X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;fp=src%2Fjalview%2Fio%2FAnnotationFile.java;h=eca27a727c3b625c333ee8a1f0deafcbd24b54b2;hb=3e98c1348b037f0972367245a524f182029a9686;hp=34fdabe0f9625ad6a54204bf32a54ab21bcb0f8d;hpb=c242d1bd498f606f87c5f3c7854b469dd7120730;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 34fdabe..eca27a7 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -28,14 +28,19 @@ 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; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.UserColourScheme; +import jalview.structure.StructureSelectionManager; import java.io.BufferedReader; +import java.io.File; import java.io.FileReader; +import java.io.IOException; import java.io.InputStreamReader; import java.io.StringReader; import java.net.URL; @@ -686,21 +691,41 @@ public class AnnotationFile public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel, String file, String protocol) { + baseUri = ""; BufferedReader in = null; try { if (protocol.equals(AppletFormatAdapter.FILE)) { in = new BufferedReader(new FileReader(file)); + baseUri = new File(file).getParent(); + if (baseUri == null) + { + baseUri = ""; + } + else + { + baseUri += "/"; + } } else if (protocol.equals(AppletFormatAdapter.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)) { in = new BufferedReader(new StringReader(file)); + // TODO - support mimencoded PDBs for a paste.. ? + baseUri = ""; } else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) { @@ -708,6 +733,8 @@ public class AnnotationFile 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) @@ -733,7 +760,14 @@ public class AnnotationFile String lastread = ""; - private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; + /** + * used for resolving absolute references to resources relative to + * annotationFile location + */ + String baseUri = ""; + + private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE", + STRUCTMODEL = "STRUCTMODEL"; public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel, BufferedReader in) throws Exception @@ -979,7 +1013,43 @@ 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(); @@ -1179,6 +1249,107 @@ public class AnnotationFile 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, modelPath = null, modelProt = null, aliPath = null, aliProt = null; + boolean added = false; + try { + // locate tempId. if it exists, will need to merge, otherwise: + SequenceI templateSeq = al.findName(tempId); + // 1. load urlToModel + modelPath = resolveAbsolute(urlToModel); + modelProt = AppletFormatAdapter.checkProtocol(modelPath); + // need to transfer to local temp file ? + PDBEntry modelpe = new PDBEntry(tempId, null, Type.FILE, modelPath); + PDBEntry templpe = new PDBEntry(tempId, null, Type.FILE, modelPath); + refSeq2.addPDBId(modelpe); + aliPath = resolveAbsolute(urlToPairwise); + aliProt = AppletFormatAdapter.checkProtocol(aliPath); + // 2. load urlToPairwise + AlignmentI pwa = new AppletFormatAdapter().readFile(aliPath, aliProt, + "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 + StructureFile pdbf = StructureSelectionManager + .getStructureSelectionManager().setMapping(false, + new SequenceI[] { refSeq2.getDatasetSequence() }, + null, modelPath, modelProt); + 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 String resolveAbsolute(String relURI) + { + 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, ",");