import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlignThread;
+import jalview.hmmer.HMMBuildThread;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.TCoffeeColourScheme;
-import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.FileReader;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
-import java.util.Scanner;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
public static final int DEFAULT_HEIGHT = 500;
+ boolean autoAlignNewSequences;
+
+ boolean recurring;
+
/*
* The currently displayed panel (selected tabbed view if more than one)
*/
init();
}
+ public void setIsRecurring(boolean status)
+ {
+ recurring = status;
+ }
+
/**
* initalise the alignframe from the underlying viewport data and the
* configurations
}
});
buildColourMenu();
+ buildHMMERMenu();
if (Desktop.desktop != null)
{
}
+ private void buildHMMERMenu()
+ {
+ hmmerMenu.removeAll();
+
+ hmmerMenu.add(changeHMMERLocation);
+ hmmerMenu.addSeparator();
+
+ hmmerMenu.add(autoAlignSeqs);
+ hmmerMenu.addSeparator();
+
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmSearch);
+
+ }
+
/**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
ap.av.updateConservation(ap);
ap.av.updateConsensus(ap);
ap.av.updateStrucConsensus(ap);
+ ap.av.updateInformation(ap);
}
}
}
@Override
+ public void hmmBuild_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
+ {
+ new Thread(new HMMBuildThread(this)).start();
+ alignPanel.repaint();
+
+ }
+
+ @Override
+ public void hmmAlign_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
+ {
+ new Thread(new HMMAlignThread(this, true)).start();
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void changeHMMERLocation_actionPerformed(ActionEvent e)
+ {
+ String location = JOptionPane.showInputDialog(
+ MessageManager.getString("label.enter_location"));
+ Cache.setProperty(Preferences.HMMER_PATH, location);
+ }
+
+ @Override
+ public void autoAlignSeqs_actionPerformed(boolean autoAlignSeqs)
+ {
+ autoAlignNewSequences = autoAlignSeqs;
+ alignPanel.repaint();
+ }
+
+ @Override
+ public void hmmSearch_actionPerformed(ActionEvent e)
+ {
+ alignPanel.repaint();
+ }
+
+ @Override
public void reload_actionPerformed(ActionEvent e)
{
if (fileName != null)
@Override
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
// Pick the tree file
JalviewFileChooser chooser = new JalviewFileChooser(
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(true);
}
*
* @param e
* DOCUMENT ME!
+ * @throws InterruptedException
+ * @throws IOException
*/
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
paste(false);
}
*
* @param newAlignment
* true to paste to a new alignment, otherwise add to this.
+ * @throws InterruptedException
+ * @throws IOException
*/
- void paste(boolean newAlignment)
+ void paste(boolean newAlignment) throws IOException, InterruptedException
{
boolean externalPaste = true;
try
System.out.println("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
-
}
@Override
*
* @param file
* either a filename or a URL string.
+ * @throws InterruptedException
+ * @throws IOException
*/
public void loadJalviewDataFile(String file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
+ throws IOException, InterruptedException
{
try
{
}
else if (FileFormat.HMMER3.equals(format))
{
- HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType)); // TODO
- // need
- // to
- // follow
- // standard
- // pipeline
- hmmFile.parse();
+ HMMFile hmmFile = new HMMFile(new FileParse(file, sourceType));
HiddenMarkovModel hmm = hmmFile.getHMM();
- AlignmentAnnotation annotation = hmm.createAnnotation(
- getViewport().getAlignment().getWidth());
- getViewport().getAlignment().addAnnotation(annotation);
- annotation.setHMM(hmm);
- isAnnotation = true;
-
- BufferedReader input = new BufferedReader(new FileReader(
- "H:/Desktop/Distributions/BadAlignment-8.csv"));
- String line = input.readLine();
-
- while (!("".equals(line)) && line != null)
- {
- Scanner scanner = new Scanner(line);
- if (scanner.hasNext())
- {
- scanner.useDelimiter(",");
- String value = scanner.next();
-
- distribution.put(value, scanner.nextFloat());
- line = input.readLine();
- }
- }
-
-
- AlignmentI alignment = getViewport().getAlignment();
- Integer alpha = 0;
- final int AMINO = 0;
- final int DNA = 1;
- if ("amino".equals(hmm.getAlphabetType()))
- {
- alpha = AMINO;
- }
- else if ("DNA".equals(hmm.getAlphabetType()))
- {
- alpha = DNA;
- }
-
-
- int size = 0;
-
- for (int l = 1; l < hmm.getLength() + 1; l++)
- {
- for (int n = 0; n < alignment.getHeight(); n++)
- {
-
- char character = alignment.getSequenceAt(n)
- .getCharAt(hmm.getNodeAlignmentColumn(l));
- character = Character.toUpperCase(character);
-
- boolean containedN;
- boolean containedA;
-
- containedN = ResidueProperties.nucleotideBackgroundFrequencies
- .containsKey(character);
- containedA = ResidueProperties.aminoBackgroundFrequencies
- .containsKey(character);
-
- if (!Comparison.isGap(character)
- && ((alpha == DNA && containedN)
- || (alpha == AMINO && containedA)))
- {
- size++;
- }
-
- }
- }
-
- for (int l = 1; l < hmm.getLength() + 1; l++)
- {
- for (int n = 0; n < alignment.getHeight(); n++)
- {
- Double prob;
- char character;
- character = alignment.getSequenceAt(n)
- .getCharAt(hmm.getNodeAlignmentColumn(l));
- character = Character.toUpperCase(character);
- boolean containedN;
- boolean containedA;
-
- containedN = ResidueProperties.nucleotideBackgroundFrequencies
- .containsKey(character);
- containedA = ResidueProperties.aminoBackgroundFrequencies
- .containsKey(character);
-
- if (!Comparison.isGap(character)
- && ((alpha == DNA && containedN)
- || (alpha == AMINO && containedA)))
- {
- prob = hmm.getMatchEmissionProbability(
- hmm.getNodeAlignmentColumn(l), character);
- if (prob == 0d)
- {
- System.out.println("?");
- }
-
- double freq = 0;
- if (alpha == AMINO)
- {
- freq = ResidueProperties.aminoBackgroundFrequencies
- .get(character);
- }
- if (alpha == DNA)
- {
- freq = ResidueProperties.nucleotideBackgroundFrequencies
- .get(character);
- }
- Double doubleValue = Math.log(prob / freq);
-
- String value = String.format("%.1f", doubleValue);
- if ("-0.0".equals(value))
- {
- value = "0.0";
- }
- if (distribution.containsKey(value))
- {
- float prev = distribution.get(value);
- prev = prev + (10000f / size);
- distribution.put(value, prev);
- }
- else
- {
- distribution.put(value, 10000f / size);
- }
-
-
- }
-
- }
- }
-
- PrintWriter writer = new PrintWriter(
- new File(
- "H:/Desktop/Distributions/BadAlignment-8.csv"));
- for (Map.Entry<String, Float> entry : distribution
- .entrySet())
- {
- writer.println(entry.getKey() + "," + entry.getValue());
-
- }
-
- writer.close();
+ SequenceI hmmSeq = hmm.initHMMSequence(this, 0);
+ getViewport().initInformation(hmmSeq);
+ getViewport().updateInformation(alignPanel);
+ isAnnotation = true;
}
else if (FileFormat.Jnet.equals(format))
else
{
new FileLoader().LoadFile(viewport, file, sourceType, format);
+ if (autoAlignNewSequences && !recurring)
+ {
+ new Thread(new HMMAlignThread(this, false)).start();
+ }
}
}
}
if (isAnnotation)
{
-
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
}
}
}
+
+
}
git://source.jalview.org / jalview.git / blobdiff