X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=a22b7a49963c1473cc6b7f1ccd7f8914ff476ab5;hb=refs%2Fheads%2Fspikes%2Fphyre;hp=7702792bee664c5135f49621f35595032ecdbc3b;hpb=efe59a09e1a7606cb837fd562bdffc44d45b9206;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 7702792..a22b7a4 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -26,16 +26,22 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DynamicData; +import jalview.datamodel.DynamicData.DataType; import jalview.datamodel.GraphLine; import jalview.datamodel.HiddenSequences; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.ResidueProperties; -import jalview.schemes.UserColourScheme; +import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; +import java.awt.Color; import java.io.BufferedReader; +import java.io.File; import java.io.FileReader; import java.io.InputStreamReader; import java.io.StringReader; @@ -51,6 +57,28 @@ import java.util.Vector; public class AnnotationFile { + StringBuffer text; + + SequenceI refSeq = null; + + String refSeqId = null; + + String[] StructModelHeader = null; + + long nlinesread = 0; + + String lastread = ""; + + /** + * used for resolving absolute references to resources relative to + * annotationFile location + */ + String baseUri = ""; + + private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE", + STRUCTMODEL = "STRUCTMODEL", + HEADER_STRUCT_MODEL = "HEADER_STRUCT_MODEL"; + public AnnotationFile() { init(); @@ -77,7 +105,6 @@ public class AnnotationFile return newline; } - StringBuffer text; private void init() { @@ -88,8 +115,8 @@ public class AnnotationFile } /** - * convenience method for pre-2.8.3 annotation files which have no view, - * hidden columns or hidden row keywords. + * convenience method for pre-2.9 annotation files which have no view, hidden + * columns or hidden row keywords. * * @param annotations * @param list @@ -294,8 +321,7 @@ public class AnnotationFile } else { - graphGroup_refs.put(key, new Object[] - { refSeq, refGroup }); + graphGroup_refs.put(key, new Object[] { refSeq, refGroup }); graphGroup.put(key, row.label); } } @@ -472,8 +498,9 @@ public class AnnotationFile text.append(properties.get(key)); } // TODO: output alignment visualization settings here if required - // iterate through one or more views, defining, marking columns and rows as visible/hidden, and emmitting view properties. - // View specific annotation is + // iterate through one or more views, defining, marking columns and rows + // as visible/hidden, and emmitting view properties. + // View specific annotation is } return text.toString(); @@ -582,7 +609,7 @@ public class AnnotationFile if (sg.cs != null) { text.append("colour="); - text.append(ColourSchemeProperty.getColourName(sg.cs)); + text.append(sg.cs.toString()); text.append("\t"); if (sg.cs.getThreshold() != 0) { @@ -656,12 +683,9 @@ public class AnnotationFile } } - SequenceI refSeq = null; - - String refSeqId = null; public boolean annotateAlignmentView(AlignViewportI viewport, - String file, String protocol) + String file, DataSourceType protocol) { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel == null) @@ -670,45 +694,67 @@ public class AnnotationFile } boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel, file, protocol); - if (rslt - && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns())) + if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns())) { viewport.setColumnSelection(colSel); } return rslt; } + public boolean readAnnotationFile(AlignmentI al, String file, - String protocol) + DataSourceType sourceType) { - return readAnnotationFile(al, null, file, protocol); + return readAnnotationFile(al, null, file, sourceType); } public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel, - String file, String protocol) + String file, DataSourceType sourceType) { + baseUri = ""; BufferedReader in = null; try { - if (protocol.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { in = new BufferedReader(new FileReader(file)); + baseUri = new File(file).getParent(); + if (baseUri == null) + { + baseUri = ""; + } + else + { + baseUri += "/"; + } } - else if (protocol.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { URL url = new URL(file); in = new BufferedReader(new InputStreamReader(url.openStream())); + String bs = url.toExternalForm(); + baseUri = bs.substring(0, bs.indexOf(url.getHost()) + + url.getHost().length()); + baseUri += url.toURI().getPath(); + if (baseUri.lastIndexOf("/") > -1) + { + baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/"; + } } - else if (protocol.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { in = new BufferedReader(new StringReader(file)); + // TODO - support mimencoded PDBs for a paste.. ? + baseUri = ""; } - else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { java.io.InputStream is = getClass().getResourceAsStream("/" + file); if (is != null) { in = new BufferedReader(new java.io.InputStreamReader(is)); + // TODO: this probably doesn't work for classloader - needs a test + baseUri = new File("/" + file).getParent() + "/"; } } if (in != null) @@ -730,15 +776,9 @@ public class AnnotationFile return false; } - long nlinesread = 0; - - String lastread = ""; - - private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel, - BufferedReader in) - throws Exception + BufferedReader in) throws Exception { nlinesread = 0; ArrayList combineAnnotation_calls = new ArrayList(); @@ -831,8 +871,8 @@ public class AnnotationFile else if (token.equalsIgnoreCase(COMBINE)) { // keep a record of current state and resolve groupRef at end - combineAnnotation_calls.add(new Object[] - { st, refSeq, groupRef }); + combineAnnotation_calls + .add(new Object[] { st, refSeq, groupRef }); modified = true; continue; } @@ -845,8 +885,8 @@ 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; } @@ -929,12 +969,6 @@ public class AnnotationFile modified = true; continue; } - // else if (token.equalsIgnoreCase("VIEW_DEF")) - // { - // addOrSetView(al,st); - // modified = true; - // continue; - // } else if (token.equalsIgnoreCase("VIEW_SETREF")) { if (refSeq != null) @@ -981,7 +1015,58 @@ public class AnnotationFile modified = true; continue; } - + else if (token.equalsIgnoreCase(HEADER_STRUCT_MODEL)) + { + int hSize = st.countTokens(); + StructModelHeader = new String[hSize]; + for (int x = 0; x < hSize; x++) + { + StructModelHeader[x] = st.nextToken(); + } + continue; + } + else if (token.equalsIgnoreCase(STRUCTMODEL)) + { + boolean failedtoadd = true; + // expects STRUCTMODEL + // + String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken(); + SequenceI querySeq = al.findName(querySeqId); + if (st.hasMoreTokens()) { + refSeq = al.findName(refSeqId = st.nextToken()); + if (refSeq == null) + { + System.err.println("Couldn't locate " + refSeqId + + " in the alignment for STRUCTMODEL"); + refSeqId = null; + } + else + { + int tSize = st.countTokens() + 2; + String[] rowData = new String[tSize]; + rowData[0] = querySeqId; + rowData[1] = refSeqId; + for (int x = 2; x < tSize; x++) + { + rowData[x] = st.nextToken(); + } + if (processStructModel(al, querySeq, refSeq, + StructModelHeader, rowData, baseUri)) + { + failedtoadd = false; + } + } + } + if (failedtoadd) + { + System.err + .println("Need minimum of as tab separated fields after" + + STRUCTMODEL); + } else { + modified = true; + } + continue; + } // Parse out the annotation row graphStyle = AlignmentAnnotation.getGraphValueFromString(token); label = st.nextToken(); @@ -1154,7 +1239,7 @@ public class AnnotationFile (SequenceI) _deferred_args[2], // refSeq (_deferred_args[3] == null) ? null : groupRefLookup .get(_deferred_args[3]) // the reference - // group, or null + // group, or null ); } } @@ -1174,16 +1259,109 @@ public class AnnotationFile (SequenceI) _combine_args[1], // refSeq (_combine_args[2] == null) ? null : groupRefLookup .get(_combine_args[2]) // the reference group, - // or null + // or null ); } } return modified; } + /** + * Resolve structural model to a reference sequence and register it to + * StructureSelectionManager + * + * @param al + * @param querySequence + * @param templateSeq + * @param structModelHeader + * @param structModelData + * @return true if model and sequence was added + */ + static boolean processStructModel(AlignmentI al, SequenceI querySequence, + SequenceI templateSeq, + String[] structModelHeader, + String[] structModelData, String baseUri) + { + String warningMessage = null; + boolean added = false; + try { + String structureModelFile = resolveAbsolutePath(structModelData[2], + baseUri); + String fastaMappingFile = resolveAbsolutePath(structModelData[3], + baseUri); + // System.out.println("Model File >> " + structureModelFile); + // System.out.println("Fasta File >> " + fastaMappingFile); + String modelName = StructureFile.safeName(structureModelFile); + PDBEntry phyre2PDBEntry = new PDBEntry(modelName, " ", + Type.PDB, + structureModelFile); + List phyreDD = generatePhyreDynamicDataList( + structModelHeader, structModelData); + phyre2PDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD); + templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry); + if (querySequence != null) + { + querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry); + } + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(); + ssm.registerPhyre2Template(structureModelFile, fastaMappingFile); + added = true; + + } catch (Exception x) + { + warningMessage = x.toString(); + } finally { + if (warningMessage !=null) + { + System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage); + } + } + return added; + } + + static List generatePhyreDynamicDataList( + String[] headerArray, + String[] dataArray) + { + + if (headerArray == null || dataArray == null) + { + throw new IllegalArgumentException( + "Header or data arrays must not be null"); + } + + if (headerArray.length != dataArray.length) + { + throw new IllegalArgumentException( + "Header and data arrays must be of same lenght"); + } + List dynamicDataList = new ArrayList(); + int x = 0; + for (String data : dataArray) + { + // first four column should be hidden; + boolean show = (x > 4); + dynamicDataList.add(new DynamicData(headerArray[x], data, DataType.S, + "PHYRE2", show)); + x++; + } + return dynamicDataList; + } + + static String resolveAbsolutePath(String relURI, String _baseUri) + { + if (relURI.indexOf(":/") > -1 || relURI.startsWith("/") + || "".equals(_baseUri) || relURI.startsWith(_baseUri)) + { + return relURI; + } + return _baseUri + relURI; + } + private void parseHideCols(ColumnSelection colSel, String nextToken) { - StringTokenizer inval = new StringTokenizer(nextToken,","); + StringTokenizer inval = new StringTokenizer(nextToken, ","); while (inval.hasMoreTokens()) { String range = inval.nextToken().trim(); @@ -1225,29 +1403,21 @@ public class AnnotationFile Annotation parseAnnotation(String string, int graphStyle) { - boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't - // do the - // glyph - // test - // if we - // don't - // want - // secondary - // structure + // don't do the glyph test if we don't want secondary structure + boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); String desc = null, displayChar = null; char ss = ' '; // secondaryStructure float value = 0; boolean parsedValue = false, dcset = false; // find colour here - java.awt.Color colour = null; + Color colour = null; int i = string.indexOf("["); int j = string.indexOf("]"); if (i > -1 && j > -1) { - UserColourScheme ucs = new UserColourScheme(); - - colour = ucs.getColourFromString(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 @@ -1301,8 +1471,8 @@ public class AnnotationFile } } if (hasSymbols - && (token.equals("H") || token.equals("E") - || token.equals("S") || token.equals(" "))) + && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz" + .contains(token))) { // Either this character represents a helix or sheet // or an integer which can be displayed @@ -1349,7 +1519,7 @@ public class AnnotationFile void colourAnnotations(AlignmentI al, String label, String colour) { - UserColourScheme ucs = new UserColourScheme(colour); + Color awtColour = ColorUtils.parseColourString(colour); Annotation[] annotations; for (int i = 0; i < al.getAlignmentAnnotation().length; i++) { @@ -1360,7 +1530,7 @@ public class AnnotationFile { if (annotations[j] != null) { - annotations[j].colour = ucs.findColour('A'); + annotations[j].colour = awtColour; } } } @@ -1430,15 +1600,22 @@ public class AnnotationFile SequenceGroup groupRef) { String group = st.nextToken(); - AlignmentAnnotation annotation = null, alannot[] = al - .getAlignmentAnnotation(); - float value = new Float(st.nextToken()).floatValue(); + AlignmentAnnotation[] alannot = al.getAlignmentAnnotation(); + String nextToken = st.nextToken(); + float value = 0f; + try + { + value = Float.valueOf(nextToken); + } catch (NumberFormatException e) + { + System.err.println("line " + nlinesread + ": Threshold '" + nextToken + + "' invalid, setting to zero"); + } String label = st.hasMoreTokens() ? st.nextToken() : null; - java.awt.Color colour = null; + Color colour = null; if (st.hasMoreTokens()) { - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - colour = ucs.findColour('A'); + colour = ColorUtils.parseColourString(st.nextToken()); } if (alannot != null) { @@ -1452,10 +1629,6 @@ public class AnnotationFile } } } - if (annotation == null) - { - return; - } } void addGroup(AlignmentI al, StringTokenizer st) @@ -1615,8 +1788,7 @@ public class AnnotationFile if (sg != null) { String keyValue, key, value; - ColourSchemeI def = sg.cs; - sg.cs = null; + ColourSchemeI def = sg.getColourScheme(); while (st.hasMoreTokens()) { keyValue = st.nextToken(); @@ -1629,7 +1801,8 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("colour")) { - sg.cs = ColourSchemeProperty.getColour(al, value); + sg.cs.setColourScheme(ColourSchemeProperty + .getColourScheme(al, value)); } else if (key.equalsIgnoreCase("pidThreshold")) { @@ -1639,8 +1812,7 @@ public class AnnotationFile else if (key.equalsIgnoreCase("consThreshold")) { sg.cs.setConservationInc(Integer.parseInt(value)); - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), + Conservation c = new Conservation("Group", sg.getSequences(null), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -1651,7 +1823,7 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("outlineColour")) { - sg.setOutlineColour(new UserColourScheme(value).findColour('A')); + sg.setOutlineColour(ColorUtils.parseColourString(value)); } else if (key.equalsIgnoreCase("displayBoxes")) { @@ -1671,11 +1843,11 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("textCol1")) { - sg.textColour = new UserColourScheme(value).findColour('A'); + sg.textColour = ColorUtils.parseColourString(value); } else if (key.equalsIgnoreCase("textCol2")) { - sg.textColour2 = new UserColourScheme(value).findColour('A'); + sg.textColour2 = ColorUtils.parseColourString(value); } else if (key.equalsIgnoreCase("textColThreshold")) { @@ -1683,9 +1855,8 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("idColour")) { - // consider warning if colour doesn't resolve to a real colour - sg.setIdColour((def = new UserColourScheme(value)) - .findColour('A')); + Color idColour = ColorUtils.parseColourString(value); + sg.setIdColour(idColour == null ? Color.black : idColour); } else if (key.equalsIgnoreCase("hide")) { @@ -1699,9 +1870,9 @@ public class AnnotationFile } sg.recalcConservation(); } - if (sg.cs == null) + if (sg.getColourScheme() == null) { - sg.cs = def; + sg.setColourScheme(def); } } } @@ -1761,6 +1932,10 @@ public class AnnotationFile */ public String printCSVAnnotations(AlignmentAnnotation[] annotations) { + if (annotations == null) + { + return ""; + } StringBuffer sp = new StringBuffer(); for (int i = 0; i < annotations.length; i++) {