import jalview.util.Format;
import java.io.BufferedReader;
-import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
{
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)
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);
return fastaMappingFile;
}
+ void setFastaMappingFile(String fastaMappingFile)
+ {
+ this.fastaMappingFile = fastaMappingFile;
+ }
+
@Override
public StringBuffer getMappingOutput(MappingOutputModel mp)
throws StructureMappingException