import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.UserColourScheme;
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;
{
boolean failedtoadd = true;
// expect
- // STRUCTMODEL <QUERYID> <TemplateID> <URL to model> <URL to
- // alignment>
+ // STRUCTMODEL <TemplateSeqId> <TemplateFileName> <Confidence> <%.I.D>
+ // <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
if (st.hasMoreTokens()) {
refSeq = al.findName(refSeqId = st.nextToken());
if (refSeq == null)
else
{
String tempId = st.nextToken();
- String urlToModel = st.nextToken();
- String urlToPairwise = st.hasMoreTokens() ? st.nextToken()
- : "";
- if (add_structmodel(al, refSeq, tempId, urlToModel,
- urlToPairwise))
+ String confidence = 100 * Double.valueOf(st.nextToken()) + "";
+ String pid = st.nextToken();
+ String alignRange = st.nextToken() + "-" + st.nextToken();
+ String otherInfo = st.hasMoreTokens() ? st.nextToken() : "";
+ String coverage = "";
+ if (add_structmodel(al, refSeq, tempId, alignRange, coverage,
+ confidence, pid, otherInfo))
{
failedtoadd = false;
}
if (failedtoadd)
{
System.err
- .println("Need <QueryId> <TemplateId> <URL to Model> [<URL to pairwise alignment>] as tab separated fields after "
- + STRUCTMODEL);
+ .println("Need <TemplateSeqId> <TemplateFileName> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
+ + STRUCTMODEL
+ + ".\nNote: other information could be provided in html format ");
} else {
modified = true;
}
* @param urlToPairwise
* @return true if model and sequence was added
*/
- private boolean add_structmodel(AlignmentI al, SequenceI refSeq2, String tempId,
- String urlToModel, String urlToPairwise)
+ private boolean add_structmodel(AlignmentI al, SequenceI refSeq,
+ String tempId, String aRange, String coverage, String confidence,
+ String pid, String otherInfo)
{
- String warningMessage = null, modelPath = null, aliPath = null;
- DataSourceType modelProt = null, aliProt = null;
+ 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
- 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,
- FileFormat.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)
+ String pdbFile = baseUri + tempId;
+ PDBEntry phyre2PDBEntry = new PDBEntry(tempId, null, Type.FILE,
+ pdbFile);
+ refSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
+ coverage, confidence, pid, otherInfo);
+ refSeq.setDescription(phyre2ModelDesc);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerPhyre2Template(pdbFile);
+ added = true;
+
+ } catch (Exception x)
{
warningMessage = x.toString();
} finally {
{
System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
}
- return added;
}
+ return added;
+ }
+
+ private String generatePhyre2InfoHTMLTable(String aRange,
+ String coverage, String confidence, String pid, String otherInfo)
+ {
+ 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())
+ {
+ 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>");
+ }
+ if (pid != null && !pid.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("%.i.d")
+ .append("</td><td>").append(pid).append("</td></tr>");
+ }
+ if (otherInfo != null && !otherInfo.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Other information")
+ .append("</td><td>").append(otherInfo).append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
+ return phyre2InfoBuilder.toString();
}
private String resolveAbsolute(String relURI)
git://source.jalview.org / jalview.git / blobdiff