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();
return newline;
}
- StringBuffer text;
private void init()
{
}
}
- SequenceI refSeq = null;
-
- String refSeqId = null;
public boolean annotateAlignmentView(AlignViewportI viewport,
String file, DataSourceType protocol)
return false;
}
- 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";
public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
BufferedReader in) throws Exception
modified = true;
continue;
}
- // else if (token.equalsIgnoreCase("VIEW_DEF"))
- // {
- // addOrSetView(al,st);
- // modified = true;
- // continue;
- // }
else if (token.equalsIgnoreCase("VIEW_SETREF"))
{
if (refSeq != null)
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;
- // expect
- // STRUCTMODEL <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile>
- // <Confidence> <%.I.D>
- // <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
+ // expects STRUCTMODEL <Query> <TemplateSeqId> <ModelFile>
+ // <FastaMappingFile>
String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
SequenceI querySeq = al.findName(querySeqId);
if (st.hasMoreTokens()) {
}
else
{
- String tempId = st.nextToken();
- String fastaMapping = st.nextToken();
- String confidence = !st.hasMoreTokens() ? "" : 100
- * Double.valueOf(st.nextToken()) + "";
- String pid = !st.hasMoreTokens() ? "" : st.nextToken();
- String alignRange = !st.hasMoreTokens() ? "" : st.nextToken()
- + "-" + st.nextToken();
- String otherInfo = !st.hasMoreTokens() ? "" : st.nextToken();
- String coverage = "";
- if (add_structmodel(al, querySeq, refSeq, tempId,
- fastaMapping,
- alignRange, coverage,
- confidence, pid, otherInfo))
+ 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 <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
- + STRUCTMODEL
- + ".\nNote: other information could be provided in html format ");
+ .println("Need minimum of <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> as tab separated fields after"
+ + STRUCTMODEL);
} else {
modified = true;
}
}
/**
- * resolve a structural model and generate and add an alignment sequence for
- * it
+ * Resolve structural model to a reference sequence and register it to
+ * StructureSelectionManager
*
- * @param refSeq2
- * @param tempId
- * @param urlToModel
- * @param urlToPairwise
+ * @param al
+ * @param querySequence
+ * @param templateSeq
+ * @param structModelHeader
+ * @param structModelData
* @return true if model and sequence was added
*/
- private boolean add_structmodel(AlignmentI al, SequenceI querySequence,
+ static boolean processStructModel(AlignmentI al, SequenceI querySequence,
SequenceI templateSeq,
- String modelFile, String fastaFile, String aRange,
- String coverage, String confidence,
- String pid, String otherInfo)
+ String[] structModelHeader,
+ String[] structModelData, String baseUri)
{
String warningMessage = null;
boolean added = false;
try {
- String structureModelFile = resolveAbsolute(modelFile);
- String fastaMappingFile = resolveAbsolute(fastaFile.replaceAll(
- ".fasta.jal", ".fasta"));
+ String structureModelFile = resolveAbsolutePath(structModelData[2],
+ baseUri);
+ String fastaMappingFile = resolveAbsolutePath(structModelData[3],
+ baseUri);
// System.out.println("Model File >> " + structureModelFile);
// System.out.println("Fasta File >> " + fastaMappingFile);
- PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
+ String modelName = StructureFile.safeName(structureModelFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelName, " ",
+ Type.PDB,
structureModelFile);
- String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
- coverage, confidence, pid, otherInfo);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(
+ structModelHeader, structModelData);
phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
if (querySequence != null)
return added;
}
- private String generatePhyre2InfoHTMLTable(String aRange,
- String coverage, String confidence, String pid, String otherInfo)
+ static String generatePhyre2InfoHTMLTable(String[] structModelHeader,
+ String[] structModelData)
{
StringBuilder phyre2InfoBuilder = new StringBuilder();
- phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>");
- phyre2InfoBuilder
- .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
- if (aRange != null && !aRange.isEmpty())
- {
- phyre2InfoBuilder.append("<tr><td>").append("Aligned range")
- .append("</td><td>").append(aRange).append("</td></tr>");
- }
- if (coverage != null && !coverage.isEmpty())
+ if (isGenerateStructInfoHtml(structModelHeader, structModelData))
{
- phyre2InfoBuilder.append("<tr><td>").append("Coverage")
- .append("</td><td>").append(coverage).append("</td></tr>");
- }
- if (confidence != null && !confidence.isEmpty())
- {
- phyre2InfoBuilder.append("<tr><td>").append("Confidence")
- .append("</td><td>").append(confidence).append("</td></tr>");
+ phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>")
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ for (int x = 4; x < structModelData.length; x++)
+ {
+ phyre2InfoBuilder.append("<tr><td>").append(structModelHeader[x])
+ .append("</td><td>").append(structModelData[x])
+ .append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
}
- if (pid != null && !pid.isEmpty())
+ return phyre2InfoBuilder.toString();
+ }
+
+ static boolean isGenerateStructInfoHtml(String[] header, String[] data)
+ {
+ boolean generate = true;
+ if (header == null || data == null)
{
- phyre2InfoBuilder.append("<tr><td>").append("%.i.d")
- .append("</td><td>").append(pid).append("</td></tr>");
+ return false;
}
- if (otherInfo != null && !otherInfo.isEmpty())
+ if (header.length < 3 || data.length < 3)
{
- phyre2InfoBuilder.append("<tr><td>").append("Other information")
- .append("</td><td>").append(otherInfo).append("</td></tr>");
+ generate = false;
}
- phyre2InfoBuilder.append("</table></html>");
- return phyre2InfoBuilder.toString();
+ return generate;
}
- private String resolveAbsolute(String relURI)
+ static String resolveAbsolutePath(String relURI, String _baseUri)
{
if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
- || "".equals(baseUri) || relURI.startsWith(baseUri))
+ || "".equals(_baseUri) || relURI.startsWith(_baseUri))
{
return relURI;
}
- return baseUri + relURI;
+ return _baseUri + relURI;
}
private void parseHideCols(ColumnSelection colSel, String nextToken)
git://source.jalview.org / jalview.git / blobdiff