import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
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 java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Deque;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
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;
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
+ Map<String, Float> distribution = new HashMap<>(); // temporary
+
public static final int DEFAULT_WIDTH = 700;
public static final int DEFAULT_HEIGHT = 500;
+ boolean autoAlignNewSequences;
+
+
/*
* The currently displayed panel (selected tabbed view if more than one)
*/
ViewportRanges vpRanges;
public AlignViewControllerI avc;
+ /*
+ * The selected HMM for this align frame
+ */
+ HiddenMarkovModel selectedHMM = null;
List<AlignmentPanel> alignPanels = new ArrayList<>();
*/
String fileName = null;
+
/**
* Creates a new AlignFrame object with specific width and height.
*
}
});
buildColourMenu();
+ buildHMMERMenu();
if (Desktop.desktop != null)
{
}
/**
+ * Adds all menu items to the HMMER menu
+ */
+ private void buildHMMERMenu()
+ {
+ hmmerMenu.removeAll();
+
+ 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);
}
}
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+ showInformationHistogram.setSelected(av.isShowInformationHistogram());
+ showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+ normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
}
@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(
if (viewport.hasHiddenColumns())
{
hiddenColumns = new ArrayList<>();
+
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
ArrayList<int[]> hiddenRegions = viewport.getAlignment()
.getHiddenColumns().getHiddenColumnsCopy();
for (int[] region : hiddenRegions)
+
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
*
* @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)
}
if (isAnnotation)
{
-
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
}
@Override
+ protected void showInformationHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowInformationHistogram(
+ showInformationHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowHMMSequenceLogo(showHMMSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
+ protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ showHMMSequenceLogo.setState(true);
+ viewport.setShowHMMSequenceLogo(true);
+ viewport.setNormaliseHMMSequenceLogo(normaliseSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ @Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
new CalculationChooser(AlignFrame.this);
}
}
+
+ /**
+ * Sets the status of the HMMER menu
+ *
+ * @param status
+ */
+ public void updateHMMERStatus(boolean status)
+ {
+ hmmerMenu.setEnabled(status);
+ }
+
+ /**
+ * Returns the selected hidden Markov model.
+ *
+ * @return
+ */
+ public HiddenMarkovModel getSelectedHMM()
+ {
+ return selectedHMM;
+ }
+
+ /**
+ * Sets the selected hidden Markov model
+ *
+ * @param selectedHMM
+ */
+ public void setSelectedHMM(HiddenMarkovModel selectedHMM)
+ {
+ this.selectedHMM = selectedHMM;
+ hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
+ + selectedHMM.getName() + "_HMM");
+ hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
+ + selectedHMM.getName() + "_HMM");
+ }
+
+ @Override
+ public void hmmerMenu_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup grp = getViewport().getSelectionGroup();
+ if (grp != null)
+ {
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
+ + grp.getName());
+ }
+ else
+ {
+ hmmBuild.setText(MessageManager.getString("label.hmmbuild")
+ + " from Alignment");
+ }
+ }
+
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff