diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 56a9e0331fb42e59f1486f0fcbfe136c1accda2f..e8dc2f1f32eff6db5aa92794554aa7f3286000a6 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -33,6 +33,7 @@ import java.util.List;
import javax.swing.JFileChooser;
+import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureEnumeration;
@@ -41,12 +42,19 @@ import uk.ac.sanger.artemis.FeaturePredicate;
import uk.ac.sanger.artemis.FeatureSegment;
import uk.ac.sanger.artemis.FeatureSegmentVector;
import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.SequenceViewer;
import uk.ac.sanger.artemis.components.StickyFileChooser;
import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
+import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.Key;
+import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.sequence.MarkerRange;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.FileDocument;
+import uk.ac.sanger.artemis.util.RemoteFileDocument;
import net.sf.samtools.util.BlockCompressedInputStream;
@@ -145,21 +153,94 @@ class IOUtils
new MessageDialog (null, "Saved Files", filterFiles, false);
}
- protected static void exportFasta(final EntryGroup entryGroup,
+ /**
+ * Write out fasta for a selected base range
+ * @param entryGroup
+ * @param vcfReaders
+ * @param chr
+ * @param vcfView
+ * @param vcf_v4
+ * @param selection
+ * @param view
+ */
+ protected static void exportFastaByRange(
+ final EntryGroup entryGroup,
final AbstractVCFReader vcfReaders[],
final String chr,
final VCFview vcfView,
- final boolean vcf_v4)
+ final boolean vcf_v4,
+ final Selection selection,
+ final boolean view)
{
- // get all CDS features that do not have the /pseudo qualifier
- final FeatureVector features = getFeatures(
- new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false), entryGroup);
- exportFasta(entryGroup, vcfReaders, chr, vcfView, vcf_v4, features, false);
+ MarkerRange marker = selection.getMarkerRange();
+ Range range = marker.getRawRange();
+ int direction = ( marker.isForwardMarker() ? Bases.FORWARD : Bases.REVERSE);
+ FeatureVector features = entryGroup.getAllFeatures();
+ FileWriter writer = null;
+ String fastaFiles = "";
+
+ String name = entryGroup.getActiveEntries().elementAt(0).getName();
+ try
+ {
+
+ if(!view)
+ {
+ File newfile = new File(
+ getBaseDirectoryFromEntry(entryGroup.getActiveEntries().elementAt(0)),
+ name);
+
+ File f = getFile(newfile.getAbsolutePath(), vcfReaders.length, ".fasta");
+ writer = new FileWriter(f);
+ fastaFiles += f.getAbsolutePath()+"\n";
+ }
+
+ int sbeg = range.getStart();
+ int send = range.getEnd();
+
+ for (int i = 0; i < vcfReaders.length; i++)
+ {
+ String basesStr = entryGroup.getBases().getSubSequence(marker.getRange(), direction);
+ if (vcfReaders[i] instanceof BCFReader)
+ {
+ BCFReaderIterator it = ((BCFReader) vcfReaders[i]).query(chr, sbeg, send);
+ VCFRecord record;
+ while ((record = it.next()) != null)
+ {
+ int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
+ if(vcfView.showVariant(record, features, basePosition) )
+ basesStr = getSeqsVariation(record, basesStr, sbeg, marker.isForwardMarker(), vcf_v4);
+ }
+ }
+
+ StringBuffer header = new StringBuffer(name+" ");
+ header.append(sbeg+":"+send+ (marker.isForwardMarker() ? "" : " reverse"));
+ header.append(" (").append(vcfReaders[i].getName()).append(")");
+
+ if(view) // sequence viewer
+ {
+ SequenceViewer viewer =
+ new SequenceViewer ("Feature base viewer for selected range: " +
+ sbeg+":"+send+(marker.isForwardMarker() ? "" : " reverse"), false);
+ viewer.setSequence(">"+header.toString(), basesStr);
+ }
+ else // write to file
+ writeSequence(writer, header.toString(), basesStr);
+ }
+
+ if(writer != null)
+ writer.close();
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+
+ if(!view)
+ new MessageDialog (null, "Saved Files", fastaFiles, false);
}
- protected static void exportFasta(final EntryGroup entryGroup,
- final AbstractVCFReader vcfReaders[],
+ protected static void exportFasta(final AbstractVCFReader vcfReaders[],
final String chr,
final VCFview vcfView,
final boolean vcf_v4,
@@ -282,6 +363,11 @@ class IOUtils
if(vcfRecord.getAlt().isDeletion(vcf_v4))
{
int ndel = vcfRecord.getAlt().getNumberOfDeletions(vcf_v4);
+ if(!vcfRecord.getAlt().toString().equals(".") && isFwd)
+ {
+ buff.append(getBase(vcfRecord.getAlt().toString(), isFwd));
+ position+=vcfRecord.getAlt().toString().length();
+ }
if(isFwd)
position+=ndel-1;
@@ -297,12 +383,7 @@ class IOUtils
buff.append("-");
}
else if(vcfRecord.getAlt().isInsertion(vcf_v4))
- {
- if(isFwd)
- buff.append(vcfRecord.getAlt().toString());
- else
- buff.append(Bases.reverseComplement(vcfRecord.getAlt().toString()));
- }
+ buff.append(getBase(vcfRecord.getAlt().toString(), isFwd));
else if(vcfRecord.getAlt().isMultiAllele())
{
String base = MultipleAlleleVariant.getIUBCode(vcfRecord);
@@ -312,29 +393,31 @@ class IOUtils
buff.append(bases.charAt(position));
}
else if(vcfRecord.getAlt().isNonVariant()) // non-variant
- {
- if(isFwd)
- buff.append(vcfRecord.getRef().toUpperCase());
- else
- buff.append(Bases.complement(vcfRecord.getRef()).toUpperCase());
- }
+ buff.append(getBase(vcfRecord.getRef(), isFwd).toUpperCase());
else
- {
- String alt = vcfRecord.getAlt().toString().toLowerCase(); // SNP
- if(isFwd)
- buff.append(alt);
- else
- buff.append(Bases.complement(alt));
- }
+ buff.append(getBase(vcfRecord.getAlt().toString().toLowerCase(), isFwd));
if(isFwd && position < bases.length())
buff.append(bases.substring(position+1));
- else if(!isFwd)
- {
+ else if(!isFwd && position < bases.length())
buff.append(bases.substring(position+1));
- }
+
return buff.toString();
}
+
+ /**
+ * Get the actual bases by reverse complementing if on the
+ * reverse strand.
+ * @param baseStr
+ * @param isFwd
+ * @return
+ */
+ private static String getBase(String baseStr, boolean isFwd)
+ {
+ if(isFwd)
+ return baseStr;
+ return Bases.reverseComplement(baseStr);
+ }
/**
* Get all features in an entry group.
@@ -382,4 +465,33 @@ class IOUtils
return false;
}
+ /**
+ * Return the dirtectory that the given entry was read from.
+ **/
+ private static File getBaseDirectoryFromEntry(final Entry entry)
+ {
+ final uk.ac.sanger.artemis.io.Entry embl_entry = entry.getEMBLEntry();
+
+ if(embl_entry instanceof DocumentEntry)
+ {
+ final DocumentEntry document_entry =(DocumentEntry) embl_entry;
+
+ if(document_entry.getDocument() instanceof FileDocument)
+ {
+ final FileDocument file_document =
+ (FileDocument) document_entry.getDocument();
+
+ if(file_document.getFile().getParent() != null)
+ return new File(file_document.getFile().getParent());
+ }
+ }
+ if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
+ instanceof RemoteFileDocument ||
+ ((DocumentEntry)entry.getEMBLEntry()).getDocument()
+ instanceof DatabaseDocument)
+ return new File(System.getProperty("user.dir"));
+
+ return null;
+ }
+
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 22834877069caaaad8ba92eef6591712ca0a379f..2f357ea395abd49ee88fb11de07d60a67345b5cc 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -516,19 +516,19 @@ public class VCFview extends JPanel
public void actionPerformed(ActionEvent e)
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- IOUtils.exportFasta(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4,
+ IOUtils.exportFasta(vcfReaders, chr, VCFview.this, vcf_v4,
selection.getAllFeatures(), false);
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
export.add(exportFastaSelected);
- final JMenuItem exportFasta = new JMenuItem("FASTA");
+ final JMenuItem exportFasta = new JMenuItem("FASTA of selected base range");
exportFasta.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- IOUtils.exportFasta(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4);
+ IOUtils.exportFastaByRange(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4, selection, false);
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
@@ -541,12 +541,23 @@ public class VCFview extends JPanel
public void actionPerformed(ActionEvent e)
{
VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- IOUtils.exportFasta(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4,
+ IOUtils.exportFasta(vcfReaders, chr, VCFview.this, vcf_v4,
selection.getAllFeatures(), true);
VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
});
view.add(viewFastaSelected);
+
+ final JMenuItem viewFasta = new JMenuItem("FASTA of selected base range");
+ viewFasta.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ IOUtils.exportFastaByRange(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4, selection, true);
+ VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ });
+ view.add(viewFasta);
}
private static EntryGroup getReference(String reference)