label.most_polymer_residues = Most Polymer Residues
label.cached_structures = Cached Structures
label.free_text_search = Free Text Search
+label.bam_file_options = BAM File Options
+label.bam_chromosome = Chromosome to load:
+label.bam_range = Region to load:
+warn.bam_params_not_set = .bam file region parameters have not been set
*/
package jalview.gui;
+import jalview.io.AlignmentFileReaderI;
+import jalview.io.BamFile;
+import jalview.util.MessageManager;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.util.Arrays;
+
+import javax.swing.BorderFactory;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JTextField;
/**
* A dialog where a user can choose import options for a bam file
public class BamFileOptionsChooser extends JPanel
{
+ // text field for start of range
+ // JFormattedTextField startRange = new JFormattedTextField(
+ // new NumberFormatter(NumberFormat.getIntegerInstance()));
+
+ // text field for end of range
+ // JFormattedTextField endRange = new JFormattedTextField(
+ // new NumberFormatter(NumberFormat.getIntegerInstance()));
+
+ JTextField startRange = new JTextField(10);
+
+ JTextField endRange = new JTextField(10);
+
+ // combo box for chromosome list
+ JComboBox<String> chroCombo;
+
+ public BamFileOptionsChooser(AlignmentFileReaderI source)
+ {
+ Object[] preprocessResult = source.preprocess();
+ String[] chromosomes = Arrays.copyOf(preprocessResult,
+ preprocessResult.length, String[].class);
+
+ setLayout(new GridBagLayout());
+ GridBagConstraints c = new GridBagConstraints();
+
+ setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
+
+ // set up chromosome input
+ JLabel chroLabel = new JLabel(
+ MessageManager.getString("label.bam_chromosome"));
+ chroCombo = new JComboBox<>(chromosomes);
+
+ // set up region input
+ JPanel range = new JPanel();
+ JLabel rangeLabel = new JLabel(
+ MessageManager.getString("label.bam_range"));
+ startRange.setColumns(8);
+ endRange.setColumns(8);
+
+ JLabel rangeSep = new JLabel("-");
+ range.add(startRange);
+ range.add(rangeSep);
+ range.add(endRange);
+
+ // chromosome label top left
+ c.gridx = 0;
+ c.gridy = 0;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.NONE;
+ this.add(chroLabel, c);
+
+ // chromosome combo top right
+ c.gridx = 1;
+ c.weightx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ this.add(chroCombo, c);
+
+ // region label mid left
+ c.gridx = 0;
+ c.gridy = 1;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.NONE;
+ this.add(rangeLabel, c);
+
+ // region input mid right
+ c.gridx = 1;
+ c.weightx = 1;
+ c.anchor = GridBagConstraints.WEST;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ this.add(range, c);
+ }
+
+ public void update(AlignmentFileReaderI source)
+ {
+
+ int start = Integer.parseInt(startRange.getText());
+ int end = Integer.parseInt(endRange.getText());
+ ((BamFile) source).setOptions((String) chroCombo.getSelectedItem(),
+ start, end);
+
+ }
+
}
*/
protected void initData()
{
- seqs = new Vector<SequenceI>();
- annotations = new Vector<AlignmentAnnotation>();
- seqGroups = new ArrayList<SequenceGroup>();
+ seqs = new Vector<>();
+ annotations = new Vector<>();
+ seqGroups = new ArrayList<>();
parseCalled = false;
}
@Override
public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
{
seqs.add(seq);
}
+
+ @Override
+ public Object[] preprocess()
+ {
+ // most AlignFiles will not need to return any preprocessing information
+ // those that do should override this method
+ return null;
+ }
+
}
*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
-import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import java.io.IOException;
+
public interface AlignmentFileReaderI
{
FeatureSettingsModelI getFeatureColourScheme();
+ /**
+ * Get a string array resulting from preprocessing the file
+ *
+ * @return preprocess result
+ */
+ Object[] preprocess();
+
+ public abstract void parse() throws IOException;
+
}
public AlignmentI readFile(String file, DataSourceType sourceType,
FileFormatI fileFormat) throws IOException
{
+ if (alignFile == null)
+ {
+ prepareFileReader(file, sourceType, fileFormat);
+ }
+ else
+ {
+ alignFile.parse();
+ }
+ return buildAlignmentFromFile();
+ }
+
+ public void prepareFileReader(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
this.inFile = file;
try
{
}
else
{
- // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
}
- return buildAlignmentFromFile();
+ return;
} catch (Exception e)
{
e.printStackTrace();
// Possible sequence is just residues with no label
alignFile = new FastaFile(">UNKNOWN\n" + inFile,
DataSourceType.PASTE);
- return buildAlignmentFromFile();
+ return;
} catch (Exception ex)
{
import java.io.File;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
import java.util.SortedMap;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
+import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import htsjdk.samtools.ValidationStringency;
public class BamFile extends AlignFile
{
+ // SAM/BAM file reader
+ private SamReader fileReader;
- SamReader fileReader;
+ // start position to read from
+ private int start = -1;
+
+ // end position to read to
+ private int end = -1;
+
+ // chromosome/contig to read
+ private String chromosome = "";
/**
* Creates a new BamFile object.
* Creates a new BamFile object.
*
* @param inFile
- * DOCUMENT ME!
+ * Name of file to read
* @param sourceType
- * DOCUMENT ME!
+ * Whether data source is file, url or other type of data source
*
* @throws IOException
- * DOCUMENT ME!
*/
public BamFile(String inFile, DataSourceType sourceType)
throws IOException
{
- super(inFile, sourceType);
+ super(true, inFile, sourceType);
final SamReaderFactory factory = SamReaderFactory.makeDefault()
.enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
fileReader = factory.open(new File(inFile));
}
+ /**
+ * Creates a new BamFile object
+ *
+ * @param source
+ * wrapper for datasource
+ * @throws IOException
+ */
public BamFile(FileParse source) throws IOException
{
+ super(true, source);
final SamReaderFactory factory = SamReaderFactory.makeDefault()
.enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
// File-based bam
fileReader = factory.open(source.inFile);
- parse();
}
@Override
}
@Override
- public void parse() throws IOException
+ public void parse()
{
- SAMRecordIterator it = fileReader.iterator();
- CigarParser parser = new CigarParser('-');
- SortedMap<Integer, Integer> insertions = parser.getInsertions(it);
- it.close();
-
- it = fileReader.iterator();
- while (it.hasNext())
+ // only actually parse if params are set
+ if (chromosome != null && chromosome != "")
{
- SAMRecord rec = it.next();
+ SAMRecordIterator it = fileReader.query(chromosome, start, end,
+ false);
+ CigarParser parser = new CigarParser('-');
+ SortedMap<Integer, Integer> insertions = parser.getInsertions(it);
+ it.close();
+
+ it = fileReader.query(chromosome, start, end, false);
+ while (it.hasNext())
+ {
+ SAMRecord rec = it.next();
- // make dataset sequence: start at 1, end at read length
- SequenceI seq = new Sequence(rec.getReadName(),
- rec.getReadString().toLowerCase());
- seq.setStart(1);
- seq.setEnd(rec.getReadLength());
+ // make dataset sequence: start at 1, end at read length
+ SequenceI seq = new Sequence(rec.getReadName(),
+ rec.getReadString().toLowerCase());
+ seq.setStart(1);
+ seq.setEnd(rec.getReadLength());
- String newRead = parser.parseCigarToSequence(rec, insertions);
+ String newRead = parser.parseCigarToSequence(rec, insertions);
- // make alignment sequences
- SequenceI alsq = seq.deriveSequence();
- alsq.setSequence(newRead);
+ // make alignment sequences
+ SequenceI alsq = seq.deriveSequence();
+ alsq.setSequence(newRead);
- // set start relative to soft clip; assume end is set by Sequence code
- alsq.setStart(rec.getStart() - rec.getUnclippedStart() + 1);
- seqs.add(alsq);
+ // set start relative to soft clip; assume end is set by Sequence code
+ alsq.setStart(rec.getStart() - rec.getUnclippedStart() + 1);
+ seqs.add(alsq);
+ }
}
}
+
+ /**
+ * Get the list of chromosomes or contigs from the file (listed in SQ entries
+ * in BAM file header)
+ *
+ * @return array of chromosome/contig strings
+ */
+ @Override
+ public Object[] preprocess()
+ {
+ List<SAMSequenceRecord> refSeqs = fileReader.getFileHeader()
+ .getSequenceDictionary().getSequences();
+ List<String> chrs = new ArrayList<>();
+
+ for (SAMSequenceRecord ref : refSeqs)
+ {
+ chrs.add(ref.getSequenceName());
+ }
+ return chrs.toArray();
+ }
+
+ public void setOptions(String chr, int s, int e)
+ {
+ chromosome = chr;
+ start = s;
+ end = e;
+ }
}
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
+import jalview.gui.BamFileOptionsChooser;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
if (FileFormat.Bam.equals(format))
{
+ FormatAdapter fa = new FormatAdapter();
+ if (source == null)
+ {
+ fa.prepareFileReader(file, protocol, format);
+ source = fa.getAlignFile();
+ }
+
+ BamFileOptionsChooser bamoptions = new BamFileOptionsChooser(
+ source);
+
// ask the user which bit of the bam they want to load
+ int confirm = JvOptionPane.showConfirmDialog(null,
+ bamoptions,
+ MessageManager.getString("label.bam_file_options"),
+ JvOptionPane.OK_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE);
+
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ Desktop.instance.stopLoading();
+ return;
+ }
+ else
+ {
+ bamoptions.update(source);
+ al = fa.readFile(file, protocol, format);
+ }
}
if (FileFormat.Jalview.equals(format))
String error = AppletFormatAdapter.getSupportedFormats();
try
{
- if (source != null)
+ if (al == null)
{
- // read from the provided source
- al = new FormatAdapter().readFromFile(source, format);
- }
- else
- {
-
- // open a new source and read from it
- FormatAdapter fa = new FormatAdapter();
- boolean downloadStructureFile = format.isStructureFile()
- && protocol.equals(DataSourceType.URL);
- if (downloadStructureFile)
+ if (source != null)
{
- String structExt = format.getExtensions().split(",")[0];
- String urlLeafName = file.substring(
- file.lastIndexOf(
- System.getProperty("file.separator")),
- file.lastIndexOf("."));
- String tempStructureFileStr = createNamedJvTempFile(
- urlLeafName, structExt);
- UrlDownloadClient.download(file, tempStructureFileStr);
- al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
- format);
- source = fa.getAlignFile();
+ // read from the provided source
+ al = new FormatAdapter().readFromFile(source, format);
}
else
{
- al = fa.readFile(file, protocol, format);
- source = fa.getAlignFile(); // keep reference for later if
- // necessary.
+
+ // open a new source and read from it
+ FormatAdapter fa = new FormatAdapter();
+ boolean downloadStructureFile = format.isStructureFile()
+ && protocol.equals(DataSourceType.URL);
+ if (downloadStructureFile)
+ {
+ String structExt = format.getExtensions().split(",")[0];
+ String urlLeafName = file.substring(
+ file.lastIndexOf(
+ System.getProperty("file.separator")),
+ file.lastIndexOf("."));
+ String tempStructureFileStr = createNamedJvTempFile(
+ urlLeafName, structExt);
+ UrlDownloadClient.download(file, tempStructureFileStr);
+ al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+ format);
+ source = fa.getAlignFile();
+ }
+ else
+ {
+ al = fa.readFile(file, protocol, format);
+ source = fa.getAlignFile(); // keep reference for later if
+ // necessary.
+ }
}
}
} catch (java.io.IOException ex)
source.getDataSourceType());
return readFromFile(fp, format);
}
-
}
git://source.jalview.org / jalview.git / commitdiff