diff --git a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
index 4fd7c1e519761c39ae1a72b649efd44b6268623b..08257af372f1557dac889091f179ca10562723fb 100644
--- a/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/AbstractVCFReader.java
@@ -30,12 +30,59 @@ import java.io.InputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
+import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
+
public abstract class AbstractVCFReader
{
private boolean vcf_v4 = false;
protected abstract String[] getSeqNames();
protected abstract String getFileName();
+ private BCFReaderIterator bcfIterator = null;
+ private TabixReader.Iterator tabixIterator = null;
+
+ /**
+ * Read and return the next record.
+ * @param chr sequence name
+ * @param sbeg start base
+ * @param send end base
+ * @return
+ * @throws IOException
+ */
+ public VCFRecord getNextRecord(String chr, int sbeg, int send) throws IOException
+ {
+ VCFRecord record;
+ if(this instanceof BCFReader)
+ {
+ if(bcfIterator == null)
+ bcfIterator = ((BCFReader)this).query(chr, sbeg, send);
+
+ record = bcfIterator.next();
+ if(record == null)
+ bcfIterator = null;
+ }
+ else
+ {
+ if(tabixIterator == null)
+ tabixIterator = ((TabixReader)this).query(chr+":"+sbeg+"-"+send);
+ if(tabixIterator == null)
+ return null;
+
+ String s = tabixIterator.next();
+ if(s == null)
+ {
+ tabixIterator = null;
+ return null;
+ }
+ record = VCFRecord.parse(s);
+
+ if(record == null)
+ tabixIterator = null;
+ }
+ return record;
+ }
+
+
protected static int readInt(final InputStream is) throws IOException {
byte[] buf = new byte[4];
is.read(buf);
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index dc7b6aabdd776ea484000c5c4a0cc9fa92e83508..e62ac259a4c3a97bec4d0a772fc92523fc52bcee 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -30,13 +30,20 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.Writer;
import java.net.URL;
+import java.util.Comparator;
import java.util.List;
+import java.util.Vector;
import javax.swing.Box;
import javax.swing.JCheckBox;
import javax.swing.JComponent;
import javax.swing.JFileChooser;
+import javax.swing.JFrame;
import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
@@ -591,12 +598,11 @@ class IOUtils
{
boolean vcf_v4 = reader.isVcf_v4();
int len = basesStr.length();
-
- if (reader instanceof BCFReader)
+
+ try
{
- BCFReaderIterator it = ((BCFReader) reader).query(chr, sbeg, send);
VCFRecord record;
- while ((record = it.next()) != null)
+ while ((record = reader.getNextRecord(chr, sbeg, send)) != null)
{
int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
if(vcfView.showVariant(record, features, basePosition, vcf_v4) )
@@ -609,7 +615,7 @@ class IOUtils
basesStr = basesStr.substring(0, position) + 'n' +
basesStr.substring(position+1);
}
-
+
if(basesStr.length() > len) // adjust for insertions
{
sbeg -= (basesStr.length()-len);
@@ -617,41 +623,133 @@ class IOUtils
}
}
}
- else
+ catch(NullPointerException e)
{
- try
+ System.err.println(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
+ }
+
+ return basesStr;
+ }
+
+
+ protected static void countVariants(final VCFview vcfView,
+ final FeatureVector features) throws IOException
+ {
+ String[] columnNames = {
+ "VCF", "Name", "Variant", "Non-variant", "Deletion", "Insertion", "Synonymous", "Non-synonymous"};
+ Vector<String> columnData = new Vector<String>();
+ for(String col: columnNames)
+ columnData.add(col);
+ Vector<Vector<Object>> rowData = new Vector<Vector<Object>>();
+
+ AbstractVCFReader vcfReaders[] = vcfView.getVcfReaders();
+ for (AbstractVCFReader reader: vcfReaders)
+ {
+
+ for (int j = 0; j < features.size(); j++)
{
- TabixReader.Iterator iter =
- (((TabixReader) reader).query(chr+":"+sbeg+"-"+send)); // get the iterator
- String s;
- while (iter != null && (s = iter.next()) != null)
+ int count[] = new int[6];
+ for(int c: count)
+ c = 0;
+
+ Feature f = features.elementAt(j);
+ FeatureSegmentVector segs = f.getSegments();
+
+ for(int k=0; k<segs.size(); k++)
{
- VCFRecord record = VCFRecord.parse(s);
- int basePosition = record.getPos() + vcfView.getSequenceOffset(record.getChrom());
- if(vcfView.showVariant(record, features, basePosition, vcf_v4) )
- basesStr = getSeqsVariation(record, basesStr, sbeg, isFwd, vcf_v4);
- else if(useNs && isSNPorNonVariant(record))
+ FeatureSegment seg = segs.elementAt(k);
+ int sbeg = seg.getRawRange().getStart();
+ int send = seg.getRawRange().getEnd();
+
+ if(vcfView.isConcatenate())
{
- int position = record.getPos()-sbeg;
- if(!isFwd)
- position = basesStr.length()-position-1;
- basesStr = basesStr.substring(0, position) + 'n' +
- basesStr.substring(position+1);
+ String[] contigs = reader.getSeqNames();
+ for(int i=0; i<contigs.length; i++)
+ {
+ int offset = vcfView.getSequenceOffset(contigs[i]);
+ int nextOffset;
+ if(i<contigs.length-1)
+ nextOffset = vcfView.getSequenceOffset(contigs[i+1]);
+ else
+ nextOffset = vcfView.seqLength;
+
+ if( (offset >= sbeg && offset < send) ||
+ (offset < sbeg && sbeg < nextOffset) )
+ {
+ int thisStart = sbeg - offset;
+ if(thisStart < 1)
+ thisStart = 1;
+ int thisEnd = send - offset;
+
+ VCFRecord record;
+ while ((record = reader.getNextRecord(vcfView.getChr(), thisStart, thisEnd)) != null)
+ count(record, count, features, reader);
+ }
+ }
}
-
- if(basesStr.length() > len) // adjust for insertions
+ else
{
- sbeg -= (basesStr.length()-len);
- len = basesStr.length();
+ VCFRecord record;
+ while ((record = reader.getNextRecord(vcfView.getChr(), sbeg, send)) != null)
+ count(record, count, features, reader);
}
}
+
+ Object row[] = {
+ reader.getName(), f.getSystematicName(), count[0], count[1], count[2], count[3], count[4], count[5] };
+
+ Vector<Object> thisRow = new Vector<Object>();
+ for(Object obj: row)
+ thisRow.add(obj);
+ rowData.add(thisRow);
}
- catch(NullPointerException e)
- {
- System.err.println(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
+ }
+
+ JTable variantData = new JTable(rowData, columnData);
+ TableRowSorter<TableModel> sorter =
+ new TableRowSorter<TableModel>(variantData.getModel());
+ variantData.setRowSorter(sorter);
+
+ Comparator<Integer> comparator = new Comparator<Integer>() {
+ public int compare(Integer i1, Integer i2) {
+ return i1.compareTo(i2);
}
+ };
+
+ for(int i=2; i< columnData.size(); i++)
+ sorter.setComparator(i, comparator);
+
+ JScrollPane jsp = new JScrollPane(variantData);
+ JFrame f = new JFrame("Variant Overview");
+ f.getContentPane().add(jsp);
+ f.pack();
+ f.setVisible(true);
+ }
+
+ private static void count(VCFRecord record, int count[], FeatureVector features, AbstractVCFReader reader)
+ {
+ if(record.getAlt().isNonVariant())
+ {
+ count[1]++;
+ return;
}
- return basesStr;
+ else
+ count[0]++;
+
+ if(record.getAlt().isDeletion(reader.isVcf_v4()))
+ count[2]++;
+ else if(record.getAlt().isInsertion(reader.isVcf_v4()))
+ count[3]++;
+
+ if(record.getAlt().length() == 1 && record.getRef().length() == 1)
+ {
+ short synFlag = record.getSynFlag(features, record.getPos());
+ switch(synFlag)
+ {
+ case 1: count[4]++; break; // synonymous
+ default: count[5]++; break; // non-synonymous
+ }
+ }
}
private static boolean isSNPorNonVariant(VCFRecord record)
@@ -876,33 +974,18 @@ class IOUtils
{
boolean vcf_v4 = reader.isVcf_v4();
Key variantKey = new Key("misc_difference");
- if (reader instanceof BCFReader)
+ try
{
- BCFReaderIterator it = ((BCFReader) reader).query(chr, sbegc, sendc);
VCFRecord record;
- while ((record = it.next()) != null)
+ while( (record = reader.getNextRecord(chr, sbegc, sendc)) != null)
{
makeFeature(record, reader.getName(), vcfView, features, bases, entry, variantKey, vcf_v4);
}
}
- else
+ catch (NullPointerException e)
{
- try
- {
- TabixReader.Iterator iter = (((TabixReader) reader).query(chr + ":"
- + sbegc + "-" + sendc)); // get the iterator
- String s;
- while (iter != null && (s = iter.next()) != null)
- {
- VCFRecord record = VCFRecord.parse(s);
- makeFeature(record, reader.getName(), vcfView, features, bases, entry, variantKey, vcf_v4);
- }
- }
- catch (NullPointerException e)
- {
- System.err.println(chr + ":" + sbegc + "-" + sendc + "\n"
- + e.getMessage());
- }
+ System.err.println(chr + ":" + sbegc + "-" + sendc + "\n"
+ + e.getMessage());
}
}
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index ee225fa48b23850152f43f6d4e7bcabea6c631d9..31070f18175f505d248354a573489c5ede4a5679 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -666,6 +666,24 @@ public class VCFview extends JPanel
}
});
+ final JMenuItem snpOverview = new JMenuItem("Overview");
+ popup.add(snpOverview);
+ snpOverview.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ IOUtils.countVariants(VCFview.this, selection.getAllFeatures());
+ }
+ catch (IOException e1)
+ {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ }
+ });
+
final JCheckBoxMenuItem labels = new JCheckBoxMenuItem("Show Labels", showLabels);
labels.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
@@ -1017,43 +1035,17 @@ public class VCFview extends JPanel
float pixPerBase,
FeatureVector features)
{
- String s;
cacheVariantLines = new Vector<Integer>(5);
- if(vcfReaders[i] instanceof BCFReader)
+ try
{
- try
- {
- BCFReader bcfReader = (BCFReader)vcfReaders[i];
- BCFReaderIterator it = bcfReader.query(chr, sbeg, send);
- VCFRecord bcfRecord;
- while((bcfRecord = it.next()) != null)
- drawVariantCall(g, bcfRecord, start, i, pixPerBase, features, vcfReaders[i].isVcf_v4());
- }
- catch (IOException e)
- {
- logger4j.warn(e.getMessage());
- e.printStackTrace();
- }
-
+ VCFRecord record;
+ while((record = vcfReaders[i].getNextRecord(chr, sbeg, send)) != null)
+ drawVariantCall(g, record, start, i, pixPerBase, features, vcfReaders[i].isVcf_v4());
}
- else
+ catch (IOException e)
{
- try
- {
- TabixReader.Iterator iter =
- ((TabixReader)vcfReaders[i]).query(chr+":"+sbeg+"-"+send); // get the iterator
- if (iter == null)
- return;
- while (iter != null && (s = iter.next()) != null)
- {
- VCFRecord vcfRecord = VCFRecord.parse(s);
- drawVariantCall(g, vcfRecord, start, i, pixPerBase, features, vcfReaders[i].isVcf_v4());
- }
- }
- catch (Exception e)
- {
- logger4j.warn(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
- }
+ logger4j.warn(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
+ e.printStackTrace();
}
}
@@ -1387,41 +1379,16 @@ public class VCFview extends JPanel
Point mousePoint, FeatureVector features,
int start, float pixPerBase)
{
- if(vcfReaders[i] instanceof BCFReader)
+ try
{
- try
- {
- BCFReader bcfReader = (BCFReader)vcfReaders[i];
- BCFReaderIterator it = bcfReader.query(chr, sbeg, send);
- VCFRecord bcfRecord;
- while((bcfRecord = it.next()) != null)
- isMouseOver(mousePoint, bcfRecord, features, i, start, pixPerBase, vcfReaders[i].isVcf_v4());
- }
- catch (IOException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ VCFRecord bcfRecord;
+ while((bcfRecord = vcfReaders[i].getNextRecord(chr, sbeg, send)) != null)
+ isMouseOver(mousePoint, bcfRecord, features, i, start, pixPerBase, vcfReaders[i].isVcf_v4());
}
- else
+ catch (IOException e)
{
- try
- {
- TabixReader.Iterator iter =
- ((TabixReader)vcfReaders[i]).query(chr+":"+sbeg+"-"+send); // get the iterator
- if (iter == null)
- return;
- String s;
- while ((s = iter.next()) != null)
- {
- VCFRecord vcfRecord = VCFRecord.parse(s);
- isMouseOver(mousePoint, vcfRecord, features, i, start, pixPerBase, vcfReaders[i].isVcf_v4());
- }
- }
- catch (Exception e)
- {
- logger4j.warn(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
- }
+ logger4j.warn(chr+":"+sbeg+"-"+send+"\n"+e.getMessage());
+ e.printStackTrace();
}
}