X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=d8f9f150c488954336d10907bf52f66022e5d5b4;hb=e84b575bede2d5a6dea85cb96000dc751d090016;hp=62503a0397b9a869cf9b7466cde2364f366ae36e;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 62503a0..d8f9f15 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -28,6 +28,8 @@ import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; 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; @@ -37,6 +39,7 @@ import jalview.schemes.UserColourScheme; import java.io.BufferedReader; import java.io.FileReader; +import java.io.IOException; import java.io.InputStreamReader; import java.io.StringReader; import java.net.URL; @@ -241,7 +244,7 @@ public class AnnotationFile && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter .equals(" ")); hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' '); - hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't + hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't // be // rendered.. hasText |= (row.annotations[j].description != null && row.annotations[j].description @@ -294,8 +297,7 @@ 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); } } @@ -331,13 +333,13 @@ public class AnnotationFile } if (hasValues) { - if (row.annotations[j].value != Float.NaN) + if (!Float.isNaN(row.annotations[j].value)) { text.append(comma + row.annotations[j].value); } else { - System.err.println("Skipping NaN - not valid value."); + // System.err.println("Skipping NaN - not valid value."); text.append(comma + 0f);// row.annotations[j].value); } comma = ","; @@ -472,8 +474,9 @@ 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(); @@ -670,14 +673,14 @@ 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) { @@ -734,11 +737,11 @@ public class AnnotationFile String lastread = ""; - private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; + private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE", + STRUCTMODEL = "STRUCTMODEL"; public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel, - BufferedReader in) - throws Exception + BufferedReader in) throws Exception { nlinesread = 0; ArrayList combineAnnotation_calls = new ArrayList(); @@ -831,8 +834,8 @@ 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 +848,8 @@ 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; } @@ -981,7 +984,43 @@ public class AnnotationFile modified = true; continue; } - + else if (token.equalsIgnoreCase(STRUCTMODEL)) + { + boolean failedtoadd = true; + // expect + // STRUCTMODEL + 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 + { + String tempId = st.nextToken(); + String urlToModel = st.nextToken(); + String urlToPairwise = st.hasMoreTokens() ? st.nextToken() + : ""; + if (add_structmodel(al, refSeq, tempId, urlToModel, + urlToPairwise)) + { + failedtoadd = false; + } + } + } + if (failedtoadd) + { + System.err + .println("Need [] as tab separated fields after " + + STRUCTMODEL); + } else { + modified = true; + } + continue; + } // Parse out the annotation row graphStyle = AlignmentAnnotation.getGraphValueFromString(token); label = st.nextToken(); @@ -1154,7 +1193,7 @@ 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 +1213,101 @@ 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 a structural model and generate and add an alignment sequence for + * it + * + * @param refSeq2 + * @param tempId + * @param urlToModel + * @param urlToPairwise + * @return true if model and sequence was added + */ + private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId, + String urlToModel, String urlToPairwise) + { + String warningMessage=null; + boolean added = false; + try { + // locate tempId. if it exists, will need to merge, otherwise: + SequenceI templateSeq = al.findName(tempId); + // 1. load urlToModel + // TODO: get base for current import operation and resolve against it + // transfer to local temp file ? + PDBEntry modelpe = new PDBEntry(tempId,null,Type.FILE,urlToModel); + PDBEntry templpe = new PDBEntry(tempId, null, Type.FILE, urlToModel); + refSeq2.addPDBId(modelpe); + + // 2. load urlToPairwise + AlignmentI pwa = new AppletFormatAdapter().readFile(urlToPairwise, + AppletFormatAdapter.checkProtocol(urlToPairwise), "FASTA"); + SequenceI qPw = null, tPw = null; + if (pwa != null) + { + // resolve query/template sequences in provided alignment + qPw = pwa.findName(refSeqId); + tPw = pwa.findName(tempId); + } + if (false) + // (qPw != null && tPw != null) + { + // not yet complete + // refalQ vvva--addrvvvtttddd + // refalT ---aaaa---sss---ddd + // profalQ ---v-v-v-a.-.-a---dd--r--vvvtt--td--dd + // profalT ---.-.-.-aa-a-a---..--.--sss..--.d--dd + // Pragmatic solution here: + // Map templpe onto refalT only where refalT and refalQ are both + // non-gaps + + // columns for start..end in refSeq2 + int[] gapMap = refSeq2.gapMap(); + // insert gaps in tPw + int curi = 0, width = refSeq2.getLength(); + // TBC + } + else + { + // assume 1:1 - so synthesise sequences to use to construct mapping ? + refSeq2.getDatasetSequence().addPDBId(modelpe); + if (templateSeq == null && tPw != null) + { + tPw.createDatasetSequence(); + tPw.getDatasetSequence().addPDBId(templpe); // needs to set mapping based on model yet... + al.addSequence(tPw); + added = true; + } + } + // 3. pad/insert gaps in urlToPairwise according to gaps already present in + // refSeq2 + // 4. add padded tempId sequence to alignment + // 4. associate urlToModel with refSeq2 based on position map provided by + // urlToPairwise + // 5. associate urlToModel with tempId based on position map provided by + // urlToPairwise + // start a thread to load urlToModel and process/annotate sequences. + } catch (IOException x) + { + warningMessage = x.toString(); + } finally { + if (warningMessage !=null) + { + System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage); + } + return added; + } + } + 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(); @@ -1301,8 +1425,8 @@ 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 @@ -1761,6 +1885,10 @@ public class AnnotationFile */ public String printCSVAnnotations(AlignmentAnnotation[] annotations) { + if (annotations == null) + { + return ""; + } StringBuffer sp = new StringBuffer(); for (int i = 0; i < annotations.length; i++) {