import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.fts.core.DecimalFormatTableCellRenderer;
+import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.util.Comparison;
import jalview.util.Format;
-import java.io.File;
+import java.io.BufferedReader;
+import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import javax.swing.JTable;
import javax.swing.table.DefaultTableModel;
-import org.jsoup.Jsoup;
-import org.jsoup.nodes.Document;
-import org.jsoup.nodes.Element;
-import org.jsoup.select.Elements;
-
public class Phyre2Client extends StructureMappingClient
{
private final static String NEWLINE = System.lineSeparator();
- public static final int UNASSIGNED = -1;
-
- private final static String PATH_SEPARATOR = File.separator;
+ private String fastaMappingFile;
public Phyre2Client(StructureFile structureFile)
{
this.structureFile = structureFile;
}
+ public StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String fMappingFile, String chain)
+ {
+ this.fastaMappingFile = fMappingFile;
+ return getStructureMapping(seq, pdbFile, chain);
+ }
+
@Override
public StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String chain)
AlignmentI seq2Phyre2ModelFastaMapping = null;
try
{
- seq2Phyre2ModelFastaMapping = new FormatAdapter().readFile(
- getFastaMappingFile(), DataSourceType.FILE, FileFormat.Fasta);
+ String fastaFile = getFastaMappingFile();
+ DataSourceType protocol = AppletFormatAdapter
+ .checkProtocol(fastaFile);
+ seq2Phyre2ModelFastaMapping = new FormatAdapter().readFile(fastaFile,
+ protocol, FileFormat.Fasta);
} catch (IOException e1)
{
e1.printStackTrace();
tStructureRes.setEnd(structureFile.getSeqsAsArray()[0].getEnd());
try
{
- int sequenceResLenght = tSequenceRes.getLength();
- int structureResLenght = tStructureRes.getLength();
- if (sequenceResLenght == structureResLenght)
+ int sequenceResLength = tSequenceRes.getLength();
+ int structureResLength = tStructureRes.getLength();
+ if (sequenceResLength == structureResLength)
{
int prevStructResNum = -1;
- int alignmentLenght = sequenceResLenght + tSequenceRes.getStart();
- for (int x = 0; x < alignmentLenght; x++)
+ int alignmentLength = sequenceResLength + tSequenceRes.getStart();
+ for (int x = 0; x < alignmentLength; x++)
{
int alignSeqResidueIndex = tSequenceRes.findIndex(x);
int structResNum = tStructureRes
.findPosition(alignSeqResidueIndex);
int sequenceResNum = tSequenceRes
.findPosition(alignSeqResidueIndex - 1);
- boolean sameResNum = (structResNum == prevStructResNum);
- // System.out.println(sequenceResNum + " : "
- // + (sameResNum ? -1 : prevStructResNum));
- mapping.put(sequenceResNum, new int[] {
- sameResNum ? -1 : prevStructResNum, -1 });
+ if (structResNum != prevStructResNum)
+ {
+ // System.out.println(sequenceResNum + " : " + prevStructResNum);
+ mapping.put(sequenceResNum, new int[] { prevStructResNum,
+ StructureMapping.UNASSIGNED });
+ }
prevStructResNum = structResNum;
}
}
e.printStackTrace();
}
+ /*
+ * now populate atom positions for structure residues (and remove
+ * residue if atom position cannot be found)
+ */
try
{
populateAtomPositions(" ", mapping);
private String getFastaMappingFile()
{
- File phyre2ModelFile = new File(structureFile.getDataName());
- String phyre2ModelResultDir = phyre2ModelFile.getParent();
- String modelId = structureFile.getId().substring(0,
- structureFile.getId().lastIndexOf(".pdb"));
- return phyre2ModelResultDir + PATH_SEPARATOR + modelId + ".fasta";
+ return fastaMappingFile;
+ }
+
+ void setFastaMappingFile(String fastaMappingFile)
+ {
+ this.fastaMappingFile = fastaMappingFile;
}
@Override
output.append(NEWLINE).append(NEWLINE);
}
float pid = (float) matchedSeqCount / seqRes.length() * 100;
- // if (pid < SiftsSettings.getFailSafePIDThreshold())
- // {
- // throw new Exception(">>> Low PID detected for Phyre2 mapping...");
- // }
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
}
-
- public static List<Phyre2SummaryPojo> parsePhyre2ResultSummaryTable(
- String html)
+ public static List<Phyre2SummaryPojo> parsePhyreCrudeList(String crudeList)
{
List<Phyre2SummaryPojo> phyre2Results = new ArrayList<Phyre2SummaryPojo>();
- try
+ try (BufferedReader br = new BufferedReader(new FileReader(crudeList)))
{
- File in = new File(html);
- Document doc = Jsoup.parse(in, null);
- // Document doc = Jsoup.connect(html).get();
- Elements tableElements = doc.select("table.midshade");
- for (Element table : tableElements)
+ String line;
+ while ((line = br.readLine()) != null)
{
- System.out.println();
- Elements tableRowElements = table.select(":not(thead) tr");
- for (int i = 0; i < tableRowElements.size(); i++)
- {
- Element row = tableRowElements.get(i);
- Elements rowItems = row.select("td");
- if (rowItems.size() > 11)
- {
- // for (int j = 0; j < rowItems.size(); j++)
- // {
- // System.out.println(">>> r:" + j + " = "
- // + rowItems.get(j).text());
- // }
-
- String c = rowItems.get(6).select("input").attr("onmouseover");
- String alignedRange = c.substring(c.indexOf("Residues ") + 9,
- c.indexOf(" of your sequence aligned "));
- String coverage = c.substring(c.lastIndexOf(" (") + 2,
- c.lastIndexOf(" coverage). Click to view detailed"));
- // System.out.println("coverage" + coverage);
- try
- {
- Phyre2SummaryPojo psp = new Phyre2SummaryPojo();
- String sn = rowItems.get(0).text();
- psp.setSerialNo(Integer.valueOf(sn));
- psp.setTemplateId(rowItems.get(1).text());
- psp.setCoverage(coverage);
- psp.setAlignedRange(alignedRange);
- psp.setConfidence(Double.valueOf(rowItems.get(8).text()));
- psp.setPid(Integer.valueOf(rowItems.get(9).text()));
- psp.setTemplateSummary(rowItems.get(10).text());
- // System.out.println("row >>>> " + psp.toString());
- // System.out.println();
- phyre2Results.add(psp);
- } catch (NumberFormatException e)
- {
- e.printStackTrace();
- } catch (IndexOutOfBoundsException e)
- {
- e.printStackTrace();
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
- }
+ String[] lineData = line.split(" ");
+ Phyre2SummaryPojo psp = new Phyre2SummaryPojo();
+ psp.setSerialNo(Integer.valueOf(lineData[0]));
+ psp.setTemplateId(lineData[1]);
+ psp.setConfidence(100 * Double.valueOf(lineData[2]));
+ psp.setPid(Integer.valueOf(lineData[3]));
+ psp.setAlignedRange(lineData[4] + " - " + lineData[5]);
+ // psp.setCoverage(coverage);
+ // psp.setTemplateSummary(templateSummary);
+ phyre2Results.add(psp);
}
- return phyre2Results;
-
} catch (Exception e)
{
e.printStackTrace();
- return null;
}
+ return phyre2Results;
}
public static DefaultTableModel getTableModel(
phyreResultTable.getColumn("#").setCellRenderer(idCellRender);
phyreResultTable.getColumn("Template").setMinWidth(60);
- phyreResultTable.getColumn("Template").setPreferredWidth(60);
- phyreResultTable.getColumn("Template").setMaxWidth(90);
+ phyreResultTable.getColumn("Template").setPreferredWidth(90);
+ phyreResultTable.getColumn("Template").setMaxWidth(150);
phyreResultTable.getColumn("Aligned Range").setMinWidth(80);
phyreResultTable.getColumn("Aligned Range").setPreferredWidth(80);
git://source.jalview.org / jalview.git / blobdiff