatException ex) + { + score = 0; + } + + sf = new SequenceFeature(type, desc, start, end, score, group); + + try + { + sf.setValue("STRAND", st.nextToken()); + sf.setValue("FRAME", st.nextToken()); + } catch (Exception ex) + { + } + + if (st.hasMoreTokens()) + { + StringBuffer attributes = new StringBuffer(); + while (st.hasMoreTokens()) + { + attributes.append("\t" + st.nextElement()); + } + // TODO validate and split GFF2 attributes field ? parse out + // ([A-Za-z][A-Za-z0-9_]*) ; and add as + // sf.setValue(attrib, val); + sf.setValue("ATTRIBUTES", attributes.toString()); + } + + seq.addSequenceFeature(sf); + while ((seq = align.findName(seq, seqId, true)) != null) + { + seq.addSequenceFeature(new SequenceFeature(sf)); + } + break; + } + } + + if (GFFFile && seq == null) + { + desc = token; + } + else + { + desc = st.nextToken(); + } + if (!st.hasMoreTokens()) + { + System.err + .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up."); + // in all probability, this isn't a file we understand, so bail + // quietly. + return false; + } + + token = st.nextToken(); + + if (!token.equals("ID_NOT_SPECIFIED")) + { + seq = findName(align, seqId = token, relaxedIdmatching); + st.nextToken(); + } + else + { + seqId = null; + try + { + index = Integer.parseInt(st.nextToken()); + seq = align.getSequenceAt(index); + } catch (NumberFormatException ex) + { + seq = null; + } + } + + if (seq == null) + { + System.out.println("Sequence not found: " + line); + break; + } + + start = Integer.parseInt(st.nextToken()); + end = Integer.parseInt(st.nextToken()); + + type = st.nextToken(); + + if (!colours.containsKey(type)) + { + // Probably the old style groups file + UserColourScheme ucs = new UserColourScheme(type); + colours.put(type, ucs.findColour('A')); + } + sf = new SequenceFeature(type, desc, "", start, end, featureGroup); + if (st.hasMoreTokens()) + { + try + { + score = new Float(st.nextToken()).floatValue(); + // update colourgradient bounds if allowed to + } catch (NumberFormatException ex) + { + score = 0; + } + sf.setScore(score); + } + if (groupLink != null && removeHTML) + { + sf.addLink(groupLink); + sf.description += "%LINK%"; + } + if (typeLink.containsKey(type) && removeHTML) + { + sf.addLink(typeLink.get(type).toString()); + sf.description += "%LINK%"; + } + + parseDescriptionHTML(sf, removeHTML); + + seq.addSequenceFeature(sf); + + while (seqId != null + && (seq = align.findName(seq, seqId, false)) != null) + { + seq.addSequenceFeature(new SequenceFeature(sf)); + } + // If we got here, its not a GFFFile + GFFFile = false; + } + } + resetMatcher(); + } catch (Exception ex) + { + System.out.println(line); + System.out.println("Error parsing feature file: " + ex + "\n" + line); + ex.printStackTrace(System.err); + resetMatcher(); + return false; + } + + return true; + } + + private AlignmentI lastmatchedAl = null; + + private SequenceIdMatcher matcher = null; + + /** + * clear any temporary handles used to speed up ID matching + */ + private void resetMatcher() + { + lastmatchedAl = null; + matcher = null; + } + + private SequenceI findName(AlignmentI align, String seqId, + boolean relaxedIdMatching) + { + SequenceI match = null; + if (relaxedIdMatching) + { + if (lastmatchedAl != align) + { + matcher = new SequenceIdMatcher( + (lastmatchedAl = align).getSequencesArray()); + } + match = matcher.findIdMatch(seqId); + } + else + { + match = align.findName(seqId, true); + } + return match; + } + + public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML) + { + if (sf.getDescription() == null) + { + return; + } + jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks( + sf.getDescription(), removeHTML, newline); + + sf.description = (removeHTML) ? parsed.getNonHtmlContent() + : sf.description; + for (String link : parsed.getLinks()) + { + sf.addLink(link); + } + + } + + /** + * generate a features file for seqs includes non-pos features by default. + * + * @param seqs + * source of sequence features + * @param visible + * hash of feature types and colours + * @return features file contents + */ + public String printJalviewFormat(SequenceI[] seqs, Hashtable visible) + { + return printJalviewFormat(seqs, visible, true, true); + } + + /** + * generate a features file for seqs with colours from visible (if any) + * + * @param seqs + * source of features + * @param visible + * hash of Colours for each feature type + * @param visOnly + * when true only feature types in 'visible' will be output + * @param nonpos + * indicates if non-positional features should be output (regardless + * of group or type) + * @return features file contents + */ + public String printJalviewFormat(SequenceI[] seqs, Hashtable visible, + boolean visOnly, boolean nonpos) + { + StringBuffer out = new StringBuffer(); + SequenceFeature[] next; + boolean featuresGen = false; + if (visOnly && !nonpos && (visible == null || visible.size() < 1)) + { + // no point continuing. + return "No Features Visible"; + } + + if (visible != null && visOnly) + { + // 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 ? + Enumeration en = visible.keys(); + String type, color; + while (en.hasMoreElements()) + { + type = en.nextElement().toString(); + + if (visible.get(type) instanceof GraduatedColor) + { + GraduatedColor gc = (GraduatedColor) visible.get(type); + 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(type) instanceof java.awt.Color) + { + color = Format.getHexString((java.awt.Color) visible.get(type)); + } + else + { + // legacy support for integer objects containing colour triplet values + color = Format.getHexString(new java.awt.Color(Integer + .parseInt(visible.get(type).toString()))); + } + out.append(type); + out.append("\t"); + out.append(color); + out.append(newline); + } + } + // Work out which groups are both present and visible + Vector groups = new Vector(); + int groupIndex = 0; + boolean isnonpos = false; + + for (int i = 0; i < seqs.length; i++) + { + next = seqs[i].getSequenceFeatures(); + if (next != null) + { + for (int j = 0; j < next.length; j++) + { + isnonpos = next[j].begin == 0 && next[j].end == 0; + if ((!nonpos && isnonpos) + || (!isnonpos && visOnly && !visible + .containsKey(next[j].type))) + { + continue; + } + + if (next[j].featureGroup != null + && !groups.contains(next[j].featureGroup)) + { + groups.addElement(next[j].featureGroup); + } + } + } + } + + String group = null; + do + { + + if (groups.size() > 0 && groupIndex < groups.size()) + { + group = groups.elementAt(groupIndex).toString(); + out.append(newline); + out.append("STARTGROUP\t"); + out.append(group); + out.append(newline); + } + else + { + group = null; + } + + for (int i = 0; i < seqs.length; i++) + { + next = seqs[i].getSequenceFeatures(); + if (next != null) + { + for (int j = 0; j < next.length; j++) + { + isnonpos = next[j].begin == 0 && next[j].end == 0; + if ((!nonpos && isnonpos) + || (!isnonpos && visOnly && !visible + .containsKey(next[j].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; + } + + if (group != null + && (next[j].featureGroup == null || !next[j].featureGroup + .equals(group))) + { + continue; + } + + if (group == null && next[j].featureGroup != null) + { + continue; + } + // we have features to output + featuresGen = true; + if (next[j].description == null + || next[j].description.equals("")) + { + out.append(next[j].type + "\t"); + } + else + { + if (next[j].links != null + && next[j].getDescription().indexOf("") == -1) + { + out.append(""); + } + + out.append(next[j].description + " "); + if (next[j].links != null) + { + for (int l = 0; l < next[j].links.size(); l++) + { + String label = next[j].links.elementAt(l).toString(); + String href = label.substring(label.indexOf("|") + 1); + label = label.substring(0, label.indexOf("|")); + + if (next[j].description.indexOf(href) == -1) + { + out.append("" + label + ""); + } + } + + if (next[j].getDescription().indexOf("") == -1) + { + out.append(""); + } + } + + out.append("\t"); + } + out.append(seqs[i].getName()); + out.append("\t-1\t"); + out.append(next[j].begin); + out.append("\t"); + out.append(next[j].end); + out.append("\t"); + out.append(next[j].type); + if (next[j].score != Float.NaN) + { + out.append("\t"); + out.append(next[j].score); + } + out.append(newline); + } + } + } + + if (group != null) + { + out.append("ENDGROUP\t"); + out.append(group); + out.append(newline); + groupIndex++; + } + else + { + break; + } + + } while (groupIndex < groups.size() + 1); + + if (!featuresGen) + { + return "No Features Visible"; + } + + return out.toString(); + } + + /** + * generate a gff file for sequence features includes non-pos features by + * default. + * + * @param seqs + * @param visible + * @return + */ + public String printGFFFormat(SequenceI[] seqs, Hashtable visible) + { + return printGFFFormat(seqs, visible, true, true); + } + + public String printGFFFormat(SequenceI[] seqs, Hashtable visible, + boolean visOnly, boolean nonpos) + { + StringBuffer out = new StringBuffer(); + SequenceFeature[] next; + String source; + boolean isnonpos; + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i].getSequenceFeatures() != null) + { + next = seqs[i].getSequenceFeatures(); + for (int j = 0; j < next.length; j++) + { + isnonpos = next[j].begin == 0 && next[j].end == 0; + if ((!nonpos && isnonpos) + || (!isnonpos && visOnly && !visible + .containsKey(next[j].type))) + { + continue; + } + + source = next[j].featureGroup; + if (source == null) + { + source = next[j].getDescription(); + } + + out.append(seqs[i].getName()); + out.append("\t"); + out.append(source); + out.append("\t"); + out.append(next[j].type); + out.append("\t"); + out.append(next[j].begin); + out.append("\t"); + out.append(next[j].end); + out.append("\t"); + out.append(next[j].score); + out.append("\t"); + + if (next[j].getValue("STRAND") != null) + { + out.append(next[j].getValue("STRAND")); + out.append("\t"); + } + else + { + out.append(".\t"); + } + + if (next[j].getValue("FRAME") != null) + { + out.append(next[j].getValue("FRAME")); + } + else + { + out.append("."); + } + // TODO: verify/check GFF - should there be a /t here before attribute + // output ? + + if (next[j].getValue("ATTRIBUTES") != null) + { + out.append(next[j].getValue("ATTRIBUTES")); + } + + out.append(newline); + + } + } + } + + return out.toString(); + } + + /** + * this is only for the benefit of object polymorphism - method does nothing. + */ + public void parse() + { + // IGNORED + } + + /** + * this is only for the benefit of object polymorphism - method does nothing. + * + * @return error message + */ + public String print() + { + return "USE printGFFFormat() or printJalviewFormat()"; + } + +} diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index ed4001e..1cdd95d 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -304,7 +304,6 @@ public class IdentifyFile public static void main(String[] args) { - for (int i = 0; args != null && i < args.length; i++) { IdentifyFile ider = new IdentifyFile(); diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index 2e2c896..b0db2e0 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -171,7 +171,7 @@ public class JalviewFileChooser extends JFileChooser { format = "PFAM"; } - + return format; } diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index bfe2156..90808de 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -51,7 +51,6 @@ public class AnnotationRenderer int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { - g.setColor(STEM_COLOUR); int sCol = (lastSSX / charWidth) + startRes; int x1 = lastSSX; diff --git a/src/jalview/schemes/RNAInteractionColourScheme.java b/src/jalview/schemes/RNAInteractionColourScheme.java index 08e699b..42f4feb 100644 --- a/src/jalview/schemes/RNAInteractionColourScheme.java +++ b/src/jalview/schemes/RNAInteractionColourScheme.java @@ -1,4 +1,21 @@ -package jalview.schemes; +/* + * 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 + * + * 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. + * + * 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 . + */ + package jalview.schemes; import jalview.datamodel.SequenceI; diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java index 266fdcd..86c3336 100644 --- a/src/jalview/workers/StrucConsensusThread.java +++ b/src/jalview/workers/StrucConsensusThread.java @@ -20,7 +20,6 @@ package jalview.workers; import java.util.Hashtable; import jalview.analysis.StructureFrequency; -import jalview.analysis.StructureFrequency; import jalview.api.AlignCalcWorkerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; diff --git a/src/jalview/ws/HttpClientUtils.java b/src/jalview/ws/HttpClientUtils.java index d018eab..01892e7 100644 --- a/src/jalview/ws/HttpClientUtils.java +++ b/src/jalview/ws/HttpClientUtils.java @@ -1,3 +1,20 @@ +/* + * 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 + * + * 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. + * + * 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 . + */ package jalview.ws; import java.io.BufferedReader; diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java index 505e15f..5457c3a 100644 --- a/src/jalview/ws/jws1/Annotate3D.java +++ b/src/jalview/ws/jws1/Annotate3D.java @@ -1,4 +1,21 @@ -package jalview.ws.jws1; +/* + * 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 + * + * 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. + * + * 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 . + */ + package jalview.ws.jws1; import java.io.BufferedInputStream; import java.io.BufferedReader; -- 1.7.10.2